diff --git a/.DS_Store b/.DS_Store index cec6999c..01c295d4 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..68a7f739 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,49 @@ +FROM node:12-alpine + +RUN apk add openjdk8 bash + +ENV JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk +ENV PATH="$JAVA_HOME/bin:${PATH}" + +WORKDIR /opt/backend + +COPY . . + +# This should be in the Dockerfile, but for now it's a script +RUN resources/build_automation/build_backend.sh + +## Build angular stuff and copy into WEB-INF +RUN apk add --update nodejs npm +RUN npm install -g @angular/cli +RUN apk add git + +WORKDIR ./SBOLCanvasFrontend +RUN npm install +RUN npm rebuild node-sass +RUN node --max-old-space-size=8192 +RUN npm run prebuild.prod +RUN ng build --prod --build-optimizer --vendor-chunk --progress --output-hashing=all --stats-json --source-map=true --base-href=/canvas/ + +#RUN resources/build_automation/build_frontend.sh + +# New container +FROM tomcat:9.0-jdk8-openjdk + +# Copy backend +COPY --from=0 /opt/backend/SBOLCanvasBackend/WebContent/api.war webapps + +# Copy frontend +COPY --from=0 /opt/backend/SBOLCanvasFrontend/dist/SBOLCanvasFrontend webapps/canvas + +# Copying configs for tomcat +ARG TOMCAT_AUTOMATION_DIR=/opt/backend/resources/server_automation/tomcat +#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/tomcat-users.xml ${TOMCAT_AUTOMATION_DIR}/base_config_files/web.xml conf/ +#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/server.xml conf/ +#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/manager-context.xml webapps/manager/META-INF/context.xml +#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/host-manager-context.xml webapps/host-manager/META-INF/context.xml +COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/ROOT_config/index.jsp webapps/ROOT/index.jsp + +COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_context.html webapps/canvas/META-INF/context.html +COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_rewrite.config webapps/canvas/WEB-INF/rewrite.config +COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_web.xml webapps/canvas/WEB-INF/web.xml + diff --git a/backend/.classpath b/SBOLCanvasBackend/.classpath similarity index 100% rename from backend/.classpath rename to SBOLCanvasBackend/.classpath diff --git a/backend/.gitignore b/SBOLCanvasBackend/.gitignore similarity index 100% rename from backend/.gitignore rename to SBOLCanvasBackend/.gitignore diff --git a/backend/.project b/SBOLCanvasBackend/.project similarity index 100% rename from backend/.project rename to SBOLCanvasBackend/.project diff --git a/backend/.settings/.jsdtscope b/SBOLCanvasBackend/.settings/.jsdtscope similarity index 100% rename from backend/.settings/.jsdtscope rename to SBOLCanvasBackend/.settings/.jsdtscope diff --git a/backend/.settings/org.eclipse.jdt.core.prefs b/SBOLCanvasBackend/.settings/org.eclipse.jdt.core.prefs similarity index 100% rename from backend/.settings/org.eclipse.jdt.core.prefs rename to SBOLCanvasBackend/.settings/org.eclipse.jdt.core.prefs diff --git a/backend/.settings/org.eclipse.wst.common.component b/SBOLCanvasBackend/.settings/org.eclipse.wst.common.component similarity index 100% rename from backend/.settings/org.eclipse.wst.common.component rename to SBOLCanvasBackend/.settings/org.eclipse.wst.common.component diff --git a/backend/.settings/org.eclipse.wst.common.project.facet.core.xml b/SBOLCanvasBackend/.settings/org.eclipse.wst.common.project.facet.core.xml similarity index 100% rename from backend/.settings/org.eclipse.wst.common.project.facet.core.xml rename to SBOLCanvasBackend/.settings/org.eclipse.wst.common.project.facet.core.xml diff --git a/backend/.settings/org.eclipse.wst.jsdt.ui.superType.container b/SBOLCanvasBackend/.settings/org.eclipse.wst.jsdt.ui.superType.container similarity index 100% rename from backend/.settings/org.eclipse.wst.jsdt.ui.superType.container rename to SBOLCanvasBackend/.settings/org.eclipse.wst.jsdt.ui.superType.container diff --git a/backend/.settings/org.eclipse.wst.jsdt.ui.superType.name b/SBOLCanvasBackend/.settings/org.eclipse.wst.jsdt.ui.superType.name similarity index 100% rename from backend/.settings/org.eclipse.wst.jsdt.ui.superType.name rename to SBOLCanvasBackend/.settings/org.eclipse.wst.jsdt.ui.superType.name diff --git a/SBOLCanvasBackend/WebContent/META-INF/MANIFEST.MF b/SBOLCanvasBackend/WebContent/META-INF/MANIFEST.MF new file mode 100644 index 00000000..254272e1 --- /dev/null +++ b/SBOLCanvasBackend/WebContent/META-INF/MANIFEST.MF @@ -0,0 +1,3 @@ +Manifest-Version: 1.0 +Class-Path: + diff --git a/SBOLCanvasBackend/WebContent/WEB-INF/classes/data/GlyphInfo.class b/SBOLCanvasBackend/WebContent/WEB-INF/classes/data/GlyphInfo.class new file mode 100644 index 00000000..b63a9c14 Binary files /dev/null and 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rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/beam-func-0.9.2.jar diff --git a/backend/lib/cdk-atomtype-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-atomtype-1.5.14.jar similarity index 100% rename from backend/lib/cdk-atomtype-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-atomtype-1.5.14.jar diff --git a/backend/lib/cdk-core-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-core-1.5.14.jar similarity index 100% rename from backend/lib/cdk-core-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-core-1.5.14.jar diff --git a/backend/lib/cdk-data-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-data-1.5.14.jar similarity index 100% rename from backend/lib/cdk-data-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-data-1.5.14.jar diff --git a/backend/lib/cdk-interfaces-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-interfaces-1.5.14.jar similarity index 100% rename from backend/lib/cdk-interfaces-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-interfaces-1.5.14.jar diff --git a/backend/lib/cdk-io-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-io-1.5.14.jar similarity index 100% rename from backend/lib/cdk-io-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-io-1.5.14.jar diff --git a/backend/lib/cdk-ioformats-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-ioformats-1.5.14.jar similarity index 100% rename from backend/lib/cdk-ioformats-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-ioformats-1.5.14.jar diff --git a/backend/lib/cdk-isomorphism-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-isomorphism-1.5.14.jar similarity index 100% rename from backend/lib/cdk-isomorphism-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-isomorphism-1.5.14.jar diff --git a/backend/lib/cdk-smiles-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-smiles-1.5.14.jar similarity index 100% rename from backend/lib/cdk-smiles-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-smiles-1.5.14.jar diff --git a/backend/lib/cdk-standard-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-standard-1.5.14.jar similarity index 100% rename from backend/lib/cdk-standard-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-standard-1.5.14.jar diff --git a/backend/lib/cdk-valencycheck-1.5.14.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-valencycheck-1.5.14.jar similarity index 100% rename from backend/lib/cdk-valencycheck-1.5.14.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/cdk-valencycheck-1.5.14.jar diff --git a/backend/lib/commons-codec-1.10.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-codec-1.10.jar similarity index 100% rename from backend/lib/commons-codec-1.10.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-codec-1.10.jar diff --git a/backend/lib/commons-codec-1.9.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-codec-1.9.jar similarity index 100% rename from backend/lib/commons-codec-1.9.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-codec-1.9.jar diff --git a/backend/lib/commons-io-1.3.2.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-io-1.3.2.jar similarity index 100% rename from backend/lib/commons-io-1.3.2.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-io-1.3.2.jar diff --git a/backend/lib/commons-io-2.5.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-io-2.5.jar similarity index 100% rename from backend/lib/commons-io-2.5.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-io-2.5.jar diff --git a/backend/lib/commons-logging-1.2.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-logging-1.2.jar similarity index 100% rename from backend/lib/commons-logging-1.2.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/commons-logging-1.2.jar diff --git a/backend/lib/gson-2.7.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/gson-2.7.jar similarity index 100% rename from backend/lib/gson-2.7.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/gson-2.7.jar diff --git a/backend/lib/guava-17.0.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/guava-17.0.jar similarity index 100% rename from backend/lib/guava-17.0.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/guava-17.0.jar diff --git a/backend/lib/hamcrest-core-1.3.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/hamcrest-core-1.3.jar similarity index 100% rename from backend/lib/hamcrest-core-1.3.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/hamcrest-core-1.3.jar diff --git a/backend/lib/httpclient-4.5.1.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/httpclient-4.5.1.jar similarity index 100% rename from backend/lib/httpclient-4.5.1.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/httpclient-4.5.1.jar diff --git a/backend/lib/httpclient-4.5.3.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/httpclient-4.5.3.jar similarity index 100% rename from backend/lib/httpclient-4.5.3.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/httpclient-4.5.3.jar diff --git a/backend/lib/httpcore-4.4.3.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/httpcore-4.4.3.jar similarity index 100% rename from backend/lib/httpcore-4.4.3.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/httpcore-4.4.3.jar diff --git a/backend/lib/httpcore-4.4.6.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/httpcore-4.4.6.jar similarity index 100% rename from backend/lib/httpcore-4.4.6.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/httpcore-4.4.6.jar diff --git a/backend/lib/httpmime-4.5.4.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/httpmime-4.5.4.jar similarity index 100% rename from backend/lib/httpmime-4.5.4.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/httpmime-4.5.4.jar diff --git a/backend/lib/javassist-3.12.1.GA.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/javassist-3.12.1.GA.jar similarity index 100% rename from backend/lib/javassist-3.12.1.GA.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/javassist-3.12.1.GA.jar diff --git a/backend/lib/javax.json-1.0.2.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/javax.json-1.0.2.jar similarity index 100% rename from backend/lib/javax.json-1.0.2.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/javax.json-1.0.2.jar diff --git a/backend/lib/jdom-1.1.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/jdom-1.1.jar similarity index 100% rename from backend/lib/jdom-1.1.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/jdom-1.1.jar diff --git a/backend/lib/joda-time-2.9.9.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/joda-time-2.9.9.jar similarity index 100% rename from backend/lib/joda-time-2.9.9.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/joda-time-2.9.9.jar diff --git a/backend/lib/json-simple-1.1.1.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/json-simple-1.1.1.jar similarity index 100% rename from backend/lib/json-simple-1.1.1.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/json-simple-1.1.1.jar diff --git a/backend/lib/junit-4.12.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/junit-4.12.jar similarity index 100% rename from backend/lib/junit-4.12.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/junit-4.12.jar diff --git a/backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar similarity index 100% rename from backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar diff --git a/backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old b/SBOLCanvasBackend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old similarity index 100% rename from backend/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/libSBOLj-2.4.1-SNAPSHOT-withDependencies.jar.old diff --git a/backend/lib/mxPdf.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/mxPdf.jar similarity index 100% rename from backend/lib/mxPdf.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/mxPdf.jar diff --git a/backend/lib/mxgraph-all.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/mxgraph-all.jar similarity index 100% rename from backend/lib/mxgraph-all.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/mxgraph-all.jar diff --git a/backend/lib/stax-utils-20070216.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/stax-utils-20070216.jar similarity index 100% rename from backend/lib/stax-utils-20070216.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/stax-utils-20070216.jar diff --git a/backend/lib/vecmath-1.5.2.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/vecmath-1.5.2.jar similarity index 100% rename from backend/lib/vecmath-1.5.2.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/vecmath-1.5.2.jar diff --git a/backend/lib/xpp3-1.1.4c.jar b/SBOLCanvasBackend/WebContent/WEB-INF/lib/xpp3-1.1.4c.jar similarity index 100% rename from backend/lib/xpp3-1.1.4c.jar rename to SBOLCanvasBackend/WebContent/WEB-INF/lib/xpp3-1.1.4c.jar diff --git a/backend/web.xml b/SBOLCanvasBackend/WebContent/WEB-INF/web.xml similarity index 100% rename from backend/web.xml rename to SBOLCanvasBackend/WebContent/WEB-INF/web.xml diff --git a/SBOLCanvasBackend/WebContent/api.war b/SBOLCanvasBackend/WebContent/api.war new file mode 100644 index 00000000..9255a407 Binary files /dev/null and b/SBOLCanvasBackend/WebContent/api.war differ diff --git a/backend/src/data/CanvasAnnotation.java b/SBOLCanvasBackend/src/data/CanvasAnnotation.java similarity index 100% rename from backend/src/data/CanvasAnnotation.java rename to SBOLCanvasBackend/src/data/CanvasAnnotation.java diff --git a/backend/src/data/CombinatorialInfo.java b/SBOLCanvasBackend/src/data/CombinatorialInfo.java similarity index 100% rename from backend/src/data/CombinatorialInfo.java rename to SBOLCanvasBackend/src/data/CombinatorialInfo.java diff --git a/backend/src/data/GlyphInfo.java b/SBOLCanvasBackend/src/data/GlyphInfo.java similarity index 100% rename from backend/src/data/GlyphInfo.java rename to SBOLCanvasBackend/src/data/GlyphInfo.java diff --git a/backend/src/data/IdentifiedInfo.java b/SBOLCanvasBackend/src/data/IdentifiedInfo.java similarity index 100% rename from backend/src/data/IdentifiedInfo.java rename to SBOLCanvasBackend/src/data/IdentifiedInfo.java diff --git a/backend/src/data/Info.java b/SBOLCanvasBackend/src/data/Info.java similarity index 100% rename from backend/src/data/Info.java rename to SBOLCanvasBackend/src/data/Info.java diff --git a/backend/src/data/InteractionInfo.java b/SBOLCanvasBackend/src/data/InteractionInfo.java similarity index 97% rename from backend/src/data/InteractionInfo.java rename to SBOLCanvasBackend/src/data/InteractionInfo.java index 4630cb9b..79c2d272 100644 --- a/backend/src/data/InteractionInfo.java +++ b/SBOLCanvasBackend/src/data/InteractionInfo.java @@ -65,7 +65,7 @@ public Hashtable getTargetRefinement() { } public void setTargetRefinement(Hashtable targetRefinement) { - this.targetRefinement = targetRefinement; + this.targetRefinement = targetRefinement; } public Hashtable getFromURI() { diff --git a/backend/src/data/ModuleInfo.java b/SBOLCanvasBackend/src/data/ModuleInfo.java similarity index 100% rename from backend/src/data/ModuleInfo.java rename to SBOLCanvasBackend/src/data/ModuleInfo.java diff --git a/backend/src/data/VariableComponentInfo.java b/SBOLCanvasBackend/src/data/VariableComponentInfo.java similarity index 100% rename from backend/src/data/VariableComponentInfo.java rename to SBOLCanvasBackend/src/data/VariableComponentInfo.java diff --git a/backend/src/json/Success.java b/SBOLCanvasBackend/src/json/Success.java similarity index 100% rename from backend/src/json/Success.java rename to SBOLCanvasBackend/src/json/Success.java diff --git a/backend/src/servlets/Convert.java b/SBOLCanvasBackend/src/servlets/Convert.java similarity index 100% rename from backend/src/servlets/Convert.java rename to SBOLCanvasBackend/src/servlets/Convert.java diff --git a/backend/src/servlets/Data.java b/SBOLCanvasBackend/src/servlets/Data.java similarity index 100% rename from backend/src/servlets/Data.java rename to SBOLCanvasBackend/src/servlets/Data.java diff --git a/backend/src/servlets/Echo.java b/SBOLCanvasBackend/src/servlets/Echo.java similarity index 100% rename from backend/src/servlets/Echo.java rename to SBOLCanvasBackend/src/servlets/Echo.java diff --git a/backend/src/servlets/Enumerate.java b/SBOLCanvasBackend/src/servlets/Enumerate.java similarity index 100% rename from backend/src/servlets/Enumerate.java rename to SBOLCanvasBackend/src/servlets/Enumerate.java diff --git a/backend/src/servlets/Export.java b/SBOLCanvasBackend/src/servlets/Export.java similarity index 100% rename from backend/src/servlets/Export.java rename to SBOLCanvasBackend/src/servlets/Export.java diff --git a/SBOLCanvasBackend/src/servlets/SynBioHub.java b/SBOLCanvasBackend/src/servlets/SynBioHub.java new file mode 100644 index 00000000..9a08ad1f --- /dev/null +++ b/SBOLCanvasBackend/src/servlets/SynBioHub.java @@ -0,0 +1,365 @@ +package servlets; + +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.net.URI; +import java.net.URISyntaxException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.TreeSet; + +import javax.servlet.ServletOutputStream; +import javax.servlet.annotation.WebServlet; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import javax.xml.parsers.ParserConfigurationException; +import javax.xml.transform.TransformerException; +import javax.xml.transform.TransformerFactoryConfigurationError; + +import org.apache.commons.io.IOUtils; +import org.apache.http.HttpStatus; +import org.sbolstandard.core2.SBOLConversionException; +import org.sbolstandard.core2.SBOLDocument; +import org.sbolstandard.core2.SBOLReader; +import org.sbolstandard.core2.SBOLValidationException; +import org.sbolstandard.core2.SBOLWriter; +import org.synbiohub.frontend.IdentifiedMetadata; +import org.synbiohub.frontend.SearchCriteria; +import org.synbiohub.frontend.SearchQuery; +import org.synbiohub.frontend.SynBioHubException; +import org.synbiohub.frontend.SynBioHubFrontend; +import org.synbiohub.frontend.WebOfRegistriesData; +import org.xml.sax.SAXException; + +import com.google.gson.Gson; + +import utils.MxToSBOL; +import utils.SBOLData; +import utils.SBOLToMx; + +@SuppressWarnings("serial") +@WebServlet(urlPatterns = { "/SynBioHub/*" }) +public class SynBioHub extends HttpServlet { + + protected void doGet(HttpServletRequest request, HttpServletResponse response) throws IOException { + Gson gson = new Gson(); + try { + String body = null; + // parameters for the different methods + String authorization = request.getHeader("Authorization"); + String email = null; + String password = null; + String user = null; + if (authorization != null && authorization.split(":").length > 1) { + String[] tokens = authorization.split(":"); + email = tokens[0]; + password = tokens[1]; + } else { + user = authorization; + } + String server = request.getParameter("server"); + + if (request.getPathInfo().equals("/registries")) { + + List registries = null; + registries = SynBioHubFrontend.getRegistries(); + LinkedList registryURLs = new LinkedList(); + for (WebOfRegistriesData registry : registries) { + registryURLs.add(registry.getInstanceUrl()); + } + body = gson.toJson(registryURLs); + + } else if (request.getPathInfo().equals("/login")) { + + if (email == null || password == null || server == null || email.equals("") || password.equals("") + || server.equals("")) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + try { + sbhf.login(email, password); + } catch (SynBioHubException e) { + if (e.getMessage().equals("org.synbiohub.frontend.PermissionException")) { + response.setStatus(HttpStatus.SC_UNAUTHORIZED); + return; + } + throw e; + } + user = sbhf.getUser(); + body = user; + + } else if (request.getPathInfo().equals("/logout")) { + + if(server == null || user == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + sbhf.logout(); + response.setStatus(HttpStatus.SC_OK); + return; + + }else if (request.getPathInfo().equals("/listMyCollections")) { + + if (server == null || user == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + List collections = sbhf.getRootCollectionMetadata(); + collections.removeIf(collection -> (collection.getUri().contains("/public/"))); + body = gson.toJson(collections); + + } else if (request.getPathInfo().equals("/listRegistryParts")) { + String collection = request.getParameter("collection"); + String type = request.getParameter("type"); + String role = request.getParameter("role"); + String mode = request.getParameter("mode"); + + if (mode == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + if (user != null) + sbhf.setUser(user); + + TreeSet roles = null; + TreeSet types = null; + TreeSet collections = null; + if (role != null && role.length() > 0) { + roles = new TreeSet(); + if (SBOLData.roles.ContainsKey(role)) + roles.add(SBOLData.roles.getValue(role)); + else + roles.add(SBOLData.refinements.getValue(role)); + } + if (type != null && type.length() > 0) { + types = new TreeSet(); + types.add(SBOLData.types.getValue(type)); + } + if (collection != null) { + collections = new TreeSet(); + collections.add(URI.create(collection)); + } + + ArrayList results = new ArrayList(); + if (mode.equals("collections")) { + if (collections == null) { + results.addAll(sbhf.getRootCollectionMetadata()); + } else { + for (URI collectionURI : collections) { + results.addAll(sbhf.getSubCollectionMetadata(collectionURI)); + } + } + } else if (mode.equals("components") && collections != null) { + results.addAll( + sbhf.getMatchingComponentDefinitionMetadata(null, roles, types, collections, null, null)); + } else if (mode.equals("modules") && collections != null) { + // SynbioHubFrontend doesn't have anything easy for modules + SearchQuery query = new SearchQuery(); + + SearchCriteria objectCriteria = new SearchCriteria(); + objectCriteria.setKey("objectType"); + objectCriteria.setValue("ModuleDefinition"); + query.addCriteria(objectCriteria); + + if (collections != null) { + for (URI uri : collections) { + SearchCriteria collectionCriteria = new SearchCriteria(); + collectionCriteria.setKey("collection"); + collectionCriteria.setValue(uri.toString()); + query.getCriteria().add(collectionCriteria); + } + } + + results.addAll(sbhf.search(query)); + } + + body = gson.toJson(results.toArray(new IdentifiedMetadata[0])); + + } else if (request.getPathInfo().equals("/listLayouts")) { + //TODO come back to me + } else if (request.getPathInfo().equals("/listCombinatorials")) { + String template = request.getParameter("template"); + + ArrayList results = new ArrayList(); + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + + SearchQuery query = new SearchQuery(); + + SearchCriteria objectTypeCriteria = new SearchCriteria(); + objectTypeCriteria.setKey("objectType"); + objectTypeCriteria.setValue("CombinatorialDerivation"); + query.addCriteria(objectTypeCriteria); + + SearchCriteria sbolTagCriteria = new SearchCriteria(); + sbolTagCriteria.setKey("template"); + sbolTagCriteria.setValue(template); + query.addCriteria(sbolTagCriteria); + + results.addAll(sbhf.search(query)); + + body = gson.toJson(results.toArray(new IdentifiedMetadata[0])); + + } else if (request.getPathInfo().equals("/getRegistryPart")) { + String uri = request.getParameter("uri"); + if (uri == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + + String combinatorial = request.getParameter("combinatorial"); + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + SBOLToMx converter = new SBOLToMx(); + + String layoutURI = uri.substring(0,uri.lastIndexOf("/"))+"_Layout"+uri.substring(uri.lastIndexOf("/"), uri.length()); + SBOLDocument document; + try { + document = sbhf.getSBOL(URI.create(layoutURI), true); + }catch(SynBioHubException e) { + document = sbhf.getSBOL(URI.create(uri), true); + } + if(document == null) { + document = sbhf.getSBOL(URI.create(uri), true); + } + + SBOLDocument combDocument = null; + if(combinatorial != null) { + combDocument = sbhf.getSBOL(URI.create(combinatorial), true); + } + + converter.toGraph(document, combDocument, response.getOutputStream()); + response.setStatus(HttpStatus.SC_OK); + return; + }else if(request.getPathInfo().equals("/importRegistryPart")) { + String uri = request.getParameter("uri"); + if(uri == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + SBOLToMx converter = new SBOLToMx(); + + String layoutURI = uri.substring(0,uri.lastIndexOf("/"))+"_Layout"+uri.substring(uri.lastIndexOf("/"), uri.length()); + SBOLDocument document; + try { + document = sbhf.getSBOL(URI.create(layoutURI), true); + if(document == null) { + document = sbhf.getSBOL(URI.create(uri), true); + } + }catch(SynBioHubException e) { + document = sbhf.getSBOL(URI.create(uri), true); + } + + converter.toGraph(document, response.getOutputStream()); + response.setStatus(HttpStatus.SC_OK); + return; + } else { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + + ServletOutputStream outputStream = response.getOutputStream(); + InputStream inputStream = new ByteArrayInputStream(body.getBytes()); + IOUtils.copy(inputStream, outputStream); + + // the request was good + response.setStatus(HttpStatus.SC_OK); + response.setContentType("application/json"); + return; + } catch (SynBioHubException | IOException | ParserConfigurationException | TransformerException | SBOLValidationException | SAXException | URISyntaxException e) { + ServletOutputStream outputStream = response.getOutputStream(); + InputStream inputStream = new ByteArrayInputStream(e.getMessage().getBytes()); + IOUtils.copy(inputStream, outputStream); + + response.setStatus(HttpStatus.SC_INTERNAL_SERVER_ERROR); + + e.printStackTrace(); + } + } + + protected void doPost(HttpServletRequest request, HttpServletResponse response) throws IOException { + try { + String server = request.getParameter("server"); + String user = request.getHeader("Authorization"); + String uri = request.getParameter("uri"); + + if (request.getPathInfo().equals("/addToCollection")) { + + if (server == null || user == null || uri == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + HashMap userTokens = new HashMap(); + String[] servers = user.split(","); + for(String serverInf : servers) { + String[] tokens = serverInf.split(" "); + userTokens.put(tokens[0], tokens[1]); + } + + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(userTokens.get(server)); + MxToSBOL converter = new MxToSBOL(userTokens); + ByteArrayOutputStream out = new ByteArrayOutputStream(); + converter.toSBOL(request.getInputStream(), out); + sbhf.addToCollection(URI.create(uri), true, new ByteArrayInputStream(out.toByteArray())); + response.setStatus(HttpStatus.SC_CREATED); + } else if(request.getPathInfo().contentEquals("/importToCollection")) { + if(server == null || user == null || uri == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + SBOLDocument document = SBOLReader.read(request.getInputStream()); + ByteArrayOutputStream out = new ByteArrayOutputStream(); + SBOLWriter.setKeepGoing(true); + SBOLWriter.write(document, out); + sbhf.addToCollection(URI.create(uri), true, new ByteArrayInputStream(out.toByteArray())); + response.setStatus(HttpStatus.SC_CREATED); + } else if(request.getPathInfo().contentEquals("/createCollection")) { + String id = request.getParameter("id"); + String version = request.getParameter("version"); + String name = request.getParameter("name"); + String description = request.getParameter("description"); + String citations = request.getParameter("citations"); + String overwrite = request.getParameter("overwrite"); + + if(server == null || user == null || id == null || version == null || name == null || description == null || overwrite == null) { + response.setStatus(HttpStatus.SC_BAD_REQUEST); + return; + } + SynBioHubFrontend sbhf = new SynBioHubFrontend(server); + sbhf.setUser(user); + sbhf.createCollection(id, version, name, description, citations, overwrite.equals("true")); + response.setStatus(HttpStatus.SC_CREATED); + } + + } catch (SynBioHubException | IOException | SBOLValidationException | SBOLConversionException | TransformerFactoryConfigurationError | TransformerException | URISyntaxException e) { + ServletOutputStream outputStream = response.getOutputStream(); + InputStream inputStream = new ByteArrayInputStream(e.getMessage().getBytes()); + IOUtils.copy(inputStream, outputStream); + + response.setStatus(HttpStatus.SC_INTERNAL_SERVER_ERROR); + } + + } + +} diff --git a/backend/src/utils/BiMap.java b/SBOLCanvasBackend/src/utils/BiMap.java similarity index 100% rename from backend/src/utils/BiMap.java rename to SBOLCanvasBackend/src/utils/BiMap.java diff --git a/backend/src/utils/Constants.java b/SBOLCanvasBackend/src/utils/Constants.java similarity index 100% rename from backend/src/utils/Constants.java rename to SBOLCanvasBackend/src/utils/Constants.java diff --git a/backend/src/utils/Converter.java b/SBOLCanvasBackend/src/utils/Converter.java similarity index 100% rename from backend/src/utils/Converter.java rename to SBOLCanvasBackend/src/utils/Converter.java diff --git a/backend/src/utils/LayoutHelper.java b/SBOLCanvasBackend/src/utils/LayoutHelper.java similarity index 100% rename from backend/src/utils/LayoutHelper.java rename to SBOLCanvasBackend/src/utils/LayoutHelper.java diff --git a/backend/src/utils/MxToSBOL.java b/SBOLCanvasBackend/src/utils/MxToSBOL.java similarity index 94% rename from backend/src/utils/MxToSBOL.java rename to SBOLCanvasBackend/src/utils/MxToSBOL.java index bb0404ac..a94c425c 100644 --- a/backend/src/utils/MxToSBOL.java +++ b/SBOLCanvasBackend/src/utils/MxToSBOL.java @@ -587,11 +587,9 @@ private void linkComponentDefinition(SBOLDocument document, mxGraph graph, mxGra Component previous = null; int count = 0, start = 0, end = 0; for (mxCell glyph : glyphs) { - - GlyphInfo info = (GlyphInfo) infoDict.get(glyph.getValue()); - // ComponentDefinition glyphCD = document.getComponentDefinition(URI.create((String) glyph.getValue())); - ComponentDefinition glyphCD = getComponentDefinitionBetter(document, URI.create((String) glyph.getValue())); - Component component = compDef.createComponent( + GlyphInfo info = (GlyphInfo) infoDict.get(glyph.getValue()); + ComponentDefinition glyphCD = document.getComponentDefinition(URI.create((String) glyph.getValue())); + Component component = compDef.createComponent( info.getDisplayID() + "_" + glyph.getParent().getIndex(glyph), AccessType.PUBLIC, URI.create((String) glyph.getValue())); @@ -911,7 +909,9 @@ private void addParticipant(SBOLDocument document, mxGraphModel model, ModuleDef participantInfo = (GlyphInfo) infoDict.get(participantCell.getValue()); participantParentCell = (mxCell) participantCell.getParent(); } - if (participantCell != null) { + // More null checking here; was getting NullPointerException sometimes + if (document != null && modDef != null && participantInfo != null && + participantCell != null && participantParentCell != null) { FunctionalComponent participantFC = getOrCreateParticipantFC(document, modDef, participantInfo, participantCell, participantParentCell); URI participantRole = getParticipantType(isSource, interaction.getTypes()); @@ -936,6 +936,9 @@ private void addParticipant(SBOLDocument document, mxGraphModel model, ModuleDef layoutHelper.addGraphicalNode(modDef.getIdentity(), participation.getDisplayId(), interactionEdge); } } + else { + System.out.println("RELATED TO GITHUB ISSUE #174: FAILED NULL CHECK"); + } } private FunctionalComponent getOrCreateParticipantFC(SBOLDocument document, ModuleDefinition modDef, @@ -993,6 +996,12 @@ private mxGraph parseGraph(InputStream graphStream) throws IOException { */ @SuppressWarnings("unchecked") private Hashtable loadDictionary(ArrayList dataContainer, int dictionaryIndex) { + // previously was getting out of bounds exception sometimes, + // hoping to catch it with this + if(dictionaryIndex >= dataContainer.size()) { + System.out.println("ARRAY INDEX OUT OF BOUNDS: " + dictionaryIndex); + return new Hashtable(); + } if (dataContainer.get(dictionaryIndex) instanceof ArrayList) { // 90% sure it only happens when it's empty meaning that we could just return a // empty hash table. @@ -1016,54 +1025,4 @@ private Hashtable loadDictionary(ArrayList d } } - /* - Not using the libSBOLj method because it skips the entire document - when one top-level throws an exception, which causes it to skip copying - the actual ComponentDefintion sometimes. - */ - private ComponentDefinition getComponentDefinitionBetter(SBOLDocument document, URI componentDefinitionURI) { - - // Try to find ComponentDefinition in document - for(ComponentDefinition cd : document.getComponentDefinitions()) { - if(cd.getIdentity().equals(componentDefinitionURI)) - return cd; - } - - // Look in SynBioHub for it - for (SynBioHubFrontend frontend : document.getRegistries()) { - - // Fetch from SynBioHub - SBOLDocument remoteDocument = null; - try { - remoteDocument = frontend.getSBOL(componentDefinitionURI); - } - catch(SynBioHubException e) { - System.out.println(e); - // e.printStackTrace(); - } - - if (remoteDocument != null) { - /* - Create a copy of each top level. - - Not using the libSBOLj method because it skips the entire document - when one top-level throws an exception, which causes it to skip copying - the actual ComponentDefintion sometimes. - */ - for (TopLevel topLevel : remoteDocument.getTopLevels()) { - try { - document.createCopy(topLevel); - } - catch(SBOLValidationException e) { - System.out.println("Failed to copy top-level:\n" + topLevel.getIdentity()); - System.out.println(e); - // e.printStackTrace(); - } - } - return remoteDocument.getComponentDefinition(componentDefinitionURI); - } - } - - return null; - } } diff --git a/backend/src/utils/SBOLData.java b/SBOLCanvasBackend/src/utils/SBOLData.java similarity index 96% rename from backend/src/utils/SBOLData.java rename to SBOLCanvasBackend/src/utils/SBOLData.java index 77bca892..c97153ff 100644 --- a/backend/src/utils/SBOLData.java +++ b/SBOLCanvasBackend/src/utils/SBOLData.java @@ -50,8 +50,7 @@ public class SBOLData { roles.put("RBS (Ribosome Binding Site)", SequenceOntology.RIBOSOME_ENTRY_SITE); roles.put("CDS (Coding Sequence)", SequenceOntology.CDS); roles.put("Ter (Terminator)", SequenceOntology.TERMINATOR); - roles.put("Cir (Circular Backbone Left)", SequenceOntology.CIRCULAR); - roles.put("Cir (Circular Backbone Right)", SequenceOntology.CIRCULAR); + roles.put("Cir (Circular Backbone)", SequenceOntology.CIRCULAR); roles.put("gRNA (Non-Coding RNA gene)", URI.create("http://identifiers.org/so/SO:0001263")); roles.put("Ori (Origin of Replication)", SequenceOntology.ORIGIN_OF_REPLICATION); roles.put("OriT (Origin of Transfer)", URI.create("http://identifiers.org/so/SO:0000724")); @@ -100,7 +99,6 @@ public class SBOLData { interactions.put("Genetic Production", SystemsBiologyOntology.GENETIC_PRODUCTION); interactions.put("Control", SystemsBiologyOntology.CONTROL); interactions.put("Dissociation", SystemsBiologyOntology.DISSOCIATION); - interactions.put("Process", SystemsBiologyOntology.PROCESS); interactionRoles = new BiMap(); interactionRoles.put("Inhibitor", SystemsBiologyOntology.INHIBITOR); @@ -121,7 +119,6 @@ public class SBOLData { interactionTargetRoles.put(SystemsBiologyOntology.GENETIC_PRODUCTION, SystemsBiologyOntology.PRODUCT); interactionTargetRoles.put(SystemsBiologyOntology.CONTROL, SystemsBiologyOntology.MODIFIED); interactionTargetRoles.put(SystemsBiologyOntology.DISSOCIATION, SystemsBiologyOntology.PRODUCT); - interactionTargetRoles.put(SystemsBiologyOntology.PROCESS, SystemsBiologyOntology.PRODUCT); interactionSourceRoles = new HashMap(); interactionSourceRoles.put(SystemsBiologyOntology.INHIBITION, SystemsBiologyOntology.INHIBITOR); @@ -132,7 +129,6 @@ public class SBOLData { interactionSourceRoles.put(SystemsBiologyOntology.GENETIC_PRODUCTION, SystemsBiologyOntology.TEMPLATE); interactionSourceRoles.put(SystemsBiologyOntology.CONTROL, SystemsBiologyOntology.MODIFIER); interactionSourceRoles.put(SystemsBiologyOntology.DISSOCIATION, SystemsBiologyOntology.REACTANT); - interactionSourceRoles.put(SystemsBiologyOntology.PROCESS, SystemsBiologyOntology.REACTANT); registries = new HashSet(); try { diff --git a/backend/src/utils/SBOLToMx.java b/SBOLCanvasBackend/src/utils/SBOLToMx.java similarity index 100% rename from backend/src/utils/SBOLToMx.java rename to SBOLCanvasBackend/src/utils/SBOLToMx.java diff --git a/SBOLCanvasFrontend/.editorconfig b/SBOLCanvasFrontend/.editorconfig new file mode 100644 index 00000000..e89330a6 --- /dev/null +++ b/SBOLCanvasFrontend/.editorconfig @@ -0,0 +1,13 @@ +# Editor configuration, see https://editorconfig.org +root = true + +[*] +charset = utf-8 +indent_style = space +indent_size = 2 +insert_final_newline = true +trim_trailing_whitespace = true + +[*.md] +max_line_length = off +trim_trailing_whitespace = false diff --git a/frontend/.gitignore b/SBOLCanvasFrontend/.gitignore similarity index 90% rename from frontend/.gitignore rename to SBOLCanvasFrontend/.gitignore index 0fc3dfbd..f4f46a5f 100644 --- a/frontend/.gitignore +++ b/SBOLCanvasFrontend/.gitignore @@ -4,10 +4,8 @@ /dist /tmp /out-tsc -*bundle.xml # Only exists if Bazel was run /bazel-out -package-lock.json # dependencies /node_modules @@ -42,8 +40,6 @@ npm-debug.log yarn-error.log testem.log /typings -*.ps1 -src/environments/versions.ts # System Files .DS_Store diff --git a/frontend/README.md b/SBOLCanvasFrontend/README.md similarity index 86% rename from frontend/README.md rename to SBOLCanvasFrontend/README.md index 2d5a88c0..3787f5fd 100644 --- a/frontend/README.md +++ b/SBOLCanvasFrontend/README.md @@ -12,7 +12,7 @@ Run `ng generate component component-name` to generate a new component. You can ## Build -Run `npm build` to build the project for production. The build artifacts will be stored in the `dist/` directory. +Run `ng build` to build the project. The build artifacts will be stored in the `dist/` directory. Use the `--prod` flag for a production build. ## Running unit tests diff --git a/frontend/angular.json b/SBOLCanvasFrontend/angular.json similarity index 98% rename from frontend/angular.json rename to SBOLCanvasFrontend/angular.json index f2c05cb8..f94dfeb7 100644 --- a/frontend/angular.json +++ b/SBOLCanvasFrontend/angular.json @@ -13,7 +13,7 @@ "build": { "builder": "@angular-devkit/build-angular:browser", "options": { - "outputPath": "dist", + "outputPath": "dist/SBOLCanvasFrontend", "index": "src/index.html", "main": "src/main.ts", "polyfills": "src/polyfills.ts", diff --git a/frontend/e2e/protractor.conf.js b/SBOLCanvasFrontend/e2e/protractor.conf.js similarity index 100% rename from frontend/e2e/protractor.conf.js rename to SBOLCanvasFrontend/e2e/protractor.conf.js diff --git a/frontend/e2e/src/app.e2e-spec.ts b/SBOLCanvasFrontend/e2e/src/app.e2e-spec.ts similarity index 100% rename from frontend/e2e/src/app.e2e-spec.ts rename to SBOLCanvasFrontend/e2e/src/app.e2e-spec.ts diff --git a/frontend/e2e/src/app.po.ts b/SBOLCanvasFrontend/e2e/src/app.po.ts similarity index 100% rename from frontend/e2e/src/app.po.ts rename to SBOLCanvasFrontend/e2e/src/app.po.ts diff --git a/frontend/e2e/tsconfig.e2e.json b/SBOLCanvasFrontend/e2e/tsconfig.e2e.json similarity index 100% rename from frontend/e2e/tsconfig.e2e.json rename to SBOLCanvasFrontend/e2e/tsconfig.e2e.json diff --git a/frontend/git.version.ts b/SBOLCanvasFrontend/git.version.ts similarity index 100% rename from frontend/git.version.ts rename to SBOLCanvasFrontend/git.version.ts diff --git a/SBOLCanvasFrontend/package-lock.json b/SBOLCanvasFrontend/package-lock.json new file mode 100644 index 00000000..342ed3f2 --- /dev/null +++ b/SBOLCanvasFrontend/package-lock.json @@ -0,0 +1,10735 @@ +{ + "name": "sbolcanvas-frontend", + "version": "0.0.0", + "lockfileVersion": 1, + "requires": true, + "dependencies": { + "@angular-devkit/architect": { + "version": "0.13.8", + "resolved": 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+ }, + "zone.js": { + "version": "0.8.29", + "resolved": "https://registry.npmjs.org/zone.js/-/zone.js-0.8.29.tgz", + "integrity": "sha512-mla2acNCMkWXBD+c+yeUrBUrzOxYMNFdQ6FGfigGGtEVBPJx07BQeJekjt9DmH1FtZek4E9rE1eRR9qQpxACOQ==" + } + } +} diff --git a/frontend/package.json b/SBOLCanvasFrontend/package.json similarity index 81% rename from frontend/package.json rename to SBOLCanvasFrontend/package.json index 0136f31f..19877e06 100644 --- a/frontend/package.json +++ b/SBOLCanvasFrontend/package.json @@ -3,10 +3,7 @@ "version": "0.0.0", "scripts": { "bundle-report": "ng build --prod --stats-json && webpack-bundle-analyzer dist/SBOLCanvasFrontend/stats.json", - "prebuild": "npm rebuild node-sass && ts-node -O \"{\\\"module\\\":\\\"commonjs\\\"}\" git.version.ts && node assetBundler.js", - "build": "ng build --prod --build-optimizer --vendor-chunk --progress --output-hashing=all --stats-json --source-map=true", - "predev": "npm run prebuild", - "dev": "ng serve -o" + "prebuild.prod": "ts-node -O \"{\\\"module\\\":\\\"commonjs\\\"}\" git.version.ts" }, "private": true, "dependencies": { @@ -29,8 +26,6 @@ "jquery": "^3.5.0", "material-community-components": "^3.4.0", "mxgraph": "^3.9.12", - "nanoid": "^4.0.0", - "nanoid-dictionary": "^4.3.0", "ng-sidebar": "^8.0.0", "ngx-bootstrap": "^4.0.0", "popper.js": "^1.15.0", @@ -61,8 +56,5 @@ "tslint": "~5.11.0", "typescript": "~3.2.2", "webpack-bundle-analyzer": "^3.6.0" - }, - "engines": { - "npm": "<7" } } diff --git a/frontend/src/app/CustomShapes.ts b/SBOLCanvasFrontend/src/app/CustomShapes.ts similarity index 97% rename from frontend/src/app/CustomShapes.ts rename to SBOLCanvasFrontend/src/app/CustomShapes.ts index 0e70cce6..24429c82 100644 --- a/frontend/src/app/CustomShapes.ts +++ b/SBOLCanvasFrontend/src/app/CustomShapes.ts @@ -69,8 +69,7 @@ export class CustomShapes { this.variant.paint(c); } else if (this.error != null && !CustomShapes.graphService.hasSequence(this.state.cell)) { this.error.bounds = this.getErrorBounds(x, y, w, h); - // disabling error painting in favor of problems panel - // this.error.paint(c); + this.error.paint(c); } } SequenceFeatureShape.prototype.getCompositeBounds = function (x, y, w, h) { //mx.mxLabel.prototype.getIndicatorBounds; diff --git a/frontend/src/app/app-routing.module.ts b/SBOLCanvasFrontend/src/app/app-routing.module.ts similarity index 100% rename from frontend/src/app/app-routing.module.ts rename to SBOLCanvasFrontend/src/app/app-routing.module.ts diff --git a/frontend/src/app/app.component.css b/SBOLCanvasFrontend/src/app/app.component.css similarity index 100% rename from frontend/src/app/app.component.css rename to SBOLCanvasFrontend/src/app/app.component.css diff --git a/frontend/src/app/app.component.html b/SBOLCanvasFrontend/src/app/app.component.html similarity index 100% rename from frontend/src/app/app.component.html rename to SBOLCanvasFrontend/src/app/app.component.html diff --git a/frontend/src/app/app.component.spec.ts b/SBOLCanvasFrontend/src/app/app.component.spec.ts similarity index 100% rename from frontend/src/app/app.component.spec.ts rename to SBOLCanvasFrontend/src/app/app.component.spec.ts diff --git a/frontend/src/app/app.component.ts b/SBOLCanvasFrontend/src/app/app.component.ts similarity index 100% rename from frontend/src/app/app.component.ts rename to SBOLCanvasFrontend/src/app/app.component.ts diff --git a/SBOLCanvasFrontend/src/app/app.module.ts b/SBOLCanvasFrontend/src/app/app.module.ts new file mode 100644 index 00000000..f349f295 --- /dev/null +++ b/SBOLCanvasFrontend/src/app/app.module.ts @@ -0,0 +1,109 @@ +import {BrowserModule} from '@angular/platform-browser'; +import {NgModule} from '@angular/core'; +import {FormsModule} from '@angular/forms'; +import {ReactiveFormsModule} from '@angular/forms'; // Added for color picker. + +import { AppComponent } from './app.component'; +import { ToolbarComponent } from './toolbar/toolbar.component'; +import { GlyphMenuComponent } from './glyph-menu/glyph-menu.component'; +import { CanvasComponent } from './canvas/canvas.component'; +import { DesignMenuComponent } from './design-menu/design-menu.component'; +import { InfoEditorComponent } from './info-editor/info-editor.component'; +import { HomeComponent } from './home/home.component'; +import { AppRoutingModule } from './app-routing.module'; +import { HttpClientModule, HTTP_INTERCEPTORS } from '@angular/common/http'; +import { AppHttpInterceptor } from './http.interceptor'; + +// for warning against leaving the page with unsaved changes +import { PendingChangesGuard} from './pending-changes.guard'; + +// Angular Material stuff. This is a different UI library than ng-bootstrap. +import {BrowserAnimationsModule} from '@angular/platform-browser/animations'; +import { MaterialModule } from './material.module'; +import { FlexLayoutModule } from '@angular/flex-layout'; + +import {GraphService} from './graph.service'; + +// Color Picker imports. +import {MccColorPickerModule} from 'material-community-components'; +import {MetadataService} from './metadata.service'; +import { BannerComponent } from './banner/banner.component'; +import { ColorPickerComponent } from './color-picker/color-picker.component'; +import { UploadGraphComponent } from './upload-graph/upload-graph.component'; +import { LoginComponent } from './login/login.component'; +import { DownloadGraphComponent } from './download-graph/download-graph.component'; +import { ErrorComponent } from './error/error.component'; +import { SearchfilterPipe } from './searchfilter.pipe'; +import { ExportImageComponent } from './export-image/export-image.component'; +import { LandingPageComponent } from './landing-page/landing-page.component'; +import { TutorialComponent } from './tutorial/tutorial.component'; +import { ConfirmComponent } from './confirm/confirm.component'; +import { FuncCompSelectorComponent } from './func-comp-selector/func-comp-selector.component'; +import { ExportDesignComponent } from './export-design/export-design.component'; +import { CollectionCreationComponent } from './collection-creation/collection-creation.component'; +import { CombinatorialDesignEditorComponent } from './combinatorial-design-editor/combinatorial-design-editor.component'; +import { LoadGraphComponent } from './load-graph/load-graph.component'; + + +@NgModule({ + declarations: [ + AppComponent, + ToolbarComponent, + GlyphMenuComponent, + CanvasComponent, + DesignMenuComponent, + InfoEditorComponent, + HomeComponent, + BannerComponent, + ColorPickerComponent, + UploadGraphComponent, + DownloadGraphComponent, + LoginComponent, + DownloadGraphComponent, + ErrorComponent, + SearchfilterPipe, + ExportImageComponent, + LandingPageComponent, + TutorialComponent, + ConfirmComponent, + FuncCompSelectorComponent, + ExportDesignComponent, + CollectionCreationComponent, + CombinatorialDesignEditorComponent, + LoadGraphComponent, + ], + imports: [ + BrowserModule, + FormsModule, + AppRoutingModule, + BrowserModule, // BrowserModule must come before all @angular/material modules for some reason. + BrowserAnimationsModule, + HttpClientModule, + MccColorPickerModule.forRoot({ + used_colors: ['#000000', '#123456', '#777666'] + }), + ReactiveFormsModule, + MaterialModule, + FlexLayoutModule + ], + providers: [PendingChangesGuard, GraphService, MetadataService, { + provide: HTTP_INTERCEPTORS, useClass: AppHttpInterceptor, multi: true + }], + bootstrap: [AppComponent], + entryComponents: [ + ToolbarComponent, + UploadGraphComponent, + DownloadGraphComponent, + ExportImageComponent, + ExportDesignComponent, + CollectionCreationComponent, + LoginComponent, + ErrorComponent, + ConfirmComponent, + FuncCompSelectorComponent, + CombinatorialDesignEditorComponent, + ColorPickerComponent, + LoadGraphComponent ] +}) +export class AppModule { +} diff --git a/frontend/src/app/banner/banner.component.css b/SBOLCanvasFrontend/src/app/banner/banner.component.css similarity index 100% rename from frontend/src/app/banner/banner.component.css rename to SBOLCanvasFrontend/src/app/banner/banner.component.css diff --git a/frontend/src/app/banner/banner.component.html b/SBOLCanvasFrontend/src/app/banner/banner.component.html similarity index 100% rename from frontend/src/app/banner/banner.component.html rename to SBOLCanvasFrontend/src/app/banner/banner.component.html diff --git a/frontend/src/app/banner/banner.component.spec.ts b/SBOLCanvasFrontend/src/app/banner/banner.component.spec.ts similarity index 100% rename from frontend/src/app/banner/banner.component.spec.ts rename to SBOLCanvasFrontend/src/app/banner/banner.component.spec.ts diff --git a/frontend/src/app/banner/banner.component.ts b/SBOLCanvasFrontend/src/app/banner/banner.component.ts similarity index 100% rename from frontend/src/app/banner/banner.component.ts rename to SBOLCanvasFrontend/src/app/banner/banner.component.ts diff --git a/frontend/src/app/canvas/canvas.component.css b/SBOLCanvasFrontend/src/app/canvas/canvas.component.css similarity index 100% rename from frontend/src/app/canvas/canvas.component.css rename to SBOLCanvasFrontend/src/app/canvas/canvas.component.css diff --git a/frontend/src/app/canvas/canvas.component.html b/SBOLCanvasFrontend/src/app/canvas/canvas.component.html similarity index 100% rename from frontend/src/app/canvas/canvas.component.html rename to SBOLCanvasFrontend/src/app/canvas/canvas.component.html diff --git a/frontend/src/app/canvas/canvas.component.spec.ts b/SBOLCanvasFrontend/src/app/canvas/canvas.component.spec.ts similarity index 100% rename from frontend/src/app/canvas/canvas.component.spec.ts rename to SBOLCanvasFrontend/src/app/canvas/canvas.component.spec.ts diff --git a/SBOLCanvasFrontend/src/app/canvas/canvas.component.ts b/SBOLCanvasFrontend/src/app/canvas/canvas.component.ts new file mode 100644 index 00000000..11007fed --- /dev/null +++ b/SBOLCanvasFrontend/src/app/canvas/canvas.component.ts @@ -0,0 +1,22 @@ +import {Component, ElementRef, OnInit, ViewChild} from '@angular/core'; +import { GraphService } from '../graph.service'; + +@Component({ + selector: 'app-canvas', + templateUrl: './canvas.component.html', + styleUrls: ['./canvas.component.css'] +}) +export class CanvasComponent implements OnInit { + + constructor( + private graphService: GraphService + ) {} + + @ViewChild('canvasContainer') canvasContainer: ElementRef; + + ngOnInit() { + const canvasContainer = this.canvasContainer.nativeElement; + const svg = this.graphService.getGraphDOM(); + canvasContainer.appendChild(svg); + } +} diff --git a/frontend/src/app/canvasAnnotation.ts b/SBOLCanvasFrontend/src/app/canvasAnnotation.ts similarity index 100% rename from frontend/src/app/canvasAnnotation.ts rename to SBOLCanvasFrontend/src/app/canvasAnnotation.ts diff --git a/frontend/src/app/collection-creation/collection-creation.component.css b/SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.css similarity index 100% rename from frontend/src/app/collection-creation/collection-creation.component.css rename to SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.css diff --git a/frontend/src/app/collection-creation/collection-creation.component.html b/SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.html similarity index 100% rename from frontend/src/app/collection-creation/collection-creation.component.html rename to SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.html diff --git a/frontend/src/app/collection-creation/collection-creation.component.spec.ts b/SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.spec.ts similarity index 100% rename from frontend/src/app/collection-creation/collection-creation.component.spec.ts rename to SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.spec.ts diff --git a/frontend/src/app/collection-creation/collection-creation.component.ts b/SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.ts similarity index 100% rename from frontend/src/app/collection-creation/collection-creation.component.ts rename to SBOLCanvasFrontend/src/app/collection-creation/collection-creation.component.ts diff --git a/frontend/src/app/color-picker/color-picker.component.css b/SBOLCanvasFrontend/src/app/color-picker/color-picker.component.css similarity index 100% rename from frontend/src/app/color-picker/color-picker.component.css rename to SBOLCanvasFrontend/src/app/color-picker/color-picker.component.css diff --git a/frontend/src/app/color-picker/color-picker.component.html b/SBOLCanvasFrontend/src/app/color-picker/color-picker.component.html similarity index 100% rename from frontend/src/app/color-picker/color-picker.component.html rename to SBOLCanvasFrontend/src/app/color-picker/color-picker.component.html diff --git a/frontend/src/app/color-picker/color-picker.component.spec.ts b/SBOLCanvasFrontend/src/app/color-picker/color-picker.component.spec.ts similarity index 100% rename from frontend/src/app/color-picker/color-picker.component.spec.ts rename to SBOLCanvasFrontend/src/app/color-picker/color-picker.component.spec.ts diff --git a/frontend/src/app/color-picker/color-picker.component.ts b/SBOLCanvasFrontend/src/app/color-picker/color-picker.component.ts similarity index 100% rename from frontend/src/app/color-picker/color-picker.component.ts rename to SBOLCanvasFrontend/src/app/color-picker/color-picker.component.ts diff --git a/frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.css b/SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.css similarity index 100% rename from frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.css rename to SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.css diff --git a/frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.html b/SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.html similarity index 100% rename from frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.html rename to SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.html diff --git a/frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.spec.ts b/SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.spec.ts similarity index 100% rename from frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.spec.ts rename to SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.spec.ts diff --git a/frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.ts b/SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.ts similarity index 100% rename from frontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.ts rename to SBOLCanvasFrontend/src/app/combinatorial-design-editor/combinatorial-design-editor.component.ts diff --git a/frontend/src/app/combinatorialInfo.ts b/SBOLCanvasFrontend/src/app/combinatorialInfo.ts similarity index 100% rename from frontend/src/app/combinatorialInfo.ts rename to SBOLCanvasFrontend/src/app/combinatorialInfo.ts diff --git a/frontend/src/app/confirm/confirm.component.css b/SBOLCanvasFrontend/src/app/confirm/confirm.component.css similarity index 100% rename from frontend/src/app/confirm/confirm.component.css rename to SBOLCanvasFrontend/src/app/confirm/confirm.component.css diff --git a/frontend/src/app/confirm/confirm.component.html b/SBOLCanvasFrontend/src/app/confirm/confirm.component.html similarity index 100% rename from frontend/src/app/confirm/confirm.component.html rename to SBOLCanvasFrontend/src/app/confirm/confirm.component.html diff --git a/frontend/src/app/confirm/confirm.component.spec.ts b/SBOLCanvasFrontend/src/app/confirm/confirm.component.spec.ts similarity index 100% rename from frontend/src/app/confirm/confirm.component.spec.ts rename to SBOLCanvasFrontend/src/app/confirm/confirm.component.spec.ts diff --git a/frontend/src/app/confirm/confirm.component.ts b/SBOLCanvasFrontend/src/app/confirm/confirm.component.ts similarity index 100% rename from frontend/src/app/confirm/confirm.component.ts rename to SBOLCanvasFrontend/src/app/confirm/confirm.component.ts diff --git a/frontend/src/app/design-menu/design-menu.component.css b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.css similarity index 96% rename from frontend/src/app/design-menu/design-menu.component.css rename to SBOLCanvasFrontend/src/app/design-menu/design-menu.component.css index 4be40c17..56ce3f07 100644 --- a/frontend/src/app/design-menu/design-menu.component.css +++ b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.css @@ -51,6 +51,3 @@ img { vertical-align:middle; } -.design-menu-container h4 { - margin: 0; -} \ No newline at end of file diff --git a/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.html b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.html new file mode 100644 index 00000000..1a9001a9 --- /dev/null +++ b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.html @@ -0,0 +1,248 @@ +
+
+ + Stroke + +
+ +
Color:
+ + +
+ +
+ +
+ +
+ +
Opacity:
+ + +
+ + + +
+ +
+ +
+ +
Width:
+ + +
+ + + +
+ +
+ + + +
+ +
+ + Fill + +
+ +
Color:
+ + +
+ +
+ +
+ +
+ +
Opacity:
+ + +
+ + + +
+ +
+
+ + + +
+ + +
+ + Edge + +
+ +
Style:
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ +
Corner:
+ + +
+ + Sharp + Rounded + Curved + +
+ +
+ +
+ +
Arrow Size:
+ + +
+ + + +
+ +
+ +
+ +
Source Margin:
+ + +
+ + + +
+ +
+
+ +
+ +
Target Margin:
+ + +
+ + + +
+ +
+
+ + +
+ + +
+ + Font + +
+ +
Color:
+ + +
+ +
+ +
+ +
+ +
Opacity:
+ + +
+ + + +
+ +
+ +
+ +
Size:
+ + +
+ + + +
+ +
+ + +
+
diff --git a/frontend/src/app/design-menu/design-menu.component.spec.ts b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.spec.ts similarity index 100% rename from frontend/src/app/design-menu/design-menu.component.spec.ts rename to SBOLCanvasFrontend/src/app/design-menu/design-menu.component.spec.ts diff --git a/frontend/src/app/design-menu/design-menu.component.ts b/SBOLCanvasFrontend/src/app/design-menu/design-menu.component.ts similarity index 100% rename from frontend/src/app/design-menu/design-menu.component.ts rename to SBOLCanvasFrontend/src/app/design-menu/design-menu.component.ts diff --git a/frontend/src/app/download-graph/download-graph.component.css b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.css similarity index 100% rename from frontend/src/app/download-graph/download-graph.component.css rename to SBOLCanvasFrontend/src/app/download-graph/download-graph.component.css diff --git a/frontend/src/app/download-graph/download-graph.component.html b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.html similarity index 98% rename from frontend/src/app/download-graph/download-graph.component.html rename to SBOLCanvasFrontend/src/app/download-graph/download-graph.component.html index b47e381b..6cf5fb1a 100644 --- a/frontend/src/app/download-graph/download-graph.component.html +++ b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.html @@ -6,7 +6,7 @@

