Issue #25: Convert all incoming gene IDs to the same naming scheme we…

… use in PhenoTips internally. Fixed.
phenotips · Aug 25, 2015 · 2fc4117 · 2fc4117
1 parent e36277a
commit 2fc4117
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Showing 4 changed files with 44 additions and 8 deletions.
diff --git a/...ient/src/main/java/org/phenotips/remote/client/internal/DefaultRemoteMatchingService.java b/...ient/src/main/java/org/phenotips/remote/client/internal/DefaultRemoteMatchingService.java
@@ -54,6 +54,7 @@
 import org.phenotips.remote.common.internal.api.DefaultJSONToMatchingPatientConverter;
 import org.phenotips.remote.hibernate.RemoteMatchingStorageManager;
 import org.phenotips.remote.hibernate.internal.DefaultOutgoingMatchRequest;
+import org.phenotips.vocabulary.Vocabulary;
 import org.slf4j.Logger;
 import org.xwiki.component.annotation.Component;
 import org.xwiki.context.Execution;
@@ -84,6 +85,10 @@ public class DefaultRemoteMatchingService implements RemoteMatchingService
     @Named("match")
     protected AccessLevel matchAccess;
 
+    @Inject
+    @Named("hgnc")
+    private Vocabulary ontologyService;
+
     @Inject
     PatientRepository patientRepository;
 
@@ -229,7 +234,7 @@ public List<PatientSimilarityView> getSimilarityResults(OutgoingMatchRequest req
         }
 
         DefaultJSONToMatchingPatientConverter patientConverter =
-                new DefaultJSONToMatchingPatientConverter(ApiConfiguration.LATEST_API_VERSION_STRING, logger);
+                new DefaultJSONToMatchingPatientConverter(ApiConfiguration.LATEST_API_VERSION_STRING, logger, ontologyService);
 
         //JSONArray processedResults = new JSONArray();
 

diff --git a/...mon/src/main/java/org/phenotips/remote/common/internal/api/DefaultIncomingJSONParser.java b/...mon/src/main/java/org/phenotips/remote/common/internal/api/DefaultIncomingJSONParser.java
@@ -24,7 +24,7 @@
 import org.phenotips.remote.api.fromjson.IncomingJSONParser;
 import org.phenotips.remote.api.fromjson.JSONToMatchingPatientConverter;
 import org.phenotips.remote.hibernate.internal.DefaultIncomingMatchRequest;
-
+import org.phenotips.vocabulary.Vocabulary;
 import org.slf4j.Logger;
 
 import net.sf.json.JSONObject;
@@ -40,12 +40,12 @@ public class DefaultIncomingJSONParser implements IncomingJSONParser
 
     private final String apiVersion;
 
-    public DefaultIncomingJSONParser(String apiVersion, Logger logger)
+    public DefaultIncomingJSONParser(String apiVersion, Logger logger, Vocabulary ontologyService)
     {
         this.apiVersion = apiVersion;
         this.logger     = logger;
 
-        this.patientConverter = new DefaultJSONToMatchingPatientConverter(apiVersion, logger);
+        this.patientConverter = new DefaultJSONToMatchingPatientConverter(apiVersion, logger, ontologyService);
     }
 
     @Override

diff --git a/.../java/org/phenotips/remote/common/internal/api/DefaultJSONToMatchingPatientConverter.java b/.../java/org/phenotips/remote/common/internal/api/DefaultJSONToMatchingPatientConverter.java
@@ -30,12 +30,17 @@
 import org.phenotips.remote.common.internal.RemotePatientFeature;
 import org.phenotips.remote.common.internal.RemotePatientGene;
 import org.phenotips.remote.common.internal.RemotePatientContactInfo;
+import org.phenotips.vocabulary.Vocabulary;
+import org.phenotips.vocabulary.VocabularyTerm;
 import org.slf4j.Logger;
 
 import java.util.HashSet;
 import java.util.Set;
 import java.util.regex.Pattern;
 
