Merge branch 'java' into java-release

Nick Bargnesi · Nick Bargnesi · commit 16a447b13c50 · 2015-11-15T21:00:45.000-05:00
diff --git a/java/buildfile.rb b/java/buildfile.rb
@@ -50,6 +50,7 @@
 REGGIE_DEPS = [ST4, TROVE, COMMONS_LANG, ANTLR]
 
 DEPS = [JENA, LOGGING, REGGIE_DEPS]
+artifacts(DEPS).each(&:invoke)
 
 # Project layout
 layout = Layout.new
diff --git a/java/src/org/openbel/reggie/rdf/generate/annotations/Main.java b/java/src/org/openbel/reggie/rdf/generate/annotations/Main.java
@@ -52,7 +52,6 @@ public void generate() {
         QuerySolutions anSchemeIter = q.annotations();
         generate(anSchemeIter);
         log.info("Completed Generating Annotations");
-        exit(0);
     }
 
     void generate(QuerySolutions anSchemeIter) {
@@ -145,6 +144,7 @@ public static void main(String... args) throws Exception {
         Dataset dataset = TDBFactory.createDataset(tdbdata);
         Main m = new Main(dataset);
         m.generate();
+        exit(0);
     }
 
     static void initLogging() {
diff --git a/java/src/org/openbel/reggie/rdf/generate/equivalences/Main.java b/java/src/org/openbel/reggie/rdf/generate/equivalences/Main.java
@@ -53,7 +53,6 @@ public void generate() {
         QuerySolutions nsSchemeIter = q.namespaces();
         generate(nsSchemeIter);
         log.info("Completed Generating Equivalences");
-        exit(0);
     }
 
     void generate(QuerySolutions nsSchemeIter) {
@@ -148,6 +147,7 @@ public static void main(String... args) throws Exception {
         Dataset dataset = TDBFactory.createDataset(tdbdata);
         Main m = new Main(dataset);
         m.generate();
+        exit(0);
     }
 
     static void initLogging() {
diff --git a/java/src/org/openbel/reggie/rdf/generate/namespaces/Main.java b/java/src/org/openbel/reggie/rdf/generate/namespaces/Main.java
@@ -52,7 +52,6 @@ public void generate() {
         QuerySolutions nsSchemeIter = q.namespaces();
         generate(nsSchemeIter);
         log.info("Completed Generating Namespaces");
-        exit(0);
     }
 
     void generate(QuerySolutions nsSchemeIter) {
@@ -148,6 +147,7 @@ public static void main(String... args) throws Exception {
         Dataset dataset = TDBFactory.createDataset(tdbdata);
         Main m = new Main(dataset);
         m.generate();
+        exit(0);
     }
 
     static void initLogging() {
diff --git a/java/templates/chembl-ids-beleq.st b/java/templates/chembl-ids-beleq.st
@@ -0,0 +1,31 @@
+chembl-ids-beleq(version, createdDateTime) ::= <<
+[Equivalence]
+NameString=ChEMBL
+DescriptionString=ChEMBL is a manually curated chemical database of bioactive molecules with drug-like properties
+VersionString=<version>
+CreatedDateTime=<createdDateTime>
+
+[NamespaceReference]
+NameString=ChEMBL
+VersionString=<version>
+
+[Author]
+NameString=OpenBEL
+CopyrightString=Copyright (c) 2015, OpenBEL Project. This work is licensed under a Creative Commons Attribution 3.0 Unported License.
+ContactInfoString=info@openbel.org
+
+[Citation]
+NameString=ChEMBL
+DescriptionString=ChEMBL is a manually curated chemical database of bioactive molecules with drug-like properties
+PublishedVersionString=2015-11-13
+PublishedDate=2015-11-13
+ReferenceURL=https://www.ebi.ac.uk/chembl/
+
+[Processing]
+CaseSensistiveFlag=yes
+DelimiterString=|
+CacheableFlag=yes
+
+[Values]
+
+>>
diff --git a/java/templates/chembl-ids-belns.st b/java/templates/chembl-ids-belns.st
@@ -0,0 +1,31 @@
+chembl-ids-belns(version, createdDateTime) ::= <<
+[Namespace]
+NameString=ChEMBL
+Keyword=CHEMBL
+DomainString=Chemical
+SpeciesString=all
+DescriptionString=ChEMBL is a manually curated chemical database of bioactive molecules with drug-like properties
+VersionString=<version>
+CreatedDateTime=<createdDateTime>
+QueryValueURL=https://www.ebi.ac.uk/chembl/
+
+[Author]
+NameString=OpenBEL
+CopyrightString=Copyright (c) 2015, OpenBEL Project. This work is licensed under a Creative Commons Attribution 3.0 Unported License.
+ContactInfoString=info@openbel.org
+
+[Citation]
+NameString=ChEMBL
+DescriptionString=ChEMBL is a manually curated chemical database of bioactive molecules with drug-like properties
+PublishedVersionString=2015-11-13
+PublishedDate=2015-11-13
+ReferenceURL=https://www.ebi.ac.uk/chembl/
+
+[Processing]
+CaseSensitiveFlag=yes
+DelimiterString=|
+CacheableFlag=yes
+
+[Values]
+
+>>

Original file line number	Diff line number	Diff line change
`@@ -52,7 +52,6 @@ public void generate() {`
`52`	`52`	`QuerySolutions anSchemeIter = q.annotations();`
`53`	`53`	`generate(anSchemeIter);`
`54`	`54`	`log.info("Completed Generating Annotations");`
`55`		`- exit(0);`
`56`	`55`	`}`
`57`	`56`
`58`	`57`	`void generate(QuerySolutions anSchemeIter) {`
`@@ -145,6 +144,7 @@ public static void main(String... args) throws Exception {`
`145`	`144`	`Dataset dataset = TDBFactory.createDataset(tdbdata);`
`146`	`145`	`Main m = new Main(dataset);`
`147`	`146`	`m.generate();`
	`147`	`+ exit(0);`
`148`	`148`	`}`
`149`	`149`
`150`	`150`	`static void initLogging() {`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,6 @@ public void generate() {`
`53`	`53`	`QuerySolutions nsSchemeIter = q.namespaces();`
`54`	`54`	`generate(nsSchemeIter);`
`55`	`55`	`log.info("Completed Generating Equivalences");`
`56`		`- exit(0);`
`57`	`56`	`}`
`58`	`57`
`59`	`58`	`void generate(QuerySolutions nsSchemeIter) {`
`@@ -148,6 +147,7 @@ public static void main(String... args) throws Exception {`
`148`	`147`	`Dataset dataset = TDBFactory.createDataset(tdbdata);`
`149`	`148`	`Main m = new Main(dataset);`
`150`	`149`	`m.generate();`
	`150`	`+ exit(0);`
`151`	`151`	`}`
`152`	`152`
`153`	`153`	`static void initLogging() {`