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PN-423: Matching algorithms should support hierarchical gene status #271

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PN-423: Matching algorithms should support hierarchical gene status #271

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5 changes: 5 additions & 0 deletions similarity-search/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,11 @@
<artifactId>patient-data-api</artifactId>
<version>${phenotips.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>patient-data-default-impl</artifactId>
<version>${phenotips.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>patient-similarity-data-api</artifactId>
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8 changes: 6 additions & 2 deletions ...ity-search/src/main/java/org/phenotips/similarity/internal/SolrSimilarPatientsFinder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
import org.phenotips.data.Patient;
import org.phenotips.data.PatientData;
import org.phenotips.data.PatientRepository;
import org.phenotips.data.internal.PhenoTipsGene;
import org.phenotips.data.permissions.EntityAccess;
import org.phenotips.data.permissions.EntityPermissionsManager;
import org.phenotips.data.permissions.Owner;
Expand Down Expand Up @@ -317,15 +318,18 @@ private void appendGenesToQuery(PatientData<Gene> allGenes, StringBuilder q)
geneName = geneName.trim();
String status = gene.getStatus();
// Treat empty status as candidate
if (StringUtils.isBlank(status) || "solved".equals(status) || "candidate".equals(status)) {
if (StringUtils.isBlank(status) || "solved".equals(status) || status.startsWith("candidate")) {
genesToSearch.add(geneName);
}
}
}
if (!genesToSearch.isEmpty()) {
String geneQuery = getQueryFromTerms(genesToSearch);
q.append(" solved_genes:" + geneQuery);
q.append(" candidate_genes:" + geneQuery);
List<String> statusValues = PhenoTipsGene.getStatusValues();
statusValues.stream()
.filter(item -> item.startsWith("candidate"))
.forEach(item -> q.append(" " + item + ":" + geneQuery));
}
}

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