+import javax.inject.Inject;
+import javax.inject.Named;
+
 import net.sf.json.JSONArray;
 import net.sf.json.JSONObject;
 
@@ -48,10 +53,13 @@ public class DefaultJSONToMatchingPatientConverter implements JSONToMatchingPati
     private final Pattern hpoTerm; // not static: may be different from api version to api version
     private final Pattern disorderTerm;
 
-    public DefaultJSONToMatchingPatientConverter(String apiVersion, Logger logger)
+    private final Vocabulary ontologyService;
+
+    public DefaultJSONToMatchingPatientConverter(String apiVersion, Logger logger, Vocabulary ontologyService)
     {
         this.apiVersion = apiVersion;
-        this.logger     = logger;
+        this.logger = logger;
+        this.ontologyService = ontologyService;
 
         this.hpoTerm      = Pattern.compile("^HP:\\d+$");
         this.disorderTerm = Pattern.compile("^MIM:\\d+$");  // TODO: Orphanet:#####
@@ -172,12 +180,29 @@ private Set<MatchingPatientGene> convertGenes(JSONObject json)
                         throw new ApiViolationException("A gene has no id");
                     }
                     // TODO: check if name is a valid gene symbol or ensembl id
-                    MatchingPatientGene gene = new RemotePatientGene(geneName);
+                    VocabularyTerm geneTerm = this.ontologyService.getTerm(geneName);
+                    if (geneTerm == null) {
+                        logger.error("Patient genomic features parser: gene id [{}] was not found in the vocabulary", geneName);
+                        throw new ApiViolationException("A gene has unsupported id [" + geneName + "]");
+                    }
+                    String symbol;
+                    try {
+                        symbol = (String)(geneTerm.get("symbol"));
+                        if (!geneName.equals(symbol)) {
+                            this.logger.debug("Converted incoming gene id [{}] to symbol [{}]", geneName, symbol);
+                        }
+                    } catch (Exception ex) {
+                        logger.error("Patient genomic features parser: can not obtain gene symbol for gene ID [{}]", geneName);
+                        throw new ApiViolationException("Internal error processing gene id [" + geneName + "]");
+                    }
+                    MatchingPatientGene gene = new RemotePatientGene(symbol);
                     geneSet.add(gene);
                     // TODO: variants
                 }
                 return geneSet;
             }
+        } catch (ApiViolationException ex) {
+            throw ex;
         } catch (Exception ex) {
             this.logger.error("Error converting genes: {}", ex);
         }

diff --git a/.../common/src/main/java/org/phenotips/remote/common/internal/api/v1/ApiDataConverterV1.java b/.../common/src/main/java/org/phenotips/remote/common/internal/api/v1/ApiDataConverterV1.java
@@ -34,6 +34,7 @@
 import org.phenotips.remote.api.fromjson.IncomingJSONParser;
 import org.phenotips.remote.api.tojson.OutgoingJSONGenerator;
 import org.phenotips.remote.api.tojson.PatientToJSONConverter;
+import org.phenotips.vocabulary.Vocabulary;
 import org.xwiki.security.authorization.AuthorizationManager;
 import org.xwiki.bridge.DocumentAccessBridge;
 import org.slf4j.Logger;
@@ -72,9 +73,14 @@ public class ApiDataConverterV1 implements ApiDataConverter, Initializable
     @Inject
     private DocumentAccessBridge bridge;
 
+    /** Used for converting gene ID between different id schemas */
+    @Inject
+    @Named("hgnc")
+    private Vocabulary ontologyService;
+
     public void initialize()
     {
-        incomingJSONParser = new DefaultIncomingJSONParser(getApiVersion(), logger);
+        incomingJSONParser = new DefaultIncomingJSONParser(getApiVersion(), logger, ontologyService);
 
         patientToJSONConverter = new DefaultPatientToJSONConverter(getApiVersion(), logger);