Download

Server + (selectionChange)="setRegistry($event.value)"> {{registry}} diff --git a/frontend/src/app/download-graph/download-graph.component.spec.ts b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.spec.ts similarity index 100% rename from frontend/src/app/download-graph/download-graph.component.spec.ts rename to SBOLCanvasFrontend/src/app/download-graph/download-graph.component.spec.ts diff --git a/frontend/src/app/download-graph/download-graph.component.ts b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.ts similarity index 93% rename from frontend/src/app/download-graph/download-graph.component.ts rename to SBOLCanvasFrontend/src/app/download-graph/download-graph.component.ts index 8de6a692..244233b4 100644 --- a/frontend/src/app/download-graph/download-graph.component.ts +++ b/SBOLCanvasFrontend/src/app/download-graph/download-graph.component.ts @@ -63,16 +63,6 @@ export class DownloadGraphComponent implements OnInit { constructor(@Inject(MAT_DIALOG_DATA) public data: any, private dialog: MatDialog, private metadataService: MetadataService, private graphService: GraphService, private filesService: FilesService, private loginService: LoginService, public dialogRef: MatDialogRef) { } ngOnInit() { - // check if there is a saved registry and collection information - if (this.metadataService.getSavedRegistry() !== undefined) this.registry = this.metadataService.getSavedRegistry(); - if (this.metadataService.getSavedCollection() !== undefined) { - this.collection = this.metadataService.getSavedCollection().collection; - this.history = this.metadataService.getSavedCollection().history; - } else { - this.collection = ""; - this.history = []; - } - this.working = true; if (this.data != null) { if (this.data.mode != null) { @@ -118,9 +108,10 @@ export class DownloadGraphComponent implements OnInit { this.working = false; }); } - this.updateParts(); this.parts.sort = this.sort; + this.history = []; + this.collection = ""; } loginDisabled(): boolean { @@ -137,7 +128,6 @@ export class DownloadGraphComponent implements OnInit { setRegistry(registry: string) { this.registry = registry; - this.metadataService.setSavedRegistry(registry); this.updateParts(); } @@ -182,9 +172,7 @@ export class DownloadGraphComponent implements OnInit { // only allowed to get here when there is one item selected, and it's a collection let row = this.selection.selected[0]; this.history.push(row); - this.metadataService.setSavedCollection({ collection: row.uri, history: this.history }); this.selection.clear(); - this.updateParts(); } @@ -234,7 +222,6 @@ export class DownloadGraphComponent implements OnInit { if (row.type === DownloadGraphComponent.collectionType) { this.history.push(row); this.collection = row.uri; - this.metadataService.setSavedCollection({ collection: this.collection, history: this.history }); this.selection.clear(); this.updateParts(); } else if (row.type === DownloadGraphComponent.componentType) { @@ -308,9 +295,7 @@ export class DownloadGraphComponent implements OnInit { } changeCollection(collection: string) { - console.log(collection) this.selection.clear(); - let found = false; for (let i = 0; i < this.history.length; i++) { if (this.history[i] === collection) { @@ -321,9 +306,7 @@ export class DownloadGraphComponent implements OnInit { } if (!found) this.history.length = 0; - this.collection = collection; - this.metadataService.setSavedCollection({ collection: collection, history: this.history }); this.updateParts(); } diff --git a/frontend/src/app/load-graph/load-graph.component.css b/SBOLCanvasFrontend/src/app/error/error.component.css similarity index 100% rename from frontend/src/app/load-graph/load-graph.component.css rename to SBOLCanvasFrontend/src/app/error/error.component.css diff --git a/SBOLCanvasFrontend/src/app/error/error.component.html b/SBOLCanvasFrontend/src/app/error/error.component.html new file mode 100644 index 00000000..e741077c --- /dev/null +++ b/SBOLCanvasFrontend/src/app/error/error.component.html @@ -0,0 +1,9 @@ + +

