Add retry-failed option for the POST request

genome-nexus · Aug 6, 2022 · 41e99ad · 41e99ad
1 parent 2c29017
commit 41e99ad
Show file tree

Hide file tree

Showing 4 changed files with 23 additions and 13 deletions.
diff --git a/annotationPipeline/src/main/java/org/cbioportal/annotation/AnnotationPipeline.java b/annotationPipeline/src/main/java/org/cbioportal/annotation/AnnotationPipeline.java
@@ -110,8 +110,11 @@ public static void main(String[] args) throws Exception
         String retryCount = commandLine.getOptionValue("retry-failed","0");
         try {
             retryFailed = Long.parseLong(retryCount);
+            if(retryFailed < 1) {
+                retryFailed = 0;
+            }
         } catch (NumberFormatException e) {
-            System.out.println("Fix the value of tha option named retry-failed");
+            System.out.println("Fix the value of the option named retry-failed");
             System.exit(0);
         }
         launchJob(args, commandLine.getOptionValue("filename"), commandLine.getOptionValue("output-filename"),commandLine.getOptionValue("isoform-override"),

diff --git a/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordReader.java b/...tationPipeline/src/main/java/org/cbioportal/annotation/pipeline/MutationRecordReader.java
@@ -95,7 +95,7 @@ public void open(ExecutionContext ec) throws ItemStreamException {
         List<MutationRecord> mutationRecords = loadMutationRecordsFromMaf();
         if (!mutationRecords.isEmpty()) {
             if (postIntervalSize > 0) {
-                this.allAnnotatedRecords = annotator.getAnnotatedRecordsUsingPOST(summaryStatistics, mutationRecords, isoformOverride, replace, postIntervalSize, true);
+                this.allAnnotatedRecords = annotator.getAnnotatedRecordsUsingPOST(summaryStatistics, mutationRecords, isoformOverride, replace, postIntervalSize, true, retryFailed);
             } else {
                 this.allAnnotatedRecords = annotator.annotateRecordsUsingGET(summaryStatistics, mutationRecords, isoformOverride, replace, true, retryFailed);
             }

diff --git a/annotator/src/main/java/org/cbioportal/annotator/Annotator.java b/annotator/src/main/java/org/cbioportal/annotator/Annotator.java
@@ -51,6 +51,7 @@ List<AnnotatedRecord> annotateRecordsUsingGET(AnnotationSummaryStatistics summar
     boolean isHgvspNullClassifications(String variantClassification);
     String getUrlForRecord(MutationRecord record, String isoformOverridesSource);
     String getVersion();
-    List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, boolean reannotate);
-    List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, Integer postIntervalSize, boolean reannotate);
+    List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, boolean reannotate, Long retryFailed);
+    List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, Integer postIntervalSize, boolean reannotate,
+                                                       Long retryFailed);
 }
diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
@@ -427,13 +427,14 @@ private static List<String> initNullClassifications() {
     }
 
     @Override
-    public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, boolean reannotate) {
+    public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, boolean reannotate, Long retryFailed) {
         // this will send everything at once
-        return getAnnotatedRecordsUsingPOST(summaryStatistics, mutationRecords, isoformOverridesSource, replace, mutationRecords.size(), reannotate);
+        return getAnnotatedRecordsUsingPOST(summaryStatistics, mutationRecords, isoformOverridesSource, replace, mutationRecords.size(), reannotate, retryFailed);
     }
 
     @Override
-    public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, Integer postIntervalSize, boolean reannotate) {
+    public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStatistics summaryStatistics, List<MutationRecord> mutationRecords, String isoformOverridesSource, Boolean replace, Integer postIntervalSize, boolean reannotate,
+                                                              Long retryFailed) {
         // construct list of genomic location objects to pass to api client
         // TODO use SortedSet (or at least Set) instead?  Do we anticipate a lot of redundancy? Probably quite a bit.
         // Maybe test which is faster with a large study
@@ -452,13 +453,18 @@ public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStati
         for (List<GenomicLocation> partitionedList : partitionedGenomicLocationList) {
             List<VariantAnnotation> gnResponseList = null;
             // Get annotations from Genome Nexus and log if server error (e.g VEP is down)
-            try {
-                 gnResponseList = apiClient.fetchVariantAnnotationByGenomicLocationPOST(partitionedList,
-                    isoformOverridesSource, "", Arrays.asList(this.enrichmentFields.split(",")));
-            } catch (Exception e) {
-                LOG.error("Annotation failed for ALL variants in this partition. " + e.getMessage());
+            for(int i = 0; i <= retryFailed; i++) {
+                try {
+                    gnResponseList = apiClient.fetchVariantAnnotationByGenomicLocationPOST(partitionedList,
+                            isoformOverridesSource, "", Arrays.asList(this.enrichmentFields.split(",")));
+                    break;
+                } catch (Exception e) {
+                    LOG.error("Annotation failed for ALL variants in this partition. " + e.getMessage());
+                    if(i != retryFailed) {
+                        LOG.warn("Retrying " + (i+1) + "/" + retryFailed);
+                    }
+                }
             }
-
             // Verify annotations coming back from Genome Nexus and log annotation failures (e.g used to be 404s)
             if (gnResponseList != null) {
                 for (VariantAnnotation gnResponse : gnResponseList) {