244 peers (#247)

* Peer service initial commit

* Change version

* Update client for when no ID is provided

* Add tests

* Fix comment, add newline

* 1kgenomes as default peer

* Change to url

ctk-cli/src/main/resources/application.properties

@@ -31,7 +31,7 @@ ctk.antfile=lib/antRunTests.xml
 # which is already in "./lib"
 # when run from command line (doesn't currently affect output when running maven)
 # THIS IS A HACK FOR ANT, we should be scanning the lib dir (soon)
-ctk.testjar=cts-java-0.6.0a7-tests.jar
+ctk.testjar=cts-java-0.6.0a10-tests.jar
 
 # this title (with ctk.tgt.urlRoot appended) goes on top of each HTML results page
 # when run from command line (doesn't currently affect output when running maven)

ctk-cli/src/main/resources/ctk

@@ -49,7 +49,7 @@ CMD_DIR="$(cd "$(dirname "$CMD")" && pwd -P)"
 # Defaults and command line options
 [ "$VERBOSE" ] ||  VERBOSE=
 [ "$DEBUG" ]   ||  DEBUG=
-[ "$CTKJAR" ]  ||  CTKJAR="ctk-cli-0.6.0a7.jar"
+[ "$CTKJAR" ]  ||  CTKJAR="ctk-cli-0.6.0a10.jar"
 [ "$TGTDIR" ] || TGTDIR="target"
 
 

ctk-server/src/main/resources/application.properties

@@ -31,7 +31,7 @@ ctk.antfile=lib/antRunTests.xml
 # which is already in "./lib"
 # when run from command line (doesn't currently affect output when running maven)
 # THIS IS A HACK FOR ANT, we should be scanning the lib dir (soon)
-ctk.testjar=cts-java-0.6.0a7-tests.jar
+ctk.testjar=cts-java-0.6.0a10-tests.jar
 
 # this title (with ctk.tgt.urlRoot appended) goes on top of each HTML results page
 # when run from command line (doesn't currently affect output when running maven)

ctk-server/src/main/resources/ctk

@@ -49,7 +49,7 @@ CMD_DIR="$(cd "$(dirname "$CMD")" && pwd -P)"
 # Defaults and command line options
 [ "$VERBOSE" ] ||  VERBOSE=
 [ "$DEBUG" ]   ||  DEBUG=
-[ "$CTKJAR" ]  ||  CTKJAR="ctk-server-0.6.0a7.jar"
+[ "$CTKJAR" ]  ||  CTKJAR="ctk-server-0.6.0a10.jar"
 [ "$TGTDIR" ] || TGTDIR="target"
 
 

ctk-testrunner/src/main/resources/application.properties

@@ -31,7 +31,7 @@ ctk.antfile=lib/antRunTests.xml
 # which is already in "./lib"
 # when run from command line (doesn't currently affect output when running maven)
 # THIS IS A HACK FOR ANT, we should be scanning the lib dir (soon)
-ctk.testjar=cts-java-0.6.0a7-tests.jar
+ctk.testjar=cts-java-0.6.0a10-tests.jar
 
 # this title (with ctk.tgt.urlRoot appended) goes on top of each HTML results page
 # when run from command line (doesn't currently affect output when running maven)

ctk-transport/src/main/java/org/ga4gh/ctk/transport/URLMAPPING.java

@@ -183,6 +183,18 @@ public interface URLMAPPING {
 
     void setGetExpressionLevel(String getExpressionLevel);
 
+    String getListPeers();
+
+    void setListPeers(String ListPeers);
+
+    String getAnnounce();
+
+    void setAnnounce(String getAnnounce);
+
+    String getInfo();
+
+    void setGetInfo(String getInfo);
+
     Map<String, String> getEndpoints();
 
     void setEndpoints(Map<String, String> endpoints);

ctk-transport/src/main/java/org/ga4gh/ctk/transport/URLMAPPINGImpl.java

@@ -99,6 +99,10 @@ public class URLMAPPINGImpl implements URLMAPPING {
         defaultEndpoints.put("ctk.tgt.searchGenotypePhenotype", "featurephenotypeassociations/search");
         defaultEndpoints.put("ctk.tgt.searchPhenotypes", "phenotypes/search");
 
