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Merge pull request #71 from julesjacobsen/master
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Adding ability to load individuals from in-memory data as well as off-disk.
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@julesjacobsen
julesjacobsen committed Mar 20, 2017
2 parents 84ce6cb + 75bf89f commit 933184c
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Showing 14 changed files with 596 additions and 132 deletions.
71 changes: 53 additions & 18 deletions owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.function.BiConsumer;
import java.util.zip.GZIPInputStream;

/**
Expand All @@ -34,13 +35,15 @@ public class Ontology {
private final OWLOntology owlOntology;

private final OWLOntologyManager ontologyManager;
private final OWLDataFactory owlDataFactory;

private Ontology(OntologySourceData sourceData, Concurrency concurrency) {
Objects.requireNonNull(sourceData, "Unable to create Ontology without data sources.");
this.sourceData = sourceData;
this.curieUtil = new CurieUtil(sourceData.getCuries());
this.ontologyManager = createOntologyManager(concurrency);
this.owlOntology = createEmptyOntology(ontologyManager);
this.owlDataFactory = ontologyManager.getOWLDataFactory();
loadOwlOntology();
}

Expand Down Expand Up @@ -81,12 +84,29 @@ public CurieUtil getCurieUtil() {
return curieUtil;
}

/**
* @param curie
* @return
*/
public OWLClass getOWLClass(String curie) {
return owlDataFactory.getOWLClass(toIri(curie));
}

public OWLNamedIndividual getOWLNamedIndividual(String curie) {
return owlDataFactory.getOWLNamedIndividual(toIri(curie));
}

public String toCurie(IRI iri) {
String iriString = iri.toString();
return curieUtil.getCurie(iriString).orElse(iriString);
}

private void loadOwlOntology() {
//Order matters here - don't change it.
mergeOntologies(sourceData.getOntologies());
mergeOntologies(sourceData.getDataOntologies());
loadDataFromTsv(sourceData.getDataTsvs());
loadDataFromPairwiseMappings(sourceData.getPairwiseMappings());
loadIndividualAssociationsFromTsv(sourceData.getIndividualAssociationTsvs());
loadIndividualAssociationsFromMap(sourceData.getIndividualAssociations());
logger.info("Ontology loaded");
}

Expand Down Expand Up @@ -118,10 +138,6 @@ private OWLOntology mergeOntologies(Collection<String> uris) {
return owlOntology;
}

private ChangeApplied addAxiom(OWLAxiom axiom) {
return ontologyManager.addAxiom(owlOntology, axiom);
}

private ChangeApplied addAxioms(Set<OWLAxiom> axioms) {
return ontologyManager.addAxioms(owlOntology, axioms);
}
Expand Down Expand Up @@ -159,12 +175,12 @@ private OWLOntology loadOwlOntology(IRI iri) {
}
}

private OWLOntology loadDataFromTsv(Collection<String> paths) {
paths.forEach(this::loadDataFromTsv);
private OWLOntology loadIndividualAssociationsFromTsv(Collection<String> paths) {
paths.forEach(this::loadIndividualAssociationsFromTsv);
return owlOntology;
}

private OWLOntology loadDataFromTsv(String path) {
private OWLOntology loadIndividualAssociationsFromTsv(String path) {
if (path.endsWith(".gz")) {
return loadDataFromTsvGzip(path);
}
Expand All @@ -191,8 +207,20 @@ private OWLOntology loadDataFromTsvGzip(String path) {
return owlOntology;
}

private void loadDataFromPairwiseMappings(Map<String, String> pairwiseMappings) {
pairwiseMappings.forEach(this::addInstanceOf);
private void loadIndividualAssociationsFromMap(Map<String, Collection<String>> individuals) {
if(!individuals.isEmpty()){
logger.info("Loading individuals from map");
}
//e.g. 'ORPHA:710': ['HP:0000194','HP:0000218','HP:0000262','HP:0000303','HP:0000316']
individuals.forEach(addIndividual());
}

private BiConsumer<String, Collection<String>> addIndividual() {
return (individual, annotations) -> {
for (String curie : annotations) {
addInstanceOf(individual, curie);
}
};
}

private void loadLineIntoDataOntology(String line) {
Expand All @@ -204,15 +232,22 @@ private void loadLineIntoDataOntology(String line) {
}

