Merge pull request #8 from icgc-argo/RC/1.0.1

RC/1.0.1
icgc-argo · Jun 18, 2020 · d5f3390 · d5f3390
2 parents 8fb37d8 + 336f8e4
commit d5f3390
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Showing 8 changed files with 14 additions and 17 deletions.
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>bio.overture</groupId>
     <artifactId>song-search</artifactId>
-    <version>1.0.0</version>
+    <version>1.0.1</version>
     <name>song-search</name>
     <description>GQL microservice for searching maestro generated song indexes</description>
 

diff --git a/src/main/java/bio/overture/songsearch/config/SearchFields.java b/src/main/java/bio/overture/songsearch/config/SearchFields.java
@@ -18,5 +18,5 @@ public class SearchFields {
   public static final String DONOR_ID = "donorId";
   public static final String SPECIMEN_ID = "specimenId";
   public static final String SAMPLE_ID = "sampleId";
-  public static final String RUN_NAME = "runName";
+  public static final String RUN_ID = "runId";
 }
diff --git a/src/main/java/bio/overture/songsearch/graphql/EntityDataFetcher.java b/src/main/java/bio/overture/songsearch/graphql/EntityDataFetcher.java
@@ -48,11 +48,11 @@ public DataFetcher getDataFetcher() {
                     }
                   }
                   if (RUN_ENTITY.equals(values.get("__typename"))) {
-                    final Object runName = values.get("runName");
-                    if (runName instanceof String) {
+                    final Object runId = values.get("runName"); // todo: will become runId after reindex
+                    if (runId instanceof String) {
                       return new Run(
-                          (String) runName,
-                          analysisService.getAnalysesByRunName((String) runName),
+                          (String) runId,
+                          analysisService.getAnalysesByRunId((String) runId),
                           "Not Implemented!");
                     }
                   }

diff --git a/src/main/java/bio/overture/songsearch/model/Run.java b/src/main/java/bio/overture/songsearch/model/Run.java
@@ -19,7 +19,7 @@
 public class Run {
     private static final ObjectMapper MAPPER = new ObjectMapper();
 
-    private String runName;
+    private String runName; // todo: will become runId after reindex
 
     private List<Analysis> producedAnalyses;
 

diff --git a/src/main/java/bio/overture/songsearch/model/Workflow.java b/src/main/java/bio/overture/songsearch/model/Workflow.java
@@ -17,8 +17,6 @@
 public class Workflow {
     private static final ObjectMapper MAPPER = new ObjectMapper();
 
-    private String runName;
-
     private String runId;
 
     private String workflowName;

diff --git a/src/main/java/bio/overture/songsearch/repository/AnalysisRepository.java b/src/main/java/bio/overture/songsearch/repository/AnalysisRepository.java
@@ -49,7 +49,7 @@ private static Map<String, Function<String, AbstractQueryBuilder<?>>> argumentPa
         .put(ANALYSIS_VERSION, value -> new TermQueryBuilder("analysis_version", value))
         .put(ANALYSIS_STATE, value -> new TermQueryBuilder("analysis_state", value))
         .put(STUDY_ID, value -> new TermQueryBuilder("study_id", value))
-        .put(RUN_NAME, value -> new TermQueryBuilder("workflow.run_id", value)) // TODO: change to run_name after migration
+        .put(RUN_ID, value -> new TermQueryBuilder("workflow.run_id", value))
         .put(
             DONOR_ID,
             value ->

diff --git a/src/main/java/bio/overture/songsearch/service/AnalysisService.java b/src/main/java/bio/overture/songsearch/service/AnalysisService.java
@@ -12,7 +12,7 @@
 import java.util.Map;
 
 import static bio.overture.songsearch.config.SearchFields.ANALYSIS_ID;
-import static bio.overture.songsearch.config.SearchFields.RUN_NAME;
+import static bio.overture.songsearch.config.SearchFields.RUN_ID;
 import static java.util.stream.Collectors.toUnmodifiableList;
 
 @Service
@@ -43,8 +43,8 @@ public Analysis getAnalysisById(String analysisId) {
     return runOpt.orElse(null);
   }
 
-  public List<Analysis> getAnalysesByRunName(String runName) {
-    val response = analysisRepository.getAnalyses(Map.of(RUN_NAME, runName), null);
+  public List<Analysis> getAnalysesByRunId(String runId) {
+    val response = analysisRepository.getAnalyses(Map.of(RUN_ID, runId), null);
     val hitStream = Arrays.stream(response.getHits().getHits());
     return hitStream.map(AnalysisService::hitToAnalysis).collect(toUnmodifiableList());
   }

diff --git a/src/main/resources/schema.graphql b/src/main/resources/schema.graphql
@@ -53,8 +53,7 @@ type Sample {
     matchedNormalSubmitterSampleId: String
 }
 
-type Workflow {
-    runName: String # TODO: swap runName to be ID post migration
+type Workflow @key(fields: "runId") {
     runId: ID!
     workflowName: String
     workflowVersion: String
@@ -118,7 +117,7 @@ input AnalysisFilter {
     donorId: String
     specimenId: String
     sampleId: String
-    runName: String
+    runId: String
 }
 
 input FileFilter {
@@ -137,7 +136,7 @@ input Page {
 }
 
 type Run @key(fields: "runName") @extends {
-    runName: ID! @external
+    runName: ID! @external # todo: runName will become runId after reindex
     producedAnalyses: [Analysis]
     inputAnalyses: String
 }