Error

+
+

{{message}}

+
+
+ +
+ diff --git a/frontend/src/app/error/error.component.spec.ts b/SBOLCanvasFrontend/src/app/error/error.component.spec.ts similarity index 100% rename from frontend/src/app/error/error.component.spec.ts rename to SBOLCanvasFrontend/src/app/error/error.component.spec.ts diff --git a/frontend/src/app/error/error.component.ts b/SBOLCanvasFrontend/src/app/error/error.component.ts similarity index 100% rename from frontend/src/app/error/error.component.ts rename to SBOLCanvasFrontend/src/app/error/error.component.ts diff --git a/frontend/src/app/export-design/export-design.component.css b/SBOLCanvasFrontend/src/app/export-design/export-design.component.css similarity index 100% rename from frontend/src/app/export-design/export-design.component.css rename to SBOLCanvasFrontend/src/app/export-design/export-design.component.css diff --git a/frontend/src/app/export-design/export-design.component.html b/SBOLCanvasFrontend/src/app/export-design/export-design.component.html similarity index 100% rename from frontend/src/app/export-design/export-design.component.html rename to SBOLCanvasFrontend/src/app/export-design/export-design.component.html diff --git a/frontend/src/app/export-design/export-design.component.spec.ts b/SBOLCanvasFrontend/src/app/export-design/export-design.component.spec.ts similarity index 100% rename from frontend/src/app/export-design/export-design.component.spec.ts rename to SBOLCanvasFrontend/src/app/export-design/export-design.component.spec.ts diff --git a/frontend/src/app/export-design/export-design.component.ts b/SBOLCanvasFrontend/src/app/export-design/export-design.component.ts similarity index 100% rename from frontend/src/app/export-design/export-design.component.ts rename to SBOLCanvasFrontend/src/app/export-design/export-design.component.ts diff --git a/frontend/src/app/export-image/export-image.component.css b/SBOLCanvasFrontend/src/app/export-image/export-image.component.css similarity index 100% rename from frontend/src/app/export-image/export-image.component.css rename to SBOLCanvasFrontend/src/app/export-image/export-image.component.css diff --git a/frontend/src/app/export-image/export-image.component.html b/SBOLCanvasFrontend/src/app/export-image/export-image.component.html similarity index 100% rename from frontend/src/app/export-image/export-image.component.html rename to SBOLCanvasFrontend/src/app/export-image/export-image.component.html diff --git a/frontend/src/app/export-image/export-image.component.spec.ts b/SBOLCanvasFrontend/src/app/export-image/export-image.component.spec.ts similarity index 100% rename from frontend/src/app/export-image/export-image.component.spec.ts rename to SBOLCanvasFrontend/src/app/export-image/export-image.component.spec.ts diff --git a/frontend/src/app/export-image/export-image.component.ts b/SBOLCanvasFrontend/src/app/export-image/export-image.component.ts similarity index 100% rename from frontend/src/app/export-image/export-image.component.ts rename to SBOLCanvasFrontend/src/app/export-image/export-image.component.ts diff --git a/frontend/src/app/files.service.spec.ts b/SBOLCanvasFrontend/src/app/files.service.spec.ts similarity index 100% rename from frontend/src/app/files.service.spec.ts rename to SBOLCanvasFrontend/src/app/files.service.spec.ts diff --git a/frontend/src/app/files.service.ts b/SBOLCanvasFrontend/src/app/files.service.ts similarity index 94% rename from frontend/src/app/files.service.ts rename to SBOLCanvasFrontend/src/app/files.service.ts index 0f83f1c7..e355206a 100644 --- a/frontend/src/app/files.service.ts +++ b/SBOLCanvasFrontend/src/app/files.service.ts @@ -93,19 +93,6 @@ export class FilesService { }); } - exportDesignToString(users: {}, format: string, contents: string): Observable { - return new Observable(observer => { - let headers = new HttpHeaders(); - headers = headers.set("Authorization", this.usersToStringArr(users)); - let params = new HttpParams(); - params = params.append("format", format); - - this.http.post(this.exportDesignURL, contents, { headers: headers, responseType: 'text', params: params }).subscribe(result => { - observer.next(result); - }); - }); - } - enumerateDesign(users: {}, filename: string, format: string, contents: string): Observable { return new Observable(observer => { let headers = new HttpHeaders(); diff --git a/frontend/src/app/func-comp-selector/func-comp-selector.component.css b/SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.css similarity index 100% rename from frontend/src/app/func-comp-selector/func-comp-selector.component.css rename to SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.css diff --git a/frontend/src/app/func-comp-selector/func-comp-selector.component.html b/SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.html similarity index 100% rename from frontend/src/app/func-comp-selector/func-comp-selector.component.html rename to SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.html diff --git a/frontend/src/app/func-comp-selector/func-comp-selector.component.spec.ts b/SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.spec.ts similarity index 100% rename from frontend/src/app/func-comp-selector/func-comp-selector.component.spec.ts rename to SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.spec.ts diff --git a/frontend/src/app/func-comp-selector/func-comp-selector.component.ts b/SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.ts similarity index 100% rename from frontend/src/app/func-comp-selector/func-comp-selector.component.ts rename to SBOLCanvasFrontend/src/app/func-comp-selector/func-comp-selector.component.ts diff --git a/frontend/src/app/glyph-menu/glyph-menu.component.css b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.css similarity index 54% rename from frontend/src/app/glyph-menu/glyph-menu.component.css rename to SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.css index 9a94e7d8..df7c87fb 100644 --- a/frontend/src/app/glyph-menu/glyph-menu.component.css +++ b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.css @@ -5,26 +5,8 @@ } .glyphContainer { - /* width: 250px; */ - /* padding: 5px; */ -} - -.flexWrapper { - display: flex; - flex-direction: column; -} - -.searchBar { - margin: 15px 10px -20px 10px; -} - -.glyphMenuSection { - box-shadow: none; - background: transparent; -} - -.glyphGrid { - margin: 0 -10px; + width: 250px; + padding: 5px; } :host ::ng-deep .mat-form-field-appearance-outline .mat-form-field-infix { diff --git a/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.html b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.html new file mode 100644 index 00000000..67b57a2d --- /dev/null +++ b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.html @@ -0,0 +1,135 @@ +
+
+ + + + + + + + + + + + + + + + + + + Sequence Features + + + + + + + + + + + + + + + + + + Molecular Species + + + + + + + + + + + + + + + + + Interactions + + + + + + + + + + + + + + + + + Interaction Nodes + + + + + + + + + + + + + + + + + Util + + + + + + + + + + + + + + + + +
+
diff --git a/frontend/src/app/glyph-menu/glyph-menu.component.spec.ts b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.spec.ts similarity index 100% rename from frontend/src/app/glyph-menu/glyph-menu.component.spec.ts rename to SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.spec.ts diff --git a/frontend/src/app/glyph-menu/glyph-menu.component.ts b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.ts similarity index 98% rename from frontend/src/app/glyph-menu/glyph-menu.component.ts rename to SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.ts index 8c03b17d..4ebad558 100644 --- a/frontend/src/app/glyph-menu/glyph-menu.component.ts +++ b/SBOLCanvasFrontend/src/app/glyph-menu/glyph-menu.component.ts @@ -149,10 +149,6 @@ export class GlyphMenuComponent implements OnInit, AfterViewInit { this.graphService.addBackbone(); } - addCircularPlasmid() { - this.graphService.addCircularPlasmid(); - } - addTextBox() { this.graphService.addTextBox(); } diff --git a/frontend/src/app/glyph.service.spec.ts b/SBOLCanvasFrontend/src/app/glyph.service.spec.ts similarity index 100% rename from frontend/src/app/glyph.service.spec.ts rename to SBOLCanvasFrontend/src/app/glyph.service.spec.ts diff --git a/SBOLCanvasFrontend/src/app/glyph.service.ts b/SBOLCanvasFrontend/src/app/glyph.service.ts new file mode 100644 index 00000000..ed29698a --- /dev/null +++ b/SBOLCanvasFrontend/src/app/glyph.service.ts @@ -0,0 +1,186 @@ +import { Injectable } from '@angular/core'; + +declare var require: any; +const mx = require('mxgraph')({ + mxImageBasePath: 'mxgraph/images', + mxBasePath: 'mxgraph' +}); + +@Injectable({ + providedIn: 'root' +}) +export class GlyphService { + + // TODO load list of xml files from server + private sequenceFeatureXMLs: string[] = [ + // Strand glyphs + 'assets/glyph_stencils/sequence_feature/engineered-region.xml', + 'assets/glyph_stencils/sequence_feature/promoter.xml', + 'assets/glyph_stencils/sequence_feature/ribosome-entry-site.xml', + 'assets/glyph_stencils/sequence_feature/cds.xml', + 'assets/glyph_stencils/sequence_feature/terminator-specification.xml', + 'assets/glyph_stencils/sequence_feature/ncrna.xml', + 'assets/glyph_stencils/sequence_feature/origin-of-replication.xml', + 'assets/glyph_stencils/sequence_feature/origin-of-transfer.xml', + 'assets/glyph_stencils/sequence_feature/primer-binding-site.xml', + 'assets/glyph_stencils/sequence_feature/five-prime-sticky-restriction-site.xml', + 'assets/glyph_stencils/sequence_feature/three-prime-sticky-restriction-site.xml', + 'assets/glyph_stencils/sequence_feature/assembly-scar.xml', + 'assets/glyph_stencils/sequence_feature/operator.xml', + 'assets/glyph_stencils/sequence_feature/insulator.xml', + 'assets/glyph_stencils/sequence_feature/blunt-restriction-site.xml', + 'assets/glyph_stencils/sequence_feature/three-prime-overhang.xml', + 'assets/glyph_stencils/sequence_feature/five-prime-overhang.xml', + 'assets/glyph_stencils/sequence_feature/aptamer.xml', + //'assets/glyph_stencils/sequence_feature/dna-stability-element.xml', + 'assets/glyph_stencils/sequence_feature/polyA.xml', + 'assets/glyph_stencils/sequence_feature/specific-recombination-site.xml', + 'assets/glyph_stencils/sequence_feature/no-glyph-assigned.xml', + 'assets/glyph_stencils/sequence_feature/signature.xml', + 'assets/glyph_stencils/sequence_feature/location-dna.xml', + 'assets/glyph_stencils/sequence_feature/location-rna.xml', + 'assets/glyph_stencils/sequence_feature/location-protein.xml', + 'assets/glyph_stencils/sequence_feature/nuclease-site.xml', + 'assets/glyph_stencils/sequence_feature/protease-site.xml', + 'assets/glyph_stencils/sequence_feature/protein-stability-element.xml', + 'assets/glyph_stencils/sequence_feature/ribonuclease-site.xml', + 'assets/glyph_stencils/sequence_feature/rna-stability-element.xml', + //'assets/glyph_stencils/sequence_feature/chromosomal-locus.xml', + //'assets/glyph_stencils/sequence_feature/circular-plasmid.xml', + 'assets/glyph_stencils/sequence_feature/transcription-end.xml', + 'assets/glyph_stencils/sequence_feature/translation-end.xml', + //'assets/glyph_stencils/sequence_feature/test.xml', + ]; + + private molecularSpeciesXMLs: string[] = [ + // 'molecular species' glyphs aka protein? + 'assets/glyph_stencils/molecular_species/macromolecule.xml', + 'assets/glyph_stencils/molecular_species/dsNA.xml', + 'assets/glyph_stencils/molecular_species/ssNA.xml', + 'assets/glyph_stencils/molecular_species/small-molecule.xml', + 'assets/glyph_stencils/molecular_species/no-glyph-assigned-ms.xml', + 'assets/glyph_stencils/molecular_species/replacement-glyph.xml', + 'assets/glyph_stencils/molecular_species/complex.xml', + ]; + + private interactionXMLs: string[] = [ + 'assets/glyph_stencils/interactions/control.xml', + 'assets/glyph_stencils/interactions/inhibition.xml', + 'assets/glyph_stencils/interactions/stimulation.xml', + 'assets/glyph_stencils/interactions/process.xml', + 'assets/glyph_stencils/interactions/degradation.xml', + ]; + + private interactionNodeXMLs: string[] = [ + 'assets/glyph_stencils/interaction_nodes/association.xml', + 'assets/glyph_stencils/interaction_nodes/dissociation.xml', + 'assets/glyph_stencils/interaction_nodes/process.xml', + 'assets/glyph_stencils/molecular_species/replacement-glyph.xml', + ] + + private indicatorXMLs: string[] = [ + 'assets/glyph_stencils/indicators/composite.xml', + 'assets/glyph_stencils/indicators/variant.xml', + 'assets/glyph_stencils/indicators/error.xml', + ]; + + private utilXMLs: string[] = [ + 'assets/backbone.xml', + 'assets/textBox.xml', + 'assets/module.xml', + ]; + + private sequenceFeatures: any = {}; + private molecularSpecies: any = {}; + private interactions: any = {}; + private interactionNodes: any = {}; + private indicators: any = {}; + private utils: any = {}; + + constructor() { + this.loadXMLs(this.sequenceFeatureXMLs, this.sequenceFeatures); + this.loadXMLs(this.molecularSpeciesXMLs, this.molecularSpecies); + this.loadXMLs(this.interactionNodeXMLs, this.interactionNodes); + this.loadXMLs(this.interactionXMLs, this.interactions); + this.loadXMLs(this.indicatorXMLs, this.indicators); + this.loadXMLs(this.utilXMLs, this.utils); + } + + loadXMLs(xml_list, glyph_list) { + xml_list.forEach((filename) => { + let req = mx.mxUtils.load(filename); + let root = req.getDocumentElement(); + let shape = root.firstChild; + + + while (shape != null) { + if (shape.nodeType == mx.mxConstants.NODETYPE_ELEMENT) { + const name = shape.getAttribute('name'); + const centered = shape.getAttribute('centered'); + + const stencil = new mx.mxStencil(shape); + + glyph_list[name] = [stencil, (centered && centered.toLowerCase() == 'true')]; + } + shape = shape.nextSibling; + } + }); + } + + getElements(glyph_list) { + const svgs = {}; + + for (const name in glyph_list) { + const stencil = glyph_list[name][0]; + + let elt = document.createElement('svg'); + let canvas = new mx.mxSvgCanvas2D(elt); + let shape = new mx.mxShape(stencil); + + canvas.setStrokeColor('#000000'); + canvas.setFillColor('none'); + + stencil.drawShape(canvas, shape, 0, 0, 50, 50); + + svgs[name] = elt; + } + + return svgs; + } + + getSequenceFeatureGlyphs() { + return this.sequenceFeatures; + } + + getMolecularSpeciesGlyphs() { + return this.molecularSpecies; + } + + getIndicatorGlyphs(){ + return this.indicators; + } + + getInteractionNodeGlyphs(){ + return this.interactionNodes; + } + + getUtilElements() { + return this.getElements(this.utils) + } + + getInteractionElements() { + return this.getElements(this.interactions); + } + + getInteractionNodeElements(){ + return this.getElements(this.interactionNodes); + } + + getMolecularSpeciesElements() { + return this.getElements(this.molecularSpecies); + } + + getSequenceFeatureElements() { + return this.getElements(this.sequenceFeatures); + } +} diff --git a/SBOLCanvasFrontend/src/app/glyphInfo.ts b/SBOLCanvasFrontend/src/app/glyphInfo.ts new file mode 100644 index 00000000..8bb9724b --- /dev/null +++ b/SBOLCanvasFrontend/src/app/glyphInfo.ts @@ -0,0 +1,130 @@ +import { ParsedEventType } from '@angular/compiler'; +import { CanvasAnnotation } from './canvasAnnotation'; +import { Info } from './info'; +import { environment } from 'src/environments/environment'; + +export class GlyphInfo extends Info{ + // Remember that when you change this you need to change the encode function in graph service + static counter: number = 0; + partType: string; + otherTypes: string[]; + partRole: string; + otherRoles: string[]; + partRefine: string; + name: string; + description: string; + version: string; + sequence: string; + sequenceURI: string; + annotations: CanvasAnnotation[]; + derivedFroms: string[]; + generatedBys: string[]; + + constructor(partType?: string) { + super(); + this.displayID = 'id' + (GlyphInfo.counter++); + if (partType) { + this.partType = partType; + } else { + this.partType = 'DNA region'; + } + } + + makeCopy() { + const copy: GlyphInfo = new GlyphInfo(); + copy.partType = this.partType; + copy.otherTypes = this.otherTypes ? this.otherTypes.slice() : null; + copy.partRole = this.partRole; + copy.otherRoles = this.otherRoles ? this.otherRoles.slice() : null; + copy.partRefine = this.partRefine; + copy.displayID = this.displayID; + copy.name = this.name; + copy.description = this.description; + copy.version = this.version; + copy.sequence = this.sequence; + copy.sequenceURI = this.sequenceURI; + copy.uriPrefix = this.uriPrefix; + copy.annotations = this.annotations ? this.annotations.slice() : null; + copy.derivedFroms = this.derivedFroms ? this.derivedFroms.slice() : null; + copy.generatedBys = this.generatedBys ? this.generatedBys.slice() : null; + return copy; + } + + copyDataFrom(other: GlyphInfo) { + this.partType = other.partType; + this.otherTypes = other.otherTypes ? other.otherTypes.slice() : null; + this.partRole = other.partRole; + this.otherRoles = other.otherRoles ? other.otherRoles.slice() : null; + this.partRefine = other.partRefine; + this.displayID = other.displayID; + this.name = other.name; + this.description = other.description; + this.version = other.version; + this.sequence = other.sequence; + this.sequenceURI = other.sequenceURI; + this.uriPrefix = other.uriPrefix; + this.annotations = other.annotations ? other.annotations.slice() : null; + this.derivedFroms = other.derivedFroms ? other.derivedFroms.slice() : null; + this.generatedBys = other.generatedBys ? other.generatedBys.slice() : null; + } + + getFullURI(): string { + let fullURI = this.uriPrefix + '/' + this.displayID; + if (this.version && this.version.length > 0) { + fullURI += '/' + this.version; + } + return fullURI; + } + + encode(enc: any) { + let node = enc.document.createElement('GlyphInfo'); + if (this.partType) + node.setAttribute("partType", this.partType); + if (this.otherTypes) { + let otherTypesNode = enc.encode(this.otherTypes); + otherTypesNode.setAttribute("as", "otherTypes"); + node.appendChild(otherTypesNode); + } + if (this.partRole) + node.setAttribute("partRole", this.partRole); + if (this.otherRoles) { + let otherRolesNode = enc.encode(this.otherRoles); + otherRolesNode.setAttribute("as", "otherRoles"); + node.appendChild(otherRolesNode); + } + if (this.partRefine) + node.setAttribute("partRefine", this.partRefine); + if (this.displayID) + node.setAttribute("displayID", this.displayID); + if (this.name && this.name.length > 0) + node.setAttribute("name", this.name); + if (this.description && this.description.length > 0) + node.setAttribute("description", this.description); + if (this.version && this.version.length > 0) + node.setAttribute("version", this.version); + if (this.sequence && this.sequence.length > 0) + node.setAttribute("sequence", this.sequence); + if(this.sequenceURI && this.sequenceURI.length > 0) + node.setAttribute("sequenceURI", this.sequenceURI); + if (this.uriPrefix) + node.setAttribute("uriPrefix", this.uriPrefix); + + if (this.annotations) { + let annotationsNode = enc.encode(this.annotations); + annotationsNode.setAttribute("as", "annotations"); + node.appendChild(annotationsNode); + } + if(this.derivedFroms){ + let derivedFromsNode = enc.encode(this.derivedFroms); + derivedFromsNode.setAttribute("as", "derivedFroms"); + node.appendChild(derivedFromsNode); + } + if(this.generatedBys){ + let generatedBysNode = enc.encode(this.generatedBys); + generatedBysNode.setAttribute("as", "generatedBys"); + node.appendChild(generatedBysNode); + } + + return node; + } +} diff --git a/frontend/src/app/graph-base.spec.ts b/SBOLCanvasFrontend/src/app/graph-base.spec.ts similarity index 100% rename from frontend/src/app/graph-base.spec.ts rename to SBOLCanvasFrontend/src/app/graph-base.spec.ts diff --git a/frontend/src/app/graph-base.ts b/SBOLCanvasFrontend/src/app/graph-base.ts similarity index 93% rename from frontend/src/app/graph-base.ts rename to SBOLCanvasFrontend/src/app/graph-base.ts index 5c912403..bfd23e64 100644 --- a/frontend/src/app/graph-base.ts +++ b/SBOLCanvasFrontend/src/app/graph-base.ts @@ -291,18 +291,18 @@ export class GraphBase { reconstructCellStyle = true; else if (cell.style === GraphBase.STYLE_MOLECULAR_SPECIES || cell.style.includes(GraphBase.STYLE_MOLECULAR_SPECIES + ";")) reconstructCellStyle = true; - else if (cell.style === GraphBase.STYLE_INTERACTION || cell.style.includes(GraphBase.STYLE_INTERACTION + ";")) + else if (cell.style === GraphBase.STYLE_INTERACTION || cell.style.includes(GraphBase.STYLE_INTERACTION+";")) reconstructCellStyle = true; - else if (cell.style === GraphBase.STYLE_INTERACTION_NODE || cell.style.includes(GraphBase.STYLE_INTERACTION_NODE + ";")) + else if (cell.style === GraphBase.STYLE_INTERACTION_NODE || cell.style.includes(GraphBase.STYLE_INTERACTION_NODE+";")) reconstructCellStyle = true; } // reconstruct the cell style if (reconstructCellStyle) { if (glyphDict[cell.value] != null) { - if (glyphDict[cell.value] instanceof ModuleInfo) { + if(glyphDict[cell.value] instanceof ModuleInfo){ // module - if (!cell.style) { + if(!cell.style){ cell.style = GraphBase.STYLE_MODULE; } cell.geometry.width = GraphBase.defaultModuleWidth; @@ -318,7 +318,7 @@ export class GraphBase { cell.geometry.width = GraphBase.sequenceFeatureGlyphWidth; if (cell.geometry.height == 0) cell.geometry.height = GraphBase.sequenceFeatureGlyphHeight; - } else if (glyphDict[cell.value] instanceof GlyphInfo) { + } else if(glyphDict[cell.value] instanceof GlyphInfo){ // molecular species if (!cell.style) cell.style = GraphBase.STYLE_MOLECULAR_SPECIES + "macromolecule"; @@ -329,17 +329,17 @@ export class GraphBase { } } else if (interactionDict[cell.value] != null) { let intInfo = interactionDict[cell.value]; - if (cell.isVertex()) { + if(cell.isVertex()){ // interaction node let name = graphBaseRef.interactionNodeTypeToName(intInfo.interactionType); - if (!cell.style) { - cell.style = GraphBase.STYLE_INTERACTION_NODE + name; - } else { + if(!cell.style){ + cell.style = GraphBase.STYLE_INTERACTION_NODE+name; + }else{ cell.style = cell.style.replace(GraphBase.STYLE_INTERACTION_NODE, GraphBase.STYLE_INTERACTION_NODE + name); } cell.geometry.width = GraphBase.interactionNodeGlyphWidth; cell.geometry.height = GraphBase.interactionNodeGlyphHeight; - } else { + }else{ // interaction let name = intInfo.interactionType; if (name == "Biochemical Reaction" || name == "Non-Covalent Binding" || name == "Genetic Production") { @@ -528,9 +528,8 @@ export class GraphBase { const layout = new mx.mxStackLayout(graph, true); layout.resizeParent = true; layout.isVertexIgnored = function (vertex) { - return vertex.isBackbone(); + return vertex.isBackbone() }; - layout.execute(this); }; @@ -776,14 +775,13 @@ export class GraphBase { // we need this if we intend on creating custom shapes with stencils let sequenceFeatureStencils = this.glyphService.getSequenceFeatureGlyphs(); - let utilStencils = this.glyphService.getUtilGlyphs() mx.mxCellRenderer.prototype.createShape = function (state) { var shape = null; if (state.style != null) { let stencilName = state.style[mx.mxConstants.STYLE_SHAPE]; var stencil = mx.mxStencilRegistry.getStencil(stencilName); - if (sequenceFeatureStencils[stencilName] != null || utilStencils[stencilName] != null) { + if (sequenceFeatureStencils[stencilName] != null) { shape = new CustomShapes.SequenceFeatureShape(stencil); } else if (stencil != null) { shape = new mx.mxShape(stencil); @@ -796,48 +794,47 @@ export class GraphBase { return shape; } - const registerSequenceFeatureShapes = stencils => { - for (const name in stencils) { - // Create a new copy of the stencil for the graph. - const stencil = stencils[name][0]; - const centered = stencils[name][1]; - let customStencil = new mx.mxStencil(stencil.desc); // Makes a deep copy - // Change the copied stencil for mxgraph - let origDrawShape = mx.mxStencil.prototype.drawShape; + // custom stencil setup + let stencils = this.glyphService.getSequenceFeatureGlyphs(); - if (centered) { - customStencil.drawShape = function (canvas, shape, x, y, w, h) { - h /= 2; - y += h / 2; - origDrawShape.apply(this, [canvas, shape, x, y, w, h]); + for (const name in stencils) { + // Create a new copy of the stencil for the graph. + const stencil = stencils[name][0]; + const centered = stencils[name][1]; + let customStencil = new mx.mxStencil(stencil.desc); // Makes a deep copy - shape.paintComposite(canvas, x, y - (h / 2), w, h * 2); - } - } else { - customStencil.drawShape = function (canvas, shape, x, y, w, h) { - h = h / 2; - origDrawShape.apply(this, [canvas, shape, x, y, w, h]); + // Change the copied stencil for mxgraph + let origDrawShape = mx.mxStencil.prototype.drawShape; - shape.paintComposite(canvas, x, y, w, h * 2); - } - } + if (centered) { + customStencil.drawShape = function (canvas, shape, x, y, w, h) { + h /= 2; + y += h / 2; + origDrawShape.apply(this, [canvas, shape, x, y, w, h]); - // Add the stencil to the registry and set its style. - mx.mxStencilRegistry.addStencil(name, customStencil); + shape.paintComposite(canvas, x, y - (h / 2), w, h * 2); + } + } else { + customStencil.drawShape = function (canvas, shape, x, y, w, h) { + h = h / 2; + origDrawShape.apply(this, [canvas, shape, x, y, w, h]); - const newGlyphStyle = mx.mxUtils.clone(this.baseSequenceFeatureGlyphStyle); - newGlyphStyle[mx.mxConstants.STYLE_SHAPE] = name; - this.graph.getStylesheet().putCellStyle(GraphBase.STYLE_SEQUENCE_FEATURE + name, newGlyphStyle); + shape.paintComposite(canvas, x, y, w, h * 2); + } } - } - registerSequenceFeatureShapes(this.glyphService.getSequenceFeatureGlyphs()) - registerSequenceFeatureShapes(this.glyphService.getUtilGlyphs()) + // Add the stencil to the registry and set its style. + mx.mxStencilRegistry.addStencil(name, customStencil); + + const newGlyphStyle = mx.mxUtils.clone(this.baseSequenceFeatureGlyphStyle); + newGlyphStyle[mx.mxConstants.STYLE_SHAPE] = name; + this.graph.getStylesheet().putCellStyle(GraphBase.STYLE_SEQUENCE_FEATURE + name, newGlyphStyle); + } // molecularSpecies glyphs are simpler, since we don't have to morph // them to always be centred on the strand - let stencils = this.glyphService.getMolecularSpeciesGlyphs(); + stencils = this.glyphService.getMolecularSpeciesGlyphs(); for (const name in stencils) { const stencil = stencils[name][0]; let customStencil = new mx.mxStencil(stencil.desc); // Makes of deep copy of the stencil. @@ -990,10 +987,10 @@ export class GraphBase { infoCopy.targetRefinement = {}; // add back refinements relating to ours - if (sourceRefinement) { + if(sourceRefinement){ infoCopy.sourceRefinement[edge.getId()] = sourceRefinement; } - if (targetRefinement) { + if(targetRefinement){ infoCopy.targetRefinement[edge.getId()] = targetRefinement; } @@ -1018,28 +1015,28 @@ export class GraphBase { let oldURI = edge.value; let nodeInfo = this.getFromInteractionDict(terminal.value).makeCopy(); this.graph.getModel().setValue(edge, nodeInfo.getFullURI()); - + // duplicate over the nescessary info // module targets - if (infoCopy.fromURI[edge.getId()]) { + if(infoCopy.fromURI[edge.getId()]){ nodeInfo.fromURI[edge.getId()] = infoCopy.fromURI[edge.getId()]; } - if (infoCopy.toURI[edge.getId()]) { + if(infoCopy.toURI[edge.getId()]){ nodeInfo.toURI[edge.getId()] = infoCopy.toURI[edge.getId()]; } // edge refinements let sourceRefinement = infoCopy.sourceRefinement[edge.getId()]; - if (sourceRefinement) { + if(sourceRefinement){ nodeInfo.sourceRefinement[edge.getId()] = sourceRefinement; } let targetRefinement = infoCopy.targetRefinement[edge.getId()]; - if (targetRefinement) { + if(targetRefinement){ nodeInfo.targetRefinement[edge.getId()] = targetRefinement; } // if the previous wasn't an interaction node, then we need to remove the info from the dictionary - if (!previous || !previous.isInteractionNode()) { + if(!previous || !previous.isInteractionNode()){ this.removeFromInteractionDict(oldURI); } @@ -1071,8 +1068,8 @@ export class GraphBase { // cell movement this.graph.addListener(mx.mxEvent.MOVE_CELLS, mx.mxUtils.bind(this, async function (sender, evt) { // sender is the graph + sender.getModel().beginUpdate(); - let cancelled = false; try { let movedCells = evt.getProperty("cells"); @@ -1080,7 +1077,7 @@ export class GraphBase { // can appear here (even if they were also selected) // sort cells: processing order is important - movedCells = movedCells.sort(function (cellA, cellB) { + movedCells = movedCells.sort(function (cellA, cellB) { if (cellA.getRootId() !== cellB.getRootId()) { // cells are not related: choose arbitrary order (but still group by root) return cellA.getRootId() < cellB.getRootId() ? -1 : 1; @@ -1128,7 +1125,6 @@ export class GraphBase { if (!movedCells[i].isSequenceFeatureGlyph()) { continue; } - // found a sequenceFeature glyph. A streak might be starting... const baseX = movedCells[i].getGeometry().x; const rootId = movedCells[i].getRootId(); @@ -1159,6 +1155,16 @@ export class GraphBase { this.horizontalSortBasedOnPosition(circuitContainer); } + // finallly, another special case: if a circuitContainer only has one sequenceFeatureGlyph, + // moving the glyph should move the circuitContainer + for (const cell of movedCells) { + if (cell.isSequenceFeatureGlyph() && cell.getParent().children.length === 2) { + const x = cell.getParent().getGeometry().x + evt.getProperty("dx"); + const y = cell.getParent().getGeometry().y + evt.getProperty("dy"); + cell.getParent().replaceGeometry(x, y, 'auto', 'auto', sender); + } + } + // sync circuit containers let circuitContainers = new Set(); for (let movedCell of movedCells) { @@ -1170,29 +1176,6 @@ export class GraphBase { this.syncCircuitContainer(circuitContainer); } - for (const cell of movedCells) { - // another special case: if a circuitContainer only has one sequenceFeatureGlyph, - // moving the glyph should move the circuitContainer - if (cell.isSequenceFeatureGlyph() && cell.getParent().children.length === 2) { - const x = cell.getParent().getGeometry().x + evt.getProperty("dx"); - const y = cell.getParent().getGeometry().y + evt.getProperty("dy"); - cell.getParent().replaceGeometry(x, y, "auto", "auto", sender); - } - - // special case where an empty circular backbone's circuit container is moved - // fixes the containers position and the right circular backbones x position - if((cell.circularBackbone && cell.children.length === 3)) { - this.repositionCircularBackbone(cell); - } - } - - // special case where a circular backbone is repositioned within a circuit container - if(movedCells[0].getParent().circularBackbone - && movedCells.filter(cell => cell.stayAtBeginning || cell.stayAtEnd).length > 0 - && movedCells[0].getParent().children.length === 3) { - this.repositionCircularBackbone(movedCells[0].getParent()); - } - // change ownership for (let container of Array.from(containers)) { this.changeOwnership(container); @@ -1227,7 +1210,7 @@ export class GraphBase { } let styleString = edge.style.slice(); - let startIdx = styleString.indexOf(GraphBase.STYLE_INTERACTION) + GraphBase.STYLE_INTERACTION.length; + let startIdx = styleString.indexOf(GraphBase.STYLE_INTERACTION)+GraphBase.STYLE_INTERACTION.length; let endIdx = styleString.indexOf(';', startIdx); endIdx = endIdx > 0 ? endIdx : styleString.length; let interactionType = styleString.slice(startIdx, endIdx); @@ -1241,7 +1224,7 @@ export class GraphBase { protected validateInteraction(interactionType: string, source: mxCell, target: mxCell) { // edges can't connect to edges - if ((source && source.isEdge()) || (target && target.isEdge())) { + if((source && source.isEdge()) || (target && target.isEdge())){ return "Edges are dissallowed to connect to edges."; } diff --git a/frontend/src/app/graph-edits.spec.ts b/SBOLCanvasFrontend/src/app/graph-edits.spec.ts similarity index 100% rename from frontend/src/app/graph-edits.spec.ts rename to SBOLCanvasFrontend/src/app/graph-edits.spec.ts diff --git a/frontend/src/app/graph-edits.ts b/SBOLCanvasFrontend/src/app/graph-edits.ts similarity index 100% rename from frontend/src/app/graph-edits.ts rename to SBOLCanvasFrontend/src/app/graph-edits.ts diff --git a/frontend/src/app/graph-helpers.spec.ts b/SBOLCanvasFrontend/src/app/graph-helpers.spec.ts similarity index 100% rename from frontend/src/app/graph-helpers.spec.ts rename to SBOLCanvasFrontend/src/app/graph-helpers.spec.ts diff --git a/frontend/src/app/graph-helpers.ts b/SBOLCanvasFrontend/src/app/graph-helpers.ts similarity index 95% rename from frontend/src/app/graph-helpers.ts rename to SBOLCanvasFrontend/src/app/graph-helpers.ts index 16bde015..af9ca3b7 100644 --- a/frontend/src/app/graph-helpers.ts +++ b/SBOLCanvasFrontend/src/app/graph-helpers.ts @@ -830,12 +830,12 @@ export class GraphHelpers extends GraphBase { let interactionInfo = this.getFromInteractionDict(interaction.value).makeCopy(); // remove an edge if the new reference is null, and this specific edge had it's old reference if (!newReference) { - if (interactionInfo.fromURI[interaction.getId()] == oldReference) { + if(interactionInfo.fromURI[interaction.getId()] == oldReference){ delete interactionInfo.fromURI[interaction.getId()]; this.updateInteractionDict(interactionInfo); this.graph.getModel().remove(interaction); } - if (interactionInfo.toURI[interaction.getId()] == oldReference) { + if(interactionInfo.toURI[interaction.getId()] == oldReference){ delete interactionInfo.toURI[interaction.getId()]; this.updateInteractionDict(interactionInfo); this.graph.getModel().remove(interaction); @@ -843,13 +843,13 @@ export class GraphHelpers extends GraphBase { continue; } // replace any interaction references that reference the oldReference - for (let key in interactionInfo.fromURI) { - if (interactionInfo.fromURI[key] == oldReference) { + for(let key in interactionInfo.fromURI){ + if(interactionInfo.fromURI[key] == oldReference){ interactionInfo.fromURI[key] = newReference; } } - for (let key in interactionInfo.toURI) { - if (interactionInfo.toURI[key] == oldReference) { + for(let key in interactionInfo.toURI){ + if(interactionInfo.toURI[key] == oldReference){ interactionInfo.toURI[key] = newReference; } } @@ -1090,22 +1090,6 @@ export class GraphHelpers extends GraphBase { var cellsRemoved = evt.getProperty('added'); var cellsAdded = evt.getProperty('removed'); - // checks if either the left or right side of a circular backbone was selected - const cirBackboneFilter = sender.cells.filter(cell => cell.stayAtBeginning || cell.stayAtEnd); - - if(cirBackboneFilter.length > 0) { - const parentCell = cirBackboneFilter[0].parent.children; - const cirBackboneCells = [parentCell[parentCell.length - 1], parentCell[1]]; - - // checks if the circular backbone is already selected - if(this.graph.getSelectionCells()[0] == cirBackboneCells[0] && this.graph.getSelectionCells()[1] == cirBackboneCells[1]) { - return; - } - - //set the selection to the circular backbone cells - this.graph.setSelectionCells(cirBackboneCells); - } - console.debug("----handleSelectionChange-----"); console.debug("cells removed: "); @@ -1136,13 +1120,13 @@ export class GraphHelpers extends GraphBase { } /** - * Updates the data in the metadata service according to the cells properties - */ + * Updates the data in the metadata service according to the cells properties + */ protected updateAngularMetadata(cells) { // start with null data, (re)add it as possible this.nullifyMetadata(); - // if there is no current root it's because we're in the middle of resetting the view + // if there is no current root it's because we're in the middle of reseting the view if (!this.graph.getCurrentRoot()) return; @@ -1153,27 +1137,19 @@ export class GraphHelpers extends GraphBase { } if (cells.length > 1) { - // multiple selections can't display glyph data unless it's a circular backbone - if(cells[1].stayAtBeginning) { - let glyphInfo; - if (!cells[1]) glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); - else glyphInfo = this.getFromInfoDict(cells[1].value); - - this.metadataService.setSelectedGlyphInfo(glyphInfo.makeCopy()); - } - + // multiple selections? can't display glyph data return; } // have to add special check as no selection cell should signify the module/component of the current view let cell; - if (cells && cells.length === 1) { + if (cells && cells.length > 0) { cell = cells[0]; } if ((!cell && this.graph.getCurrentRoot().isModuleView()) || (cell && cell.isModule())) { let moduleInfo; - if (!cell) + if (!cell) moduleInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); else moduleInfo = this.getFromInfoDict(cell.value); @@ -1655,10 +1631,10 @@ export class GraphHelpers extends GraphBase { // edge case, module view, need to check parent circuit container toCheck.add(cell.getParent().getValue()); } - } else if (cell.isCircuitContainer() && cell.getParent().isModuleView()) { + } else if(cell.isCircuitContainer() && cell.getParent().isModuleView()){ // transition state to module views toCheck.add(cell.getParent().getId()); - } else if (cell.isModule()) { + } else if(cell.isModule()){ toCheck.add(cell.getParent().getId()); } } @@ -1858,8 +1834,8 @@ export class GraphHelpers extends GraphBase { return false; } - protected flipInteractionEdge(cell) { - if (!cell.isInteraction()) { + protected flipInteractionEdge(cell){ + if(!cell.isInteraction()){ console.error("flipInteraction attempted on something other than an interaction!"); return; } @@ -1871,10 +1847,10 @@ export class GraphHelpers extends GraphBase { let targetPoint = cell.geometry.getTerminalPoint(false); cell.geometry.setTerminalPoint(null, true); cell.geometry.setTerminalPoint(null, false); - if (sourcePoint) { + if(sourcePoint){ cell.geometry.setTerminalPoint(sourcePoint, false); } - if (targetPoint) { + if(targetPoint){ cell.geometry.setTerminalPoint(targetPoint, true); } // reverse the info to/from @@ -1883,10 +1859,10 @@ export class GraphHelpers extends GraphBase { let oldFrom = newInfo.toURI[cell.id]; delete newInfo.toURI[cell.id]; delete newInfo.fromURI[cell.id]; - if (oldTo) { + if(oldTo){ newInfo.fromURI[cell.id] = oldTo; } - if (oldFrom) { + if(oldFrom){ newInfo.toURI[cell.id] = oldFrom; } // nuke the refinemnets, as source refinements don't match target refinements @@ -2059,51 +2035,18 @@ export class GraphHelpers extends GraphBase { } } - /** - * If a circuit container contains only a circular backbone the container's width is for some - * reason set to 1 and the right side of the circular backbone is moved right next to the left - * side, this method fixes the formatting - * - * @param circuitContainer The circuit container that contains the circular backbone - */ - repositionCircularBackbone(circuitContainer) { - const childrenCopy = circuitContainer.children.slice().filter(cell => cell.stayAtEnd); - const containerCopy = childrenCopy[0].getParent(); - - containerCopy.replaceGeometry("auto", "auto", 52, "auto", this.graph); - childrenCopy[0].replaceGeometry( - childrenCopy[0].getGeometry().x + 49, "auto", "auto", "auto", this.graph); - } - horizontalSortBasedOnPosition(circuitContainer) { - // pull out children that should be sorted - let childrenCopy = circuitContainer.children.slice() - .filter(cell => !cell.stayAtBeginning); - // sort the children - childrenCopy.sort((cellA, cellB) => - cellA.getGeometry().x - cellB.getGeometry().x - ); - + let childrenCopy = circuitContainer.children.slice(); + childrenCopy.sort(function (cellA, cellB) { + return cellA.getGeometry().x - cellB.getGeometry().x; + }); // and have the model reflect the sort in an undoable way - childrenCopy.forEach((child, i) => { + for (let i = 0; i < childrenCopy.length; i++) { + const child = childrenCopy[i]; this.graph.getModel().add(circuitContainer, child, i); - }); - - // add in children that should stay at the beginning - circuitContainer.children - .filter(cell => cell.stayAtBeginning) - .forEach(child => { - this.graph.getModel().add(circuitContainer, child, 0); - }); + } - // add in children that should stay at the end - circuitContainer.children - .filter(cell => cell.stayAtEnd) - .forEach(child => { - this.graph.getModel().add(circuitContainer, child, circuitContainer.children.length); - }); - circuitContainer.refreshCircuitContainer(this.graph); } diff --git a/frontend/src/app/graph.service.spec.ts b/SBOLCanvasFrontend/src/app/graph.service.spec.ts similarity index 100% rename from frontend/src/app/graph.service.spec.ts rename to SBOLCanvasFrontend/src/app/graph.service.spec.ts diff --git a/SBOLCanvasFrontend/src/app/graph.service.ts b/SBOLCanvasFrontend/src/app/graph.service.ts new file mode 100644 index 00000000..b2b9b717 --- /dev/null +++ b/SBOLCanvasFrontend/src/app/graph.service.ts @@ -0,0 +1,1621 @@ +/* +* GraphService +* +* This service controls the main editing canvas +*/ + +///// + +import { Injectable } from '@angular/core'; +import * as mxCell from 'mxgraph'; +import { GlyphInfo } from './glyphInfo'; +import { MetadataService } from './metadata.service'; +import { GlyphService } from './glyph.service'; +import { InteractionInfo } from './interactionInfo'; +import { environment } from 'src/environments/environment'; +import { MatDialog } from '@angular/material'; +import { GraphEdits } from './graph-edits'; +import { GraphBase, mx } from './graph-base'; +import { GraphHelpers } from './graph-helpers'; +import { StyleInfo } from './style-info'; +import { ModuleInfo } from './moduleInfo'; +import { Info } from './info'; +import { CombinatorialInfo } from './combinatorialInfo'; + +@Injectable({ + providedIn: 'root' +}) +export class GraphService extends GraphHelpers { + + constructor(dialog: MatDialog, metadataService: MetadataService, glyphService: GlyphService) { + super(dialog, metadataService, glyphService); + + this.graph.getSelectionModel().addListener(mx.mxEvent.CHANGE, mx.mxUtils.bind(this, this.handleSelectionChange)); + } + + isSelectedAGlyph(): boolean { + let selected = this.graph.getSelectionCells(); + if (selected.length != 1) { + return false; + } + return selected[0].isSequenceFeatureGlyph(); + } + + isRootAComponentView(): boolean { + return this.viewStack[0].isComponentView(); + } + + isComposite(sequenceFeature): boolean { + if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { + return false; + } + return sequenceFeature.getCircuitContainer(this.graph).children.length > 1; + } + + isVariant(sequenceFeature): boolean { + if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { + return false; + } + let combinatorial = this.getCombinatorialWithTemplate(sequenceFeature.getParent().value); + if (!combinatorial) + return false; + return combinatorial.getVariableComponentInfo(sequenceFeature.getId()); + } + + /** + * Given the interaction type, checks the selected cells source and target to see if it's allowed. + * @param interactionType + * @returns + */ + isInteractionTypeAllowed(interactionType: string): boolean { + let selected = this.graph.getSelectionCells(); + if (selected.length > 1 || selected.length == 0 || (!selected[0].isInteraction() && !selected[0].isInteractionNode)) { + return false; + } + + if (selected[0].isInteraction()) { + let result = this.validateInteraction(interactionType, selected[0].source, selected[0].target); + if (result == null || result == '') { + return true; + }else{ + return false; + } + } + + if (selected[0].isInteractionNode()) { + return interactionType == "Biochemical Reaction" || interactionType == "Dissociation" || interactionType == "Genetic Production" || interactionType == "Non-Covalent Binding"; + } + + return false; + } + + isSelectedTargetEdge(): boolean{ + let selected = this.graph.getSelectionCells(); + if(selected.lengh > 1 || selected.length == 0 || !selected[0].isInteraction()){ + return false; + } + + return selected[0].target == null || !selected[0].target.isInteractionNode(); + } + + isSelectedSourceEdge(): boolean{ + let selected = this.graph.getSelectionCells(); + if(selected.lengh > 1 || selected.length == 0 || !selected[0].isInteraction()){ + return false; + } + + return selected[0].source == null || !selected[0].source.isInteractionNode(); + } + + /** + * Recursively checks that all leaf children have sequences + * @param sequenceFeature A cell representing a sequence feature + */ + hasSequence(sequenceFeature): boolean { + if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { + return false; + } + // check if the child view has more than just a backbone + let circuitContainer = sequenceFeature.getCircuitContainer(this.graph); + if (circuitContainer.children.length > 1) { + for (let child of circuitContainer.children) { + if (child.isSequenceFeatureGlyph() && !this.hasSequence(child)) { + return false; + } + } + return true; + } + // no children? we must be a leaf node, check for a sequence + let glyphInfo = (this.getFromInfoDict(sequenceFeature.getValue())); + if (!glyphInfo || !glyphInfo.sequence || glyphInfo.sequence.length <= 0) { + return false; + } + return true; + } + + /** + * Forces the graph to redraw + */ + repaint() { + this.graph.refresh(); + } + + getSelectedCellID(): string { + let selected = this.graph.getSelectionCells(); + if (selected.length != 1) { + return null; + } + return selected[0].getId(); + } + + /** + * This method is called by the UI when the user turns scars on + * or off. + */ + toggleScars() { + // Toggle showing scars + if (this.showingScars) { + this.showingScars = false; + } else { this.showingScars = true; } + + // We hide scar glyphs by setting their widths to 0. + console.debug("showing scars now equals " + this.showingScars); + this.setAllScars(this.showingScars); + } + + /** + * Sets all scars in the current view + * @param isCollapsed + */ + setAllScars(isCollapsed: boolean) { + this.graph.getModel().beginUpdate(); + try { + let allGraphCells = this.graph.getDefaultParent().children; + for (let i = 0; i < allGraphCells.length; i++) { + if (allGraphCells[i].isCircuitContainer()) { + this.setScars(allGraphCells[i], this.showingScars); + } + } + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Changes all scars in a circuit container. + * @param circuitContainer + * @param isCollapsed + */ + setScars(circuitContainer, isCollapsed: boolean) { + let children = circuitContainer.children; + for (let i = 0; i < children.length; i++) { + if (children[i].isScar()) { + console.debug("scar found"); + let child = children[i]; + const geo = new mx.mxGeometry(0, 0, 0, 0); + geo.x = 0; + geo.y = 0; + geo.height = GraphBase.sequenceFeatureGlyphHeight; + + if (this.showingScars) { + geo.width = GraphBase.sequenceFeatureGlyphWidth; + } else { + geo.width = 0; + } + this.graph.getModel().setGeometry(child, geo); + } + } + circuitContainer.refreshCircuitContainer(this.graph) + } + + /** + * This method is called by the UI when the user asks to flip a + * sequence feature glyph. + * It swaps direction east/west. + */ + async flipSequenceFeatureGlyph() { + let selectionCells = this.graph.getSelectionCells(); + + // flip any selected glyphs + let parentInfos = new Set(); + for (let cell of selectionCells) { + if (cell.isSequenceFeatureGlyph()) { + // add the item to check ownership + parentInfos.add(this.getParentInfo(cell)); + } + } + for (let parentInfo of Array.from(parentInfos.values())) { + if (parentInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(parentInfo.displayID)) { + return; + } + } + + try { + this.graph.getModel().beginUpdate(); + + for (let cell of selectionCells) { + if (cell.isSequenceFeatureGlyph()) { + + // Make the cell face east/west + let direction = this.graph.getCellStyle(cell)[mx.mxConstants.STYLE_DIRECTION]; + console.debug("current glyph direction setting = " + direction); + + if (direction == undefined) { + console.warn("direction style undefined. Assuming east, and turning to west"); + this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "west", [cell]); + } else if (direction === "east") { + this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "west", [cell]); + console.debug("turning west"); + } else if (direction == "west") { + this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "east", [cell]); + console.debug("turning east"); + } + } else if (cell.isInteraction()) { + this.flipInteractionEdge(cell); + }else if (cell.isInteractionNode()){ + let edges = this.graph.getModel().getEdges(cell); + for(let edge of edges){ + this.flipInteractionEdge(edge); + } + } + } + + // sync circuit containers + let circuitContainers = []; + for (let cell of selectionCells) { + if (cell.isSequenceFeatureGlyph()) { + this.syncCircuitContainer(cell.getParent()); + } + } + + for (let parentInfo of Array.from(parentInfos.values())) { + // change the owner + this.changeOwnership(parentInfo.getFullURI()); + } + + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * "Drills in" to replace the canvas with the selected glyph's component/module view + */ + enterGlyph() { + let selection = this.graph.getSelectionCells(); + if (selection.length != 1) { + return; + } + + if (!selection[0].isSequenceFeatureGlyph() && !selection[0].isModule()) { + return; + } + + this.graph.getModel().beginUpdate(); + try { + let viewCell = this.graph.getModel().getCell(selection[0].getValue()); + // doing this in the graph edit breaks things in the undo, so we put it here + viewCell.refreshViewCell(this.graph); + let zoomEdit = new GraphEdits.zoomEdit(this.graph.getView(), selection[0], this); + this.graph.getModel().execute(zoomEdit); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Moves up the drilling hierarchy, restoring the canvas to how it was before "Drilling in" + * (If "enterGlyph" has not been called, ie the canvas is already + * at the top of the drilling hierarchy, does nothing) + */ + exitGlyph() { + // the root view should always be left on the viewStack + if (this.viewStack.length > 1) { + let zoomEdit = new GraphEdits.zoomEdit(this.graph.getView(), null, this); + this.graph.getModel().execute(zoomEdit); + } + } + + /** + * Turns the given element into a dragsource for creating empty DNA strands + */ + makeBackboneDragsource(element) { + const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addBackboneAt(x - GraphBase.sequenceFeatureGlyphWidth / 2, y - GraphBase.sequenceFeatureGlyphHeight / 2); + }); + + this.makeGeneralDragsource(element, insertGlyph); + } + + /** + * Creates an empty DNA strand at the center of the current view + */ + addBackbone() { + const pt = this.getDefaultNewCellCoords(); + this.addBackboneAt(pt.x, pt.y); + } + + /** + * Creates an empty DNA strand at the given coordinates + */ + addBackboneAt(x, y) { + this.graph.getModel().beginUpdate(); + try { + let glyphInfo; + if (this.graph.getCurrentRoot().isModuleView()) { + glyphInfo = new GlyphInfo(); + super.addToInfoDict(glyphInfo); + } else { + glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); + } + const circuitContainer = this.graph.insertVertex(this.graph.getDefaultParent(), null, glyphInfo.getFullURI(), x, y, GraphBase.sequenceFeatureGlyphWidth, GraphBase.sequenceFeatureGlyphHeight, GraphBase.STYLE_CIRCUIT_CONTAINER); + const backbone = this.graph.insertVertex(circuitContainer, null, '', 0, GraphBase.sequenceFeatureGlyphHeight / 2, GraphBase.sequenceFeatureGlyphWidth, 1, GraphBase.STYLE_BACKBONE); + + backbone.refreshBackbone(this.graph); + + circuitContainer.setConnectable(false); + backbone.setConnectable(false); + + // The new circuit should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(circuitContainer); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Returns the