private void addInstanceOf(String individual, String ontologyClass) {
// logger.info("Adding axiom " + individual + ": " + ontologyClass);
OWLDataFactory owlDataFactory = ontologyManager.getOWLDataFactory();
OWLClass owlClass = owlDataFactory.getOWLClass(toIri(ontologyClass));
OWLNamedIndividual owlNamedIndividual = owlDataFactory.getOWLNamedIndividual(toIri(individual));
OWLClassAssertionAxiom axiom = owlDataFactory.getOWLClassAssertionAxiom(owlClass, owlNamedIndividual);
addAxiom(axiom);
Objects.requireNonNull(individual, "Individual identifier cannot be null. Check your input.");
Objects.requireNonNull(ontologyClass, "Class identifier(s) cannot be null. Check your input.");
if (!ontologyClass.isEmpty()) {
// logger.info("Adding axiom " + individual + ": " + ontologyClass);
OWLClass owlClass = getOWLClass(ontologyClass);
OWLNamedIndividual owlNamedIndividual = getOWLNamedIndividual(individual);
OWLClassAssertionAxiom axiom = owlDataFactory.getOWLClassAssertionAxiom(owlClass, owlNamedIndividual);
addAxiom(axiom);
}
}

private ChangeApplied addAxiom(OWLAxiom axiom) {
return ontologyManager.addAxiom(owlOntology, axiom);
}

private IRI toIri(String id) {
IRI toIri(String id) {
return IRI.create(curieUtil.getIri(id).orElse(id));
}

Expand Down
57 changes: 31 additions & 26 deletions owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,16 +20,16 @@ public class OntologySourceData {
private final List<String> dataOntologies;

private final Map<String, String> curies;
private final List<String> dataTsvs;
//TODO: add these so people can programmatically add individual assertions
private final Map<String, String> pairwiseMappings;
private final List<String> individualAssociationTsvs;
private final Map<String, Collection<String>> individualAssociations;
//TODO - labels?

private OntologySourceData(Builder builder) {
this.ontologies = distinctImmutableListOf(builder.ontologies);
this.dataOntologies = distinctImmutableListOf(builder.dataOntologies);
this.curies = ImmutableMap.copyOf(builder.curies);
this.dataTsvs = distinctImmutableListOf(builder.dataTsvs);
this.pairwiseMappings = ImmutableMap.copyOf(builder.pairwiseMappings);
this.individualAssociationTsvs = distinctImmutableListOf(builder.individualAssociationTsvs);
this.individualAssociations = ImmutableMap.copyOf(builder.individualAssociations);
}

private ImmutableList<String> distinctImmutableListOf(List<String> list) {
Expand All @@ -48,12 +48,12 @@ public Map<String, String> getCuries() {
return curies;
}

public List<String> getDataTsvs() {
return dataTsvs;
public List<String> getIndividualAssociationTsvs() {
return individualAssociationTsvs;
}

public Map<String, String> getPairwiseMappings() {
return pairwiseMappings;
public Map<String, Collection<String>> getIndividualAssociations() {
return individualAssociations;
}

@Override
Expand All @@ -64,13 +64,13 @@ public boolean equals(Object o) {
return Objects.equals(ontologies, that.ontologies) &&
Objects.equals(dataOntologies, that.dataOntologies) &&
Objects.equals(curies, that.curies) &&
Objects.equals(dataTsvs, that.dataTsvs) &&
Objects.equals(pairwiseMappings, that.pairwiseMappings);
Objects.equals(individualAssociationTsvs, that.individualAssociationTsvs) &&
Objects.equals(individualAssociations, that.individualAssociations);
}

@Override
public int hashCode() {
return Objects.hash(ontologies, dataOntologies, curies, dataTsvs, pairwiseMappings);
return Objects.hash(ontologies, dataOntologies, curies, individualAssociationTsvs, individualAssociations);
}

@Override
Expand All @@ -79,8 +79,8 @@ public String toString() {
"ontologies=" + ontologies +
", dataOntologies=" + dataOntologies +
", curies=" + curies +
", dataTsvs=" + dataTsvs +
", pairwiseMappings=" + pairwiseMappings +
", individualAssociationTsvs=" + individualAssociationTsvs +
", individualAssociations=" + individualAssociations +
'}';
}