+        defaultEndpoints.put("ctk.tgt.listPeers", "peers/list");
+        defaultEndpoints.put("ctk.tgt.announce", "announce");
+        defaultEndpoints.put("ctk.tgt.getInfo", "info");
+
         dumpToStdOut = Boolean.getBoolean("ctk.tgt.urlmapper.dump"); // so, -Dctk.tgt.urlmapper.dump=true
 
         log.info("set default URLMAPPING urlRoot to " + defaultEndpoints.get("ctk.tgt.urlRoot"));
@@ -667,4 +671,31 @@ public void setSearchPhenotypeAssociationSets(String searchPhenotypeAssociationS
         endpoints.put("ctk.tgt.searchPhenotypeAssociationSets", searchPhenotypeAssociationSets);
     }
 
+    @Override
+    public String getListPeers() { return endpoints.get("ctk.tgt.listPeers"); }
+
+    @Override
+    public void setListPeers(String listPeers) {
+        assert(listPeers != null);
+        endpoints.put("ctk.tgt.listPeers", listPeers);
+    }
+
+    @Override
+    public String getAnnounce() { return endpoints.get("ctk.tgt.announce"); }
+
+    @Override
+    public void setAnnounce(String announce) {
+        assert(announce != null);
+        endpoints.put("ctk.tgt.announce", announce);
+    }
+
+    @Override
+    public String getInfo() { return endpoints.get("ctk.tgt.getInfo"); }
+
+    @Override
+    public void setGetInfo(String info) {
+        assert(info != null);
+        endpoints.put("ctk.tgt.getInfo", info);
+    }
+
 }

ctk-transport/src/main/java/org/ga4gh/ctk/transport/protobuf/Get.java

@@ -25,11 +25,19 @@ protected HttpResponse<JsonNode> queryServer(String url) throws UnirestException
         if (log.isDebugEnabled()) {
             log.debug("begin jsonGet to " + url + " id = " + id);
         }
-        HttpResponse<JsonNode> response = Unirest.get(url)
-                .header("accept", "application/json")
-                .routeParam("id", id)
-                .queryString(queryParams)
-                .asJson();
+        HttpResponse<JsonNode> response;
+        if (id != null) {
+            response = Unirest.get(url)
+                    .header("accept", "application/json")
+                    .routeParam("id", id)
+                    .queryString(queryParams)
+                    .asJson();
+        } else {
+            response = Unirest.get(url)
+                    .header("accept", "application/json")
+                    .queryString(queryParams)
+                    .asJson();
+        }
         if (log.isDebugEnabled()) {
             log.debug("exit jsonGet to " + url + " with status " + response.getStatusText());
         }

ctk-transport/src/main/java/org/ga4gh/ctk/transport/protocols/Client.java

@@ -50,6 +50,8 @@
 import ga4gh.BioMetadataServiceOuterClass.SearchBiosamplesResponse;
 import ga4gh.BioMetadataServiceOuterClass.SearchIndividualsRequest;
 import ga4gh.BioMetadataServiceOuterClass.SearchIndividualsResponse;
+import ga4gh.PeerServiceOuterClass.Peer;
+import ga4gh.PeerServiceOuterClass.*;
 import org.ga4gh.ctk.transport.GAWrapperException;
 import org.ga4gh.ctk.transport.URLMAPPING;
 import org.ga4gh.ctk.transport.WireTracker;
@@ -149,6 +151,9 @@ public class Client {
 
     public final BioMetadata bioMetadata = new BioMetadata();
 
