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Merge pull request #501 from geneontology/issue-500
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Add command to dump models to JSON files.
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@kltm
kltm authored Sep 28, 2022
2 parents f01b5af + 6c0b6ae commit bce7e99
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Showing 2 changed files with 112 additions and 5 deletions.
115 changes: 111 additions & 4 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 @@ -28,6 +28,7 @@
import org.geneontology.minerva.model.GoCamModel;
import org.geneontology.minerva.model.GoCamModelStats;
import org.geneontology.minerva.server.StartUpTool;
import org.geneontology.minerva.server.handler.OperationsTools;
import org.geneontology.minerva.server.inferences.InferenceProviderCreator;
import org.geneontology.minerva.server.validation.MinervaShexValidator;
import org.geneontology.minerva.util.BlazegraphMutationCounter;
Expand All @@ -37,12 +38,16 @@
import org.geneontology.minerva.validation.pipeline.BatchPipelineValidationReport;
import org.geneontology.minerva.validation.pipeline.ErrorMessage;
import org.obolibrary.robot.CatalogXmlIRIMapper;
import org.openrdf.model.Statement;
import org.openrdf.model.ValueFactory;
import org.openrdf.model.impl.URIImpl;
import org.openrdf.model.vocabulary.OWL;
import org.openrdf.model.vocabulary.RDF;
import org.openrdf.query.MalformedQueryException;
import org.openrdf.query.QueryLanguage;
import org.openrdf.query.UpdateExecutionException;
import org.openrdf.repository.RepositoryException;
import org.openrdf.rio.RDFHandlerException;
import org.openrdf.rio.RDFParseException;
import org.openrdf.rio.*;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
import org.semanticweb.owlapi.io.IRIDocumentSource;
Expand All @@ -62,6 +67,8 @@
import java.nio.file.Paths;
import java.util.*;

import static org.geneontology.minerva.server.handler.OperationsTools.createModelRenderer;


public class CommandLineInterface {
private static final Logger LOGGER = Logger.getLogger(CommandLineInterface.class);
Expand All @@ -72,6 +79,12 @@ public static void main(String[] args) {
Options main_options = new Options();
OptionGroup methods = new OptionGroup();
methods.setRequired(true);
Option dumpJSON = Option.builder()
.longOpt("dump-owl-json")
.desc("export JSON format GO-CAM models from journal")
.hasArg(false)
.build();
methods.addOption(dumpJSON);
Option dump = Option.builder()
.longOpt("dump-owl-models")
.desc("export OWL GO-CAM models from journal")
Expand Down Expand Up @@ -210,6 +223,21 @@ public static void main(String[] args) {
String outputFolder = cmd.getOptionValue("f"); //--folder
String modelIdPrefix = cmd.getOptionValue("p"); //--prefix
modelsToOWL(journalFilePath, outputFolder, modelIdPrefix);
} else if (cmd.hasOption("dump-owl-json")) {
Options jsonDumpOptions = new Options();
jsonDumpOptions.addOption(dumpJSON);
jsonDumpOptions.addOption("j", "journal", true, "Sets the Blazegraph journal file for the database");
jsonDumpOptions.addOption("ontojournal", "ontojournal", true, "Specify a blazegraph journal file containing the merged, pre-reasoned tbox aka go-lego.owl");
jsonDumpOptions.addOption("f", "folder", true, "Sets the output folder the GO-CAM model files");
jsonDumpOptions.addOption("p", "model-id-prefix", true, "prefix for GO-CAM model ids");
jsonDumpOptions.addOption("prefixes", "prefixes", true, "Prefix mappings file");
cmd = parser.parse(jsonDumpOptions, args, false);
String journalFilePath = cmd.getOptionValue("j"); //--journal
String ontojournalFilePath = cmd.getOptionValue("ontojournal");
String outputFolder = cmd.getOptionValue("f"); //--folder
String modelIdPrefix = cmd.getOptionValue("p"); //--prefix
String prefixMappingsFileLoc = cmd.getOptionValue("prefixes");
modelsToJSON(journalFilePath, ontojournalFilePath, outputFolder, modelIdPrefix, prefixMappingsFileLoc);
} else if (cmd.hasOption("import-owl-models")) {
Options import_options = new Options();
import_options.addOption(import_owl);
Expand Down Expand Up @@ -423,6 +451,85 @@ public static void modelsToOWL(String journalFilePath, String outputFolder, Stri
m3.dispose();
}