that this graph displays to + */ + getGraphDOM() { + return this.graphContainer; + } + + /** + * Deletes the currently selected cell + */ + async delete() { + const selectedCells = this.graph.getSelectionCells(); + if (selectedCells == null) { + return; + } + + // check for ownership prompt + let containers = new Set(); + if (this.graph.getCurrentRoot()) { + let ownershipPrompt = false; + for (let cell of selectedCells) { + if (cell.isSequenceFeatureGlyph()) { + ownershipPrompt = true; + containers.add(cell.getParent().getValue()); + } + } + for (let container of Array.from(containers.values())) { + let glyphInfo; + if (this.graph.getCurrentRoot().isComponentView()) { + glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); + } else { + glyphInfo = this.getFromInfoDict(container); + } + if (ownershipPrompt && glyphInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(glyphInfo.displayID)) { + return; + } + } + } + + this.graph.getModel().beginUpdate(); + try { + let circuitContainers = []; + for (let cell of selectedCells) { + if (cell.isSequenceFeatureGlyph()) { + circuitContainers.push(cell.getParent()); + + // if it's a sequence feature and it has a combinatorial, remove the variable component + if (cell.isSequenceFeatureGlyph()) { + let combinatorial = this.getCombinatorialWithTemplate(cell.getParent().getValue()); + // TODO make this undoable + if (combinatorial) + combinatorial.removeVariableComponentInfo(cell.getId()); + } + } else if (cell.isCircuitContainer() && this.graph.getCurrentRoot() && this.graph.getCurrentRoot().isComponentView()) + circuitContainers.push(cell); + } + + // If we are not at the top level, we need to check + // for a corner case where we can't allow the backbone + // to be deleted + if (this.graph.getCurrentRoot() != null && this.graph.getCurrentRoot().isComponentView()) { + let newSelection = []; + for (let cell of selectedCells) { + // Anything other than the backbone gets added to + // the revised selection + if (!(cell.isBackbone() || cell.isCircuitContainer())) { + newSelection.push(cell); + } else { + let circuitContainer; + if (cell.isBackbone()) { + circuitContainer = cell.getParent(); + } else if (cell.isCircuitContainer()) { + circuitContainer = cell; + } + + // If we find a backbone is selected, add all it's children + if (circuitContainer.children) { + for (let child of circuitContainer.children) { + if (!child.isBackbone()) { + newSelection.push(child); + } + } + } + } + } + this.graph.setSelectionCells(newSelection); + } + + + + // remove interactions with modules if the item it connects to is being removed + for (let selectedCell of selectedCells) { + if (selectedCell.isCircuitContainer() || selectedCell.isMolecularSpeciesGlyph()) { + this.updateInteractions(selectedCell.getValue() + "_" + selectedCell.getId(), null); + } + } + + this.editor.execute('delete'); + + this.trimUnreferencedCells(); + this.trimUnreferencedCombinatorials(); + this.trimUnreferencedInfos(); + + // sync circuit containers + for (let circuitContainer of circuitContainers) { + this.syncCircuitContainer(circuitContainer); + } + + // obtain ownership + for (let container of Array.from(containers)) { + this.changeOwnership(container); + } + + for (let cell of circuitContainers) { + cell.refreshCircuitContainer(this.graph); + } + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Undoes the most recent changes + */ + undo() { + // (un/re)doing is managed by the editor; it only works + // if all changes are encapsulated by graphModel.(begin/end)Update + + // clearing the selection avoids a lot of exceptions from mxgraph code for some reason. + this.graph.clearSelection(); + this.editor.execute('undo'); + + //console.log(this.editor.undoManager); + + // If the undo caused scars to become visible, we should update + this.showingScars = this.getScarsVisible(); + + // refresh to update cell labels + if (this.graph.getCurrentRoot()) { + this.graph.refresh(this.graph.getCurrentRoot()); + } + + // selections after an undo break things if annother undo/redo happens + this.filterSelectionCells(); + } + + /** + * Redoes the most recent changes + */ + redo() { + //console.log(this.editor.undoManager); + + this.graph.clearSelection(); + this.editor.execute('redo'); + + // If the undo caused scars to become visible, we should update + this.showingScars = this.getScarsVisible(); + + // refresh to update cell labels + if (this.graph.getCurrentRoot()) { + this.graph.refresh(this.graph.getCurrentRoot()); + } + + // selections after an undo break things if annother undo/redo happens + this.filterSelectionCells(); + } + + zoomIn() { + this.graph.zoomIn(); + } + + zoomOut() { + this.graph.zoomOut(); + } + + setZoom(scale: number) { + this.graph.zoomTo(scale); + } + + getZoom(): number { + return this.graph.getView().getScale(); + } + + sendSelectionToFront() { + this.graph.orderCells(false) + } + + sendSelectionToBack() { + this.graph.orderCells(true) + } + + fitCamera() { + // graph.fit() does most of the work. however by default it will zoom in far too much. + // Instead, it makes sense to stay at the user's zoom level unless it is too small to + // contain everything. + let currentScale = this.graph.getView().getScale(); + this.graph.maxFitScale = currentScale; + this.graph.fit(); + + // if the user had it widely zoomed out, however, stupidly graph.fit() + // doesn't center the view on cells. It puts them in the top left. + this.graph.center(); + } + + + + /** + * Turns the given element into a dragsource for creating + * sequenceFeatureGlyphs of the type specified by 'stylename.' + */ + makeSequenceFeatureDragsource(element, stylename) { + const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addSequenceFeatureAt(stylename, x - GraphBase.sequenceFeatureGlyphWidth / 2, y - GraphBase.sequenceFeatureGlyphHeight / 2); + }); + this.makeGeneralDragsource(element, insertGlyph); + } + + /** + * Adds a sequenceFeatureGlyph. + * The new glyph's location is based off the user's selection. + */ + addSequenceFeature(name) { + this.graph.getModel().beginUpdate(); + try { + if (!this.atLeastOneCircuitContainerInGraph()) { + // if there is no strand, quietly make one + // stupid user + this.addBackbone(); + // this changes the selection, so the rest of this method works fine + } + + // let the graph choose an arbitrary cell from the selection, + // we'll pretend it's the only one selected + const selection = this.graph.getSelectionCell(); + + // if selection is nonexistent, or is not part of a strand, there is no suitable place. + if (!selection || !(selection.isSequenceFeatureGlyph() || selection.isCircuitContainer())) { + return; + } + + const circuitContainer = selection.isCircuitContainer() ? selection : selection.getParent(); + + // use y coord of the strand + let y = circuitContainer.getGeometry().y; + + // x depends on the exact selection + let x; + if (selection.isCircuitContainer()) { + x = selection.getGeometry().x + selection.getGeometry().width; + } else { + x = circuitContainer.getGeometry().x + selection.getGeometry().x + 1; + } + + // Add it + this.addSequenceFeatureAt(name, x, y, circuitContainer); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Adds a sequenceFeatureGlyph. + * + * circuitContainer (optional) specifies the strand to add to. + * If not specified, it is inferred by x,y. + * + * x,y are also used to determine where on the strand the new + * glyph is added (first, second, etc) + */ + async addSequenceFeatureAt(name, x, y, circuitContainer?) { + + // ownership change check + if (this.graph.getCurrentRoot()) { + let glyphInfo; + if (this.graph.getCurrentRoot().isComponentView()) { + // normal case + glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); + } else if (this.atLeastOneCircuitContainerInGraph()) { + // edge case that we're adding to a container in a module view + if (!circuitContainer) { + circuitContainer = this.getClosestCircuitContainerToPoint(x, y); + } + glyphInfo = this.getFromInfoDict(circuitContainer.getValue()); + } + if (glyphInfo && glyphInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(glyphInfo.displayID)) { + return; + } + } + + this.graph.getModel().beginUpdate(); + try { + // Make sure scars are/become visible if we're adding one + if (name.includes(GraphBase.STYLE_SCAR) && !this.showingScars) { + this.toggleScars(); + } + + if (!this.atLeastOneCircuitContainerInGraph()) { + // if there is no strand, quietly make one + this.addBackboneAt(x, y); + } + + if (!circuitContainer) { + circuitContainer = this.getClosestCircuitContainerToPoint(x, y); + } + + // transform coords to be relative to parent + x = x - circuitContainer.getGeometry().x; + y = y - circuitContainer.getGeometry().y; + + // create the glyph info and add it to the dictionary + const glyphInfo = new GlyphInfo(); + glyphInfo.partRole = name; + this.addToInfoDict(glyphInfo); + + // Insert new glyph and its components + const sequenceFeatureCell = this.graph.insertVertex(circuitContainer, null, glyphInfo.getFullURI(), x, y, GraphBase.sequenceFeatureGlyphWidth, GraphBase.sequenceFeatureGlyphHeight, GraphBase.STYLE_SEQUENCE_FEATURE + name); + + this.createViewCell(glyphInfo.getFullURI()); + sequenceFeatureCell.setConnectable(true); + + // Sorts the new SequenceFeature into the correct position in parent's array + this.horizontalSortBasedOnPosition(circuitContainer); + + // The new glyph should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(sequenceFeatureCell); + + // perform the ownership change + if (this.graph.getCurrentRoot()) { + let glyphInfo; + if (this.graph.getCurrentRoot().isComponentView()) { + // normal case + glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); + } else { + // edge case that we're adding to a container in a module view + glyphInfo = this.getFromInfoDict(circuitContainer.getValue()); + } + if (glyphInfo.uriPrefix != environment.baseURI) { + this.changeOwnership(glyphInfo.getFullURI()); + } + } + + // synchronize circuit containers + this.syncCircuitContainer(circuitContainer); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Turns the given element into a dragsource for creating molecular species glyphs + */ + makeMolecularSpeciesDragsource(element, stylename) { + const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addMolecularSpeciesAt(stylename, x - GraphBase.molecularSpeciesGlyphWidth / 2, y - GraphBase.molecularSpeciesGlyphHeight / 2); + }); + this.makeGeneralDragsource(element, insertGlyph); + } + + /** + * Creates a molecular species glyph of the given type at the center of the current view + */ + addMolecularSpecies(name) { + const pt = this.getDefaultNewCellCoords(); + this.addMolecularSpeciesAt(name, pt.x, pt.y); + } + + /** + * Creates a molecular species glyph of the given type at the given location + */ + addMolecularSpeciesAt(name, x, y) { + this.graph.getModel().beginUpdate(); + try { + + //TODO partRoles for proteins + let proteinInfo = new GlyphInfo(); + proteinInfo.partType = this.moleculeNameToType(name); + this.addToInfoDict(proteinInfo); + + const molecularSpeciesGlyph = this.graph.insertVertex(this.graph.getDefaultParent(), null, proteinInfo.getFullURI(), x, y, + GraphBase.molecularSpeciesGlyphWidth, GraphBase.molecularSpeciesGlyphHeight, GraphBase.STYLE_MOLECULAR_SPECIES + name); + molecularSpeciesGlyph.setConnectable(true); + + // The new glyph should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(molecularSpeciesGlyph); + } finally { + this.graph.getModel().endUpdate(); + } + + console.log(this.graph.getModel().cells); + } + + makeInteractionNodeDragsource(element, stylename) { + const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addInteractionNodeAt(stylename, x - GraphBase.interactionNodeGlyphWidth / 2, y - GraphBase.interactionNodeGlyphHeight / 2); + }); + this.makeGeneralDragsource(element, insertGlyph); + } + + addInteractionNode(name) { + const pt = this.getDefaultNewCellCoords(); + this.addInteractionNodeAt(name, pt.x, pt.y); + } + + addInteractionNodeAt(name: string, x, y) { + this.graph.getModel().beginUpdate(); + try { + let interactionInfo = new InteractionInfo(); + const interactionNodeGlyph = this.graph.insertVertex(this.graph.getDefaultParent(), null, interactionInfo.getFullURI(), x, y, + GraphBase.interactionNodeGlyphWidth, GraphBase.interactionNodeGlyphHeight, GraphBase.STYLE_INTERACTION_NODE + name); + interactionInfo.interactionType = this.interactionNodeNametoType(name); + this.addToInteractionDict(interactionInfo); + interactionNodeGlyph.setConnectable(true); + + // The new glyph should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(interactionNodeGlyph); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Turns the given HTML element into a dragsource for creating interaction glyphs + */ + makeInteractionDragsource(element, stylename) { + const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addInteractionAt(stylename, x - GraphBase.defaultInteractionSize / 2, y - GraphBase.defaultInteractionSize / 2); + }); + this.makeGeneralDragsource(element, insertGlyph); + } + + /** + * Creates an interaction edge of the given type at the center of the current view + */ + addInteraction(name) { + const selectionCells = this.graph.getSelectionCells(); + if (selectionCells.length > 0 && selectionCells.length < 3) { + let selectedCell = selectionCells[0]; + const selectedParent = selectedCell.getParent(); + if (selectedParent.geometry && !selectedParent.isViewCell()) { + this.addInteractionAt(name, selectedParent.geometry.x + selectedCell.geometry.x + (selectedCell.geometry.width / 2), + selectedParent.geometry.y); + } else { + this.addInteractionAt(name, selectedCell.geometry.x + (selectedCell.geometry.width / 2), + selectedCell.geometry.y); + } + } else { + const pt = this.getDefaultNewCellCoords(); + this.addInteractionAt(name, pt.x, pt.y); + } + } + + /** + * Creates an interaction edge of the given type at the given coordiantes + * @param name The name identifying the type of interaction this should be. + * @param x The x coordinate that the interaction should appear at + * @param y The y coordinate that the interaction should appear at + */ + async addInteractionAt(name: string, x, y) { + let cell; + + this.graph.getModel().beginUpdate(); + try { + let addToDictionary = true; + let interactionInfo = new InteractionInfo(); + cell = new mx.mxCell(interactionInfo.getFullURI(), new mx.mxGeometry(x, y, 0, 0), GraphBase.STYLE_INTERACTION + name); + + const selectionCells = this.graph.getSelectionCells(); + if (selectionCells.length == 1) { + + // one cell is selected, set the edges source + const selectedCell = this.graph.getSelectionCell(); + // check for any restrictions on valid edges + let error = this.graph.getEdgeValidationError(cell, selectedCell, null); + if (error) { + this.showError(error); + return; + } + if (selectedCell.isModule()) { + // if the cell is a module, we need to prompt what subpart we want to connect to + let result = await this.promptChooseFunctionalComponent(selectedCell, true); + if (!result) + return; + interactionInfo.fromURI[this.graph.getModel().nextId] = result; + } else if (selectedCell.isInteractionNode()) { + // if the source is a interaction node, we want to inherit it's information + cell.value = selectedCell.value; + addToDictionary = false; + interactionInfo = this.getFromInteractionDict(selectedCell.value).makeCopy() + } + cell.geometry.setTerminalPoint(new mx.mxPoint(x, y - GraphBase.defaultInteractionSize), false); + cell.edge = true; + this.graph.addEdge(cell, this.graph.getCurrentRoot(), selectedCell, null); + + } else if (selectionCells.length == 2) { + + // two cells were selected, set the first one as the source, and the second as the target + const sourceCell = selectionCells[0]; + const destCell = selectionCells[1]; + // check for restrictions on the edge + let error = this.graph.getEdgeValidationError(cell, sourceCell, destCell); + if (error) { + this.showError(error); + return; + } + // check source or target are interaction nodes to couple with them before making modifications to the interaction + // don't worry, edge validation rules prevent both from being interaction nodes. + if(sourceCell.isInteractionNode()){ + // inherit the information + cell.value = sourceCell.value; + addToDictionary = false; + interactionInfo = this.getFromInteractionDict(sourceCell.value).makeCopy(); + } + if(destCell.isInteractionNode()){ + // inherit the information + cell.value = destCell.value; + addToDictionary = false; + interactionInfo = this.getFromInteractionDict(destCell.value).makeCopy(); + } + + if (sourceCell.isModule()) { + // prompt for the subpart to keep track of + let result = await this.promptChooseFunctionalComponent(sourceCell, true); + if (!result) + return; + interactionInfo.fromURI[this.graph.getModel().nextId] = result; + } + if (destCell.isModule()) { + // prompt for the subpart to keep track of + let result = await this.promptChooseFunctionalComponent(destCell, false); + if (!result) + return; + interactionInfo.toURI[this.graph.getModel().nextId] = result; + } + cell.edge = true; + this.graph.addEdge(cell, this.graph.getCurrentRoot(), sourceCell, destCell); + + } else { + cell.geometry.setTerminalPoint(new mx.mxPoint(x, y + GraphBase.defaultInteractionSize), true); + cell.geometry.setTerminalPoint(new mx.mxPoint(x + GraphBase.defaultInteractionSize, y), false); + cell.edge = true; + this.graph.addEdge(cell, this.graph.getCurrentRoot(), null, null); + } + + + // Default name for a process interaction + if (name == "Process") { + name = "Genetic Production" + } + + if (addToDictionary) { + interactionInfo.interactionType = name; + this.addToInteractionDict(interactionInfo); + } else { + this.updateInteractionDict(interactionInfo); + this.mutateInteractionGlyph(interactionInfo.interactionType, cell); + } + + // The new glyph should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(cell); + } finally { + this.graph.getModel().endUpdate(); + } + + return cell; + } + + /** + * Turns the given HTML element into a dragsource for creating textboxes + */ + makeTextboxDragsource(element) { + const insert = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addTextBoxAt(x - GraphBase.defaultTextWidth / 2, y - GraphBase.defaultTextHeight / 2); + }); + this.makeGeneralDragsource(element, insert); + } + + /** + * Creates a textbox at the center of the current view + */ + addTextBox() { + const pt = this.getDefaultNewCellCoords(); + this.addTextBoxAt(pt.x, pt.y); + } + + /** + * Creates a textbox at the given location + */ + addTextBoxAt(x, y) { + this.graph.getModel().beginUpdate(); + try { + const cell = this.graph.insertVertex(this.graph.getDefaultParent(), null, 'Sample Text', x, y, GraphBase.defaultTextWidth, GraphBase.defaultTextHeight, GraphBase.STYLE_TEXTBOX); + cell.setConnectable(false); + + // The new cell should be selected + this.graph.clearSelection(); + this.graph.setSelectionCell(cell); + } finally { + this.graph.getModel().endUpdate(); + } + } + + makeModuleDragsource(element) { + const insert = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { + this.addModuleAt(x - GraphBase.defaultModuleWidth / 2, y - GraphBase.defaultModuleHeight / 2); + }); + this.makeGeneralDragsource(element, insert); + } + + addModule() { + const pt = this.getDefaultNewCellCoords(); + this.addModuleAt(pt.x, pt.y); + } + + addModuleAt(x, y) { + this.graph.getModel().beginUpdate(); + try { + let moduleInfo = new ModuleInfo(); + this.addToInfoDict(moduleInfo); + + const moduleCell = this.graph.insertVertex(this.graph.getDefaultParent(), null, moduleInfo.getFullURI(), x, y, GraphBase.defaultModuleWidth, GraphBase.defaultModuleHeight, GraphBase.STYLE_MODULE); + moduleCell.setConnectable(true); + + this.createViewCell(moduleInfo.getFullURI(), true); + + this.graph.clearSelection(); + this.graph.setSelectionCell(moduleCell); + } finally { + this.graph.getModel().endUpdate(); + } + } + + /** + * Find the selected cell, and if there is a glyph selected, update its metadata. + */ + async setSelectedCellInfo(info: Info) { + const selectedCell = this.graph.getSelectionCell(); + + this.graph.getModel().beginUpdate(); + try { + // figure out which type of info object it is + if (info instanceof ModuleInfo && (!selectedCell || selectedCell.isModule())) { + this.updateSelectedModuleInfo(info); + return; + } + + if (info instanceof GlyphInfo && (!selectedCell || selectedCell.isSequenceFeatureGlyph() || selectedCell.isCircuitContainer() || selectedCell.isMolecularSpeciesGlyph())) { + if (!selectedCell || !selectedCell.isMolecularSpeciesGlyph()) { + // The logic for updating the glyphs was getting a bit big, so I moved it into it's own method + this.updateSelectedGlyphInfo(info); + } else { + this.updateSelectedMolecularSpecies(info); + } + return; + } + + if (info instanceof InteractionInfo && (selectedCell.isInteraction() || selectedCell.isInteractionNode())) { + this.updateSelectedInteractionInfo(info); + } + + } finally { + this.graph.getModel().endUpdate(); + this.graph.refresh(selectedCell); + //this.updateAngularMetadata(this.graph.getSelectionCells()); + } + } + + /** + * Sets the combinatorial info associated to the selected cell + * @param info + * @param prevURI + */ + setSelectedCombinatorialInfo(info: CombinatorialInfo, prevURI?: string) { + const selectedCell = this.graph.getSelectionCell(); + + this.graph.getModel().beginUpdate(); + try { + if (info instanceof CombinatorialInfo && selectedCell.isSequenceFeatureGlyph()) { + if (!prevURI) { + prevURI = info.getFullURI(); + } + this.updateSelectedCombinatorialInfo(info, prevURI); + } + } finally { + this.graph.getModel().endUpdate(); + } + } + + setSelectedCellStyle(styleInfo: StyleInfo) { + this.graph.getModel().beginUpdate(); + try { + let selectedCells = this.graph.getSelectionCells().slice(); + // filter out the circuit containers + for (let i = 0; i < selectedCells.length; i++) { + if (selectedCells[i].isCircuitContainer()) { + selectedCells[i] = selectedCells[i].getBackbone(); + } + } + for (let key in styleInfo.styles) { + this.graph.setCellStyles(key, styleInfo.styles[key], selectedCells); + } + + // sync circuit containers + let circuitContainers = new Set(); + for (let cell of selectedCells) { + if (cell.isSequenceFeatureGlyph() || cell.isBackbone()) { + circuitContainers.add(cell.getParent()); + } + } + for (let circuitContainer of Array.from(circuitContainers.values())) { + this.syncCircuitContainer(circuitContainer); + } + + } finally { + this.graph.getModel().endUpdate(); + } + } + + exportSVG(filename: string) { + var background = '#ffffff'; + var scale = 1; + var border = 1; + + var imgExport = new mx.mxImageExport(); + var bounds = this.graph.getGraphBounds(); + var vs = this.graph.view.scale; + + // Prepares SVG document that holds the output + var svgDoc = mx.mxUtils.createXmlDocument(); + var root = (svgDoc.createElementNS != null) ? + svgDoc.createElementNS(mx.mxConstants.NS_SVG, 'svg') : svgDoc.createElement('svg'); + + if (background != null) { + if (root.style != null) { + root.style.backgroundColor = background; + } else { + root.setAttribute('style', 'background-color:' + background); + } + } + + if (svgDoc.createElementNS == null) { + root.setAttribute('xmlns', mx.mxConstants.NS_SVG); + root.setAttribute('xmlns:xlink', mx.mxConstants.NS_XLINK); + } else { + // KNOWN: Ignored in IE9-11, adds namespace for each image element instead. No workaround. + root.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', mx.mxConstants.NS_XLINK); + } + + root.setAttribute('width', (Math.ceil(bounds.width * scale / vs) + 2 * border) + 'px'); + root.setAttribute('height', (Math.ceil(bounds.height * scale / vs) + 2 * border) + 'px'); + root.setAttribute('version', '1.1'); + + // Adds group for anti-aliasing via transform + var group = (svgDoc.createElementNS != null) ? svgDoc.createElementNS(mx.mxConstants.NS_SVG, 'g') : svgDoc.createElement('g'); + group.setAttribute('transform', 'translate(0.5,0.5)'); + root.appendChild(group); + svgDoc.appendChild(root); + + // Renders graph. Offset will be multiplied with state's scale when painting state. + var svgCanvas = new mx.mxSvgCanvas2D(group); + svgCanvas.translate(Math.floor((border / scale - bounds.x) / vs), Math.floor((border / scale - bounds.y) / vs)); + svgCanvas.scale(scale / vs); + + // Displayed if a viewer does not support foreignObjects (which is needed to HTML output) + svgCanvas.foAltText = '[Not supported by viewer]'; + imgExport.drawState(this.graph.getView().getState(this.graph.getCurrentRoot()), svgCanvas); + + var xml = encodeURIComponent(mx.mxUtils.getXml(root)); + new mx.mxXmlRequest(environment.backendURL + '/echo', 'filename=' + filename + '.svg&format=svg' + '&xml=' + xml).simulate(document, '_blank'); + } + + exportImage(filename: string, format: string) { + let bg = '#ffffff'; + let scale = 1; + let b = 1; + + let imgExport = new mx.mxImageExport(); + let bounds = this.graph.getGraphBounds(); + let vs = this.graph.view.scale; + + let xmlDoc = mx.mxUtils.createXmlDocument(); + let root = xmlDoc.createElement('output'); + xmlDoc.appendChild(root); + + let xmlCanvas = new mx.mxXmlCanvas2D(root); + xmlCanvas.translate(Math.floor((b / scale - bounds.x) / vs), Math.floor((b / scale - bounds.y) / vs)); + xmlCanvas.scale(1 / vs); + + imgExport.drawState(this.graph.getView().getState(this.graph.getCurrentRoot()), xmlCanvas); + + let w = Math.ceil(bounds.width * scale / vs + 2 * b); + let h = Math.ceil(bounds.height * scale / vs + 2 * b); + + let xml = mx.mxUtils.getXml(root); + + if (bg != null) { + bg = '&bg=' + bg; + } + + new mx.mxXmlRequest(environment.backendURL + '/export', 'filename=' + filename + '.' + format + '&format=' + format + bg + '&w=' + w + '&h=' + h + '&xml=' + encodeURIComponent(xml)).simulate(document, '_blank'); + } + + /** + * Encodes the current graph to a string (xml) representation + */ + getGraphXML(): string { + const encoder = new mx.mxCodec(); + const result = encoder.encode(this.graph.getModel()); + return mx.mxUtils.getXml(result); + } + + /** + * Decodes the given string (xml) representation of a graph + * and uses it to replace the current graph + */ + setGraphToXML(graphString: string) { + GraphBase.unFormatedCells.clear(); + this.graph.home(); + this.graph.getModel().clear(); + + const doc = mx.mxUtils.parseXml(graphString); + const codec = new mx.mxCodec(doc); + codec.decode(doc.documentElement, this.graph.getModel()); + + // The child of cell 1 that isn't a view cell points to the root view + const cell1 = this.graph.getModel().getCell("1"); + let viewCells = this.graph.getModel().getChildren(cell1); + let rootViewCell; + for (let child of viewCells) { + if (!child.isViewCell()) { + rootViewCell = this.graph.getModel().getCell(child.getValue()); + this.graph.getModel().remove(child); + break; + } + } + this.graph.enterGroup(rootViewCell); + this.viewStack = []; + this.viewStack.push(rootViewCell); + this.selectionStack = []; + + let children = this.graph.getModel().getChildren(this.graph.getDefaultParent()); + if (children) { + children.forEach(element => { + if (element.isCircuitContainer()) + element.refreshCircuitContainer(this.graph); + }); + } + + if (GraphBase.unFormatedCells.size > 0) { + console.log("FORMATTING !!!!!!!!!!!!!!!!"); + this.autoFormat(GraphBase.unFormatedCells); + GraphBase.unFormatedCells.clear(); + } + + this.fitCamera(); + + this.metadataService.setComponentDefinitionMode(this.graph.getCurrentRoot().isComponentView()); + + // top level compDefs may not have cells referencing them, but they still end up with view cells for other reasons + this.trimUnreferencedCells(); + + this.editor.undoManager.clear(); + + this.graph.refresh(); // for some reason unformatted edges don't render correctly the first time without this + } + + /** + * Decodes the given string (xml) representation of a cell + * and uses it ot replace the currently selected cell + * @param cellString + */ + async setSelectedToXML(cellString: string) { + const selectionCells = this.graph.getSelectionCells(); + + if (selectionCells.length == 0 || (selectionCells.length == 1 && (selectionCells[0].isSequenceFeatureGlyph() || selectionCells[0].isCircuitContainer() || selectionCells[0].isModule()))) { + // We're making a new cell to replace the selected one + let selectedCell; + if (selectionCells.length > 0) { + selectedCell = selectionCells[0]; + } else { + // nothing selected means we're replacing the view cell + selectedCell = this.graph.getCurrentRoot(); + } + + this.graph.getModel().beginUpdate(); + try { + let inModuleView = this.graph.getCurrentRoot().isModuleView(); + + // prompt ownership change + let parentInfo = this.getParentInfo(selectedCell); + if (parentInfo && parentInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(parentInfo.displayID)) { + return; + } + + // change ownership + if (parentInfo) { + if (selectedCell.isViewCell()) { + this.changeOwnership(parentInfo.getFullURI()); + selectedCell = this.graph.getCurrentRoot(); + } else if (selectedCell.isCircuitContainer() || selectedCell.isModule()) { + let selectedIndex = selectedCell.getParent().getIndex(selectedCell); + this.changeOwnership(parentInfo.getFullURI()); + selectedCell = this.graph.getCurrentRoot().children[selectedIndex]; + } else { + let parentIndex = this.graph.getCurrentRoot().getIndex(selectedCell.getParent()); + let selectedIndex = selectedCell.getParent().getIndex(selectedCell); + this.changeOwnership(parentInfo.getFullURI()); + selectedCell = this.graph.getCurrentRoot().children[parentIndex].children[selectedIndex]; + } + } + + // if we're in a non top level circuit container, module, or view cell zoom out to make things easier + let zoomOut = false; + if (((selectedCell.isCircuitContainer() || selectedCell.isComponentView()) && this.graph.getCurrentRoot().isComponentView() && this.viewStack.length > 1) || + ((selectedCell.isModule() || selectedCell.isModuleView()) && this.viewStack.length > 1)) { + zoomOut = true; + selectedCell = this.selectionStack[this.selectionStack.length - 1]; + this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), null, this)); + } + + // setup the decoding info + const doc = mx.mxUtils.parseXml(cellString); + const codec = new mx.mxCodec(doc); + + // store the information in a temp graph for easy access + const subGraph = new mx.mxGraph(); + codec.decode(doc.documentElement, subGraph.getModel()); + + // get the new cell + let newCell = subGraph.getModel().cloneCell(subGraph.getModel().getCell("1").children[0]); + + // not part of a module or a top level component definition + let origParent; + if (selectedCell.isSequenceFeatureGlyph()) { + // store old cell's parent + origParent = selectedCell.getParent(); + + // generated cells don't have a proper geometry + newCell.setStyle(selectedCell.getStyle()); + this.graph.getModel().setGeometry(newCell, selectedCell.geometry); + + // add new cell to the graph + this.graph.getModel().add(origParent, newCell, origParent.getIndex(selectedCell)); + + // remove the old cell's view cell if it doesn't have any references + if (this.getCoupledGlyphs(selectedCell.value).length < 2) { + this.removeViewCell(this.graph.getModel().getCell(selectedCell.value)); + } + + // remove the old cell + this.graph.getModel().remove(selectedCell); + + // move any edges from selectedCell to newCell + if (selectedCell.edges != null) { + let edgeCache = []; + selectedCell.edges.forEach(edge => { + edgeCache.push(edge); + }); + + edgeCache.forEach(edge => { + if (edge.source == selectedCell) { + this.graph.getModel().setTerminal(edge, newCell, true); + } + if (edge.target == selectedCell) { + this.graph.getModel().setTerminal(edge, newCell, false); + } + }); + } + } else if (selectedCell.isModule()) { + // store old cell's parent + origParent = selectedCell.getParent(); + + // generated cells don't have a proper geometry + newCell.setStyle(selectedCell.getStyle()); + this.graph.getModel().setGeometry(newCell, selectedCell.geometry); + + // add new cell to the graph + this.graph.getModel().add(origParent, newCell, origParent.getIndex(selectedCell)); + + // remove the old cell's view cell if it doesn't have any references + if (this.getCoupledModules(selectedCell.value).length < 2) { + this.removeViewCell(this.graph.getModel().getCell(selectedCell.value)); + } + + // remove the old cell + this.graph.getModel().remove(selectedCell); + } + + // Now create all children of the new cell + let viewCells = subGraph.getModel().getCell("1").children; + let subGlyphDict = subGraph.getModel().getCell("0").getValue(); + let cell1 = this.graph.getModel().getCell("1"); + for (let i = 1; i < viewCells.length; i++) { // start at cell 1 because the glyph is at 0 + // If we already have it skip it + if (this.graph.getModel().getCell(viewCells[i].getId())) { + continue; + } + + // clone the cell otherwise viewCells get's messed up + let viewClone = subGraph.getModel().cloneCell(viewCells[i]); + // cloning doesn't keep the id for some reason + viewClone.id = viewCells[i].id; + + // add the cell to the graph + this.graph.addCell(viewClone, cell1); + + // add the info to the dictionary + if (this.getFromInfoDict(viewCells[i].getId()) != null) { + this.removeFromInfoDict(viewCells[i].getId()); + } + this.addToInfoDict(subGlyphDict[GraphBase.INFO_DICT_INDEX][viewCells[i].getId()]); + + // add any molecular species or interactions to the info dict + for(let child of viewClone.children){ + if(child.isMolecularSpeciesGlyph()){ + if(this.getFromInfoDict(child.value) != null){ + this.removeFromInfoDict(child.value); + } + this.addToInfoDict(subGlyphDict[GraphBase.INFO_DICT_INDEX][child.value]); + }else if(child.isInteractionNode()){ + if(this.getFromInteractionDict(child.value) != null){ + this.removeFromInteractionDict(child.value); + } + this.addToInteractionDict(subGlyphDict[GraphBase.INTERACTION_DICT_INDEX][child.value]); + }else if(child.isInteraction()){ + // if either end is an interaction node, we don't need to bother + if((child.source && child.source.isInteractionNode()) || (child.target && child.target.isInteractionNode())){ + continue; + } + if(this.getFromInteractionDict(child.value) != null){ + this.removeFromInteractionDict(child.value); + } + this.addToInteractionDict(subGlyphDict[GraphBase.INTERACTION_DICT_INDEX][child.value]); + } + } + } + + // relink the interactions now that their ID's have likely changed + for(let i = 1; i < viewCells.length; i++){ + let viewClone = this.graph.getModel().getCell(viewCells[i].getId()); + for(let j = 0; j < viewClone.children.length; j++){ + // for now it seems that cloning the cell keeps the child order in tact + let child = viewClone.children[j]; + let originalChild = viewCells[i].children[j]; + if(child.isInteractionNode()){ + // copy to new dict as new id's may conflict with old + let newTo = [] + let newFrom = [] + let newSource = [] + let newTarget = [] + let infoCopy = this.getFromInteractionDict(child.value).makeCopy(); + for(let k = 0; k < child.edges.length; k++){ + let edge = child.edges[k]; + let originalEdge = originalChild.edges[k]; + if(infoCopy.toURI[originalEdge.getId()]){ + // find the original cell + let cellRef = infoCopy.toURI[originalEdge.getId()]; + let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_")+1)); + let oldParentView = oldCell.getParent(); + let newParentView = this.graph.getModel().getCell(oldParentView.getId()); + // replace with the new id + newTo[edge.getId()] = cellRef.substring(0,cellRef.lastIndexOf("_")+1)+newParentView.children[oldParentView.getIndex(oldCell)].getId(); + } + if(infoCopy.fromURI[originalEdge.getId()]){ + // find the original cell + let cellRef = infoCopy.fromURI[originalEdge.getId()]; + let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_")+1)); + let oldParentView = oldCell.getParent(); + let newParentView = this.graph.getModel().getCell(oldParentView.getId()); + // replace with the new id + newFrom[edge.getId()] = cellRef.substring(0,cellRef.lastIndexOf("_")+1)+newParentView.children[oldParentView.getIndex(oldCell)].getId(); + } + if(infoCopy.sourceRefinement[originalEdge.getId()]){ + newSource[edge.getId()] = infoCopy.sourceRefinement[originalEdge.getId()]; + } + if(infoCopy.targetRefinement[originalEdge.getId()]){ + newTarget[edge.getId()] = infoCopy.targetRefinement[originalEdge.getId()]; + } + } + infoCopy.toURI = newTo; + infoCopy.fromURI = newFrom; + infoCopy.sourceRefinement = newSource; + infoCopy.targetRefinement = newTarget; + this.updateInteractionDict(infoCopy); + } + if(child.isInteraction()){ + // skip edges connected to interaction nodes + if((child.source && child.source.isInteractionNode()) || (child.target && child.target.isInteractionNode())){ + continue; + } + let infoCopy = this.getFromInteractionDict(child.value).makeCopy(); + if(infoCopy.fromURI[originalChild.getId()]){ + let cellRef = infoCopy.fromURI[originalChild.getId()]; + delete infoCopy.fromURI[originalChild.getId()]; + let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_")+1)); + let oldParentView = oldCell.getParent(); + let newParentView = this.graph.getModel().getCell(oldParentView.getId()); + infoCopy.fromURI[child.getId()] = cellRef.substring(0,cellRef.lastIndexOf("_")+1)+newParentView.children[oldParentView.getIndex(oldCell)].getId();; + } + if(infoCopy.toURI[originalChild.getId()]){ + let cellRef = infoCopy.toURI[originalChild.getId()]; + delete infoCopy.toURI[originalChild.getId()]; + let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_")+1)); + let oldParentView = oldCell.getParent(); + let newParentView = this.graph.getModel().getCell(oldParentView.getId()); + infoCopy.toURI[child.getId()] = cellRef.substring(0,cellRef.lastIndexOf("_")+1)+newParentView.children[oldParentView.getIndex(oldCell)].getId();; + } + if(infoCopy.sourceRefinement[originalChild.getId()]){ + let value = infoCopy.sourceRefinement[originalChild.getId()]; + delete infoCopy.sourceRefinement[originalChild.getId()]; + infoCopy.sourceRefinement[child.getId()] = value; + } + if(infoCopy.targetRefinement[originalChild.getId()]){ + let value = infoCopy.targetRefinement[originalChild.getId()]; + delete infoCopy.targetRefinement[originalChild.getId()]; + infoCopy.targetRefinement[child.getId()] = value; + } + this.updateInteractionDict(infoCopy); + } + } + } + + if (selectedCell.isSequenceFeatureGlyph()) { + origParent.refreshCircuitContainer(this.graph); + this.graph.setSelectionCell(newCell); + this.mutateSequenceFeatureGlyph((this.getFromInfoDict(newCell.value)).partRole); + } + + // if we zoomed out zoom back in + if (zoomOut) { + if (selectedCell.isSequenceFeatureGlyph()) { + // if the selected cell is a sequenceFeature that means we came from a sub view + this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newCell, this)); + } else { + // if it isn't, that means we are in a module, or at the root + let newRootView = this.graph.getModel().getCell(newCell.getValue()); + let circuitContainer = this.graph.getModel().filterCells(newRootView.children, cell => cell.isCircuitContainer())[0]; + if (inModuleView) { + // get the circuit container so we can replace our current one + this.graph.getModel().setGeometry(circuitContainer, selectedCell.geometry); + if (this.getCoupledGlyphs(newRootView.getId()).length < 1) + // we don't need the root view if nothing references it, we only need it's circuit container + this.graph.getModel().remove(newRootView); + circuitContainer = this.graph.getModel().add(selectedCell.getParent(), circuitContainer); + this.graph.getModel().remove(selectedCell); + circuitContainer.refreshCircuitContainer(this.graph); + } else { + // at the root, just zoom back in + this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newRootView, this)); + circuitContainer.refreshCircuitContainer(this.graph); + } + } + } + + // root cells won't be zoomed out, so just zoom into the correct one, and remove the old one + if (selectedCell.isViewCell()) { + let newViewId = newCell.getValue(); + const newView = this.graph.getModel().getCell(newViewId); + this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), null, this)); + this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newView, this)); + this.removeViewCell(selectedCell); + } + + // top level circuit containers need to be synced to get the changes before the trim + if (selectedCell.isCircuitContainer()) { + let previousReference = selectedCell.getValue() + "_" + selectedCell.getId(); + let selectedParent = selectedCell.getParent(); + let selectedIndex = selectedParent.getIndex(selectedCell); + this.graph.getModel().setValue(selectedCell, newCell.getValue()); + const viewCell = this.graph.getModel().getCell(newCell.getValue()); + if (viewCell.children) { + for (let viewChild of viewCell.children) { + if (viewChild.isCircuitContainer()) { + this.syncCircuitContainer(viewChild); + break; + } + } + } + selectedCell = selectedParent.children[selectedIndex]; + this.updateInteractions(previousReference, newCell.getValue() + "_" + selectedCell.getId()); + } + + if (GraphBase.unFormatedCells.size > 0) { + console.log("FORMATTING !!!!!!!!!!!!!!!!"); + this.autoFormat(GraphBase.unFormatedCells); + GraphBase.unFormatedCells.clear(); + } + + // sync circuit containers + if (origParent) { + this.syncCircuitContainer(origParent); + } + + this.trimUnreferencedCells(); + } finally { + this.graph.getModel().endUpdate(); + } + } + } + + resetGraph(moduleMode: boolean = true) { + this.graph.home(); + this.graph.getModel().clear(); + + this.viewStack = []; + this.selectionStack = []; + + // initalize the GlyphInfoDictionary + const cell0 = this.graph.getModel().getCell(0); + const infoDict = []; + const combinatorialDict = []; + var dataContainer = []; + dataContainer[GraphBase.INFO_DICT_INDEX] = infoDict; + dataContainer[GraphBase.COMBINATORIAL_DICT_INDEX] = combinatorialDict; + this.graph.getModel().setValue(cell0, dataContainer); + + const cell1 = this.graph.getModel().getCell(1); + let rootViewCell; + + // initalize the root view cell of the graph + if (moduleMode) { + let rootModuleInfo = new ModuleInfo(); + this.addToInfoDict(rootModuleInfo); + rootViewCell = this.graph.insertVertex(cell1, rootModuleInfo.getFullURI(), "", 0, 0, 0, 0, GraphBase.STYLE_MODULE_VIEW); + this.graph.enterGroup(rootViewCell); + this.viewStack.push(rootViewCell); + } else { + let info = new GlyphInfo(); + this.addToInfoDict(info); + rootViewCell = this.graph.insertVertex(cell1, info.getFullURI(), "", 0, 0, 0, 0, GraphBase.STYLE_COMPONENT_VIEW); + this.graph.enterGroup(rootViewCell); + this.viewStack.push(rootViewCell); + this.addBackbone(); + } + + this.metadataService.setComponentDefinitionMode(!moduleMode); + + this.updateAngularMetadata(this.graph.getSelectionCells()); + + this.editor.undoManager.clear(); + } + + /** + * Sets the graph to component definition mode or module mode. + * wrapper for metadataService.setComponentDefinitionMode. + * @param componentMode True if you want to be in component mode, false if module mode. + */ + public setComponentDefinitionMode(componentMode: boolean) { + this.metadataService.setComponentDefinitionMode(componentMode); + } + +} diff --git a/frontend/src/app/home/home.component.css b/SBOLCanvasFrontend/src/app/home/home.component.css similarity index 73% rename from frontend/src/app/home/home.component.css rename to SBOLCanvasFrontend/src/app/home/home.component.css index 0cb35284..afdad6d2 100644 --- a/frontend/src/app/home/home.component.css +++ b/SBOLCanvasFrontend/src/app/home/home.component.css @@ -7,10 +7,6 @@ } -/deep/ .mat-tab-body-wrapper { - padding: 20px; -} - /deep/ .mat-tab-label { min-width: 130px!important; } diff --git a/frontend/src/app/home/home.component.html b/SBOLCanvasFrontend/src/app/home/home.component.html similarity index 85% rename from frontend/src/app/home/home.component.html rename to SBOLCanvasFrontend/src/app/home/home.component.html index 6225f4fb..81c35cb9 100644 --- a/frontend/src/app/home/home.component.html +++ b/SBOLCanvasFrontend/src/app/home/home.component.html @@ -17,7 +17,7 @@ - + @@ -30,9 +30,6 @@
- - -
diff --git a/frontend/src/app/home/home.component.spec.ts b/SBOLCanvasFrontend/src/app/home/home.component.spec.ts similarity index 100% rename from frontend/src/app/home/home.component.spec.ts rename to SBOLCanvasFrontend/src/app/home/home.component.spec.ts diff --git a/frontend/src/app/home/home.component.ts b/SBOLCanvasFrontend/src/app/home/home.component.ts similarity index 93% rename from frontend/src/app/home/home.component.ts rename to SBOLCanvasFrontend/src/app/home/home.component.ts index eae0113a..ef7b1641 100644 --- a/frontend/src/app/home/home.component.ts +++ b/SBOLCanvasFrontend/src/app/home/home.component.ts @@ -5,7 +5,6 @@ import { ToolbarComponent } from "../toolbar/toolbar.component"; import {ComponentCanDeactivate} from '../pending-changes.guard'; import {Observable} from 'rxjs'; import {Title} from "@angular/platform-browser"; -import { EmbeddedService } from '../embedded.service'; export enum KEY_CODE { DELETE = "Delete", @@ -26,7 +25,7 @@ export class HomeComponent implements OnInit, ComponentCanDeactivate { rightBarOpened = true; leftBarOpened = true; - constructor(private graphService: GraphService, private titleService: Title, private embeddedService: EmbeddedService) { + constructor(private graphService: GraphService, private titleService: Title) { this.titleService.setTitle('SBOL Canvas'); } @@ -78,6 +77,6 @@ export class HomeComponent implements OnInit, ComponentCanDeactivate { // insert logic to check if there are pending changes here; // returning true will navigate without confirmation // returning false will show a confirm dialog before navigating away - return this.embeddedService.isAppEmbedded(); + return false; } } diff --git a/frontend/src/app/http.interceptor.ts b/SBOLCanvasFrontend/src/app/http.interceptor.ts similarity index 69% rename from frontend/src/app/http.interceptor.ts rename to SBOLCanvasFrontend/src/app/http.interceptor.ts index 82549454..10f8b07f 100644 --- a/frontend/src/app/http.interceptor.ts +++ b/SBOLCanvasFrontend/src/app/http.interceptor.ts @@ -4,19 +4,10 @@ import { Observable, of, throwError } from "rxjs"; import { tap, catchError } from "rxjs/operators"; import { MatDialog } from '@angular/material'; import { ErrorComponent } from './error/error.component'; -import { ActivatedRoute } from '@angular/router' - @Injectable() export class AppHttpInterceptor implements HttpInterceptor { - - ignoreHTTPErrors: boolean - - constructor(public dialog: MatDialog, private route: ActivatedRoute) { - this.route.queryParams.subscribe(params => { - this.ignoreHTTPErrors = !!params.ignoreHTTPErrors - }) - } + constructor(public dialog: MatDialog) {} intercept( req: HttpRequest, next: HttpHandler @@ -28,7 +19,7 @@ intercept( }), catchError((err: any) => { if(err instanceof HttpErrorResponse && err.status === 500) { - !this.ignoreHTTPErrors && this.dialog.open(ErrorComponent, {data: err.error}); + this.dialog.open(ErrorComponent, {data: err.error}); } return throwError(err); })); diff --git a/frontend/src/app/identifiedInfo.ts b/SBOLCanvasFrontend/src/app/identifiedInfo.ts similarity index 100% rename from frontend/src/app/identifiedInfo.ts rename to SBOLCanvasFrontend/src/app/identifiedInfo.ts diff --git a/frontend/src/app/info-editor/info-editor.component.css b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.css similarity index 100% rename from frontend/src/app/info-editor/info-editor.component.css rename to SBOLCanvasFrontend/src/app/info-editor/info-editor.component.css diff --git a/frontend/src/app/info-editor/info-editor.component.html b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.html similarity index 100% rename from frontend/src/app/info-editor/info-editor.component.html rename to SBOLCanvasFrontend/src/app/info-editor/info-editor.component.html diff --git a/frontend/src/app/info-editor/info-editor.component.spec.ts b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.spec.ts similarity index 100% rename from frontend/src/app/info-editor/info-editor.component.spec.ts rename to SBOLCanvasFrontend/src/app/info-editor/info-editor.component.spec.ts diff --git a/frontend/src/app/info-editor/info-editor.component.ts b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.ts similarity index 94% rename from frontend/src/app/info-editor/info-editor.component.ts rename to SBOLCanvasFrontend/src/app/info-editor/info-editor.component.ts index 6121880f..e57741fc 100644 --- a/frontend/src/app/info-editor/info-editor.component.ts +++ b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.ts @@ -89,8 +89,6 @@ export class InfoEditorComponent implements OnInit { break; } case 'partRole': { - if(event.value.includes("Cir (Circular Backbone")) break; - this.glyphInfo.partRole = event.value; this.glyphInfo.partRefine = ''; if (event.value !== '') { @@ -170,7 +168,6 @@ export class InfoEditorComponent implements OnInit { } case 'sequence': { this.glyphInfo.sequence = event.target.value; - break; } default: { console.log('Unexpected id encountered in info menu input = ' + id); @@ -243,8 +240,8 @@ export class InfoEditorComponent implements OnInit { this.interactionInfo = interactionInfo; if (interactionInfo != null) { if (interactionInfo.interactionType != null) { - this.getInteractionSourceRefinements(this.getSourceInteractionRole()); - this.getInteractionTargetRefinements(this.getTargetInteractionRole()); + this.getInteractionSourceRefinements(this.interactionRoles[interactionInfo.interactionType][0]); + this.getInteractionTargetRefinements(this.interactionRoles[interactionInfo.interactionType][1]); } else { this.interactionSourceRefinements = []; this.interactionTargetRefinements = []; @@ -287,15 +284,13 @@ export class InfoEditorComponent implements OnInit { } getSourceInteractionRole() { - const interactionRole = this.interactionRoles[this.interactionInfo.interactionType] - const NA = "NA" - return interactionRole ? interactionRole[0] || NA : NA; + let sourceRole = this.interactionRoles[this.interactionInfo.interactionType][0]; + return sourceRole ? sourceRole : "NA"; } getTargetInteractionRole() { - const interactionRole = this.interactionRoles[this.interactionInfo.interactionType] - const NA = "NA" - return interactionRole ? interactionRole[1] || NA : NA; + let targetRole = this.interactionRoles[this.interactionInfo.interactionType][1]; + return targetRole ? targetRole : "NA"; } hasSourceRefinements(): boolean { diff --git a/frontend/src/app/info.ts b/SBOLCanvasFrontend/src/app/info.ts similarity index 100% rename from frontend/src/app/info.ts rename to SBOLCanvasFrontend/src/app/info.ts diff --git a/frontend/src/app/interactionInfo.ts b/SBOLCanvasFrontend/src/app/interactionInfo.ts similarity index 100% rename from frontend/src/app/interactionInfo.ts rename to SBOLCanvasFrontend/src/app/interactionInfo.ts diff --git a/frontend/src/app/landing-page/landing-page.component.css b/SBOLCanvasFrontend/src/app/landing-page/landing-page.component.css similarity index 100% rename from frontend/src/app/landing-page/landing-page.component.css rename to SBOLCanvasFrontend/src/app/landing-page/landing-page.component.css diff --git a/frontend/src/app/landing-page/landing-page.component.html b/SBOLCanvasFrontend/src/app/landing-page/landing-page.component.html similarity index 100% rename from frontend/src/app/landing-page/landing-page.component.html rename to SBOLCanvasFrontend/src/app/landing-page/landing-page.component.html diff --git a/frontend/src/app/landing-page/landing-page.component.spec.ts b/SBOLCanvasFrontend/src/app/landing-page/landing-page.component.spec.ts similarity index 100% rename from frontend/src/app/landing-page/landing-page.component.spec.ts rename to SBOLCanvasFrontend/src/app/landing-page/landing-page.component.spec.ts diff --git a/frontend/src/app/landing-page/landing-page.component.ts b/SBOLCanvasFrontend/src/app/landing-page/landing-page.component.ts similarity index 100% rename from frontend/src/app/landing-page/landing-page.component.ts rename to SBOLCanvasFrontend/src/app/landing-page/landing-page.component.ts diff --git a/frontend/src/assets/.gitkeep b/SBOLCanvasFrontend/src/app/load-graph/load-graph.component.css similarity index 100% rename from frontend/src/assets/.gitkeep rename to SBOLCanvasFrontend/src/app/load-graph/load-graph.component.css diff --git a/frontend/src/app/load-graph/load-graph.component.html b/SBOLCanvasFrontend/src/app/load-graph/load-graph.component.html similarity index 100% rename from frontend/src/app/load-graph/load-graph.component.html rename to SBOLCanvasFrontend/src/app/load-graph/load-graph.component.html diff --git a/frontend/src/app/load-graph/load-graph.component.spec.ts b/SBOLCanvasFrontend/src/app/load-graph/load-graph.component.spec.ts similarity index 100% rename from frontend/src/app/load-graph/load-graph.component.spec.ts rename to SBOLCanvasFrontend/src/app/load-graph/load-graph.component.spec.ts diff --git a/frontend/src/app/load-graph/load-graph.component.ts b/SBOLCanvasFrontend/src/app/load-graph/load-graph.component.ts similarity index 100% rename from frontend/src/app/load-graph/load-graph.component.ts rename to SBOLCanvasFrontend/src/app/load-graph/load-graph.component.ts diff --git a/frontend/src/app/login.service.spec.ts b/SBOLCanvasFrontend/src/app/login.service.spec.ts similarity index 100% rename from frontend/src/app/login.service.spec.ts rename to SBOLCanvasFrontend/src/app/login.service.spec.ts diff --git a/frontend/src/app/login.service.ts b/SBOLCanvasFrontend/src/app/login.service.ts similarity index 100% rename from frontend/src/app/login.service.ts rename to SBOLCanvasFrontend/src/app/login.service.ts diff --git a/frontend/src/app/login/login.component.css b/SBOLCanvasFrontend/src/app/login/login.component.css similarity index 100% rename from frontend/src/app/login/login.component.css rename to SBOLCanvasFrontend/src/app/login/login.component.css diff --git a/frontend/src/app/login/login.component.html b/SBOLCanvasFrontend/src/app/login/login.component.html similarity index 100% rename from frontend/src/app/login/login.component.html rename to SBOLCanvasFrontend/src/app/login/login.component.html diff --git a/frontend/src/app/login/login.component.spec.ts b/SBOLCanvasFrontend/src/app/login/login.component.spec.ts similarity index 100% rename from frontend/src/app/login/login.component.spec.ts rename to SBOLCanvasFrontend/src/app/login/login.component.spec.ts diff --git a/frontend/src/app/login/login.component.ts b/SBOLCanvasFrontend/src/app/login/login.component.ts similarity index 95% rename from frontend/src/app/login/login.component.ts rename to SBOLCanvasFrontend/src/app/login/login.component.ts index 73babc88..17bf4e8f 100644 --- a/frontend/src/app/login/login.component.ts +++ b/SBOLCanvasFrontend/src/app/login/login.component.ts @@ -32,7 +32,7 @@ export class LoginComponent implements OnInit { this.working = true; this.badLogin = false; this.loginService.login(this.email, this.password, this.data.server).subscribe(result => { - this.loginService.users[this.data.server] = JSON.parse(result); + this.loginService.users[this.data.server] = result; this.working = false; this.dialogRef.close(true); }, diff --git a/frontend/src/app/material.module.ts b/SBOLCanvasFrontend/src/app/material.module.ts similarity index 100% rename from frontend/src/app/material.module.ts rename to SBOLCanvasFrontend/src/app/material.module.ts diff --git a/frontend/src/app/metadata.service.spec.ts b/SBOLCanvasFrontend/src/app/metadata.service.spec.ts similarity index 100% rename from frontend/src/app/metadata.service.spec.ts rename to SBOLCanvasFrontend/src/app/metadata.service.spec.ts diff --git a/frontend/src/app/metadata.service.ts b/SBOLCanvasFrontend/src/app/metadata.service.ts similarity index 89% rename from frontend/src/app/metadata.service.ts rename to SBOLCanvasFrontend/src/app/metadata.service.ts index d5f42d92..6c4f9c73 100644 --- a/frontend/src/app/metadata.service.ts +++ b/SBOLCanvasFrontend/src/app/metadata.service.ts @@ -66,32 +66,10 @@ export class MetadataService { private componentDefinitionModeSource = new BehaviorSubject(null); componentDefinitionMode = this.componentDefinitionModeSource.asObservable(); - private savedRegistry: string; - private savedCollection: { collection: string, history: Array }; - // TODO: DNA strand info constructor(private http: HttpClient) { } - getSavedRegistry() { - return this.savedRegistry; - } - - getSavedCollection() { - return this.savedCollection; - } - - setSavedRegistry(registry: string) { - this.savedRegistry = registry; - } - - setSavedCollection(collectionInfo: { collection: string, history: Array }) { - this.savedCollection = { - collection: collectionInfo.collection, - history: collectionInfo.history - } - } - loadTypes(): Observable { return this.http.get(this.typesURL); } diff --git a/frontend/src/app/moduleInfo.ts b/SBOLCanvasFrontend/src/app/moduleInfo.ts similarity index 100% rename from frontend/src/app/moduleInfo.ts rename to SBOLCanvasFrontend/src/app/moduleInfo.ts diff --git a/frontend/src/app/pending-changes.guard.spec.ts b/SBOLCanvasFrontend/src/app/pending-changes.guard.spec.ts similarity index 100% rename from frontend/src/app/pending-changes.guard.spec.ts rename to SBOLCanvasFrontend/src/app/pending-changes.guard.spec.ts diff --git a/SBOLCanvasFrontend/src/app/pending-changes.guard.ts b/SBOLCanvasFrontend/src/app/pending-changes.guard.ts new file mode 100644 index 00000000..79fedb23 --- /dev/null +++ b/SBOLCanvasFrontend/src/app/pending-changes.guard.ts @@ -0,0 +1,24 @@ +import { CanDeactivate } from '@angular/router'; +import { Injectable } from '@angular/core'; +import {Observable} from 'rxjs'; + +export interface ComponentCanDeactivate { + canDeactivate: () => boolean | Observable; +} + +@Injectable() +export class PendingChangesGuard implements CanDeactivate { + canDeactivate(component: ComponentCanDeactivate): boolean | Observable { + + // if there are no pending changes, just allow deactivation; else confirm first + console.log("NOpe\n"); + if (component.canDeactivate()) { + return true; + } else { + // NOTE: this warning message will only be shown when navigating elsewhere within your angular app; + // when navigating away from your angular app, the browser will show a generic warning message + // see http://stackoverflow.com/a/42207299/7307355 + return confirm('WARNING: You have unsaved changes. Press Cancel to go back and save these changes, or OK to lose these changes.'); + } + } +} diff --git a/frontend/src/app/searchfilter.pipe.spec.ts b/SBOLCanvasFrontend/src/app/searchfilter.pipe.spec.ts similarity index 100% rename from frontend/src/app/searchfilter.pipe.spec.ts rename to SBOLCanvasFrontend/src/app/searchfilter.pipe.spec.ts diff --git a/frontend/src/app/searchfilter.pipe.ts b/SBOLCanvasFrontend/src/app/searchfilter.pipe.ts similarity index 100% rename from frontend/src/app/searchfilter.pipe.ts rename to SBOLCanvasFrontend/src/app/searchfilter.pipe.ts diff --git a/frontend/src/app/style-info.spec.ts b/SBOLCanvasFrontend/src/app/style-info.spec.ts similarity index 100% rename from frontend/src/app/style-info.spec.ts rename to SBOLCanvasFrontend/src/app/style-info.spec.ts diff --git a/frontend/src/app/style-info.ts b/SBOLCanvasFrontend/src/app/style-info.ts similarity index 100% rename from frontend/src/app/style-info.ts rename to SBOLCanvasFrontend/src/app/style-info.ts diff --git a/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.css b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.css new file mode 100644 index 00000000..6906574e --- /dev/null +++ b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.css @@ -0,0 +1,39 @@ +/* This sets the space between sets of buttons */ +.toolbar-spacer { + flex: 1 1 auto; +} + +/* Not sure exactly how this works but it makes the menu + bigger so that it can fit the buttons. */ +::ng-deep .mat-menu-panel { + padding: 0 10px!important; + width: 100%!important; +} + +/* This sets the css for the buttons on the row */ +.toolbar-row-button { + margin-right: 8px; + margin-left: 8px; +} + +.zoom-input { + text-align: right; + padding-left: 10px; + padding-right: 10px; + max-width: 50px; + font-size: .8em; +} + +/* There is a bug with vertical dividers in + toolbar rows so you have to manually fix + the styling for the divider. + */ +mat-divider.toolbar-divider-style-fix { + height: 40px; + margin-left: 8px; + margin-right: 8px; +} + +.toolbar-row { + padding: 8px; +} diff --git a/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.html b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.html new file mode 100644 index 00000000..ff72c8eb --- /dev/null +++ b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.html @@ -0,0 +1,155 @@ + + + + + + + + + SynBioHub + + + + + + Local Device + + + + + + + + + + + + New + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/frontend/src/app/toolbar/toolbar.component.spec.ts b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.spec.ts similarity index 100% rename from frontend/src/app/toolbar/toolbar.component.spec.ts rename to SBOLCanvasFrontend/src/app/toolbar/toolbar.component.spec.ts diff --git a/frontend/src/app/toolbar/toolbar.component.ts b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.ts similarity index 96% rename from frontend/src/app/toolbar/toolbar.component.ts rename to SBOLCanvasFrontend/src/app/toolbar/toolbar.component.ts index afafb41f..be078b04 100644 --- a/frontend/src/app/toolbar/toolbar.component.ts +++ b/SBOLCanvasFrontend/src/app/toolbar/toolbar.component.ts @@ -8,7 +8,6 @@ import { ExportImageComponent } from '../export-image/export-image.component'; import { ExportDesignComponent } from '../export-design/export-design.component'; import { ConfirmComponent } from '../confirm/confirm.component'; import { LoadGraphComponent } from '../load-graph/load-graph.component'; -import { EmbeddedService } from '../embedded.service'; export interface SaveDialogData { filename: string; @@ -31,7 +30,7 @@ export class ToolbarComponent implements OnInit, AfterViewInit { users: {}; constructor(public graphService: GraphService, private filesService: FilesService, - public dialog: MatDialog, public embeddedService: EmbeddedService) { + public dialog: MatDialog) { } ngOnInit() { diff --git a/frontend/src/app/tutorial/tutorial.component.css b/SBOLCanvasFrontend/src/app/tutorial/tutorial.component.css similarity index 100% rename from frontend/src/app/tutorial/tutorial.component.css rename to SBOLCanvasFrontend/src/app/tutorial/tutorial.component.css diff --git a/frontend/src/app/tutorial/tutorial.component.html b/SBOLCanvasFrontend/src/app/tutorial/tutorial.component.html similarity index 100% rename from frontend/src/app/tutorial/tutorial.component.html rename to SBOLCanvasFrontend/src/app/tutorial/tutorial.component.html diff --git a/frontend/src/app/tutorial/tutorial.component.spec.ts b/SBOLCanvasFrontend/src/app/tutorial/tutorial.component.spec.ts similarity index 100% rename from frontend/src/app/tutorial/tutorial.component.spec.ts rename to SBOLCanvasFrontend/src/app/tutorial/tutorial.component.spec.ts diff --git a/frontend/src/app/tutorial/tutorial.component.ts b/SBOLCanvasFrontend/src/app/tutorial/tutorial.component.ts similarity index 100% rename from frontend/src/app/tutorial/tutorial.component.ts rename to SBOLCanvasFrontend/src/app/tutorial/tutorial.component.ts diff --git a/frontend/src/app/upload-graph/upload-graph.component.css b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.css similarity index 100% rename from frontend/src/app/upload-graph/upload-graph.component.css rename to SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.css diff --git a/frontend/src/app/upload-graph/upload-graph.component.html b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.html similarity index 100% rename from frontend/src/app/upload-graph/upload-graph.component.html rename to SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.html diff --git a/frontend/src/app/upload-graph/upload-graph.component.spec.ts b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.spec.ts similarity index 100% rename from frontend/src/app/upload-graph/upload-graph.component.spec.ts rename to SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.spec.ts diff --git a/frontend/src/app/upload-graph/upload-graph.component.ts b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.ts similarity index 100% rename from frontend/src/app/upload-graph/upload-graph.component.ts rename to SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.ts diff --git a/frontend/src/app/useful_code_snippets.txt b/SBOLCanvasFrontend/src/app/useful_code_snippets.txt similarity index 100% rename from frontend/src/app/useful_code_snippets.txt rename to SBOLCanvasFrontend/src/app/useful_code_snippets.txt diff --git a/frontend/src/app/variableComponentInfo.ts b/SBOLCanvasFrontend/src/app/variableComponentInfo.ts similarity index 100% rename from frontend/src/app/variableComponentInfo.ts rename to SBOLCanvasFrontend/src/app/variableComponentInfo.ts diff --git a/frontend/src/app/window-ref.service.ts b/SBOLCanvasFrontend/src/app/window-ref.service.ts similarity index 100% rename from frontend/src/app/window-ref.service.ts rename to SBOLCanvasFrontend/src/app/window-ref.service.ts diff --git a/SBOLCanvasFrontend/src/assets/.gitkeep b/SBOLCanvasFrontend/src/assets/.gitkeep new file mode 100644 index 00000000..e69de29b diff --git a/frontend/src/assets/glyph_stencils/utils/backbone.xml b/SBOLCanvasFrontend/src/assets/backbone.