+
+    public final Peers peers = new Peers();
+
     /**
      * Create a new client that can make requests on a GA4GH server.
      *
@@ -807,4 +812,54 @@ public SearchPhenotypeAssociationSetsResponse searchPhenotypeAssociationSets(Sea
             return builder.build();
         }
     }
+
+    /**
+     * Inner class holding all peer service related methods.
+     */
+    public class Peers {
+        /**
+         * Lists available peers at the /peers/list endpoint using the given request.
+         * @param request   A ListPeers request
+         * @return ListPeersResponse
+         * @throws GAWrapperException if the server finds the request invalid in some way
+         * @throws UnirestException if there's a problem speaking HTTP to the server
+         * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+         */
+        public ListPeersResponse listPeers(ListPeersRequest request) throws InvalidProtocolBufferException, GAWrapperException, UnirestException {
+            String path = urls.getListPeers();
+            ListPeersResponse.Builder responseBuilder = ListPeersResponse.newBuilder();
+            new Post<>(urls.getUrlRoot(), path, request, responseBuilder, wireTracker).performQuery();
+            return responseBuilder.build();
+        }
+
+        /**
+         * Get info about the server at the /info endpoint.
+         * @return Info
+         * @throws GAWrapperException if the server finds the request invalid in some way
+         * @throws UnirestException if there's a problem speaking HTTP to the server
+         * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+         */
+        public GetInfoResponse getInfo() throws InvalidProtocolBufferException, GAWrapperException, UnirestException {
+            String path = urls.getInfo();
+            GetInfoResponse.Builder builder = GetInfoResponse.newBuilder();
+            new Get<>(urls.getUrlRoot(), path, null, null, builder, wireTracker).performQuery();
+            return builder.build();
+        }
+
+        /**
+         * Announces a peer to the /announce endpoint.
+         * @param request   A AnnouncePeer request
+         * @return AnnouncePeerResponse
+         * @throws GAWrapperException if the server finds the request invalid in some way
+         * @throws UnirestException if there's a problem speaking HTTP to the server
+         * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+         */
+        public AnnouncePeerResponse announcePeer(AnnouncePeerRequest request) throws InvalidProtocolBufferException, GAWrapperException, UnirestException {
+            String path = urls.getAnnounce();
+            AnnouncePeerResponse.Builder responseBuilder = AnnouncePeerResponse.newBuilder();
+            new Post<>(urls.getUrlRoot(), path, request, responseBuilder, wireTracker).performQuery();
+            return responseBuilder.build();
+        }
+
+    }
 }

ctk-transport/src/main/resources/defaulttransport.properties

@@ -34,3 +34,6 @@ ctk.tgt.searchFeatureSets=featuresets/search
 ctk.tgt.searchContinuous=continuous/search
 ctk.tgt.searchContinuousSets=continuoussets/search
 ctk.tgt.searchPhenotypeAssociationSets=phenotypeassociationsets/search
+ctk.tgt.listPeers=peers/list
+ctk.tgt.getInfo=info
+ctk.tgt.announce=announce

cts-java/src/main/resources/defaulttransport.properties

@@ -34,3 +34,6 @@ ctk.tgt.searchFeatureSets=featuresets/search
 ctk.tgt.searchContinuous=continuous/search
 ctk.tgt.searchContinuousSets=continuoussets/search
 ctk.tgt.searchPhenotypeAssociationSets=phenotypeassociationsets/search
+ctk.tgt.listPeers=peers/list
+ctk.tgt.getInfo=info
+ctk.tgt.announce=announce