/**
* Given a blazegraph journal with go-cams in it, write them all out as JSON files.
* cli --dump-owl-json
*
* @param journalFilePath
* @param outputFolder
* @param modelIdPrefix
* @throws Exception
*/
public static void modelsToJSON(String journalFilePath, String ontojournalFilePath, String outputFolder, String modelIdPrefix, String prefixMappingsFilePath) throws Exception {
final String idPrefix;
if (modelIdPrefix == null) {
idPrefix = "http://model.geneontology.org/";
} else {
idPrefix = modelIdPrefix;
}
// minimal inputs
if (journalFilePath == null) {
System.err.println("No journal file was configured.");
System.exit(-1);
return;
}
if (ontojournalFilePath == null) {
System.err.println("No ontology journal file was configured.");
System.exit(-1);
return;
}
if (outputFolder == null) {
System.err.println("No output folder was configured.");
System.exit(-1);
return;
}
final CurieMappings mappings;
if (prefixMappingsFilePath != null) {
mappings = DefaultCurieHandler.loadMappingsFromFile(new File(prefixMappingsFilePath));
} else {
mappings = DefaultCurieHandler.loadDefaultMappings();
}
CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap("gomodel", idPrefix));
CurieHandler curieHandler = new MappedCurieHandler(mappings, localMappings);
OWLOntology dummy = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://example.org/dummy"));
BlazegraphMolecularModelManager<Void> m3 = new BlazegraphMolecularModelManager<>(dummy, curieHandler, idPrefix, journalFilePath, outputFolder, ontojournalFilePath, true);
InferenceProvider inferenceProvider = null;
Gson gson = new Gson();
FileUtils.forceMkdir(new File(outputFolder));
m3.getStoredModelIds().forEach(iri -> {
ModelContainer mc = m3.getModel(iri);
final MolecularModelJsonRenderer renderer = OperationsTools.createModelRenderer(mc, m3.getGolego_repo(), inferenceProvider, curieHandler, m3.getTboxLabelIndex());
JsonModel jsonModel = renderer.renderModel();
String fileName = StringUtils.replaceOnce(iri.toString(), idPrefix, "") + ".json";
File targetFile = new File(outputFolder, fileName).getAbsoluteFile();
if (targetFile.exists()) {
if (!targetFile.isFile()) {
throw new RuntimeException(new IOException("For modelId: '" + iri + "', the resulting path is not a file: " + targetFile.getAbsolutePath()));
}
if (!targetFile.canWrite()) {
throw new RuntimeException(new IOException("For modelId: '" + iri + "', Cannot write to the file: " + targetFile.getAbsolutePath()));
}
}
File tempFile = null;
try {
// create tempFile
String prefix = iri.toString(); // TODO escape
tempFile = File.createTempFile(prefix, ".json");
try (FileWriter writer = new FileWriter(tempFile)) {
gson.toJson(jsonModel, writer);
}
FileUtils.copyFile(tempFile, targetFile);
} catch (IOException e) {
throw new RuntimeException(e);
} finally {
// delete temp file
FileUtils.deleteQuietly(tempFile);
}
m3.unlinkModel(iri);
});
m3.dispose();
}

/**
* Load the go-cam files in the input folder into the journal
* cli import-owl-models
Expand Down Expand Up @@ -852,7 +959,7 @@ public static void validateGoCams(String input, String outputFolder,
modelid_filename.put(modeluri, file.getName());
}
} catch (OWLOntologyCreationException | RepositoryException | RDFParseException
| RDFHandlerException | IOException e) {
| RDFHandlerException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
Expand All @@ -863,7 +970,7 @@ public static void validateGoCams(String input, String outputFolder,
try {
m3.importModelToDatabase(i, true);
} catch (OWLOntologyCreationException | RepositoryException | RDFParseException
| RDFHandlerException | IOException e) {
| RDFHandlerException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
Expand Down
2 changes: 1 addition & 1 deletion minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsTools.java
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ static MolecularModelJsonRenderer createModelRenderer(
}

//BlazegraphOntologyManager
static MolecularModelJsonRenderer createModelRenderer(
public static MolecularModelJsonRenderer createModelRenderer(
final ModelContainer model,
final BlazegraphOntologyManager go_lego_repo,
final InferenceProvider inferenceProvider,
Expand Down

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