add robot release script

ontology/dev/build/RELEASE_PROCESS.md

@@ -0,0 +1,63 @@
+## REALEASE PROCESS:
+The release process uses the ROBOT tool produce the ontology release file `data-source-ontology.owl`.
+
+Information about downloading and installing ROBOT is found at:
+- http://robot.obolibrary.org/
+- https://github.com/ontodev/robot
+
+Since the robot.jar file is in the directory, calls to robot are made using the `java -jar ./robot.jar` command.
+Alternatively, if your system is configured properly, you can edit the script to call robot directly. 
+For example, if the path to robot is in your `PATH` environment variable, you can replace `java -jar ./robot.jar` with `robot`.
+
+## MERGE ERRORS AND THE CATALOG-V001.XML FILE
+As you create new import files for the ontology, robot may throw an error saying it cannot locate the import ontology.
+This error is most likely fixed by editing the catalog-v001.xml file in the build directory to include the new import.
+For example, suppose the catalog-v001.xml only references the `ontology_annotations_import.owl` like so:
+```
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri name="http://purl.roswellpark.org/ontology_annotations_import.owl" uri="ontology_annotations_import.owl"/>
+</catalog>
+```
+
+You then create a file named `foo.owl` in the imports directory. 
+In order for the robot merge operation to execute, you need to modify the catalog file to reference `foo.owl`:
+```
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri name="http://purl.roswellpark.org/ontology_annotations_import.owl" uri="ontology_annotations_import.owl"/>
+    <uri name="http://purl.roswellpark.org/foo.owl" uri="foo.owl"/>
+</catalog>
+```
+
+## RUNNING THE RELEASE SCRIPT
+To release a version of `data-source-ontology.owl`, run the `robot_release.sh` command
+
+This will copy the `data-source-ontology-dev.owl` file and the imports into build directory, and produce the temp files:
+
+- `data-source-ontology-merged.owl`
+- `data-source-ontology-annotated.owl`
+- `data-source-ontology.owl`
+
+The `data-source-ontology.owl` is the **release file**. Open this file and check that the ontology IRI was produced correctly and that are not any errors.
+The `data-source-ontology-merged.owl` and `data-source-ontology-annotated.owl` are intermediary files produced in the release process. 
+They are deleted after the build process completes, but they can be helpful in tracking down errors. 
+To prevent them from being deleted, comment out the following lines in the build script:
+```
+rm data-source-ontology-merged.owl
+rm data-source-ontology-annotated.owl
+```
+
+Finally, when you are satisfied with the ontology generated by the release script:
+
+- copy the build `data-source-ontology.owl` file to the ontology directory
+- commit and push your changes:
+```
+git commit -am "create release ontology $(date '+%Y-%m-%dT%H:%M:%S')"
+git push
+```
+- tag the repo with the date and time and push the tag: 
+```
+git tag data_source_ontology_release_$(date '+%Y-%m-%dT%H_%M_%S') -m "ONTOLOGY REALEASE $(date '+%Y-%m-%d %H:%M:%S')"
+git push origin --tags
+```

ontology/dev/build/catalog-v001.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri name="http://purl.roswellpark.org/ontology_annotations_import.owl" uri="ontology_annotations_import.owl"/>
+</catalog>

ontology/dev/build/robot_release.sh

@@ -0,0 +1,43 @@
+# remove any existing owl files in the directory
+rm *.owl
+
+# copy dev ontology and imports into directory
+cp ../data-source-ontology-dev.owl .
+cp ../imports/*import.owl .
+
+# since the robot.jar file is in the directory, calls to robot are made using the java -jar ./robot.jar command
+# alternatively, you can call robot directly if your system is configured properly 
+# for example, if the path to robot is in your PATH environment variable 
+# you can perform merge by simple executing robot merge
+
+# merge owl files
+# you can also call robot merge ...; but I have placed the jar file in the directory
+java -jar ./robot.jar merge \
+  --inputs "*.owl" \
+  --include-annotations true \
+  --collapse-import-closure true \
+  --output data-source-ontology-merged.owl
+
+# # add date to IRI version; e.g.: http://purl.obolibrary.org/obo/2018-06-05/data-source-ontology.owl
+java -jar ./robot.jar annotate \
+  --input data-source-ontology-merged.owl \
+  --ontology-iri "http://purl.data-source-translation.org/data-source-translation.owl" \
+  --version-iri "http://purl.data-source-translation.org/`date '+%Y-%m-%d'`/data-source-translation.owl" \
+  --output data-source-ontology-annotated.owl
+
+# run reasoner on the ontology and add inferred axioms to final output
+java -jar ./robot.jar reason \
+	--input data-source-ontology-annotated.owl \
+  --reasoner HermiT \
+  --annotate-inferred-axioms true \
+  --output data-source-ontology.owl
+
+# clean up
+# remove imports
+rm *import.owl
+
+# remove dev, merge, annotated temp ontologies
+# comment out these lines if you wish to examine them
+rm data-source-ontology-dev.owl
+rm data-source-ontology-merged.owl
+rm data-source-ontology-annotated.owl

ontology/dev/catalog-v001.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="imports" prefer="public" xml:base="">
-    		<uri name="http://purl.roswellpark.org/ontology-annotations.owl" uri="imports/ontology-annotations.owl"/>
+        <uri name="http://purl.data-source-translation.org/data-source-translation.owl" uri="data-source-translation.owl"/>
+        <uri name="http://purl.roswellpark.org/ontology_annotations_import.owl" uri="imports/ontology_annotations_import.owl"/>
     </group>
 </catalog>

ontology/dev/data-source-ontology-dev.owl

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
-<rdf:RDF xmlns="http://purl.data-source-translation.org/dev/data-source-translation.owl#"
-     xml:base="http://purl.data-source-translation.org/dev/data-source-translation.owl"
+<rdf:RDF xmlns="http://purl.data-source-translation.org/data-source-translation.owl/"
+     xml:base="http://purl.data-source-translation.org/data-source-translation.owl/"
      xmlns:annotation="http://purl.data-source-translation.org/annotation/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
      xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
@@ -14,8 +14,8 @@
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:dc="http://purl.org/dc/elements/1.1/">
-    <owl:Ontology rdf:about="http://purl.data-source-translation.org/dev/data-source-translation.owl">
-        <owl:imports rdf:resource="http://purl.roswellpark.org/ontology-annotations.owl"/>
+    <owl:Ontology rdf:about="http://purl.data-source-translation.org/data-source-translation.owl">
+        <owl:imports rdf:resource="http://purl.roswellpark.org/ontology_annotations_import.owl"/>
     </owl:Ontology>
 
 

ontology/dev/imports/catalog-v001.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
-        <uri id="Automatically generated entry, Timestamp=1527625362484" name="http://purl.roswellpark.org/ontology-annotations.owl/" uri="ontology-annotations.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1530912005722" name="http://purl.roswellpark.org/ontology_annotations_import.owl/" uri="ontology_annotations_import.owl"/>
     </group>
 </catalog>