cts-java/src/test/java/org/ga4gh/cts/api/peers/PeersIT.java

@@ -0,0 +1,80 @@
+package org.ga4gh.cts.api.peers;
+
+import com.google.protobuf.InvalidProtocolBufferException;
+import com.mashape.unirest.http.exceptions.UnirestException;
+import ga4gh.PeerServiceOuterClass;
+import ga4gh.PeerServiceOuterClass.ListPeersRequest;
+import ga4gh.PeerServiceOuterClass.ListPeersResponse;
+import ga4gh.PeerServiceOuterClass.GetInfoResponse;
+import ga4gh.PeerServiceOuterClass.GetInfoRequest;
+import ga4gh.PeerServiceOuterClass.AnnouncePeerRequest;
+import ga4gh.PeerServiceOuterClass.AnnouncePeerResponse;
+import ga4gh.PeerServiceOuterClass.Peer;
+import org.ga4gh.ctk.transport.GAWrapperException;
+import org.ga4gh.ctk.transport.URLMAPPING;
+import org.ga4gh.ctk.transport.protocols.Client;
+import org.ga4gh.cts.api.TestData;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Tests for the BioMetadata endpoints
+ */
+@Category(PeersTests.class)
+public class PeersIT {
+
+    private static Client client = new Client(URLMAPPING.getInstance());
+
+    /**
+     * Tests the /peers/list endpoint to ensure a well formed peer (1kgenomes.ga4gh.org) is returned.
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    @Test
+    public void checkListPeers() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+        final ListPeersRequest req =
+                ListPeersRequest.newBuilder()
+                        .build();
+
+        final ListPeersResponse resp = client.peers.listPeers(req);
+        assertThat(resp.getPeersCount()).isGreaterThan(0);
+        final Peer peer = Peer.newBuilder().setUrl("http://1kgenomes.ga4gh.org").build();
+        assertThat(resp.getPeersList()).contains(peer);
+    }
+
+    /**
+     * Tests that the service will receive a well formed announce message without throwing an error.
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    @Test
+    public void checkValidAnnounce() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+        final Peer peer = Peer.newBuilder().setUrl("http://1kgenomes.ga4gh.org").build();
+        final AnnouncePeerRequest req =
+                AnnouncePeerRequest.newBuilder()
+                        .setPeer(peer)
+                        .build();
+
+        final AnnouncePeerResponse resp = client.peers.announcePeer(req);
+        assertThat(resp).isNotNull();
+        assertThat(resp.getSuccess()).isTrue();
+    }
+
+    /**
+     * Tests that the service returns an expected info response at the /info endpoint including the protocol version.
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    @Test
+    public void checkGetInfo() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+        final GetInfoResponse resp = client.peers.getInfo();
+        assertThat(resp).isNotNull();
+        assertThat(resp.getProtocolVersion()).isNotEmpty();
+    }
+
+}

cts-java/src/test/java/org/ga4gh/cts/api/peers/PeersTests.java

@@ -0,0 +1,5 @@
+package org.ga4gh.cts.api.peers;
+
+
+public interface PeersTests {  /* category marker */
+}

docs/ConfigTheCTK.md

@@ -16,7 +16,7 @@ You can configure the CTK via the properties used by the:
 If you're working with CTK/CTS source (in an IDE or for a Maven build) it's easiest to just edit `ctk-cli/src/main/resources/application.properties`, `ctk-server/src/main/resources/application.properties`, and `ctk-testrunner/src/main/resources/application.properties`, but these changes will have no effect until you rebuild (because the rebuild copies the files from `src/main/resources/` into `target/` which is where the code runs from). But, you can make temporary changes to the text properties files directly in the output build `target` tree.
 
 If you're working with the CTK/CTS at the command line, you can extract that file from the packaged jar file and have it in the dir where the jar runs from
-(`jar xvf ctk-cli-v.0.6.0a7.jar application.properties`) ... if you're using the ZIP distribution, it will already have extracted that properties file (and other control files) for you.
+(`jar xvf ctk-cli-v.0.6.0a10.jar application.properties`) ... if you're using the ZIP distribution, it will already have extracted that properties file (and other control files) for you.
 
 Note that individual test suites (`cts-java` etc) might have individual configuration mechanisms or properties files - refer to their documentation.
 
@@ -41,7 +41,7 @@ The Properties list is available by looking at the javadoc for the `ctk-testrunn
 
 Because URLMAPPING initialization is a static action which might happen without logs being available, the URLMAPPING class has a special Java system property property to cause it to dump all the static initialization actions directly to stdout:
 
-`java -Dctk.tgt.urlmapper.dump=true -jar ctk-cli-0.6.0a7.jar`
+`java -Dctk.tgt.urlmapper.dump=true -jar ctk-cli-0.6.0a10.jar`
 
 Note that many tests reinitialize the URLMAPPER in a @BeforeClass, so you may see the initialization get dumped multiple times!
 
