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Add cli option to allow running checks against a graphstore journal. #542

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merged 2 commits into from
May 15, 2024
Merged

Add cli option to allow running checks against a graphstore journal. #542

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1a089de
Add cli option to allow running checks against a graphstore journal.
balhoff May 14, 2024
2bc3911
Merge branch 'master' into issue-541
balhoff May 14, 2024
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20 changes: 18 additions & 2 deletions minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down Expand Up @@ -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: "
Expand Down Expand Up @@ -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";
Expand Down Expand Up @@ -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
Expand Down
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