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/utils/backbone.xml rename to SBOLCanvasFrontend/src/assets/backbone.xml diff --git a/frontend/src/assets/banner.png b/SBOLCanvasFrontend/src/assets/banner.png similarity index 100% rename from frontend/src/assets/banner.png rename to SBOLCanvasFrontend/src/assets/banner.png diff --git a/frontend/src/assets/glyph_stencils/indicators/composite.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/composite.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/indicators/composite.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/composite.xml diff --git a/frontend/src/assets/glyph_stencils/indicators/error.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/error.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/indicators/error.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/error.xml diff --git a/frontend/src/assets/glyph_stencils/indicators/variant.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/variant.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/indicators/variant.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/indicators/variant.xml diff --git a/frontend/src/assets/glyph_stencils/interactionNodes/association.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/association.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactionNodes/association.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/association.xml diff --git a/frontend/src/assets/glyph_stencils/interactionNodes/dissociation.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/dissociation.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactionNodes/dissociation.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/dissociation.xml diff --git a/frontend/src/assets/glyph_stencils/interactionNodes/process.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/process.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactionNodes/process.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/process.xml diff --git a/frontend/src/assets/glyph_stencils/interactionNodes/replacement-glyph.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/replacement-glyph.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactionNodes/replacement-glyph.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interaction_nodes/replacement-glyph.xml diff --git a/frontend/src/assets/glyph_stencils/interactions/control.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/control.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactions/control.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/control.xml diff --git a/frontend/src/assets/glyph_stencils/interactions/degradation.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/degradation.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactions/degradation.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/degradation.xml diff --git a/frontend/src/assets/glyph_stencils/interactions/inhibition.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/inhibition.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactions/inhibition.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/inhibition.xml diff --git a/frontend/src/assets/glyph_stencils/interactions/process.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/process.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactions/process.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/process.xml diff --git a/frontend/src/assets/glyph_stencils/interactions/stimulation.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/stimulation.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/interactions/stimulation.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/interactions/stimulation.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/complex.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/complex.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/complex.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/complex.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/dsNA.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/dsNA.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/dsNA.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/dsNA.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/macromolecule.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/macromolecule.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/macromolecule.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/macromolecule.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/no-glyph-assigned-ms.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/no-glyph-assigned-ms.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/no-glyph-assigned-ms.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/no-glyph-assigned-ms.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/replacement-glyph.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/replacement-glyph.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/replacement-glyph.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/replacement-glyph.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/small-molecule.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/small-molecule.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/small-molecule.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/small-molecule.xml diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/ssNA.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/ssNA.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/molecularSpecies/ssNA.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/molecular_species/ssNA.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/aptamer.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/aptamer.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/aptamer.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/aptamer.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/assembly-scar.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/assembly-scar.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/assembly-scar.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/assembly-scar.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/blunt-restriction-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/blunt-restriction-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/blunt-restriction-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/blunt-restriction-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/cds.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/cds.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/cds.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/cds.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/chromosomal-locus.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/chromosomal-locus.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/chromosomal-locus.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/chromosomal-locus.xml diff --git a/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/circular-plasmid.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/circular-plasmid.xml new file mode 100644 index 00000000..9e1af997 --- /dev/null +++ b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/circular-plasmid.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/dna-stability-element.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/dna-stability-element.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/dna-stability-element.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/dna-stability-element.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/engineered-region.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/engineered-region.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/engineered-region.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/engineered-region.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/five-prime-overhang.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/five-prime-overhang.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/five-prime-overhang.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/five-prime-overhang.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/five-prime-sticky-restriction-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/five-prime-sticky-restriction-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/five-prime-sticky-restriction-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/five-prime-sticky-restriction-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/insulator.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/insulator.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/insulator.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/insulator.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/location-dna.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-dna.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/location-dna.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-dna.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/location-protein.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-protein.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/location-protein.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-protein.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/location-rna.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-rna.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/location-rna.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/location-rna.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/ncrna.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ncrna.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/ncrna.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ncrna.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/no-glyph-assigned.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/no-glyph-assigned.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/no-glyph-assigned.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/no-glyph-assigned.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/nuclease-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/nuclease-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/nuclease-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/nuclease-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/operator.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/operator.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/operator.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/operator.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/origin-of-replication.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/origin-of-replication.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/origin-of-replication.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/origin-of-replication.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/origin-of-transfer.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/origin-of-transfer.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/origin-of-transfer.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/origin-of-transfer.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/polyA.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/polyA.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/polyA.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/polyA.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/primer-binding-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/primer-binding-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/primer-binding-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/primer-binding-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/promoter.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/promoter.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/promoter.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/promoter.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/protease-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/protease-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/protease-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/protease-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/protein-stability-element.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/protein-stability-element.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/protein-stability-element.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/protein-stability-element.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/ribonuclease-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ribonuclease-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/ribonuclease-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ribonuclease-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/ribosome-entry-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ribosome-entry-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/ribosome-entry-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/ribosome-entry-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/rna-stability-element.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/rna-stability-element.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/rna-stability-element.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/rna-stability-element.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/signature.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/signature.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/signature.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/signature.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/specific-recombination-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/specific-recombination-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/specific-recombination-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/specific-recombination-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/terminator-specification.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/terminator-specification.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/terminator-specification.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/terminator-specification.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/test.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/test.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/test.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/test.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/three-prime-overhang.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/three-prime-overhang.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/three-prime-overhang.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/three-prime-overhang.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/three-prime-sticky-restriction-site.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/three-prime-sticky-restriction-site.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/three-prime-sticky-restriction-site.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/three-prime-sticky-restriction-site.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/transcription-end.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/transcription-end.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/transcription-end.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/transcription-end.xml diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/translation-end.xml b/SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/translation-end.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/sequenceFeatures/translation-end.xml rename to SBOLCanvasFrontend/src/assets/glyph_stencils/sequence_feature/translation-end.xml diff --git a/frontend/src/assets/grid.png b/SBOLCanvasFrontend/src/assets/grid.png similarity index 100% rename from frontend/src/assets/grid.png rename to SBOLCanvasFrontend/src/assets/grid.png diff --git a/frontend/src/assets/icons/diagonalEdgeStyle.png b/SBOLCanvasFrontend/src/assets/icons/diagonalEdgeStyle.png similarity index 100% rename from frontend/src/assets/icons/diagonalEdgeStyle.png rename to SBOLCanvasFrontend/src/assets/icons/diagonalEdgeStyle.png diff --git a/frontend/src/assets/icons/entityRelationEdgeStyle.png b/SBOLCanvasFrontend/src/assets/icons/entityRelationEdgeStyle.png similarity index 100% rename from frontend/src/assets/icons/entityRelationEdgeStyle.png rename to SBOLCanvasFrontend/src/assets/icons/entityRelationEdgeStyle.png diff --git a/frontend/src/assets/icons/orthogonalEdgeStyle.png b/SBOLCanvasFrontend/src/assets/icons/orthogonalEdgeStyle.png similarity index 100% rename from frontend/src/assets/icons/orthogonalEdgeStyle.png rename to SBOLCanvasFrontend/src/assets/icons/orthogonalEdgeStyle.png diff --git a/frontend/src/assets/icons/sideToSideEdgeStyle.png b/SBOLCanvasFrontend/src/assets/icons/sideToSideEdgeStyle.png similarity index 100% rename from frontend/src/assets/icons/sideToSideEdgeStyle.png rename to SBOLCanvasFrontend/src/assets/icons/sideToSideEdgeStyle.png diff --git a/frontend/src/assets/icons/topToBottomEdgeStyle.png b/SBOLCanvasFrontend/src/assets/icons/topToBottomEdgeStyle.png similarity index 100% rename from frontend/src/assets/icons/topToBottomEdgeStyle.png rename to SBOLCanvasFrontend/src/assets/icons/topToBottomEdgeStyle.png diff --git a/frontend/src/assets/glyph_stencils/utils/module.xml b/SBOLCanvasFrontend/src/assets/module.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/utils/module.xml rename to SBOLCanvasFrontend/src/assets/module.xml diff --git a/frontend/src/assets/profile_jared.jpeg b/SBOLCanvasFrontend/src/assets/profile_jared.jpeg similarity index 100% rename from frontend/src/assets/profile_jared.jpeg rename to SBOLCanvasFrontend/src/assets/profile_jared.jpeg diff --git a/frontend/src/assets/profile_logan.jpg b/SBOLCanvasFrontend/src/assets/profile_logan.jpg similarity index 100% rename from frontend/src/assets/profile_logan.jpg rename to SBOLCanvasFrontend/src/assets/profile_logan.jpg diff --git a/frontend/src/assets/profile_sam.jpg b/SBOLCanvasFrontend/src/assets/profile_sam.jpg similarity index 100% rename from frontend/src/assets/profile_sam.jpg rename to SBOLCanvasFrontend/src/assets/profile_sam.jpg diff --git a/frontend/src/assets/glyph_stencils/utils/textBox.xml b/SBOLCanvasFrontend/src/assets/textBox.xml similarity index 100% rename from frontend/src/assets/glyph_stencils/utils/textBox.xml rename to SBOLCanvasFrontend/src/assets/textBox.xml diff --git a/frontend/src/assets/textBoxSource.png b/SBOLCanvasFrontend/src/assets/textBoxSource.png similarity index 100% rename from frontend/src/assets/textBoxSource.png rename to SBOLCanvasFrontend/src/assets/textBoxSource.png diff --git a/frontend/src/assets/tutorial_pics/AddingInteractions/freeFloatingInteraction.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/freeFloatingInteraction.png similarity index 100% rename from frontend/src/assets/tutorial_pics/AddingInteractions/freeFloatingInteraction.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/freeFloatingInteraction.png diff --git a/frontend/src/assets/tutorial_pics/AddingInteractions/moduleInteraction.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/moduleInteraction.png similarity index 100% rename from frontend/src/assets/tutorial_pics/AddingInteractions/moduleInteraction.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/moduleInteraction.png diff --git a/frontend/src/assets/tutorial_pics/AddingInteractions/selectionAfter.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/selectionAfter.png similarity index 100% rename from frontend/src/assets/tutorial_pics/AddingInteractions/selectionAfter.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/selectionAfter.png diff --git a/frontend/src/assets/tutorial_pics/AddingInteractions/selectionBefore.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/selectionBefore.png similarity index 100% rename from frontend/src/assets/tutorial_pics/AddingInteractions/selectionBefore.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/AddingInteractions/selectionBefore.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/circuit.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/circuit.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/circuit.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/circuit.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialButton.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialButton.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialButton.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialButton.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialEditor.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialEditor.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialEditor.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialEditor.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialIndicator.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialIndicator.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialIndicator.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/combinatorialIndicator.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerateButton.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerateButton.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerateButton.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerateButton.png diff --git a/frontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerationMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerationMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerationMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/CombinatorialDerivation/enumerationMenu.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/colorEditor.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/colorEditor.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/colorEditor.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/colorEditor.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/designMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/designMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/designMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/designMenu.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/importComponentMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/importComponentMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/importComponentMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/importComponentMenu.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/infoMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/infoMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/infoMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/infoMenu.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/selection_glyph_vs_strand.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/selection_glyph_vs_strand.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/selection_glyph_vs_strand.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/selection_glyph_vs_strand.png diff --git a/frontend/src/assets/tutorial_pics/EditingParts/simple_toolbar_options.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/simple_toolbar_options.png similarity index 100% rename from frontend/src/assets/tutorial_pics/EditingParts/simple_toolbar_options.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/EditingParts/simple_toolbar_options.png diff --git a/frontend/src/assets/tutorial_pics/GettingStarted/backbone.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/backbone.png similarity index 100% rename from frontend/src/assets/tutorial_pics/GettingStarted/backbone.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/backbone.png diff --git a/frontend/src/assets/tutorial_pics/GettingStarted/backbone_menu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/backbone_menu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/GettingStarted/backbone_menu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/backbone_menu.png diff --git a/frontend/src/assets/tutorial_pics/GettingStarted/circuit.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/circuit.png similarity index 100% rename from frontend/src/assets/tutorial_pics/GettingStarted/circuit.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/GettingStarted/circuit.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/downloadButton.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/downloadButton.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/downloadButton.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/downloadButton.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/downloadMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/downloadMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/downloadMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/downloadMenu.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/exportButton.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/exportButton.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/exportButton.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/exportButton.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/exportMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/exportMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/exportMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/exportMenu.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/uploadButton.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/uploadButton.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/uploadButton.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/uploadButton.png diff --git a/frontend/src/assets/tutorial_pics/SavingAndLoading/uploadMenu.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/uploadMenu.png similarity index 100% rename from frontend/src/assets/tutorial_pics/SavingAndLoading/uploadMenu.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/SavingAndLoading/uploadMenu.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/enterPart.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/enterPart.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/enterPart.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/enterPart.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/module.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/module.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/module.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/module.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/moduleSubstructure.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/moduleSubstructure.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/moduleSubstructure.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/moduleSubstructure.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/terminator.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminator.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/terminator.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminator.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/terminatorComposite.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminatorComposite.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/terminatorComposite.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminatorComposite.png diff --git a/frontend/src/assets/tutorial_pics/Substructure/terminatorSubParts.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminatorSubParts.png similarity index 100% rename from frontend/src/assets/tutorial_pics/Substructure/terminatorSubParts.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/Substructure/terminatorSubParts.png diff --git a/frontend/src/assets/tutorial_pics/front_and_back.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/front_and_back.png similarity index 100% rename from frontend/src/assets/tutorial_pics/front_and_back.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/front_and_back.png diff --git a/frontend/src/assets/tutorial_pics/glyph_flip.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/glyph_flip.png similarity index 100% rename from frontend/src/assets/tutorial_pics/glyph_flip.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/glyph_flip.png diff --git a/frontend/src/assets/tutorial_pics/search_bar.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/search_bar.png similarity index 100% rename from frontend/src/assets/tutorial_pics/search_bar.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/search_bar.png diff --git a/frontend/src/assets/tutorial_pics/side_menu_top.png b/SBOLCanvasFrontend/src/assets/tutorial_pics/side_menu_top.png similarity index 100% rename from frontend/src/assets/tutorial_pics/side_menu_top.png rename to SBOLCanvasFrontend/src/assets/tutorial_pics/side_menu_top.png diff --git a/frontend/src/browserslist b/SBOLCanvasFrontend/src/browserslist similarity index 100% rename from frontend/src/browserslist rename to SBOLCanvasFrontend/src/browserslist diff --git a/SBOLCanvasFrontend/src/environments/environment.prod.ts b/SBOLCanvasFrontend/src/environments/environment.prod.ts new file mode 100644 index 00000000..37ec29aa --- /dev/null +++ b/SBOLCanvasFrontend/src/environments/environment.prod.ts @@ -0,0 +1,5 @@ +export const environment = { + production: true, + backendURL: '../api', + baseURI: "https://sbolcanvas.org" +}; diff --git a/frontend/src/environments/environment.ts b/SBOLCanvasFrontend/src/environments/environment.ts similarity index 92% rename from frontend/src/environments/environment.ts rename to SBOLCanvasFrontend/src/environments/environment.ts index 937471b7..c77a7fa0 100644 --- a/frontend/src/environments/environment.ts +++ b/SBOLCanvasFrontend/src/environments/environment.ts @@ -4,7 +4,7 @@ export const environment = { production: false, - backendURL: 'http://localhost:8080/api', + backendURL: 'http://localhost:8080/SBOLCanvasBackend', baseURI: "https://sbolcanvas.org" }; diff --git a/SBOLCanvasFrontend/src/environments/versions.ts b/SBOLCanvasFrontend/src/environments/versions.ts new file mode 100644 index 00000000..c7a84ff9 --- /dev/null +++ b/SBOLCanvasFrontend/src/environments/versions.ts @@ -0,0 +1,7 @@ + +// this file is automatically generated by git.version.ts script +export const versions = { + revision: 'dev', + branch: 'AboutPageFix', + version: 'Development' +}; \ No newline at end of file diff --git a/frontend/src/favicon.ico b/SBOLCanvasFrontend/src/favicon.ico similarity index 100% rename from frontend/src/favicon.ico rename to SBOLCanvasFrontend/src/favicon.ico diff --git a/frontend/src/index.html b/SBOLCanvasFrontend/src/index.html similarity index 100% rename from frontend/src/index.html rename to SBOLCanvasFrontend/src/index.html diff --git a/frontend/src/karma.conf.js b/SBOLCanvasFrontend/src/karma.conf.js similarity index 100% rename from frontend/src/karma.conf.js rename to SBOLCanvasFrontend/src/karma.conf.js diff --git a/frontend/src/main.ts b/SBOLCanvasFrontend/src/main.ts similarity index 100% rename from frontend/src/main.ts rename to SBOLCanvasFrontend/src/main.ts diff --git a/frontend/src/mxgraph.d.ts b/SBOLCanvasFrontend/src/mxgraph.d.ts similarity index 100% rename from frontend/src/mxgraph.d.ts rename to SBOLCanvasFrontend/src/mxgraph.d.ts diff --git a/frontend/src/polyfills.ts b/SBOLCanvasFrontend/src/polyfills.ts similarity index 100% rename from frontend/src/polyfills.ts rename to SBOLCanvasFrontend/src/polyfills.ts diff --git a/frontend/src/scrap_html.html b/SBOLCanvasFrontend/src/scrap_html.html similarity index 100% rename from frontend/src/scrap_html.html rename to SBOLCanvasFrontend/src/scrap_html.html diff --git a/frontend/src/styles.scss b/SBOLCanvasFrontend/src/styles.scss similarity index 100% rename from frontend/src/styles.scss rename to SBOLCanvasFrontend/src/styles.scss diff --git a/frontend/src/test.ts b/SBOLCanvasFrontend/src/test.ts similarity index 100% rename from frontend/src/test.ts rename to SBOLCanvasFrontend/src/test.ts diff --git a/frontend/src/tsconfig.app.json b/SBOLCanvasFrontend/src/tsconfig.app.json similarity index 100% rename from frontend/src/tsconfig.app.json rename to SBOLCanvasFrontend/src/tsconfig.app.json diff --git a/frontend/src/tsconfig.spec.json b/SBOLCanvasFrontend/src/tsconfig.spec.json similarity index 100% rename from frontend/src/tsconfig.spec.json rename to SBOLCanvasFrontend/src/tsconfig.spec.json diff --git a/frontend/src/tslint.json b/SBOLCanvasFrontend/src/tslint.json similarity index 100% rename from frontend/src/tslint.json rename to SBOLCanvasFrontend/src/tslint.json diff --git a/frontend/tsconfig.json b/SBOLCanvasFrontend/tsconfig.json similarity index 96% rename from frontend/tsconfig.json rename to SBOLCanvasFrontend/tsconfig.json index 7e0b410b..b271fd9f 100644 --- a/frontend/tsconfig.json +++ b/SBOLCanvasFrontend/tsconfig.json @@ -15,7 +15,7 @@ "node_modules/@types" ], "lib": [ - "esnext", + "es2018", "dom" ] } diff --git a/frontend/tslint.json b/SBOLCanvasFrontend/tslint.json similarity index 100% rename from frontend/tslint.json rename to SBOLCanvasFrontend/tslint.json diff --git a/backend/Dockerfile b/backend/Dockerfile deleted file mode 100644 index db7ae07f..00000000 --- a/backend/Dockerfile +++ /dev/null @@ -1,25 +0,0 @@ -FROM tomcat:9.0-jdk8-openjdk - -# Set up working directory -WORKDIR /opt/backend - -# Variables to make building easier -ARG web_content_dir=WEB-INF -ARG compile_source_dir=src -ARG compile_dest_dir=${web_content_dir}/classes -ARG dependencies_dir=${web_content_dir}/lib -ARG tomcat_dependencies=/usr/local/tomcat/lib - -# Set up build directory -RUN mkdir -p ${compile_dest_dir} - -# Copy source, dependencies, and web.xml -COPY src src -COPY lib ${web_content_dir}/lib -COPY web.xml ${web_content_dir} - -# Compile java files into the backend/WebContent/WEB-INF/classes directory -RUN javac -source 1.8 -target 1.8 -sourcepath ${compile_source_dir} -d ${compile_dest_dir} -cp ".:${dependencies_dir}/*:${tomcat_dependencies}/*" ${compile_source_dir}/**/*.java - -# Build .war file -RUN jar -cf /usr/local/tomcat/webapps/api.war ${web_content_dir}/* diff --git a/backend/nodemon.json b/backend/nodemon.json deleted file mode 100644 index b2ff50c2..00000000 --- a/backend/nodemon.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "ext": "java", - "watch": [ "src/" ], - "exec": "docker build -t canvas-api:working . && docker run --rm --name CanvasAPI -p 8080:8080 canvas-api:working", - "events": { - "restart": "docker stop CanvasAPI" - } -} \ No newline at end of file diff --git a/backend/src/servlets/SynBioHub.java b/backend/src/servlets/SynBioHub.java deleted file mode 100644 index ab0b8d85..00000000 --- a/backend/src/servlets/SynBioHub.java +++ /dev/null @@ -1,378 +0,0 @@ -package servlets; - -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.net.URI; -import java.net.URISyntaxException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedList; -import java.util.List; -import java.util.TreeSet; - -import javax.servlet.ServletOutputStream; -import javax.servlet.annotation.WebServlet; -import javax.servlet.http.HttpServlet; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; -import javax.xml.parsers.ParserConfigurationException; -import javax.xml.transform.TransformerException; -import javax.xml.transform.TransformerFactoryConfigurationError; - -import org.apache.commons.io.IOUtils; -import org.apache.http.HttpStatus; -import org.sbolstandard.core2.SBOLConversionException; -import org.sbolstandard.core2.SBOLDocument; -import org.sbolstandard.core2.SBOLReader; -import org.sbolstandard.core2.SBOLValidationException; -import org.sbolstandard.core2.SBOLWriter; -import org.synbiohub.frontend.IdentifiedMetadata; -import org.synbiohub.frontend.SearchCriteria; -import org.synbiohub.frontend.SearchQuery; -import org.synbiohub.frontend.SynBioHubException; -import org.synbiohub.frontend.SynBioHubFrontend; -import org.synbiohub.frontend.WebOfRegistriesData; -import org.xml.sax.SAXException; - -import com.google.gson.Gson; - -import utils.MxToSBOL; -import utils.SBOLData; -import utils.SBOLToMx; - -@SuppressWarnings("serial") -@WebServlet(urlPatterns = { "/SynBioHub/*" }) -public class SynBioHub extends HttpServlet { - - protected void doGet(HttpServletRequest request, HttpServletResponse response) throws IOException { - try { - - // parse auth header - String authorization = request.getHeader("Authorization"); - String email = null; - String password = null; - String user = null; - if (authorization != null && authorization.split(":").length > 1) { - String[] tokens = authorization.split(":"); - email = tokens[0]; - password = tokens[1]; - } else { - user = authorization; - } - - // setup SBH server - String server = request.getParameter("server"); - SynBioHubFrontend sbhf = null; - if(server != null) { - sbhf = new SynBioHubFrontend(server); - if(user != null) - sbhf.setUser(user); - } - - // handle routes - // NOTE: using nested scopes in each case to prevent naming collisions - switch(request.getPathInfo()) { - - case "/registries": { - LinkedList registryURLs = new LinkedList(); - for (WebOfRegistriesData registry : SynBioHubFrontend.getRegistries()) { - registryURLs.add(registry.getInstanceUrl()); - } - writeJSONBody(response, registryURLs); - cacheResponse(response); - } - break; - - case "/login": { - if (sbhf == null || email == null || password == null || email.isEmpty() || password.isEmpty() - || server.isEmpty()) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - try { - sbhf.login(email, password); - } catch (SynBioHubException e) { - if (e.getMessage().equals("org.synbiohub.frontend.PermissionException")) { - response.setStatus(HttpStatus.SC_UNAUTHORIZED); - return; - } - throw e; - } - writeJSONBody(response, sbhf.getUser()); - } - break; - - case "/logout": { - if(sbhf == null || user == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - sbhf.logout(); - } - break; - - case "/listMyCollections": { - if (sbhf == null || user == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - List collections = sbhf.getRootCollectionMetadata(); - collections.removeIf(collection -> (collection.getUri().contains("/public/"))); - writeJSONBody(response, collections); - } - break; - - case "/listRegistryParts": { - String collection = request.getParameter("collection"); - String type = request.getParameter("type"); - String role = request.getParameter("role"); - String mode = request.getParameter("mode"); - - if (sbhf == null || mode == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - TreeSet roles = null; - TreeSet types = null; - TreeSet collections = null; - if (role != null && role.length() > 0) { - roles = new TreeSet(); - if (SBOLData.roles.ContainsKey(role)) - roles.add(SBOLData.roles.getValue(role)); - else - roles.add(SBOLData.refinements.getValue(role)); - } - if (type != null && type.length() > 0) { - types = new TreeSet(); - types.add(SBOLData.types.getValue(type)); - } - if (collection != null) { - collections = new TreeSet(); - collections.add(URI.create(collection)); - } - - ArrayList results = new ArrayList(); - if (mode.equals("collections")) { - if (collections == null) { - results.addAll(sbhf.getRootCollectionMetadata()); - } else { - for (URI collectionURI : collections) { - results.addAll(sbhf.getSubCollectionMetadata(collectionURI)); - } - } - } else if (mode.equals("components") && collections != null) { - results.addAll( - sbhf.getMatchingComponentDefinitionMetadata(null, roles, types, collections, null, null)); - } else if (mode.equals("modules") && collections != null) { - // SynbioHubFrontend doesn't have anything easy for modules - SearchQuery query = new SearchQuery(); - - SearchCriteria objectCriteria = new SearchCriteria(); - objectCriteria.setKey("objectType"); - objectCriteria.setValue("ModuleDefinition"); - query.addCriteria(objectCriteria); - - if (collections != null) { - for (URI uri : collections) { - SearchCriteria collectionCriteria = new SearchCriteria(); - collectionCriteria.setKey("collection"); - collectionCriteria.setValue(uri.toString()); - query.getCriteria().add(collectionCriteria); - } - } - - results.addAll(sbhf.search(query)); - } - - writeJSONBody(response, results.toArray(new IdentifiedMetadata[0])); - } - break; - - case "/listLayouts": - // TO DO: implement - break; - - case "/listCombinatorials": { - if(sbhf == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - String template = request.getParameter("template"); - - ArrayList results = new ArrayList(); - - SearchQuery query = new SearchQuery(); - - SearchCriteria objectTypeCriteria = new SearchCriteria(); - objectTypeCriteria.setKey("objectType"); - objectTypeCriteria.setValue("CombinatorialDerivation"); - query.addCriteria(objectTypeCriteria); - - SearchCriteria sbolTagCriteria = new SearchCriteria(); - sbolTagCriteria.setKey("template"); - sbolTagCriteria.setValue(template); - query.addCriteria(sbolTagCriteria); - - results.addAll(sbhf.search(query)); - - writeJSONBody(response, results.toArray(new IdentifiedMetadata[0])); - } - break; - - case "/getRegistryPart": { - String uri = request.getParameter("uri"); - if (uri == null || sbhf == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - String combinatorial = request.getParameter("combinatorial"); - SBOLToMx converter = new SBOLToMx(); - String layoutURI = uri.substring(0,uri.lastIndexOf("/"))+"_Layout"+uri.substring(uri.lastIndexOf("/"), uri.length()); - SBOLDocument document; - try { - document = sbhf.getSBOL(URI.create(layoutURI), true); - }catch(SynBioHubException e) { - document = sbhf.getSBOL(URI.create(uri), true); - } - if(document == null) { - document = sbhf.getSBOL(URI.create(uri), true); - } - - SBOLDocument combDocument = null; - if(combinatorial != null) { - combDocument = sbhf.getSBOL(URI.create(combinatorial), true); - } - - converter.toGraph(document, combDocument, response.getOutputStream()); - } - break; - - case "/importRegistryPart": { - String uri = request.getParameter("uri"); - if(uri == null || sbhf == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - SBOLToMx converter = new SBOLToMx(); - - String layoutURI = uri.substring(0,uri.lastIndexOf("/"))+"_Layout"+uri.substring(uri.lastIndexOf("/"), uri.length()); - SBOLDocument document; - try { - document = sbhf.getSBOL(URI.create(layoutURI), true); - if(document == null) { - document = sbhf.getSBOL(URI.create(uri), true); - } - }catch(SynBioHubException e) { - document = sbhf.getSBOL(URI.create(uri), true); - } - - converter.toGraph(document, response.getOutputStream()); - } - break; - - default: - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - - // if it made it out, status is OK - response.setStatus(HttpStatus.SC_OK); - - } catch (SynBioHubException | IOException | ParserConfigurationException | TransformerException | SBOLValidationException | SAXException | URISyntaxException e) { - ServletOutputStream outputStream = response.getOutputStream(); - InputStream inputStream = new ByteArrayInputStream(e.getMessage().getBytes()); - IOUtils.copy(inputStream, outputStream); - - response.setStatus(HttpStatus.SC_INTERNAL_SERVER_ERROR); - - e.printStackTrace(); - } - } - - protected void doPost(HttpServletRequest request, HttpServletResponse response) throws IOException { - try { - String server = request.getParameter("server"); - String user = request.getHeader("Authorization"); - String uri = request.getParameter("uri"); - - if (request.getPathInfo().equals("/addToCollection")) { - - if (server == null || user == null || uri == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - HashMap userTokens = new HashMap(); - String[] servers = user.split(","); - for(String serverInf : servers) { - String[] tokens = serverInf.split(" "); - userTokens.put(tokens[0], tokens[1]); - } - - SynBioHubFrontend sbhf = new SynBioHubFrontend(server); - sbhf.setUser(userTokens.get(server)); - MxToSBOL converter = new MxToSBOL(userTokens); - ByteArrayOutputStream out = new ByteArrayOutputStream(); - converter.toSBOL(request.getInputStream(), out); - sbhf.addToCollection(URI.create(uri), true, new ByteArrayInputStream(out.toByteArray())); - response.setStatus(HttpStatus.SC_CREATED); - } else if(request.getPathInfo().contentEquals("/importToCollection")) { - if(server == null || user == null || uri == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - SynBioHubFrontend sbhf = new SynBioHubFrontend(server); - sbhf.setUser(user); - SBOLDocument document = SBOLReader.read(request.getInputStream()); - ByteArrayOutputStream out = new ByteArrayOutputStream(); - SBOLWriter.setKeepGoing(true); - SBOLWriter.write(document, out); - sbhf.addToCollection(URI.create(uri), true, new ByteArrayInputStream(out.toByteArray())); - response.setStatus(HttpStatus.SC_CREATED); - } else if(request.getPathInfo().contentEquals("/createCollection")) { - String id = request.getParameter("id"); - String version = request.getParameter("version"); - String name = request.getParameter("name"); - String description = request.getParameter("description"); - String citations = request.getParameter("citations"); - String overwrite = request.getParameter("overwrite"); - - if(server == null || user == null || id == null || version == null || name == null || description == null || overwrite == null) { - response.setStatus(HttpStatus.SC_BAD_REQUEST); - return; - } - SynBioHubFrontend sbhf = new SynBioHubFrontend(server); - sbhf.setUser(user); - sbhf.createCollection(id, version, name, description, citations, overwrite.equals("true")); - response.setStatus(HttpStatus.SC_CREATED); - } - - } catch (SynBioHubException | IOException | SBOLValidationException | SBOLConversionException | TransformerFactoryConfigurationError | TransformerException | URISyntaxException e) { - ServletOutputStream outputStream = response.getOutputStream(); - InputStream inputStream = new ByteArrayInputStream(e.getMessage().getBytes()); - IOUtils.copy(inputStream, outputStream); - - response.setStatus(HttpStatus.SC_INTERNAL_SERVER_ERROR); - } - - } - - private void writeJSONBody(HttpServletResponse response, Object data) throws IOException { - Gson gson = new Gson(); - InputStream bodyStream = new ByteArrayInputStream(gson.toJson(data).getBytes()); - IOUtils.copy(bodyStream, response.getOutputStream()); - response.setContentType("application/json"); - } - - private void cacheResponse(HttpServletResponse response) { - response.setHeader("Cache-Control", "max-age=3600"); - } -} diff --git a/frontend/assetBundler.js b/frontend/assetBundler.js deleted file mode 100644 index 0a7dca82..00000000 --- a/frontend/assetBundler.js +++ /dev/null @@ -1,100 +0,0 @@ -const fs = require("fs").promises -const path = require("path") - -const BUNDLE_DIRS = [ - "src/assets/glyph_stencils/sequenceFeatures", - "src/assets/glyph_stencils/molecularSpecies", - "src/assets/glyph_stencils/interactions", - "src/assets/glyph_stencils/interactionNodes", - "src/assets/glyph_stencils/indicators", - "src/assets/glyph_stencils/utils", -] - -const BUNDLE_FILENAME = "bundle.xml" -const BUNDLE_ORDER_FILENAME = ".bundle_order" -const OUTPUT_DIR = "src/assets/glyph_stencils" - - -async function bundle() { - // create bundle for each directory - // using for loop instead of map so logs are in order - const bundles = [] - for (const dir of BUNDLE_DIRS) - bundles.push(await bundleDir(dir)) - - // join them all together into one string - const entireBundle = ` - ${bundles.join("\n")} -` - - // write bundle out - const bundlePath = path.join(OUTPUT_DIR, BUNDLE_FILENAME) - await fs.writeFile(bundlePath, entireBundle) - console.log("\nWrote final bundle:", bundlePath) -} - - -async function bundleDir(dir) { - console.log("\nBundling assets in", dir) - - // read in all files in directory - const files = await fs.readdir(dir) - console.log("\tFound", files.length, "files.") - - // try to sort files according to .bundle_order file - try { - // read in file - const bundleOrderContent = (await fs.readFile(path.join(dir, BUNDLE_ORDER_FILENAME), "utf8")) - .split(/\r?\n/) // split by line - .filter(item => !!item.trim()) // remove blanks - const bundleOrder = bundleOrderContent.filter(item => !item.startsWith("!")) - console.log("\tUsing bundle order.") - - // find exclusions - const exclude = bundleOrderContent - .filter(item => item.startsWith("!")) - .map(item => item.replace("!", "")) - - // sort files array - const findOrderIndex = fileName => { - const index = bundleOrder.findIndex(item => fileName.includes(item)) - return index == -1 ? bundleOrder.length + 1 : index - } - files.sort( - (a, b) => findOrderIndex(a) - findOrderIndex(b) - ) - - // filter out files that are in the exclusions - const filesExcluded = [] - exclude.forEach(exclusion => { - const index = files.findIndex(file => file.includes(exclusion)) - index != -1 && filesExcluded.push(files.splice(index, 1)) - }) - console.log("\tExcluding", filesExcluded.length, "files.") - } - catch (err) { console.error(err) } - - // await all file content to be loaded in - const filesContents = await Promise.all( - files - // grab only XMLs - .filter(fileName => fileName.endsWith('.xml')) - // make sure we don't grab a preexisting bundle - .filter(fileName => fileName != BUNDLE_FILENAME) - // read in file content - .map(fileName => fs.readFile(path.join(dir, fileName), "utf8")) - ) - - // combine content - const joinedContent = filesContents - // remove tag - .map(content => content.replace(/\<[\/]*shapes\>/g, "")) - // add subdir attribute to tag - .map(content => content.replace(/\ -
- -

