Add cli option to allow running checks against a graphstore journal.

geneontology · May 14, 2024 · 1a089de · 1a089de
1 parent f66b4bb
commit 1a089de
Showing 1 changed file with 18 additions and 2 deletions.
diff --git a/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java b/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java
@@ -358,6 +358,7 @@ public static void main(String[] args) {
                 validate_options.addOption("s", "shexpath", true, "Specify a shex schema file.  Otherwise will download from go_shapes repo.");
                 validate_options.addOption("ontojournal", "ontojournal", true, "Specify a blazegraph journal file containing the merged, pre-reasoned tbox aka go-lego.owl");
                 validate_options.addOption("reasoner_report", "reasoner_report", false, "Add a report with reasoning results to the output of the validation. ");
+                validate_options.addOption("graph", "check-graph-type", false, "Run the checks agains a GO graphstore journal; check only graphs with graphType noctuaCam.");
 
 
                 cmd = parser.parse(validate_options, args, false);
@@ -403,7 +404,11 @@ public static void main(String[] args) {
                 if (cmd.hasOption("reasoner_report")) {
                     run_reasoner_report = true;
                 }
-                validateGoCams(input, outputFolder, ontologyIRI, catalog, modelIdPrefix, modelIdcurie, shexpath, shapemappath, travisMode, shouldFail, checkShex, go_lego_journal_file, run_reasoner_report);
+                boolean checkGraphType = false;
+                if (cmd.hasOption("check-graph-type")) {
+                    checkGraphType = true;
+                }
+                validateGoCams(input, outputFolder, ontologyIRI, catalog, modelIdPrefix, modelIdcurie, shexpath, shapemappath, travisMode, shouldFail, checkShex, go_lego_journal_file, run_reasoner_report, checkGraphType);
             }
         } catch (ParseException exp) {
             System.out.println("Parameter parse exception.  Note that the first parameter must be one of: "
@@ -881,7 +886,7 @@ public static void legoToAnnotationsSPARQL(String modelIdPrefix, String modelIdc
     public static void validateGoCams(String input, String outputFolder,
                                       String ontologyIRI, String catalog, String modelIdPrefix, String modelIdcurie,
                                       String shexpath, String shapemappath, boolean travisMode, boolean shouldFail, boolean checkShex,
-                                      String go_lego_journal_file, boolean run_reasoner_report) throws OWLOntologyCreationException, IOException {
+                                      String go_lego_journal_file, boolean run_reasoner_report, boolean checkGraphType) throws OWLOntologyCreationException, IOException {
         LOGGER.setLevel(Level.INFO);
         String inputDB = "blazegraph.jnl";
         String shexFileUrl = "https://raw.githubusercontent.com/geneontology/go-shapes/master/shapes/go-cam-shapes.shex";
@@ -1092,6 +1097,17 @@ public static void validateGoCams(String input, String outputFolder,
                 //this is where everything actually happens
                 ModelContainer mc = m3.getModel(modelIRI);
                 OWLOntology gocam = mc.getAboxOntology();
+                final IRI graphType = IRI.create("http://model.geneontology.org/graphType");
+                final IRI noctuaCam = IRI.create("http://model.geneontology.org/noctuaCam");
+                if (checkGraphType) {
+                    if (gocam.getAnnotations().stream().noneMatch(annotation ->
+                            annotation.getProperty().getIRI().equals(graphType)
+                                    && annotation.getValue().isIRI()
+                                    && annotation.getValue().equals(noctuaCam))) {
+                        System.out.println("SKIPPING: " + modelIRI);
+                        continue;
+                    }
+                }
                 try {
                     //if a model does not have an import statement that links in an ontology that defines all of its classes and object properties
                     //or if the model does not define the classes and object properties itself, parsing problems will prevail