Merge pull request #470 from geneontology/status-version

Include git revision and ontology version IRI in status service.
geneontology · Mar 28, 2022 · 8b1473d · 8b1473d
2 parents 54365e5 + 230866e
commit 8b1473d
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Showing 3 changed files with 36 additions and 2 deletions.
diff --git a/minerva-server/pom.xml b/minerva-server/pom.xml
@@ -11,6 +11,26 @@
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>pl.project13.maven</groupId>
+                <artifactId>git-commit-id-plugin</artifactId>
+                <version>4.0.3</version>
+                <executions>
+                    <execution>
+                        <id>git-commit-id</id>
+                        <goals>
+                            <goal>revision</goal>
+                        </goals>
+                        <phase>validate</phase>
+                        <configuration>
+                            <skipPoms>false</skipPoms>
+                            <gitDescribe>
+                                <skip>false</skip>
+                            </gitDescribe>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>

diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java b/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java
@@ -21,7 +21,9 @@
 import org.geneontology.minerva.server.validation.MinervaShexValidator;
 import org.glassfish.jersey.server.ResourceConfig;
 import org.glassfish.jersey.servlet.ServletContainer;
+import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
 import owltools.cli.Opts;
 import owltools.gaf.eco.EcoMapperFactory;
 import owltools.gaf.eco.SimpleEcoMapper;
@@ -303,8 +305,13 @@ public static Server startUp(final MinervaStartUpConfig conf)
 
         //grab ontology metadata and store for status service
         Map<IRI, Set<OWLAnnotation>> ont_annos = new HashMap<IRI, Set<OWLAnnotation>>();
+        OWLDataFactory factory = OWLManager.getOWLDataFactory();
+        OWLAnnotationProperty versionIRI = factory.getOWLAnnotationProperty(OWLRDFVocabulary.OWL_VERSION_IRI.getIRI());
         for (OWLOntology ont : graph.getAllOntologies()) {
-            ont_annos.put(ont.getOWLOntologyManager().getOntologyDocumentIRI(ont), ont.getAnnotations());
+            Set<OWLAnnotation> maybeVersionAnnotation = ont.getOntologyID().getVersionIRI().transform(iri -> factory.getOWLAnnotation(versionIRI, iri)).asSet();
+            Set<OWLAnnotation> annotations = ont.getAnnotations();
+            annotations.addAll(maybeVersionAnnotation);
+            ont_annos.put(ont.getOWLOntologyManager().getOntologyDocumentIRI(ont), annotations);
         }
 
         OWLOntology full_tbox = forceMergeImports(graph.getSourceOntology(), graph.getAllOntologies());

diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/StatusHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/StatusHandler.java
@@ -9,6 +9,7 @@
 import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Set;
 
 
@@ -24,6 +25,7 @@ public class StatusHandler {
 
     public class Status {
         public String startup_date = started_at;
+        public String gitRevision;
         // data configuration
         public String ontology;
         public String catalog;
@@ -80,10 +82,15 @@ public Status(MinervaStartUpConfig conf) {
             this.sparqlEndpointTimeout = conf.sparqlEndpointTimeout;
             this.shexFileUrl = conf.shexFileUrl;
             this.goshapemapFileUrl = conf.goshapemapFileUrl;
-
+            this.gitRevision = getManifestVersionEntry("git-revision-sha1").orElse("UNKNOWN");
         }
     }
 
+    private static Optional<String> getManifestVersionEntry(String key) {
+        String value = owltools.version.VersionInfo.getManifestVersion(key);
+        return Optional.ofNullable(value);
+    }
+
     /**
      * @param ont_annos
      * @param started_at