Stroke

- -
- -
Color:
- - -
- -
- -
- -
- -
Opacity:
- - -
- - - -
- -
- -
- -
Width:
- - -
- - - -
- -
- - -
- -
- -

Fill

- -
- -
Color:
- - -
- -
- -
- -
- -
Opacity:
- - -
- - - -
- -
-
- - - -
- -
- -

Edge

- -
- -
Style:
- - -
- - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- -
- -
Corner:
- - -
- - Sharp - Rounded - Curved - -
- -
- -
- -
Arrow Size:
- - -
- - - -
- -
- -
- -
Source Margin:
- - -
- - - -
- -
-
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Target Margin:
- - -
- - - -
- -
-
- - -
- -
- -

Font

- -
- -
Color:
- - -
- -
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- -
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Opacity:
- - -
- - - -
- -
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Size:
- - -
- - - -
- -
- - -
- \ No newline at end of file diff --git a/frontend/src/app/embedded.service.ts b/frontend/src/app/embedded.service.ts deleted file mode 100644 index f01a49f8..00000000 --- a/frontend/src/app/embedded.service.ts +++ /dev/null @@ -1,42 +0,0 @@ -import { Injectable } from '@angular/core' -import { GraphService } from './graph.service' -import { ActivatedRoute } from '@angular/router' -import { Observable } from 'rxjs' - - -@Injectable({ - providedIn: 'root' -}) - -export class EmbeddedService { - - private parent: any - public sbol: Observable - - constructor(private route: ActivatedRoute) { - - // create observable that watches for messages - this.sbol = new Observable(observer => { - window.addEventListener('message', ({data, source}) => { - // check that message is coming from external window - if(source != window) { - this.parent = source - - // check if message includes SBOL - if(data && data.sbol) { - console.debug('[Embedded] Received SBOL from up above:', data.sbol.substring(0, 20) + '...') - observer.next(data.sbol) - } - } - }) - }) - } - - public isAppEmbedded(): boolean { - return !!this.parent - } - - public postMessage(message: any): void { - this.parent && this.parent.postMessage(message, '*') - } -} \ No newline at end of file diff --git a/frontend/src/app/error/error.component.css b/frontend/src/app/error/error.component.css deleted file mode 100644 index 525d55f1..00000000 --- a/frontend/src/app/error/error.component.css +++ /dev/null @@ -1,10 +0,0 @@ - -#error-frame { - width: 100%; - height: 400px; - border: none; -} - -#error-content-size { - width: 900px; -} \ No newline at end of file diff --git a/frontend/src/app/error/error.component.html b/frontend/src/app/error/error.component.html deleted file mode 100644 index 2c5685d3..00000000 --- a/frontend/src/app/error/error.component.html +++ /dev/null @@ -1,18 +0,0 @@ -

An error has occurred.

