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WIP: Early draft owlet query expansion #1139

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904df79
First draft owlet query expansion
matentzn Aug 6, 2023
6324064
Update robot-core/pom.xml
matentzn Aug 8, 2023
fe00192
Update robot-core/pom.xml
matentzn Aug 8, 2023
b543ba7
Update pom.xml
matentzn Aug 8, 2023
b8734f4
add dl query command
matentzn Aug 8, 2023
5a42a6f
add comment to owlet expand query string
matentzn Aug 8, 2023
5a02b4e
Update to Owlet 2.0.0. Upgrade Jena, add jackson-databind dependency …
balhoff Sep 9, 2023
d269e86
Reformat.
balhoff Sep 9, 2023
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27 changes: 24 additions & 3 deletions robot-command/src/main/java/org/obolibrary/robot/QueryCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,10 @@
import org.apache.jena.query.Dataset;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.tdb.TDBFactory;
import org.phenoscape.owlet.Owlet;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -239,14 +242,27 @@ private static void executeInMemory(
CommandLine line, OWLOntology inputOntology, List<List<String>> queries) throws Exception {
boolean useGraphs = CommandLineHelper.getBooleanValue(line, "use-graphs", false);
Dataset dataset = QueryOperation.loadOntologyAsDataset(inputOntology, useGraphs);
boolean useOwlet = CommandLineHelper.getBooleanValue(line, "owlet", false);

Owlet owlet = getOwlet(line, inputOntology, useOwlet);
try {
runQueries(line, dataset, queries);
runQueries(line, dataset, queries, owlet);
} finally {
dataset.close();
// TDBFactory.release(dataset);
}
}

private static Owlet getOwlet(CommandLine line, OWLOntology inputOntology, boolean useOwlet) {
Owlet owlet = null;
if(useOwlet) {
OWLReasonerFactory rf = CommandLineHelper.getReasonerFactory(line);
OWLReasoner r = rf.createReasoner(inputOntology);
owlet = new Owlet(r);
}
return owlet;
}

/**
* Given a command line and a list of queries, execute 'query' using TDB and writing mappings to
* disk.
Expand All @@ -260,8 +276,9 @@ private static void executeOnDisk(CommandLine line, List<List<String>> queries)
Dataset dataset = createTDBDataset(line);
boolean keepMappings = CommandLineHelper.getBooleanValue(line, "keep-tdb-mappings", false);
String tdbDir = CommandLineHelper.getDefaultValue(line, "tdb-directory", ".tdb");

try {
runQueries(line, dataset, queries);
runQueries(line, dataset, queries, null);
} finally {
dataset.close();
TDBFactory.release(dataset);
Expand Down Expand Up @@ -396,7 +413,7 @@ private static List<List<String>> getQueries(CommandLine line) {
* @param queries List of queries
* @throws IOException on issue reading or writing files
*/
private static void runQueries(CommandLine line, Dataset dataset, List<List<String>> queries)
private static void runQueries(CommandLine line, Dataset dataset, List<List<String>> queries, Owlet owlet)
throws IOException {
String format = CommandLineHelper.getOptionalValue(line, "format");
String outputDir = CommandLineHelper.getDefaultValue(line, "output-dir", "");
Expand All @@ -406,6 +423,10 @@ private static void runQueries(CommandLine line, Dataset dataset, List<List<Stri
String outputPath = q.get(1);

String query = FileUtils.readFileToString(new File(queryPath), Charset.defaultCharset());

if(owlet != null) {
query = owlet.expandQueryString(query, false);
}

String formatName = format;
if (formatName == null) {
Expand Down
20 changes: 18 additions & 2 deletions robot-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>3.17.0</version>
<version>4.9.0</version>
<exclusions>
<exclusion>
<groupId>com.github.jsonld-java</groupId>
Expand All @@ -134,7 +134,7 @@
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-tdb</artifactId>
<version>3.17.0</version>
<version>4.9.0</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
Expand Down Expand Up @@ -288,6 +288,22 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>4.9.0</version>
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</dependency>
<dependency>
<groupId>org.phenoscape</groupId>
<artifactId>owlet_2.13</artifactId>
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<version>1.9</version>
<exclusions>
<exclusion>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
Expand Down