Expand All @@ -93,8 +93,8 @@ public static class Builder {
private List<String> dataOntologies = new ArrayList<>();
//Curies need to be supplied if people are adding data using TSV files or pairwise mappings using curies.
private Map<String, String> curies = Collections.emptyMap();
private List<String> dataTsvs = new ArrayList<>();
private Map<String, String> pairwiseMappings = Collections.emptyMap();
private List<String> individualAssociationTsvs = new ArrayList<>();
private Map<String, Collection<String>> individualAssociations = new HashMap<>();

private Builder(){
//use the static method.
Expand Down Expand Up @@ -161,33 +161,38 @@ public Builder dataOntologies(Collection<String> paths) {
return this;
}

public Builder dataTsv(String path) {
dataTsvs.add(path);
public Builder individualAssociationsTsv(String path) {
individualAssociationTsvs.add(path);
return this;
}

public Builder dataTsv(String... paths) {
dataTsvs.addAll(Arrays.asList(paths));
public Builder individualAssociationsTsv(String... paths) {
individualAssociationTsvs.addAll(Arrays.asList(paths));
return this;
}

public Builder dataTsv(Collection<String> paths) {
dataTsvs.addAll(paths);
public Builder individualAssociationsTsv(Collection<String> paths) {
individualAssociationTsvs.addAll(paths);
return this;
}

public Builder individualAssociations(Map<String, ? extends Collection<String>> mappings) {
individualAssociations.putAll(mappings);
return this;
}

public OntologySourceData build() {
if(ontologies.isEmpty()) {
throw new OntologyLoadException("No ontology defined.");
}
if (curies.isEmpty() && hasNonOntologyData()) {
throw new OntologyLoadException("Cannot load TSV data sources or pairwise mappings when curies have not been defined.");
if (curies.isEmpty() && hasIndividualAssociationData()) {
throw new OntologyLoadException("Cannot load individual class associations when curies have not been defined.");
}
return new OntologySourceData(this);
}

private boolean hasNonOntologyData() {
return !dataTsvs.isEmpty() || !pairwiseMappings.isEmpty();
private boolean hasIndividualAssociationData() {
return !individualAssociationTsvs.isEmpty() || !individualAssociations.isEmpty();
}
}
}
18 changes: 11 additions & 7 deletions owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,6 @@ public Loader loadCuries(Map<String, String> curies) {
* @param file
*/
public Loader loadOntology(File file) {
Math.random();
sourceDataBuilder.ontology(file);
return this;
}
Expand Down Expand Up @@ -103,18 +102,23 @@ public Loader loadDataFromOntologies(Collection<String> paths) {
return this;
}

public Loader loadDataFromTsv(String path) {
sourceDataBuilder.dataTsv(path);
public Loader loadIndividualAssociationsFromTsv(String path) {
sourceDataBuilder.individualAssociationsTsv(path);
return this;
}

public Loader loadDataFromTsv(String... paths) {
sourceDataBuilder.dataTsv(paths);
public Loader loadIndividualAssociationsFromTsv(String... paths) {
sourceDataBuilder.individualAssociationsTsv(paths);
return this;
}

public Loader loadDataFromTsv(Collection<String> paths) {
sourceDataBuilder.dataTsv(paths);
public Loader loadIndividualAssociationsFromTsv(Collection<String> paths) {
sourceDataBuilder.individualAssociationsTsv(paths);
return this;
}

public Loader loadIndividualAssociations(Map<String, ? extends Collection<String>> data) {
sourceDataBuilder.individualAssociations(data);
return this;
}

Expand Down
12 changes: 7 additions & 5 deletions owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
package org.monarchinitiative.owlsim.kb;

import java.util.Map;
import java.util.Set;

import com.googlecode.javaewah.EWAHCompressedBitmap;
import org.monarchinitiative.owlsim.io.OwlKnowledgeBase;
import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
import org.monarchinitiative.owlsim.model.kb.Attribute;
import org.monarchinitiative.owlsim.model.kb.Entity;

import com.googlecode.javaewah.EWAHCompressedBitmap;
import java.util.Map;
import java.util.Set;

/**
* An interface to an ontology in which the fundamental unit of representation of
Expand Down Expand Up @@ -351,7 +351,9 @@ public interface BMKnowledgeBase {
public int getRootIndex();



public static OwlKnowledgeBase.Loader owlLoader() {
return OwlKnowledgeBase.loader();
}



Expand Down
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