- - - - - Click to view more details. - - - -
- - - - - -
- -
\ No newline at end of file diff --git a/frontend/src/app/glyph-menu/glyph-menu.component.html b/frontend/src/app/glyph-menu/glyph-menu.component.html deleted file mode 100644 index 83e1a8eb..00000000 --- a/frontend/src/app/glyph-menu/glyph-menu.component.html +++ /dev/null @@ -1,153 +0,0 @@ -
-
- - - - - - - - - - - - - - - - - - - - - Sequence Features - - - - - - - - - - - - - - - - - - Molecular Species - - - - - - - - - - - - - - - - - Interactions - - - - - - - - - - - - - - - - - Interaction Nodes - - - - - - - - - - - - - - - - - Util - - - - - - - - - - - - - - - - - - - -
-
\ No newline at end of file diff --git a/frontend/src/app/glyph.service.ts b/frontend/src/app/glyph.service.ts deleted file mode 100644 index 2200d99f..00000000 --- a/frontend/src/app/glyph.service.ts +++ /dev/null @@ -1,213 +0,0 @@ -import { Injectable } from '@angular/core'; - -declare var require: any; -const mx = require('mxgraph')({ - mxImageBasePath: 'mxgraph/images', - mxBasePath: 'mxgraph' -}); - -@Injectable({ - providedIn: 'root' -}) -export class GlyphService { - - private sequenceFeatureXMLBundle: string = "assets/glyph_stencils/sequence_feature/bundle.xml"; - private sequenceFeatureXMLs: string[] = [ - // Strand glyphs - 'assets/glyph_stencils/sequence_feature/engineered-region.xml', - 'assets/glyph_stencils/sequence_feature/promoter.xml', - 'assets/glyph_stencils/sequence_feature/ribosome-entry-site.xml', - 'assets/glyph_stencils/sequence_feature/cds.xml', - 'assets/glyph_stencils/sequence_feature/terminator-specification.xml', - 'assets/glyph_stencils/sequence_feature/ncrna.xml', - 'assets/glyph_stencils/sequence_feature/origin-of-replication.xml', - 'assets/glyph_stencils/sequence_feature/origin-of-transfer.xml', - 'assets/glyph_stencils/sequence_feature/primer-binding-site.xml', - 'assets/glyph_stencils/sequence_feature/five-prime-sticky-restriction-site.xml', - 'assets/glyph_stencils/sequence_feature/three-prime-sticky-restriction-site.xml', - 'assets/glyph_stencils/sequence_feature/assembly-scar.xml', - 'assets/glyph_stencils/sequence_feature/operator.xml', - 'assets/glyph_stencils/sequence_feature/insulator.xml', - 'assets/glyph_stencils/sequence_feature/blunt-restriction-site.xml', - 'assets/glyph_stencils/sequence_feature/three-prime-overhang.xml', - 'assets/glyph_stencils/sequence_feature/five-prime-overhang.xml', - 'assets/glyph_stencils/sequence_feature/aptamer.xml', - //'assets/glyph_stencils/sequence_feature/dna-stability-element.xml', - 'assets/glyph_stencils/sequence_feature/polyA.xml', - 'assets/glyph_stencils/sequence_feature/specific-recombination-site.xml', - 'assets/glyph_stencils/sequence_feature/no-glyph-assigned.xml', - 'assets/glyph_stencils/sequence_feature/signature.xml', - 'assets/glyph_stencils/sequence_feature/location-dna.xml', - 'assets/glyph_stencils/sequence_feature/location-rna.xml', - 'assets/glyph_stencils/sequence_feature/location-protein.xml', - 'assets/glyph_stencils/sequence_feature/nuclease-site.xml', - 'assets/glyph_stencils/sequence_feature/protease-site.xml', - 'assets/glyph_stencils/sequence_feature/protein-stability-element.xml', - 'assets/glyph_stencils/sequence_feature/ribonuclease-site.xml', - 'assets/glyph_stencils/sequence_feature/rna-stability-element.xml', - //'assets/glyph_stencils/sequence_feature/chromosomal-locus.xml', - //'assets/glyph_stencils/sequence_feature/circular-plasmid.xml', - 'assets/glyph_stencils/sequence_feature/transcription-end.xml', - 'assets/glyph_stencils/sequence_feature/translation-end.xml', - //'assets/glyph_stencils/sequence_feature/test.xml', - ]; - - private molecularSpeciesXMLBundle: string = "assets/glyph_stencils/molecular_species/bundle.xml"; - private molecularSpeciesXMLs: string[] = [ - // 'molecular species' glyphs aka protein? - 'assets/glyph_stencils/molecular_species/macromolecule.xml', - 'assets/glyph_stencils/molecular_species/dsNA.xml', - 'assets/glyph_stencils/molecular_species/ssNA.xml', - 'assets/glyph_stencils/molecular_species/small-molecule.xml', - 'assets/glyph_stencils/molecular_species/no-glyph-assigned-ms.xml', - 'assets/glyph_stencils/molecular_species/replacement-glyph.xml', - 'assets/glyph_stencils/molecular_species/complex.xml', - ]; - - private interactionXMLBundle: string = "assets/glyph_stencils/interactions/bundle.xml"; - private interactionXMLs: string[] = [ - 'assets/glyph_stencils/interactions/control.xml', - 'assets/glyph_stencils/interactions/inhibition.xml', - 'assets/glyph_stencils/interactions/stimulation.xml', - 'assets/glyph_stencils/interactions/process.xml', - 'assets/glyph_stencils/interactions/degradation.xml', - ]; - - private interactionNodeXMLBundle: string = "assets/glyph_stencils/interaction_nodes/bundle.xml"; - private interactionNodeXMLs: string[] = [ - 'assets/glyph_stencils/interaction_nodes/association.xml', - 'assets/glyph_stencils/interaction_nodes/dissociation.xml', - 'assets/glyph_stencils/interaction_nodes/process.xml', - 'assets/glyph_stencils/molecular_species/replacement-glyph.xml', - ]; - - private indicatorXMLBundle: string = "assets/glyph_stencils/indicators/bundle.xml"; - private indicatorXMLs: string[] = [ - 'assets/glyph_stencils/indicators/composite.xml', - 'assets/glyph_stencils/indicators/variant.xml', - 'assets/glyph_stencils/indicators/error.xml', - ]; - - private utilXMLBundle: string = "assets/glyph_stencils/util/bundle.xml"; - private utilXMLs: string[] = [ - 'assets/backbone.xml', - 'assets/textBox.xml', - 'assets/module.xml', - ]; - - private sequenceFeatures: any = {}; - private molecularSpecies: any = {}; - private interactions: any = {}; - private interactionNodes: any = {}; - private indicators: any = {}; - private utils: any = {}; - - private xmlBundle: string = "assets/glyph_stencils/bundle.xml" - - constructor() { - this.loadXMLBundle(this.xmlBundle) - } - - loadXMLBundle(bundleFile) { - let req = mx.mxUtils.load(bundleFile); - let root = req.getDocumentElement(); - let shape = root.firstChild; - - while (shape != null) { - if (shape.nodeType == mx.mxConstants.NODETYPE_ELEMENT) { - const name = shape.getAttribute('name'); - const subDir = shape.getAttribute('subdir'); - const centered = shape.getAttribute('centered'); - - const stencil = new mx.mxStencil(shape); - this[subDir][name] = [stencil, (centered && centered.toLowerCase() == 'true')]; - } - shape = shape.nextSibling; - } - } - - // unused now - loadXMLs(xml_list, glyph_list) { - xml_list.forEach((filename) => this.loadXML(filename, glyph_list)); - } - - // unused now - loadXML(xmlFile, glyph_list) { - let req = mx.mxUtils.load(xmlFile); - let root = req.getDocumentElement(); - let shape = root.firstChild; - - while (shape != null) { - if (shape.nodeType == mx.mxConstants.NODETYPE_ELEMENT) { - const name = shape.getAttribute('name'); - const centered = shape.getAttribute('centered'); - - const stencil = new mx.mxStencil(shape); - - glyph_list[name] = [stencil, (centered && centered.toLowerCase() == 'true')]; - } - shape = shape.nextSibling; - } - } - - getElements(glyph_list) { - const svgs = {}; - - for (const name in glyph_list) { - const stencil = glyph_list[name][0]; - - let elt = document.createElement('svg'); - let canvas = new mx.mxSvgCanvas2D(elt); - let shape = new mx.mxShape(stencil); - - canvas.setStrokeColor('#000000'); - canvas.setFillColor('none'); - - stencil.drawShape(canvas, shape, 0, 0, 50, 50); - - svgs[name] = elt; - } - - return svgs; - } - - getSequenceFeatureGlyphs() { - return this.sequenceFeatures; - } - - getMolecularSpeciesGlyphs() { - return this.molecularSpecies; - } - - getIndicatorGlyphs() { - return this.indicators; - } - - getInteractionNodeGlyphs() { - return this.interactionNodes; - } - - getUtilGlyphs() { - return this.utils; - } - - getUtilElements() { - return this.getElements(this.utils) - } - - getInteractionElements() { - return this.getElements(this.interactions); - } - - getInteractionNodeElements() { - return this.getElements(this.interactionNodes); - } - - getMolecularSpeciesElements() { - return this.getElements(this.molecularSpecies); - } - - getSequenceFeatureElements() { - return this.getElements(this.sequenceFeatures); - } -} diff --git a/frontend/src/app/glyphInfo.ts b/frontend/src/app/glyphInfo.ts deleted file mode 100644 index 2eed4b19..00000000 --- a/frontend/src/app/glyphInfo.ts +++ /dev/null @@ -1,141 +0,0 @@ -import { ParsedEventType } from '@angular/compiler'; -import { CanvasAnnotation } from './canvasAnnotation'; -import { Info } from './info'; -import { environment } from 'src/environments/environment'; -import { customAlphabet } from 'nanoid'; -import { alphanumeric } from 'nanoid-dictionary'; - -export class GlyphInfo extends Info { - // Remember that when you change this you need to change the encode function in graph service - static counter: number = 0; - partType: string; - otherTypes: string[]; - partRole: string; - otherRoles: string[]; - partRefine: string; - name: string; - description: string; - version: string; - sequence: string; - sequenceURI: string; - annotations: CanvasAnnotation[]; - derivedFroms: string[]; - generatedBys: string[]; - - constructor(partType?: string, id?: string) { - super(); - - this.version = "1" - - if (id) { - this.displayID = id - // this.displayID = 'id_' + (customAlphabet(alphanumeric, 5)()); - } - else - this.displayID = 'id' + (GlyphInfo.counter++); - - if (partType) { - this.partType = partType; - } else { - this.partType = 'DNA region'; - } - } - - makeCopy() { - const copy: GlyphInfo = new GlyphInfo(); - copy.partType = this.partType; - copy.otherTypes = this.otherTypes ? this.otherTypes.slice() : null; - copy.partRole = this.partRole; - copy.otherRoles = this.otherRoles ? this.otherRoles.slice() : null; - copy.partRefine = this.partRefine; - copy.displayID = this.displayID; - copy.name = this.name; - copy.description = this.description; - copy.version = this.version; - copy.sequence = this.sequence; - copy.sequenceURI = this.sequenceURI; - copy.uriPrefix = this.uriPrefix; - copy.annotations = this.annotations ? this.annotations.slice() : null; - copy.derivedFroms = this.derivedFroms ? this.derivedFroms.slice() : null; - copy.generatedBys = this.generatedBys ? this.generatedBys.slice() : null; - return copy; - } - - copyDataFrom(other: GlyphInfo) { - this.partType = other.partType; - this.otherTypes = other.otherTypes ? other.otherTypes.slice() : null; - this.partRole = other.partRole; - this.otherRoles = other.otherRoles ? other.otherRoles.slice() : null; - this.partRefine = other.partRefine; - this.displayID = other.displayID; - this.name = other.name; - this.description = other.description; - this.version = other.version; - this.sequence = other.sequence; - this.sequenceURI = other.sequenceURI; - this.uriPrefix = other.uriPrefix; - this.annotations = other.annotations ? other.annotations.slice() : null; - this.derivedFroms = other.derivedFroms ? other.derivedFroms.slice() : null; - this.generatedBys = other.generatedBys ? other.generatedBys.slice() : null; - } - - getFullURI(): string { - let fullURI = this.uriPrefix + '/' + this.displayID; - if (this.version && this.version.length > 0) { - fullURI += '/' + this.version; - } - return fullURI; - } - - encode(enc: any) { - let node = enc.document.createElement('GlyphInfo'); - if (this.partType) - node.setAttribute("partType", this.partType); - if (this.otherTypes) { - let otherTypesNode = enc.encode(this.otherTypes); - otherTypesNode.setAttribute("as", "otherTypes"); - node.appendChild(otherTypesNode); - } - if (this.partRole) - node.setAttribute("partRole", this.partRole); - if (this.otherRoles) { - let otherRolesNode = enc.encode(this.otherRoles); - otherRolesNode.setAttribute("as", "otherRoles"); - node.appendChild(otherRolesNode); - } - if (this.partRefine) - node.setAttribute("partRefine", this.partRefine); - if (this.displayID) - node.setAttribute("displayID", this.displayID); - if (this.name && this.name.length > 0) - node.setAttribute("name", this.name); - if (this.description && this.description.length > 0) - node.setAttribute("description", this.description); - if (this.version && this.version.length > 0) - node.setAttribute("version", this.version); - if (this.sequence && this.sequence.length > 0) - node.setAttribute("sequence", this.sequence); - if (this.sequenceURI && this.sequenceURI.length > 0) - node.setAttribute("sequenceURI", this.sequenceURI); - if (this.uriPrefix) - node.setAttribute("uriPrefix", this.uriPrefix); - - if (this.annotations) { - let annotationsNode = enc.encode(this.annotations); - annotationsNode.setAttribute("as", "annotations"); - node.appendChild(annotationsNode); - } - if (this.derivedFroms) { - let derivedFromsNode = enc.encode(this.derivedFroms); - derivedFromsNode.setAttribute("as", "derivedFroms"); - node.appendChild(derivedFromsNode); - } - if (this.generatedBys) { - let generatedBysNode = enc.encode(this.generatedBys); - generatedBysNode.setAttribute("as", "generatedBys"); - node.appendChild(generatedBysNode); - } - - return node; - } -} diff --git a/frontend/src/app/graph.service.ts b/frontend/src/app/graph.service.ts deleted file mode 100644 index c61e852f..00000000 --- a/frontend/src/app/graph.service.ts +++ /dev/null @@ -1,1770 +0,0 @@ -/* -* GraphService -* -* This service controls the main editing canvas -*/ - -///// - -import { Injectable } from '@angular/core'; -import * as mxCell from 'mxgraph'; -import { GlyphInfo } from './glyphInfo'; -import { MetadataService } from './metadata.service'; -import { GlyphService } from './glyph.service'; -import { InteractionInfo } from './interactionInfo'; -import { environment } from 'src/environments/environment'; -import { MatDialog } from '@angular/material'; -import { GraphEdits } from './graph-edits'; -import { GraphBase, mx } from './graph-base'; -import { GraphHelpers } from './graph-helpers'; -import { StyleInfo } from './style-info'; -import { ModuleInfo } from './moduleInfo'; -import { Info } from './info'; -import { CombinatorialInfo } from './combinatorialInfo'; -import { EmbeddedService } from './embedded.service'; -import { FilesService } from './files.service'; -import { Observable } from 'rxjs'; -import { debounceTime } from 'rxjs/operators'; - -@Injectable({ - providedIn: 'root' -}) -export class GraphService extends GraphHelpers { - - constructor(dialog: MatDialog, metadataService: MetadataService, glyphService: GlyphService, embeddedService: EmbeddedService, fileService: FilesService) { - super(dialog, metadataService, glyphService); - - // handle selection changes - this.graph.getSelectionModel().addListener(mx.mxEvent.CHANGE, mx.mxUtils.bind(this, this.handleSelectionChange)); - - // handle double click on glyph to enter it - this.graph.addListener(mx.mxEvent.DOUBLE_CLICK, mx.mxUtils.bind(this, this.enterGlyph)); - - - // --- For when SBOLCanvas is embedded in another app --- - - // send changes in mxgraph model to parent - // doing this via an Observable so we can debounce - new Observable(observer => { - this.graph.getModel().addListener(mx.mxEvent.CHANGE, mx.mxUtils.bind(this, () => { - observer.next(this.getGraphXML()) - })) - }) - .pipe(debounceTime(100)) - .subscribe(graphXml => { - if (embeddedService.isAppEmbedded()) { - console.debug('[GraphService] Model changed. Sending to parent.') - fileService.exportDesignToString({}, 'SBOL2', graphXml).subscribe(sbol => { - embeddedService.postMessage({ sbol }) - }) - } - }) - - // observe changes in parent SBOL - embeddedService.sbol.subscribe(sbolContent => { - console.debug('[GraphService] Loading SBOL from external message...') - fileService.convertToMxGraph(sbolContent).subscribe(result => { - this.setGraphToXML(result) - console.debug('[GraphService] Done.') - - // post message back letting parent know it loaded - embeddedService.postMessage('graphServiceLoadedSBOL') - }) - }) - } - - isSelectedAGlyph(): boolean { - let selected = this.graph.getSelectionCells(); - if (selected.length != 1) { - return false; - } - return selected[0].isSequenceFeatureGlyph(); - } - - isRootAComponentView(): boolean { - return this.viewStack[0].isComponentView(); - } - - isComposite(sequenceFeature): boolean { - if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { - return false; - } - return sequenceFeature.getCircuitContainer(this.graph).children.length > 1; - } - - isVariant(sequenceFeature): boolean { - if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { - return false; - } - let combinatorial = this.getCombinatorialWithTemplate(sequenceFeature.getParent().value); - if (!combinatorial) - return false; - return combinatorial.getVariableComponentInfo(sequenceFeature.getId()); - } - - /** - * Given the interaction type, checks the selected cells source and target to see if it's allowed. - * @param interactionType - * @returns - */ - isInteractionTypeAllowed(interactionType: string): boolean { - let selected = this.graph.getSelectionCells(); - if (selected.length > 1 || selected.length == 0 || (!selected[0].isInteraction() && !selected[0].isInteractionNode)) { - return false; - } - - if (selected[0].isInteraction()) { - let result = this.validateInteraction(interactionType, selected[0].source, selected[0].target); - if (result == null || result == '') { - return true; - } else { - return false; - } - } - - if (selected[0].isInteractionNode()) { - return interactionType == "Biochemical Reaction" || interactionType == "Dissociation" || interactionType == "Genetic Production" || interactionType == "Non-Covalent Binding"; - } - - return false; - } - - isSelectedTargetEdge(): boolean { - let selected = this.graph.getSelectionCells(); - if (selected.lengh > 1 || selected.length == 0 || !selected[0].isInteraction()) { - return false; - } - - return selected[0].target == null || !selected[0].target.isInteractionNode(); - } - - isSelectedSourceEdge(): boolean { - let selected = this.graph.getSelectionCells(); - if (selected.lengh > 1 || selected.length == 0 || !selected[0].isInteraction()) { - return false; - } - - return selected[0].source == null || !selected[0].source.isInteractionNode(); - } - - /** - * Recursively checks that all leaf children have sequences - * @param sequenceFeature A cell representing a sequence feature - */ - hasSequence(sequenceFeature): boolean { - if (!sequenceFeature || !sequenceFeature.isSequenceFeatureGlyph()) { - return false; - } - // check if the child view has more than just a backbone - let circuitContainer = sequenceFeature.getCircuitContainer(this.graph); - if (circuitContainer.children.length > 1) { - for (let child of circuitContainer.children) { - if (child.isSequenceFeatureGlyph() && !this.hasSequence(child)) { - return false; - } - } - return true; - } - // no children? we must be a leaf node, check for a sequence - let glyphInfo = (this.getFromInfoDict(sequenceFeature.getValue())); - if (!glyphInfo || !glyphInfo.sequence || glyphInfo.sequence.length <= 0) { - return false; - } - return true; - } - - /** - * Forces the graph to redraw - */ - repaint() { - this.graph.refresh(); - } - - getSelectedCellID(): string { - let selected = this.graph.getSelectionCells(); - if (selected.length != 1) { - return null; - } - return selected[0].getId(); - } - - /** - * This method is called by the UI when the user turns scars on - * or off. - */ - toggleScars() { - // Toggle showing scars - if (this.showingScars) { - this.showingScars = false; - } else { this.showingScars = true; } - - // We hide scar glyphs by setting their widths to 0. - console.debug("showing scars now equals " + this.showingScars); - this.setAllScars(this.showingScars); - } - - /** - * Sets all scars in the current view - * @param isCollapsed - */ - setAllScars(isCollapsed: boolean) { - this.graph.getModel().beginUpdate(); - try { - let allGraphCells = this.graph.getDefaultParent().children; - for (let i = 0; i < allGraphCells.length; i++) { - if (allGraphCells[i].isCircuitContainer()) { - this.setScars(allGraphCells[i], this.showingScars); - } - } - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Changes all scars in a circuit container. - * @param circuitContainer - * @param isCollapsed - */ - setScars(circuitContainer, isCollapsed: boolean) { - let children = circuitContainer.children; - for (let i = 0; i < children.length; i++) { - if (children[i].isScar()) { - console.debug("scar found"); - let child = children[i]; - const geo = new mx.mxGeometry(0, 0, 0, 0); - geo.x = 0; - geo.y = 0; - geo.height = GraphBase.sequenceFeatureGlyphHeight; - - if (this.showingScars) { - geo.width = GraphBase.sequenceFeatureGlyphWidth; - } else { - geo.width = 0; - } - this.graph.getModel().setGeometry(child, geo); - } - } - circuitContainer.refreshCircuitContainer(this.graph) - } - - /** - * This method is called by the UI when the user asks to flip a - * sequence feature glyph. - * It swaps direction east/west. - */ - async flipSequenceFeatureGlyph() { - let selectionCells = this.graph.getSelectionCells(); - - // a circular backbone cannot be flipped - if(selectionCells.filter(cell => cell.stayAtBeginning || cell.stayAtEnd).length > 0) { - this.showError("A circular backbone cannot be flipped."); - return; - } - - // flip any selected glyphs - let parentInfos = new Set(); - for (let cell of selectionCells) { - if (cell.isSequenceFeatureGlyph()) { - // add the item to check ownership - parentInfos.add(this.getParentInfo(cell)); - } - } - for (let parentInfo of Array.from(parentInfos.values())) { - if (parentInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(parentInfo.displayID)) { - return; - } - } - - try { - this.graph.getModel().beginUpdate(); - - for (let cell of selectionCells) { - if (cell.isSequenceFeatureGlyph()) { - - // Make the cell face east/west - let direction = this.graph.getCellStyle(cell)[mx.mxConstants.STYLE_DIRECTION]; - console.debug("current glyph direction setting = " + direction); - - if (direction == undefined) { - console.warn("direction style undefined. Assuming east, and turning to west"); - this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "west", [cell]); - } else if (direction === "east") { - this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "west", [cell]); - console.debug("turning west"); - } else if (direction == "west") { - this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "east", [cell]); - console.debug("turning east"); - } - } else if (cell.isInteraction()) { - this.flipInteractionEdge(cell); - } else if (cell.isInteractionNode()) { - let edges = this.graph.getModel().getEdges(cell); - for (let edge of edges) { - this.flipInteractionEdge(edge); - } - } - } - - // sync circuit containers - let circuitContainers = []; - for (let cell of selectionCells) { - if (cell.isSequenceFeatureGlyph()) { - this.syncCircuitContainer(cell.getParent()); - } - } - - for (let parentInfo of Array.from(parentInfos.values())) { - // change the owner - this.changeOwnership(parentInfo.getFullURI()); - } - - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * "Drills in" to replace the canvas with the selected glyph's component/module view - */ - enterGlyph() { - let selection = this.graph.getSelectionCells(); - if (selection.length != 1) { - return; - } - - if (!selection[0].isSequenceFeatureGlyph() && !selection[0].isModule()) { - return; - } - - this.graph.getModel().beginUpdate(); - try { - let viewCell = this.graph.getModel().getCell(selection[0].getValue()); - // doing this in the graph edit breaks things in the undo, so we put it here - viewCell.refreshViewCell(this.graph); - let zoomEdit = new GraphEdits.zoomEdit(this.graph.getView(), selection[0], this); - this.graph.getModel().execute(zoomEdit); - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Moves up the drilling hierarchy, restoring the canvas to how it was before "Drilling in" - * (If "enterGlyph" has not been called, ie the canvas is already - * at the top of the drilling hierarchy, does nothing) - */ - exitGlyph() { - // the root view should always be left on the viewStack - if (this.viewStack.length > 1) { - let zoomEdit = new GraphEdits.zoomEdit(this.graph.getView(), null, this); - this.graph.getModel().execute(zoomEdit); - } - } - - /** - * Turns the given element into a dragsource for creating empty DNA strands - */ - makeBackboneDragsource(element) { - const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addBackboneAt(x - GraphBase.sequenceFeatureGlyphWidth / 2, y - GraphBase.sequenceFeatureGlyphHeight / 2); - }); - - this.makeGeneralDragsource(element, insertGlyph); - } - - /** - * Creates an empty DNA strand at the center of the current view - */ - addBackbone() { - const pt = this.getDefaultNewCellCoords(); - this.addBackboneAt(pt.x, pt.y); - } - - /** - * Creates an empty DNA strand at the given coordinates - */ - addBackboneAt(x, y) { - this.graph.getModel().beginUpdate(); - try { - let glyphInfo; - if (this.graph.getCurrentRoot().isModuleView()) { - glyphInfo = new GlyphInfo(); - super.addToInfoDict(glyphInfo); - } else { - glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); - } - const circuitContainer = this.graph.insertVertex(this.graph.getDefaultParent(), null, glyphInfo.getFullURI(), x, y, GraphBase.sequenceFeatureGlyphWidth, GraphBase.sequenceFeatureGlyphHeight, GraphBase.STYLE_CIRCUIT_CONTAINER); - const backbone = this.graph.insertVertex(circuitContainer, null, '', 0, GraphBase.sequenceFeatureGlyphHeight / 2, GraphBase.sequenceFeatureGlyphWidth, 1, GraphBase.STYLE_BACKBONE); - - backbone.refreshBackbone(this.graph); - - circuitContainer.setConnectable(false); - backbone.setConnectable(false); - - // The new circuit should be selected - this.graph.clearSelection(); - this.graph.setSelectionCell(circuitContainer); - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Returns the
that this graph displays to - */ - getGraphDOM() { - return this.graphContainer; - } - - /** - * Deletes the currently selected cell - */ - async delete() { - const selectedCells = this.graph.getSelectionCells(); - if (selectedCells == null) { - return; - } - - // check for ownership prompt - let containers = new Set(); - if (this.graph.getCurrentRoot()) { - let ownershipPrompt = false; - for (let cell of selectedCells) { - if (cell.isSequenceFeatureGlyph()) { - ownershipPrompt = true; - containers.add(cell.getParent().getValue()); - } - } - for (let container of Array.from(containers.values())) { - let glyphInfo; - if (this.graph.getCurrentRoot().isComponentView()) { - glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); - } else { - glyphInfo = this.getFromInfoDict(container); - } - if (ownershipPrompt && glyphInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(glyphInfo.displayID)) { - return; - } - } - } - - this.graph.getModel().beginUpdate(); - try { - let circuitContainers = []; - for (let cell of selectedCells) { - if (cell.isSequenceFeatureGlyph()) { - // if it's a sequence feature and it has a combinatorial, remove the variable component - if (cell.isSequenceFeatureGlyph()) { - let combinatorial = this.getCombinatorialWithTemplate(cell.getParent().getValue()); - // TODO make this undoable - if (combinatorial) - combinatorial.removeVariableComponentInfo(cell.getId()); - - if(cell.stayAtBeginning || cell.stayAtEnd) cell.getParent().circularBackbone = false; - - circuitContainers.push(cell.getParent()); - } - } else if (cell.isCircuitContainer() && this.graph.getCurrentRoot() && this.graph.getCurrentRoot().isComponentView()) - circuitContainers.push(cell); - } - - // If we are not at the top level, we need to check - // for a corner case where we can't allow the backbone - // to be deleted - if (this.graph.getCurrentRoot() != null && this.graph.getCurrentRoot().isComponentView()) { - let newSelection = []; - for (let cell of selectedCells) { - // Anything other than the backbone gets added to - // the revised selection - if (!(cell.isBackbone() || cell.isCircuitContainer())) { - newSelection.push(cell); - } else { - let circuitContainer; - if (cell.isBackbone()) { - circuitContainer = cell.getParent(); - } else if (cell.isCircuitContainer()) { - circuitContainer = cell; - } - - // If we find a backbone is selected, add all it's children - if (circuitContainer.children) { - for (let child of circuitContainer.children) { - if (!child.isBackbone()) { - newSelection.push(child); - } - } - } - } - } - this.graph.setSelectionCells(newSelection); - } - - // remove interactions with modules if the item it connects to is being removed - for (let selectedCell of selectedCells) { - if (selectedCell.isCircuitContainer() || selectedCell.isMolecularSpeciesGlyph()) { - this.updateInteractions(selectedCell.getValue() + "_" + selectedCell.getId(), null); - } - } - - this.editor.execute('delete'); - - this.trimUnreferencedCells(); - this.trimUnreferencedCombinatorials(); - this.trimUnreferencedInfos(); - - // sync circuit containers - for (let circuitContainer of circuitContainers) { - this.syncCircuitContainer(circuitContainer); - } - - // obtain ownership - for (let container of Array.from(containers)) { - this.changeOwnership(container); - } - - for (let cell of circuitContainers) { - cell.refreshCircuitContainer(this.graph); - } - - // repositions the circular backbone if the circular backbone is now empty - if(circuitContainers.length > 0 && circuitContainers[0].children.length === 3 - && circuitContainers[0].circularBackbone) { - this.repositionCircularBackbone(circuitContainers[0]); - } - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Undoes the most recent changes - */ - undo() { - // (un/re)doing is managed by the editor; it only works - // if all changes are encapsulated by graphModel.(begin/end)Update - - // clearing the selection avoids a lot of exceptions from mxgraph code for some reason. - this.graph.clearSelection(); - this.editor.execute('undo'); - - //console.log(this.editor.undoManager); - - // If the undo caused scars to become visible, we should update - this.showingScars = this.getScarsVisible(); - - // refresh to update cell labels - if (this.graph.getCurrentRoot()) { - this.graph.refresh(this.graph.getCurrentRoot()); - } - - // selections after an undo break things if annother undo/redo happens - this.filterSelectionCells(); - } - - /** - * Redoes the most recent changes - */ - redo() { - //console.log(this.editor.undoManager); - - this.graph.clearSelection(); - this.editor.execute('redo'); - - // If the undo caused scars to become visible, we should update - this.showingScars = this.getScarsVisible(); - - // refresh to update cell labels - if (this.graph.getCurrentRoot()) { - this.graph.refresh(this.graph.getCurrentRoot()); - } - - // selections after an undo break things if annother undo/redo happens - this.filterSelectionCells(); - } - - zoomIn() { - this.graph.zoomIn(); - } - - zoomOut() { - this.graph.zoomOut(); - } - - setZoom(scale: number) { - this.graph.zoomTo(scale); - } - - getZoom(): number { - return this.graph.getView().getScale(); - } - - sendSelectionToFront() { - this.graph.orderCells(false) - } - - sendSelectionToBack() { - this.graph.orderCells(true) - } - - fitCamera() { - // graph.fit() does most of the work. however by default it will zoom in far too much. - // Instead, it makes sense to stay at the user's zoom level unless it is too small to - // contain everything. - let currentScale = this.graph.getView().getScale(); - this.graph.maxFitScale = currentScale; - this.graph.fit(); - - // if the user had it widely zoomed out, however, stupidly graph.fit() - // doesn't center the view on cells. It puts them in the top left. - this.graph.center(); - } - - /** - * Turns the given element into a dragsource for creating - * sequenceFeatureGlyphs of the type specified by 'stylename.' - */ - makeSequenceFeatureDragsource(element, stylename) { - const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addSequenceFeatureAt(stylename, x - GraphBase.sequenceFeatureGlyphWidth / 2, y - GraphBase.sequenceFeatureGlyphHeight / 2); - }); - this.makeGeneralDragsource(element, insertGlyph); - } - - /** - * Adds a sequenceFeatureGlyph. - * The new glyph's location is based off the user's selection. - */ - async addSequenceFeature(name) { - this.graph.getModel().beginUpdate(); - try { - if (!this.atLeastOneCircuitContainerInGraph()) { - // if there is no strand, quietly make one - // stupid user - this.addBackbone(); - // this changes the selection, so the rest of this method works fine - } - - // let the graph choose an arbitrary cell from the selection, - // we'll pretend it's the only one selected - const selection = this.graph.getSelectionCell(); - - // if selection is nonexistent, or is not part of a strand, there is no suitable place. - if (!selection || !(selection.isSequenceFeatureGlyph() || selection.isCircuitContainer())) { - return; - } - - const circuitContainer = selection.isCircuitContainer() ? selection : selection.getParent(); - - // use y coord of the strand - let y = circuitContainer.getGeometry().y; - - // x depends on the exact selection - let x; - if (selection.isCircuitContainer()) { - x = selection.getGeometry().x + selection.getGeometry().width; - } else { - x = circuitContainer.getGeometry().x + selection.getGeometry().x + 1; - } - - // Add it - await this.addSequenceFeatureAt(name, x, y, circuitContainer); - } finally { - this.graph.getModel().endUpdate(); - } - } - - async addCircularPlasmid() { - this.graph.getModel().beginUpdate(); - try { - if (!this.atLeastOneCircuitContainerInGraph()) { - // if there is no strand, quietly make one - // stupid user - this.addBackbone(); - // this changes the selection, so the rest of this method works fine - } - - // let the graph choose an arbitrary cell from the selection, - // we'll pretend it's the only one selected - const selection = this.graph.getSelectionCell(); - - // if selection is nonexistent, or is not part of a strand, there is no suitable place. - if (!selection || !(selection.isSequenceFeatureGlyph() || selection.isCircuitContainer())) { - return; - } - - const circuitContainer = selection.isCircuitContainer() ? selection : selection.getParent(); - - // there cannot be more than one circular backbone on a circuit container - if(circuitContainer.circularBackbone) return; - - circuitContainer.circularBackbone = true; - - // x is at the beginning of the circuit container - let x = circuitContainer.getGeometry().x; - - // use y coord of the strand - let y = circuitContainer.getGeometry().y; - - // add the left side of the circular cell - const circCellLeft = await this.addSequenceFeatureAt("Cir (Circular Backbone Left)", - x, y, circuitContainer, { - connectable: false, - glyphWidth: 1, - }); - circCellLeft.stayAtBeginning = true; - - // add the right side of the circular cell - const circCellRight = await this.addSequenceFeatureAt("Cir (Circular Backbone Right)", - x + circuitContainer.getGeometry().width, y, - circuitContainer, { - connectable: false, - glyphWidth: 1, - }); - circCellRight.stayAtEnd = true; - - // if the only cells are the backbone and the circular backbone the right circular backbone needs - // to be repositioned and the size of the circuit container needs to reflect that - if(circuitContainer.getGeometry().width == 2) { - this.repositionCircularBackbone(circuitContainer); - } - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Adds a sequenceFeatureGlyph. - * - * circuitContainer (optional) specifies the strand to add to. - * If not specified, it is inferred by x,y. - * - * x,y are also used to determine where on the strand the new - * glyph is added (first, second, etc) - */ - async addSequenceFeatureAt(name, x, y, circuitContainer?, { - connectable = true, - glyphWidth = GraphBase.sequenceFeatureGlyphWidth, - glyphStyle = undefined, - cellValue = undefined, - } = {}) { - let sequenceFeatureCell; - let cirBackboneLeftCell; - - // ownership change check - if (this.graph.getCurrentRoot()) { - let glyphInfo; - if (this.graph.getCurrentRoot().isComponentView()) { - // normal case - glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); - } else if (this.atLeastOneCircuitContainerInGraph()) { - // edge case that we're adding to a container in a module view - if (!circuitContainer) { - circuitContainer = this.getClosestCircuitContainerToPoint(x, y); - } - glyphInfo = this.getFromInfoDict(circuitContainer.getValue()); - } - if (glyphInfo && glyphInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(glyphInfo.displayID)) { - return; - } - } - - this.graph.getModel().beginUpdate(); - try { - // Make sure scars are/become visible if we're adding one - if (name.includes(GraphBase.STYLE_SCAR) && !this.showingScars) { - this.toggleScars(); - } - - if (!this.atLeastOneCircuitContainerInGraph()) { - // if there is no strand, quietly make one - this.addBackboneAt(x, y); - } - - if (!circuitContainer) { - circuitContainer = this.getClosestCircuitContainerToPoint(x, y); - } - - // transform coords to be relative to parent - x = x - circuitContainer.getGeometry().x; - y = y - circuitContainer.getGeometry().y; - - let glyphInfo = new GlyphInfo(); - - // if the container is a circular backbone then both sides should have the same cellValue - if (glyphWidth == 1) { - circuitContainer.children - .filter(cell => cell.stayAtBeginning) - .forEach(child => { - cellValue = child.value; - cirBackboneLeftCell = child; - }); - } - - if(cellValue == null) { - // create the glyph info and add it to the dictionary - glyphInfo.partRole = name; - this.addToInfoDict(glyphInfo); - } - - // Insert new glyph and its components - sequenceFeatureCell = this.graph.insertVertex( - circuitContainer, - null, - cellValue == null ? glyphInfo.getFullURI() : cellValue, - x, y, glyphWidth, GraphBase.sequenceFeatureGlyphHeight, - glyphStyle || GraphBase.STYLE_SEQUENCE_FEATURE + name - ); - - this.createViewCell(glyphInfo.getFullURI()); - sequenceFeatureCell.setConnectable(connectable); - - // Sorts the new SequenceFeature into the correct position in parent's array - this.horizontalSortBasedOnPosition(circuitContainer); - - // The new glyph should be selected - this.graph.clearSelection(); - - // if the new sequence feature is a circular backbone both circular backbones should be selected - if(cirBackboneLeftCell !== undefined) this.graph.setSelectionCells([cirBackboneLeftCell, sequenceFeatureCell]); - else if(glyphWidth !