@@ -70,7 +70,7 @@ To set properties as a command line variable (the highest priority) for a Maven
 ### Configuring a Command Line invocation
 From the directory where the executable jar is, you can edit `application.properties`. The zip distribution has this file pre-extracted, but if you don't already have it, just extract it from the executable jar like this
 
-    jar xvf ctk-cli-0.6.0a7.jar application.properties
+    jar xvf ctk-cli-0.6.0a10.jar application.properties
 
 Edit the properties file, and leave it in the launch directory or put it in a `config` subdirectory.
 

docs/README-Server.txt

@@ -1,14 +1,14 @@
 This is an experimental web-server wrapper for the GA4GH Conformance Test Kit (CTK).
 
 Run it using the included 'ctk' script, or simply as
-    java -jar ctk-server-0.6.0a7.jar
+    java -jar ctk-server-0.6.0a10.jar
 
 Once it is running, it exposes a server at port 8080. (Being a Spring Boot app,
 you can modify the port number with the normal --server.port= ... setting, like this:
 
    ./ctk --server.port=8088
    or
-   java -jar ctk-server-0.6.0a7.jar --server.port=8088
+   java -jar ctk-server-0.6.0a10.jar --server.port=8088
 
 To run the tests, you just browse to that server using a web browser; it
 will run using the defaults and values set in the application properties file.

docs/RunningTests_maven.md

@@ -122,7 +122,7 @@ processes):
     2. edit `application-properties` (or set environment properties) to point to the in-source location of files, for example:
         1. `ctk.antfile=../ctk-testrunner/src/main/resources/antRunTests.xml`
         2. `ctk.defaulttransportfile=../ctk-transport/src/main/resources/defaulttransport.properties/defaulttransport.properties`
-        3. `ctk.testjar=../cts-java/target/cts-java-0.6.0a7-tests.jar`
+        3. `ctk.testjar=../cts-java/target/cts-java-0.6.0a10-tests.jar`
         4. `ctk.testclassroots=../cts-java/target/test-classes`
         5. `ctk.domaintypesfile=../ctk-domain/src/main/resources/avro-types.json`
     2. manually create a `ctk-cli/lib` directory and copy into it the logging control file(s) from

parent/pom.xml

@@ -29,7 +29,7 @@
 
 
     <properties>
-        <compliance.version>0.6.0a7</compliance.version>
+        <compliance.version>0.6.0a10</compliance.version>
         <!--
           Use this section to indicate the repository and branch of schemas
           your tests will be compiled against.
@@ -38,8 +38,8 @@
           Then change the schemas.version to be the commit hash, release, 
           or branch snapshot you would like to test.
         -->
-        <ga4gh.schemas.groupId>com.github.ga4gh</ga4gh.schemas.groupId>
-        <ga4gh.schemas.version>master-SNAPSHOT</ga4gh.schemas.version>
+        <ga4gh.schemas.groupId>com.github.david4096</ga4gh.schemas.groupId>
+        <ga4gh.schemas.version>760_peers-SNAPSHOT</ga4gh.schemas.version>
         <ga4gh.schemas.artifactId>schemas</ga4gh.schemas.artifactId>
         <ctk.tgt.urlRoot>http://localhost:8000</ctk.tgt.urlRoot>
         <!-- Controls skipping of cts-java IT tests during build; skip the tests by passing
@@ -248,7 +248,7 @@
 
             <!--Comment to use local schema build-->
             <dependency>
-                <groupId>com.github.ga4gh</groupId>
+                <groupId>com.github.david4096</groupId>
                 <artifactId>schemas</artifactId>
                 <version>${ga4gh.schemas.version}</version>
             </dependency>