== 1) this.graph.setSelectionCell(sequenceFeatureCell); - - // perform the ownership change - if (this.graph.getCurrentRoot()) { - let glyphInfo; - if (this.graph.getCurrentRoot().isComponentView()) { - // normal case - glyphInfo = this.getFromInfoDict(this.graph.getCurrentRoot().getId()); - } else { - // edge case that we're adding to a container in a module view - glyphInfo = this.getFromInfoDict(circuitContainer.getValue()); - } - if (glyphInfo.uriPrefix != environment.baseURI) { - this.changeOwnership(glyphInfo.getFullURI()); - } - } - - // synchronize circuit containers - this.syncCircuitContainer(circuitContainer); - } finally { - this.graph.getModel().endUpdate(); - } - - return sequenceFeatureCell; - } - - /** - * Turns the given element into a dragsource for creating molecular species glyphs - */ - makeMolecularSpeciesDragsource(element, stylename) { - const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addMolecularSpeciesAt(stylename, x - GraphBase.molecularSpeciesGlyphWidth / 2, y - GraphBase.molecularSpeciesGlyphHeight / 2); - }); - this.makeGeneralDragsource(element, insertGlyph); - } - - /** - * Creates a molecular species glyph of the given type at the center of the current view - */ - addMolecularSpecies(name) { - const pt = this.getDefaultNewCellCoords(); - this.addMolecularSpeciesAt(name, pt.x, pt.y); - } - - /** - * Creates a molecular species glyph of the given type at the given location - */ - addMolecularSpeciesAt(name, x, y) { - this.graph.getModel().beginUpdate(); - try { - - //TODO partRoles for proteins - let proteinInfo = new GlyphInfo(); - proteinInfo.partType = this.moleculeNameToType(name); - this.addToInfoDict(proteinInfo); - - const molecularSpeciesGlyph = this.graph.insertVertex(this.graph.getDefaultParent(), null, proteinInfo.getFullURI(), x, y, - GraphBase.molecularSpeciesGlyphWidth, GraphBase.molecularSpeciesGlyphHeight, GraphBase.STYLE_MOLECULAR_SPECIES + name); - molecularSpeciesGlyph.setConnectable(true); - - // The new glyph should be selected - this.graph.clearSelection(); - this.graph.setSelectionCell(molecularSpeciesGlyph); - } finally { - this.graph.getModel().endUpdate(); - } - - console.log(this.graph.getModel().cells); - } - - makeInteractionNodeDragsource(element, stylename) { - const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addInteractionNodeAt(stylename, x - GraphBase.interactionNodeGlyphWidth / 2, y - GraphBase.interactionNodeGlyphHeight / 2); - }); - this.makeGeneralDragsource(element, insertGlyph); - } - - addInteractionNode(name) { - const pt = this.getDefaultNewCellCoords(); - this.addInteractionNodeAt(name, pt.x, pt.y); - } - - addInteractionNodeAt(name: string, x, y) { - this.graph.getModel().beginUpdate(); - try { - let interactionInfo = new InteractionInfo(); - const interactionNodeGlyph = this.graph.insertVertex(this.graph.getDefaultParent(), null, interactionInfo.getFullURI(), x, y, - GraphBase.interactionNodeGlyphWidth, GraphBase.interactionNodeGlyphHeight, GraphBase.STYLE_INTERACTION_NODE + name); - interactionInfo.interactionType = this.interactionNodeNametoType(name); - this.addToInteractionDict(interactionInfo); - interactionNodeGlyph.setConnectable(true); - - // The new glyph should be selected - this.graph.clearSelection(); - this.graph.setSelectionCell(interactionNodeGlyph); - } finally { - this.graph.getModel().endUpdate(); - } - } - - /** - * Turns the given HTML element into a dragsource for creating interaction glyphs - */ - makeInteractionDragsource(element, stylename) { - const insertGlyph = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addInteractionAt(stylename, x - GraphBase.defaultInteractionSize / 2, y - GraphBase.defaultInteractionSize / 2); - }); - this.makeGeneralDragsource(element, insertGlyph); - } - - /** - * Creates an interaction edge of the given type at the center of the current view - */ - addInteraction(name) { - const selectionCells = this.graph.getSelectionCells(); - if (selectionCells.length > 0 && selectionCells.length < 3) { - let selectedCell = selectionCells[0]; - const selectedParent = selectedCell.getParent(); - if (selectedParent.geometry && !selectedParent.isViewCell()) { - this.addInteractionAt(name, selectedParent.geometry.x + selectedCell.geometry.x + (selectedCell.geometry.width / 2), - selectedParent.geometry.y); - } else { - this.addInteractionAt(name, selectedCell.geometry.x + (selectedCell.geometry.width / 2), - selectedCell.geometry.y); - } - } else { - const pt = this.getDefaultNewCellCoords(); - this.addInteractionAt(name, pt.x, pt.y); - } - } - - /** - * Creates an interaction edge of the given type at the given coordiantes - * @param name The name identifying the type of interaction this should be. - * @param x The x coordinate that the interaction should appear at - * @param y The y coordinate that the interaction should appear at - */ - async addInteractionAt(name: string, x, y) { - let cell; - - this.graph.getModel().beginUpdate(); - try { - let addToDictionary = true; - let interactionInfo = new InteractionInfo(); - cell = new mx.mxCell(interactionInfo.getFullURI(), new mx.mxGeometry(x, y, 0, 0), GraphBase.STYLE_INTERACTION + name); - - const selectionCells = this.graph.getSelectionCells(); - if (selectionCells.length == 1) { - - // one cell is selected, set the edges source - const selectedCell = this.graph.getSelectionCell(); - // check for any restrictions on valid edges - let error = this.graph.getEdgeValidationError(cell, selectedCell, null); - if (error) { - this.showError(error); - return; - } - if (selectedCell.isModule()) { - // if the cell is a module, we need to prompt what subpart we want to connect to - let result = await this.promptChooseFunctionalComponent(selectedCell, true); - if (!result) - return; - interactionInfo.fromURI[this.graph.getModel().nextId] = result; - } else if (selectedCell.isInteractionNode()) { - // if the source is a interaction node, we want to inherit it's information - cell.value = selectedCell.value; - addToDictionary = false; - interactionInfo = this.getFromInteractionDict(selectedCell.value).makeCopy() - } - cell.geometry.setTerminalPoint(new mx.mxPoint(x, y - GraphBase.defaultInteractionSize), false); - cell.edge = true; - this.graph.addEdge(cell, this.graph.getCurrentRoot(), selectedCell, null); - - } else if (selectionCells.length == 2) { - - // two cells were selected, set the first one as the source, and the second as the target - const sourceCell = selectionCells[0]; - const destCell = selectionCells[1]; - // check for restrictions on the edge - let error = this.graph.getEdgeValidationError(cell, sourceCell, destCell); - if (error) { - this.showError(error); - return; - } - // check source or target are interaction nodes to couple with them before making modifications to the interaction - // don't worry, edge validation rules prevent both from being interaction nodes. - if (sourceCell.isInteractionNode()) { - // inherit the information - cell.value = sourceCell.value; - addToDictionary = false; - interactionInfo = this.getFromInteractionDict(sourceCell.value).makeCopy(); - } - if (destCell.isInteractionNode()) { - // inherit the information - cell.value = destCell.value; - addToDictionary = false; - interactionInfo = this.getFromInteractionDict(destCell.value).makeCopy(); - } - - if (sourceCell.isModule()) { - // prompt for the subpart to keep track of - let result = await this.promptChooseFunctionalComponent(sourceCell, true); - if (!result) - return; - interactionInfo.fromURI[this.graph.getModel().nextId] = result; - } - if (destCell.isModule()) { - // prompt for the subpart to keep track of - let result = await this.promptChooseFunctionalComponent(destCell, false); - if (!result) - return; - interactionInfo.toURI[this.graph.getModel().nextId] = result; - } - cell.edge = true; - this.graph.addEdge(cell, this.graph.getCurrentRoot(), sourceCell, destCell); - - } else { - cell.geometry.setTerminalPoint(new mx.mxPoint(x, y + GraphBase.defaultInteractionSize), true); - cell.geometry.setTerminalPoint(new mx.mxPoint(x + GraphBase.defaultInteractionSize, y), false); - cell.edge = true; - this.graph.addEdge(cell, this.graph.getCurrentRoot(), null, null); - } - - - // Default name for a process interaction - if (name == "Process") { - name = "Genetic Production" - } - - if (addToDictionary) { - interactionInfo.interactionType = name; - this.addToInteractionDict(interactionInfo); - } else { - this.updateInteractionDict(interactionInfo); - this.mutateInteractionGlyph(interactionInfo.interactionType, cell); - } - - // The new glyph should be selected - this.graph.clearSelection(); - this.graph.setSelectionCell(cell); - } finally { - this.graph.getModel().endUpdate(); - } - - return cell; - } - - /** - * Turns the given HTML element into a dragsource for creating textboxes - */ - makeTextboxDragsource(element) { - const insert = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addTextBoxAt(x - GraphBase.defaultTextWidth / 2, y - GraphBase.defaultTextHeight / 2); - }); - this.makeGeneralDragsource(element, insert); - } - - /** - * Creates a textbox at the center of the current view - */ - addTextBox() { - const pt = this.getDefaultNewCellCoords(); - this.addTextBoxAt(pt.x, pt.y); - } - - /** - * Creates a textbox at the given location - */ - addTextBoxAt(x, y) { - this.graph.getModel().beginUpdate(); - try { - const cell = this.graph.insertVertex(this.graph.getDefaultParent(), null, 'Sample Text', x, y, GraphBase.defaultTextWidth, GraphBase.defaultTextHeight, GraphBase.STYLE_TEXTBOX); - cell.setConnectable(false); - - // The new cell should be selected - this.graph.clearSelection(); - this.graph.setSelectionCell(cell); - } finally { - this.graph.getModel().endUpdate(); - } - } - - makeModuleDragsource(element) { - const insert = mx.mxUtils.bind(this, function (graph, evt, target, x, y) { - this.addModuleAt(x - GraphBase.defaultModuleWidth / 2, y - GraphBase.defaultModuleHeight / 2); - }); - this.makeGeneralDragsource(element, insert); - } - - addModule() { - const pt = this.getDefaultNewCellCoords(); - this.addModuleAt(pt.x, pt.y); - } - - addModuleAt(x, y) { - this.graph.getModel().beginUpdate(); - try { - let moduleInfo = new ModuleInfo(); - this.addToInfoDict(moduleInfo); - - const moduleCell = this.graph.insertVertex(this.graph.getDefaultParent(), null, moduleInfo.getFullURI(), x, y, GraphBase.defaultModuleWidth, GraphBase.defaultModuleHeight, GraphBase.STYLE_MODULE); - moduleCell.setConnectable(true); - - this.createViewCell(moduleInfo.getFullURI(), true); - - this.graph.clearSelection(); - this.graph.setSelectionCell(moduleCell); - } finally { - this.graph.getModel().endUpdate(); - } - } -x - /** - * Find the selected cell, and if there is a glyph selected, update its metadata. - */ - async setSelectedCellInfo(info: Info) { - const selectedCell = this.graph.getSelectionCell(); - - this.graph.getModel().beginUpdate(); - try { - // figure out which type of info object it is - if (info instanceof ModuleInfo && (!selectedCell || selectedCell.isModule())) { - this.updateSelectedModuleInfo(info); - return; - } - - if (info instanceof GlyphInfo && (!selectedCell || selectedCell.isSequenceFeatureGlyph() || selectedCell.isCircuitContainer() || selectedCell.isMolecularSpeciesGlyph())) { - if (!selectedCell || !selectedCell.isMolecularSpeciesGlyph()) { - // The logic for updating the glyphs was getting a bit big, so I moved it into it's own method - this.updateSelectedGlyphInfo(info); - } else { - this.updateSelectedMolecularSpecies(info); - } - return; - } - - if (info instanceof InteractionInfo && (selectedCell.isInteraction() || selectedCell.isInteractionNode())) { - this.updateSelectedInteractionInfo(info); - } - - } finally { - this.graph.getModel().endUpdate(); - this.graph.refresh(selectedCell); - //this.updateAngularMetadata(this.graph.getSelectionCells()); - } - } - - /** - * Sets the combinatorial info associated to the selected cell - * @param info - * @param prevURI - */ - setSelectedCombinatorialInfo(info: CombinatorialInfo, prevURI?: string) { - const selectedCell = this.graph.getSelectionCell(); - - this.graph.getModel().beginUpdate(); - try { - if (info instanceof CombinatorialInfo && selectedCell.isSequenceFeatureGlyph()) { - if (!prevURI) { - prevURI = info.getFullURI(); - } - this.updateSelectedCombinatorialInfo(info, prevURI); - } - } finally { - this.graph.getModel().endUpdate(); - } - } - - setSelectedCellStyle(styleInfo: StyleInfo) { - this.graph.getModel().beginUpdate(); - try { - let selectedCells = this.graph.getSelectionCells().slice(); - // filter out the circuit containers - for (let i = 0; i < selectedCells.length; i++) { - if (selectedCells[i].isCircuitContainer()) { - selectedCells[i] = selectedCells[i].getBackbone(); - } - } - for (let key in styleInfo.styles) { - this.graph.setCellStyles(key, styleInfo.styles[key], selectedCells); - } - - // sync circuit containers - let circuitContainers = new Set(); - for (let cell of selectedCells) { - if (cell.isSequenceFeatureGlyph() || cell.isBackbone()) { - circuitContainers.add(cell.getParent()); - } - } - for (let circuitContainer of Array.from(circuitContainers.values())) { - this.syncCircuitContainer(circuitContainer); - } - - } finally { - this.graph.getModel().endUpdate(); - } - } - - exportSVG(filename: string) { - var background = '#ffffff'; - var scale = 1; - var border = 1; - - var imgExport = new mx.mxImageExport(); - var bounds = this.graph.getGraphBounds(); - var vs = this.graph.view.scale; - - // Prepares SVG document that holds the output - var svgDoc = mx.mxUtils.createXmlDocument(); - var root = (svgDoc.createElementNS != null) ? - svgDoc.createElementNS(mx.mxConstants.NS_SVG, 'svg') : svgDoc.createElement('svg'); - - if (background != null) { - if (root.style != null) { - root.style.backgroundColor = background; - } else { - root.setAttribute('style', 'background-color:' + background); - } - } - - if (svgDoc.createElementNS == null) { - root.setAttribute('xmlns', mx.mxConstants.NS_SVG); - root.setAttribute('xmlns:xlink', mx.mxConstants.NS_XLINK); - } else { - // KNOWN: Ignored in IE9-11, adds namespace for each image element instead. No workaround. - root.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', mx.mxConstants.NS_XLINK); - } - - root.setAttribute('width', (Math.ceil(bounds.width * scale / vs) + 2 * border) + 'px'); - root.setAttribute('height', (Math.ceil(bounds.height * scale / vs) + 2 * border) + 'px'); - root.setAttribute('version', '1.1'); - - // Adds group for anti-aliasing via transform - var group = (svgDoc.createElementNS != null) ? svgDoc.createElementNS(mx.mxConstants.NS_SVG, 'g') : svgDoc.createElement('g'); - group.setAttribute('transform', 'translate(0.5,0.5)'); - root.appendChild(group); - svgDoc.appendChild(root); - - // Renders graph. Offset will be multiplied with state's scale when painting state. - var svgCanvas = new mx.mxSvgCanvas2D(group); - svgCanvas.translate(Math.floor((border / scale - bounds.x) / vs), Math.floor((border / scale - bounds.y) / vs)); - svgCanvas.scale(scale / vs); - - // Displayed if a viewer does not support foreignObjects (which is needed to HTML output) - svgCanvas.foAltText = '[Not supported by viewer]'; - imgExport.drawState(this.graph.getView().getState(this.graph.getCurrentRoot()), svgCanvas); - - var xml = encodeURIComponent(mx.mxUtils.getXml(root)); - new mx.mxXmlRequest(environment.backendURL + '/echo', 'filename=' + filename + '.svg&format=svg' + '&xml=' + xml).simulate(document, '_blank'); - } - - exportImage(filename: string, format: string) { - let bg = '#ffffff'; - let scale = 1; - let b = 1; - - let imgExport = new mx.mxImageExport(); - let bounds = this.graph.getGraphBounds(); - let vs = this.graph.view.scale; - - let xmlDoc = mx.mxUtils.createXmlDocument(); - let root = xmlDoc.createElement('output'); - xmlDoc.appendChild(root); - - let xmlCanvas = new mx.mxXmlCanvas2D(root); - xmlCanvas.translate(Math.floor((b / scale - bounds.x) / vs), Math.floor((b / scale - bounds.y) / vs)); - xmlCanvas.scale(1 / vs); - - imgExport.drawState(this.graph.getView().getState(this.graph.getCurrentRoot()), xmlCanvas); - - let w = Math.ceil(bounds.width * scale / vs + 2 * b); - let h = Math.ceil(bounds.height * scale / vs + 2 * b); - - let xml = mx.mxUtils.getXml(root); - - if (bg != null) { - bg = '&bg=' + bg; - } - - new mx.mxXmlRequest(environment.backendURL + '/export', 'filename=' + filename + '.' + format + '&format=' + format + bg + '&w=' + w + '&h=' + h + '&xml=' + encodeURIComponent(xml)).simulate(document, '_blank'); - } - - /** - * Encodes the current graph to a string (xml) representation - */ - getGraphXML(): string { - const encoder = new mx.mxCodec(); - const result = encoder.encode(this.graph.getModel()); - return mx.mxUtils.getXml(result); - } - - /** - * Decodes the given string (xml) representation of a graph - * and uses it to replace the current graph - */ - setGraphToXML(graphString: string) { - GraphBase.unFormatedCells.clear(); - this.graph.home(); - this.graph.getModel().clear(); - - const doc = mx.mxUtils.parseXml(graphString); - const codec = new mx.mxCodec(doc); - codec.decode(doc.documentElement, this.graph.getModel()); - - // The child of cell 1 that isn't a view cell points to the root view - const cell1 = this.graph.getModel().getCell("1"); - let viewCells = this.graph.getModel().getChildren(cell1); - let rootViewCell; - for (let child of viewCells) { - if (!child.isViewCell()) { - rootViewCell = this.graph.getModel().getCell(child.getValue()); - this.graph.getModel().remove(child); - break; - } - } - this.graph.enterGroup(rootViewCell); - this.viewStack = []; - this.viewStack.push(rootViewCell); - this.selectionStack = []; - - let children = this.graph.getModel().getChildren(this.graph.getDefaultParent()); - if (children) { - children.forEach(element => { - if (element.isCircuitContainer()) - element.refreshCircuitContainer(this.graph); - }); - } - - if (GraphBase.unFormatedCells.size > 0) { - console.log("FORMATTING !!!!!!!!!!!!!!!!"); - this.autoFormat(GraphBase.unFormatedCells); - GraphBase.unFormatedCells.clear(); - } - - this.fitCamera(); - - this.metadataService.setComponentDefinitionMode(this.graph.getCurrentRoot().isComponentView()); - - // top level compDefs may not have cells referencing them, but they still end up with view cells for other reasons - this.trimUnreferencedCells(); - - this.editor.undoManager.clear(); - - this.graph.refresh(); // for some reason unformatted edges don't render correctly the first time without this - } - - /** - * Decodes the given string (xml) representation of a cell - * and uses it to replace the currently selected cell - * @param cellString - */ - async setSelectedToXML(cellString: string) { - const selectionCells = this.graph.getSelectionCells(); - - if (selectionCells.length == 0 || (selectionCells.length == 1 && (selectionCells[0].isSequenceFeatureGlyph() || selectionCells[0].isCircuitContainer() || selectionCells[0].isModule()))) { - // We're making a new cell to replace the selected one - let selectedCell; - if (selectionCells.length > 0) { - selectedCell = selectionCells[0]; - } else { - // nothing selected means we're replacing the view cell - selectedCell = this.graph.getCurrentRoot(); - } - - this.graph.getModel().beginUpdate(); - try { - let inModuleView = this.graph.getCurrentRoot().isModuleView(); - - // prompt ownership change - let parentInfo = this.getParentInfo(selectedCell); - if (parentInfo && parentInfo.uriPrefix != environment.baseURI && !await this.promptMakeEditableCopy(parentInfo.displayID)) { - return; - } - - // change ownership - if (parentInfo) { - if (selectedCell.isViewCell()) { - this.changeOwnership(parentInfo.getFullURI()); - selectedCell = this.graph.getCurrentRoot(); - } else if (selectedCell.isCircuitContainer() || selectedCell.isModule()) { - let selectedIndex = selectedCell.getParent().getIndex(selectedCell); - this.changeOwnership(parentInfo.getFullURI()); - selectedCell = this.graph.getCurrentRoot().children[selectedIndex]; - } else { - let parentIndex = this.graph.getCurrentRoot().getIndex(selectedCell.getParent()); - let selectedIndex = selectedCell.getParent().getIndex(selectedCell); - this.changeOwnership(parentInfo.getFullURI()); - selectedCell = this.graph.getCurrentRoot().children[parentIndex].children[selectedIndex]; - } - } - - // if we're in a non top level circuit container, module, or view cell zoom out to make things easier - let zoomOut = false; - if (((selectedCell.isCircuitContainer() || selectedCell.isComponentView()) && this.graph.getCurrentRoot().isComponentView() && this.viewStack.length > 1) || - ((selectedCell.isModule() || selectedCell.isModuleView()) && this.viewStack.length > 1)) { - zoomOut = true; - selectedCell = this.selectionStack[this.selectionStack.length - 1]; - this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), null, this)); - } - - // setup the decoding info - const doc = mx.mxUtils.parseXml(cellString); - const codec = new mx.mxCodec(doc); - - // store the information in a temp graph for easy access - const subGraph = new mx.mxGraph(); - codec.decode(doc.documentElement, subGraph.getModel()); - - // get the new cell - let newCell = subGraph.getModel().cloneCell(subGraph.getModel().getCell("1").children[0]); - - // not part of a module or a top level component definition - let origParent; - if (selectedCell.isSequenceFeatureGlyph()) { - // store old cell's parent - origParent = selectedCell.getParent(); - - // generated cells don't have a proper geometry - newCell.setStyle(selectedCell.getStyle()); - this.graph.getModel().setGeometry(newCell, selectedCell.geometry); - - // add new cell to the graph - this.graph.getModel().add(origParent, newCell, origParent.getIndex(selectedCell)); - - // remove the old cell's view cell if it doesn't have any references - if (this.getCoupledGlyphs(selectedCell.value).length < 2) { - this.removeViewCell(this.graph.getModel().getCell(selectedCell.value)); - } - - // remove the old cell - this.graph.getModel().remove(selectedCell); - - // move any edges from selectedCell to newCell - if (selectedCell.edges != null) { - let edgeCache = []; - selectedCell.edges.forEach(edge => { - edgeCache.push(edge); - }); - - edgeCache.forEach(edge => { - if (edge.source == selectedCell) { - this.graph.getModel().setTerminal(edge, newCell, true); - } - if (edge.target == selectedCell) { - this.graph.getModel().setTerminal(edge, newCell, false); - } - }); - } - } else if (selectedCell.isModule()) { - // store old cell's parent - origParent = selectedCell.getParent(); - - // generated cells don't have a proper geometry - newCell.setStyle(selectedCell.getStyle()); - this.graph.getModel().setGeometry(newCell, selectedCell.geometry); - - // add new cell to the graph - this.graph.getModel().add(origParent, newCell, origParent.getIndex(selectedCell)); - - // remove the old cell's view cell if it doesn't have any references - if (this.getCoupledModules(selectedCell.value).length < 2) { - this.removeViewCell(this.graph.getModel().getCell(selectedCell.value)); - } - - // remove the old cell - this.graph.getModel().remove(selectedCell); - } - - // Now create all children of the new cell - let viewCells = subGraph.getModel().getCell("1").children; - let subGlyphDict = subGraph.getModel().getCell("0").getValue(); - let cell1 = this.graph.getModel().getCell("1"); - for (let i = 1; i < viewCells.length; i++) { // start at cell 1 because the glyph is at 0 - // If we already have it skip it - if (this.graph.getModel().getCell(viewCells[i].getId())) { - continue; - } - - // clone the cell otherwise viewCells get's messed up - let viewClone = subGraph.getModel().cloneCell(viewCells[i]); - // cloning doesn't keep the id for some reason - viewClone.id = viewCells[i].id; - - // add the cell to the graph - this.graph.addCell(viewClone, cell1); - - // add the info to the dictionary - if (this.getFromInfoDict(viewCells[i].getId()) != null) { - this.removeFromInfoDict(viewCells[i].getId()); - } - this.addToInfoDict(subGlyphDict[GraphBase.INFO_DICT_INDEX][viewCells[i].getId()]); - - // add any molecular species or interactions to the info dict - for (let child of viewClone.children) { - if (child.isMolecularSpeciesGlyph()) { - if (this.getFromInfoDict(child.value) != null) { - this.removeFromInfoDict(child.value); - } - this.addToInfoDict(subGlyphDict[GraphBase.INFO_DICT_INDEX][child.value]); - } else if (child.isInteractionNode()) { - if (this.getFromInteractionDict(child.value) != null) { - this.removeFromInteractionDict(child.value); - } - this.addToInteractionDict(subGlyphDict[GraphBase.INTERACTION_DICT_INDEX][child.value]); - } else if (child.isInteraction()) { - // if either end is an interaction node, we don't need to bother - if ((child.source && child.source.isInteractionNode()) || (child.target && child.target.isInteractionNode())) { - continue; - } - if (this.getFromInteractionDict(child.value) != null) { - this.removeFromInteractionDict(child.value); - } - this.addToInteractionDict(subGlyphDict[GraphBase.INTERACTION_DICT_INDEX][child.value]); - } - } - } - - // relink the interactions now that their ID's have likely changed - for (let i = 1; i < viewCells.length; i++) { - let viewClone = this.graph.getModel().getCell(viewCells[i].getId()); - for (let j = 0; j < viewClone.children.length; j++) { - // for now it seems that cloning the cell keeps the child order in tact - let child = viewClone.children[j]; - let originalChild = viewCells[i].children[j]; - if (child.isInteractionNode()) { - // copy to new dict as new id's may conflict with old - let newTo = [] - let newFrom = [] - let newSource = [] - let newTarget = [] - let infoCopy = this.getFromInteractionDict(child.value).makeCopy(); - for (let k = 0; k < child.edges.length; k++) { - let edge = child.edges[k]; - let originalEdge = originalChild.edges[k]; - if (infoCopy.toURI[originalEdge.getId()]) { - // find the original cell - let cellRef = infoCopy.toURI[originalEdge.getId()]; - let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_") + 1)); - let oldParentView = oldCell.getParent(); - let newParentView = this.graph.getModel().getCell(oldParentView.getId()); - // replace with the new id - newTo[edge.getId()] = cellRef.substring(0, cellRef.lastIndexOf("_") + 1) + newParentView.children[oldParentView.getIndex(oldCell)].getId(); - } - if (infoCopy.fromURI[originalEdge.getId()]) { - // find the original cell - let cellRef = infoCopy.fromURI[originalEdge.getId()]; - let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_") + 1)); - let oldParentView = oldCell.getParent(); - let newParentView = this.graph.getModel().getCell(oldParentView.getId()); - // replace with the new id - newFrom[edge.getId()] = cellRef.substring(0, cellRef.lastIndexOf("_") + 1) + newParentView.children[oldParentView.getIndex(oldCell)].getId(); - } - if (infoCopy.sourceRefinement[originalEdge.getId()]) { - newSource[edge.getId()] = infoCopy.sourceRefinement[originalEdge.getId()]; - } - if (infoCopy.targetRefinement[originalEdge.getId()]) { - newTarget[edge.getId()] = infoCopy.targetRefinement[originalEdge.getId()]; - } - } - infoCopy.toURI = newTo; - infoCopy.fromURI = newFrom; - infoCopy.sourceRefinement = newSource; - infoCopy.targetRefinement = newTarget; - this.updateInteractionDict(infoCopy); - } - if (child.isInteraction()) { - // skip edges connected to interaction nodes - if ((child.source && child.source.isInteractionNode()) || (child.target && child.target.isInteractionNode())) { - continue; - } - let infoCopy = this.getFromInteractionDict(child.value).makeCopy(); - if (infoCopy.fromURI[originalChild.getId()]) { - let cellRef = infoCopy.fromURI[originalChild.getId()]; - delete infoCopy.fromURI[originalChild.getId()]; - let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_") + 1)); - let oldParentView = oldCell.getParent(); - let newParentView = this.graph.getModel().getCell(oldParentView.getId()); - infoCopy.fromURI[child.getId()] = cellRef.substring(0, cellRef.lastIndexOf("_") + 1) + newParentView.children[oldParentView.getIndex(oldCell)].getId();; - } - if (infoCopy.toURI[originalChild.getId()]) { - let cellRef = infoCopy.toURI[originalChild.getId()]; - delete infoCopy.toURI[originalChild.getId()]; - let oldCell = subGraph.getModel().getCell(cellRef.substring(cellRef.lastIndexOf("_") + 1)); - let oldParentView = oldCell.getParent(); - let newParentView = this.graph.getModel().getCell(oldParentView.getId()); - infoCopy.toURI[child.getId()] = cellRef.substring(0, cellRef.lastIndexOf("_") + 1) + newParentView.children[oldParentView.getIndex(oldCell)].getId();; - } - if (infoCopy.sourceRefinement[originalChild.getId()]) { - let value = infoCopy.sourceRefinement[originalChild.getId()]; - delete infoCopy.sourceRefinement[originalChild.getId()]; - infoCopy.sourceRefinement[child.getId()] = value; - } - if (infoCopy.targetRefinement[originalChild.getId()]) { - let value = infoCopy.targetRefinement[originalChild.getId()]; - delete infoCopy.targetRefinement[originalChild.getId()]; - infoCopy.targetRefinement[child.getId()] = value; - } - this.updateInteractionDict(infoCopy); - } - } - } - - if (selectedCell.isSequenceFeatureGlyph()) { - origParent.refreshCircuitContainer(this.graph); - this.graph.setSelectionCell(newCell); - this.mutateSequenceFeatureGlyph((this.getFromInfoDict(newCell.value)).partRole); - } - - // if we zoomed out zoom back in - if (zoomOut) { - if (selectedCell.isSequenceFeatureGlyph()) { - // if the selected cell is a sequenceFeature that means we came from a sub view - this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newCell, this)); - } else { - // if it isn't, that means we are in a module, or at the root - let newRootView = this.graph.getModel().getCell(newCell.getValue()); - let circuitContainer = this.graph.getModel().filterCells(newRootView.children, cell => cell.isCircuitContainer())[0]; - if (inModuleView) { - // get the circuit container so we can replace our current one - this.graph.getModel().setGeometry(circuitContainer, selectedCell.geometry); - if (this.getCoupledGlyphs(newRootView.getId()).length < 1) - // we don't need the root view if nothing references it, we only need it's circuit container - this.graph.getModel().remove(newRootView); - circuitContainer = this.graph.getModel().add(selectedCell.getParent(), circuitContainer); - this.graph.getModel().remove(selectedCell); - circuitContainer.refreshCircuitContainer(this.graph); - } else { - // at the root, just zoom back in - this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newRootView, this)); - circuitContainer.refreshCircuitContainer(this.graph); - } - } - } - - // root cells won't be zoomed out, so just zoom into the correct one, and remove the old one - if (selectedCell.isViewCell()) { - let newViewId = newCell.getValue(); - const newView = this.graph.getModel().getCell(newViewId); - this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), null, this)); - this.graph.getModel().execute(new GraphEdits.zoomEdit(this.graph.getView(), newView, this)); - this.removeViewCell(selectedCell); - } - - // top level circuit containers need to be synced to get the changes before the trim - if (selectedCell.isCircuitContainer()) { - let previousReference = selectedCell.getValue() + "_" + selectedCell.getId(); - let selectedParent = selectedCell.getParent(); - let selectedIndex = selectedParent.getIndex(selectedCell); - this.graph.getModel().setValue(selectedCell, newCell.getValue()); - const viewCell = this.graph.getModel().getCell(newCell.getValue()); - if (viewCell.children) { - for (let viewChild of viewCell.children) { - if (viewChild.isCircuitContainer()) { - this.syncCircuitContainer(viewChild); - break; - } - } - } - selectedCell = selectedParent.children[selectedIndex]; - this.updateInteractions(previousReference, newCell.getValue() + "_" + selectedCell.getId()); - } - - if (GraphBase.unFormatedCells.size > 0) { - console.log("FORMATTING !!!!!!!!!!!!!!!!"); - this.autoFormat(GraphBase.unFormatedCells); - GraphBase.unFormatedCells.clear(); - } - - // sync circuit containers - if (origParent) { - this.syncCircuitContainer(origParent); - } - - this.trimUnreferencedCells(); - } finally { - this.graph.getModel().endUpdate(); - } - } - } - - resetGraph(moduleMode: boolean = true) { - this.graph.home(); - this.graph.getModel().clear(); - - this.viewStack = []; - this.selectionStack = []; - - // initalize the GlyphInfoDictionary - const cell0 = this.graph.getModel().getCell(0); - const infoDict = []; - const combinatorialDict = []; - var dataContainer = []; - dataContainer[GraphBase.INFO_DICT_INDEX] = infoDict; - dataContainer[GraphBase.COMBINATORIAL_DICT_INDEX] = combinatorialDict; - this.graph.getModel().setValue(cell0, dataContainer); - - const cell1 = this.graph.getModel().getCell(1); - let rootViewCell; - - // initalize the root view cell of the graph - if (moduleMode) { - let rootModuleInfo = new ModuleInfo(); - this.addToInfoDict(rootModuleInfo); - rootViewCell = this.graph.insertVertex(cell1, rootModuleInfo.getFullURI(), "", 0, 0, 0, 0, GraphBase.STYLE_MODULE_VIEW); - this.graph.enterGroup(rootViewCell); - this.viewStack.push(rootViewCell); - } else { - let info = new GlyphInfo(); - this.addToInfoDict(info); - rootViewCell = this.graph.insertVertex(cell1, info.getFullURI(), "", 0, 0, 0, 0, GraphBase.STYLE_COMPONENT_VIEW); - this.graph.enterGroup(rootViewCell); - this.viewStack.push(rootViewCell); - this.addBackbone(); - } - - this.metadataService.setComponentDefinitionMode(!moduleMode); - - this.updateAngularMetadata(this.graph.getSelectionCells()); - - this.editor.undoManager.clear(); - } - - /** - * Sets the graph to component definition mode or module mode. - * wrapper for metadataService.setComponentDefinitionMode. - * @param componentMode True if you want to be in component mode, false if module mode. - */ - public setComponentDefinitionMode(componentMode: boolean) { - this.metadataService.setComponentDefinitionMode(componentMode); - } - - - public lookupInfo(glyphURI: string) { - return this.getFromInfoDict(glyphURI) as GlyphInfo - } - - public getCurrentRoot() { - return this.graph.getCurrentRoot() - } - -} diff --git a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.css b/frontend/src/app/hierarchy-preview/hierarchy-preview.component.css deleted file mode 100644 index 3640918c..00000000 --- a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.css +++ /dev/null @@ -1,31 +0,0 @@ -.hierarchy-controls { - position: absolute; - bottom: 0; - right: 0; - display: flex; - flex-direction: column; - align-items: center; - padding: 8px; - max-height: 500px; -} - -.hierarchy-controls .level { - width: 4em; - height: 3em; - margin: 8px; - font-family: 'Roboto'; - cursor: pointer; - border-radius: 8px; - - border: 3px solid #ddd; - color: grey; - - display: flex; - align-items: center; - justify-content: center; -} - -.hierarchy-controls .level:last-child { - border-color: black; - color: black; -} \ No newline at end of file diff --git a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.html b/frontend/src/app/hierarchy-preview/hierarchy-preview.component.html deleted file mode 100644 index a38b2eb9..00000000 --- a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.html +++ /dev/null @@ -1,8 +0,0 @@ -
-
- - {{i == 0 && "Top" || i}} - - -
-
\ No newline at end of file diff --git a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.ts b/frontend/src/app/hierarchy-preview/hierarchy-preview.component.ts deleted file mode 100644 index f9eef3aa..00000000 --- a/frontend/src/app/hierarchy-preview/hierarchy-preview.component.ts +++ /dev/null @@ -1,26 +0,0 @@ -import { Component } from '@angular/core' -import { GraphService } from '../graph.service' - - -@Component({ - selector: 'app-hierarchy-preview', - templateUrl: './hierarchy-preview.component.html', - styleUrls: ['./hierarchy-preview.component.css'] -}) - -export class HierarchyPreviewComponent { - - constructor(private graphService: GraphService) { } - - getViewStack() { - // console.log(this.glyphMenu.sequenceFeatureDict) - return this.graphService.viewStack - } - - switchView(depth) { - let levels = this.graphService.viewStack.length - depth - 1 - - for (let i = 0; i < levels; i++) - this.graphService.exitGlyph() - } -} diff --git a/frontend/src/app/pending-changes.guard.ts b/frontend/src/app/pending-changes.guard.ts deleted file mode 100644 index b614e7bd..00000000 --- a/frontend/src/app/pending-changes.guard.ts +++ /dev/null @@ -1,28 +0,0 @@ -import { CanDeactivate } from '@angular/router'; -import { Injectable } from '@angular/core'; -import { Observable } from 'rxjs'; -import { EmbeddedService } from './embedded.service'; - -export interface ComponentCanDeactivate { - canDeactivate: () => boolean | Observable; -} - -@Injectable() -export class PendingChangesGuard implements CanDeactivate { - - constructor(private embeddedService: EmbeddedService) { } - - canDeactivate(component: ComponentCanDeactivate): boolean | Observable { - - // if there are no pending changes, just allow deactivation; else confirm first - console.log("NOpe\n"); - if (component.canDeactivate() || this.embeddedService.isAppEmbedded()) { - return true; - } else { - // NOTE: this warning message will only be shown when navigating elsewhere within your angular app; - // when navigating away from your angular app, the browser will show a generic warning message - // see http://stackoverflow.com/a/42207299/7307355 - return confirm('WARNING: You have unsaved changes. Press Cancel to go back and save these changes, or OK to lose these changes.'); - } - } -} diff --git a/frontend/src/app/problems/problems.component.css b/frontend/src/app/problems/problems.component.css deleted file mode 100644 index adbfc20a..00000000 --- a/frontend/src/app/problems/problems.component.css +++ /dev/null @@ -1,48 +0,0 @@ - -.problem-icon { - color: lightgray; -} - -.warning { - color: #ffca28; -} - -.warning span, span.warning { - color: #c79a00; -} - -.error { - color: #f44336; -} - -.problem-qty { - font-weight: bolder; - display: inline-block; - padding: 0 6px 0 10px; -} - -.success { - color: #4caf50; -} - -/* .error span, span.error { - color: #ba000d; -} */ - -#problems-expand { - width: 100px; - border-radius: 20px; - margin: 10px; - margin-right: 20px; - position: absolute; - right: 0; -} - -.problem-item { - /* width: 300px; */ - line-height: 28px; - height: 2.5em; -} -/deep/ .problems-panel { - max-width: 500px !important; -} \ No newline at end of file diff --git a/frontend/src/app/problems/problems.component.html b/frontend/src/app/problems/problems.component.html deleted file mode 100644 index 2c29028a..00000000 --- a/frontend/src/app/problems/problems.component.html +++ /dev/null @@ -1,36 +0,0 @@ - - -
- -
-
- -
- \ No newline at end of file diff --git a/frontend/src/app/problems/problems.component.ts b/frontend/src/app/problems/problems.component.ts deleted file mode 100644 index f3846a56..00000000 --- a/frontend/src/app/problems/problems.component.ts +++ /dev/null @@ -1,95 +0,0 @@ -import { Component } from '@angular/core' -import { GraphService } from '../graph.service' - - -@Component({ - selector: 'app-problems', - templateUrl: './problems.component.html', - styleUrls: ['./problems.component.css'] -}) - -export class ProblemsComponent { - - warnings: string[] - errors: string[] - - constructor(private graphService: GraphService) { } - - ngOnInit() { - this.warnings = [] - this.errors = [] - - setInterval(this.validate.bind(this), 750) - } - - validate() { - const warnings = [] - const errors = [] - - // Validation functions - this.validateCurrentView(warnings, errors) - this.validateComponents(warnings, errors) - // more here... - - // Transpose to separate errors and warnings - this.warnings = warnings - this.errors = errors - } - - validateCurrentView(warnings: string[], errors: string[]) { - - const currentView = this.graphService.getCurrentRoot() - const children = currentView.children || [] - - // Warning: No children in current view - if (!children.length) { - const cellType = currentView.isModuleView() ? 'Module' : currentView.isComponentView() ? 'Component' : 'Current view' - warnings.push(`${cellType} does not contain any children.`) - } - - // TO DO: other validations - } - - validateComponents(warnings: string[], errors: string[]) { - const currentView = this.graphService.getCurrentRoot() - const circuitContainers = currentView.children || [] - const components = circuitContainers - .map(container => container.children || []) - .flat() - .filter(comp => comp.value) - - components.forEach(comp => this.validateComponent(comp, warnings, errors)) - } - - validateComponent(component, warnings: string[], errors: string[]) { - const info = this.graphService.lookupInfo(component.value) - const sequence = (info.sequence || '').toUpperCase() - const version = (info.version || '') - - // Error: No ID - !info.displayID && errors.push(`${info.partRole} is missing an ID.`) - - // Error: Non-IUPAC compliant sequence - const negativeIUPACSequenceRegex = /[^ACGTURYSWKMBDHVN\.\-]/g - var compliant = !sequence.match(negativeIUPACSequenceRegex) - const sequencePreview = sequence.substring(0, 10) - !compliant && errors.push(`Component '${info.displayID}' has illegal sequence: ${sequencePreview}...`) - - // Warning: No sequence - !sequence && warnings.push(`Component '${info.displayID}' does not have a sequence.`) - - // Warning: No version - !version && warnings.push(`Component '${info.displayID}' does not have a version.`) - - // Warning: Non-Semver compliant version - // Got Regex from https://ihateregex.io/expr/semver/# - // const semverVersionRegex = /^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$/gm - - // using less strict expression now -- SBOL interpreted Semver improperly and actually intended - // to allow versions like 1 or 1.3 - const versionRegex = /^[0-9]+[\\p{L}0-9_\\.-]*$/ - compliant = !!version.match(versionRegex) - version && !compliant && - warnings.push(`Component '${info.displayID}' has incompliant version: ${version}`) - } -} diff --git a/frontend/src/app/toolbar/toolbar.component.css b/frontend/src/app/toolbar/toolbar.component.css deleted file mode 100644 index 88fe0fa5..00000000 --- a/frontend/src/app/toolbar/toolbar.component.css +++ /dev/null @@ -1,31 +0,0 @@ -/* This sets the space between sets of buttons */ -.toolbar-spacer { - flex: 1 1 auto; -} - -/* Not sure exactly how this works but it makes the menu - bigger so that it can fit the buttons. */ -::ng-deep .mat-menu-panel { - padding: 0 10px !important; - width: 100% !important; -} - -/* This sets the css for the buttons on the row */ -.toolbar-row-button { - margin: 0 3px; - border: none; -} - -.mat-toolbar { - min-height: 0; -} - -.toolbar-row { - height: 44px; - padding-bottom: 2px; - gap: 40px; -} - -.toolbar-row-section.grow { - flex-grow: 1; -} \ No newline at end of file diff --git a/frontend/src/app/toolbar/toolbar.component.html b/frontend/src/app/toolbar/toolbar.component.html deleted file mode 100644 index 754d8875..00000000 --- a/frontend/src/app/toolbar/toolbar.component.html +++ /dev/null @@ -1,138 +0,0 @@ - - - - - -
- - - - - SynBioHub - - - - - - Local Device - - - - - - - - - - - - New - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- - - - - - - -
- - -
- - - - - -
- - -
- - - - - - - -
- - - \ No newline at end of file diff --git a/frontend/src/app/zoom-controls/zoom-controls.component.css b/frontend/src/app/zoom-controls/zoom-controls.component.css deleted file mode 100644 index c667125e..00000000 --- a/frontend/src/app/zoom-controls/zoom-controls.component.css +++ /dev/null @@ -1,16 +0,0 @@ -.zoom-controls { - position: absolute; - top: -8px; - left: 4px; - display: flex; - flex-direction: column; - align-items: center; - padding: 8px; - - transform: scale(0.9); -} - -.zoom-controls .zoom-input { - width: 6ch; - text-align: center; -} \ No newline at end of file diff --git a/frontend/src/app/zoom-controls/zoom-controls.component.html b/frontend/src/app/zoom-controls/zoom-controls.component.html deleted file mode 100644 index fe7c6392..00000000 --- a/frontend/src/app/zoom-controls/zoom-controls.component.html +++ /dev/null @@ -1,16 +0,0 @@ -
- - - - - - - - - -
\ No newline at end of file diff --git a/frontend/src/app/zoom-controls/zoom-controls.component.ts b/frontend/src/app/zoom-controls/zoom-controls.component.ts deleted file mode 100644 index 25956166..00000000 --- a/frontend/src/app/zoom-controls/zoom-controls.component.ts +++ /dev/null @@ -1,40 +0,0 @@ -import { Component } from '@angular/core' -import { GraphService } from '../graph.service' - - -@Component({ - selector: 'app-zoom-controls', - templateUrl: './zoom-controls.component.html', - styleUrls: ['./zoom-controls.component.css'] -}) - -export class ZoomControlsComponent { - - constructor(public graphService: GraphService) { } - - zoomSliderChanged($event) { - this.graphService.setZoom($event.value / 100); - } - - zoomInputChanged($event) { - let number = parseInt($event.target.value); - if (!isNaN(number)) { - const percent = number / 100; - this.graphService.setZoom(percent); - } - - // if they entered nonsense the zoom doesn't change, which - // means angular won't refresh the input box on its own - $event.target.value = this.getZoomDisplayValue(); - } - - getZoomSliderValue() { - return this.graphService.getZoom() * 100; - } - - getZoomDisplayValue() { - let percent = this.graphService.getZoom() * 100; - let string = percent.toFixed(0); - return string.toString() + '%'; - } -} diff --git a/frontend/src/assets/glyph_stencils/indicators/.bundle_order b/frontend/src/assets/glyph_stencils/indicators/.bundle_order deleted file mode 100644 index 906d53af..00000000 --- a/frontend/src/assets/glyph_stencils/indicators/.bundle_order +++ /dev/null @@ -1,3 +0,0 @@ -composite -variant -error \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/interactionNodes/.bundle_order b/frontend/src/assets/glyph_stencils/interactionNodes/.bundle_order deleted file mode 100644 index 0ba51741..00000000 --- a/frontend/src/assets/glyph_stencils/interactionNodes/.bundle_order +++ /dev/null @@ -1,4 +0,0 @@ -association -dissociation -process -replacement-glyph \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/interactions/.bundle_order b/frontend/src/assets/glyph_stencils/interactions/.bundle_order deleted file mode 100644 index 5157227a..00000000 --- a/frontend/src/assets/glyph_stencils/interactions/.bundle_order +++ /dev/null @@ -1,5 +0,0 @@ -control -inhibition -stimulation -process -degradation \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/molecularSpecies/.bundle_order b/frontend/src/assets/glyph_stencils/molecularSpecies/.bundle_order deleted file mode 100644 index fcb7d43a..00000000 --- a/frontend/src/assets/glyph_stencils/molecularSpecies/.bundle_order +++ /dev/null @@ -1,7 +0,0 @@ -macromolecule -dsNA -ssNA -small-molecule -no-glyph-assigned-ms -replacement-glyph -complex \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/sequenceFeatures/.bundle_order b/frontend/src/assets/glyph_stencils/sequenceFeatures/.bundle_order deleted file mode 100644 index 9b7f7aa2..00000000 --- a/frontend/src/assets/glyph_stencils/sequenceFeatures/.bundle_order +++ /dev/null @@ -1,36 +0,0 @@ -engineered-region -promoter -ribosome-entry-site -cds -terminator-specification -ncrna -origin-of-replication -origin-of-transfer -primer-binding-site -five-prime-sticky-restriction-site -three-prime-sticky-restriction-site -assembly-scar -operator -insulator -blunt-restriction-site -three-prime-overhang -five-prime-overhang -aptamer -polyA -specific-recombination-site -no-glyph-assigned -signature -location-dna -location-rna -location-protein -nuclease-site -protease-site -protein-stability-element -ribonuclease-site -rna-stability-element -transcription-end -translation-end - -!test -!chromosomal-locus -!dna-stability-element \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/utils/.bundle_order b/frontend/src/assets/glyph_stencils/utils/.bundle_order deleted file mode 100644 index 72634336..00000000 --- a/frontend/src/assets/glyph_stencils/utils/.bundle_order +++ /dev/null @@ -1,5 +0,0 @@ -backbone -circular-plasmid-left -circular-plasmid-right -textBox -module \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/utils/circular-plasmid-left.xml b/frontend/src/assets/glyph_stencils/utils/circular-plasmid-left.xml deleted file mode 100644 index 9802d91f..00000000 --- a/frontend/src/assets/glyph_stencils/utils/circular-plasmid-left.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/frontend/src/assets/glyph_stencils/utils/circular-plasmid-right.xml b/frontend/src/assets/glyph_stencils/utils/circular-plasmid-right.xml deleted file mode 100644 index 59cfb579..00000000 --- a/frontend/src/assets/glyph_stencils/utils/circular-plasmid-right.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/frontend/src/environments/environment.prod.ts b/frontend/src/environments/environment.prod.ts deleted file mode 100644 index 330366be..00000000 --- a/frontend/src/environments/environment.prod.ts +++ /dev/null @@ -1,5 +0,0 @@ -export const environment = { - production: true, - backendURL: 'https://canvas-api.greensky-6cc75ee4.westus.azurecontainerapps.io/api', - baseURI: "https://sbolcanvas.org" -}; diff --git a/frontend/staticwebapp.config.json b/frontend/staticwebapp.config.json deleted file mode 100644 index 7b94283d..00000000 --- a/frontend/staticwebapp.config.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "routes": [ - { - "route": "/about", - "rewrite": "/index.html" - }, - { - "route": "/tutorial", - "rewrite": "/index.html" - } - ] -} \ No newline at end of file diff --git a/resources/build_automation/build_backend.sh b/resources/build_automation/build_backend.sh new file mode 100755 index 00000000..40045ac4 --- /dev/null +++ b/resources/build_automation/build_backend.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +BACKEND_DIR=$(pwd)/SBOLCanvasBackend +compile_dest_dir=${BACKEND_DIR}/WebContent/WEB-INF/classes +compile_source_dir=${BACKEND_DIR}/src +tomcat_dependencies=$(pwd)/resources/server_automation/tomcat/apache-tomcat-9.0.26/lib +other_dependencies=${BACKEND_DIR}/WebContent/WEB-INF/lib +war_filename=api.war +cur_dir=$(pwd) + +# Compile java files into the SBOLCanvasBackend/WebContent/WEB-INF/classes directory +[[ -d ${compile_dest_dir} ]] && rm -rf ${compile_dest_dir} # Make sure we have a clean slate +mkdir ${compile_dest_dir} + +javac -source 1.8 -target 1.8 -sourcepath ${compile_source_dir} -d ${compile_dest_dir} -cp ".:${other_dependencies}/*:${tomcat_dependencies}/*" ${compile_source_dir}/**/*.java\ + +# Build .war file and deploy +cd ${BACKEND_DIR}/WebContent +jar -cf ${war_filename} * +echo "$PWD" +echo $(ls)