analysis: Fix VariantStatsAnalysis when using a cohort instead of a l…

…ist of samples. #1376
opencb · Nov 26, 2019 · 2451070 · 2451070
1 parent 7bc5d18
commit 2451070
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Showing 6 changed files with 16 additions and 10 deletions.
diff --git a/...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantStorageManager.java b/...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantStorageManager.java
@@ -334,7 +334,8 @@ public DataResult<ProjectMetadata.VariantAnnotationMetadata> getAnnotationMetada
     public void stats(String study, List<String> cohorts, List<String> samples,
                       String outDir, boolean index, ObjectMap config, String sessionId)
             throws AnalysisException {
-        stats(study, cohorts, new Query(SampleDBAdaptor.QueryParams.ID.key(), samples), outDir, index, config, sessionId);
+        Query samplesQuery = CollectionUtils.isEmpty(samples) ? new Query() : new Query(SampleDBAdaptor.QueryParams.ID.key(), samples);
+        stats(study, cohorts, samplesQuery, outDir, index, config, sessionId);
     }
 
     public void stats(String study, List<String> cohorts, Query samplesQuery,

diff --git a/...nalysis/src/main/java/org/opencb/opencga/analysis/variant/stats/VariantStatsAnalysis.java b/...nalysis/src/main/java/org/opencb/opencga/analysis/variant/stats/VariantStatsAnalysis.java
@@ -284,7 +284,12 @@ protected void run() throws Exception {
                 });
 
                 if (!emptyCohorts.isEmpty()) {
-                    throw new AnalysisException("Unable to compute variant stats for cohorts " + emptyCohorts);
+                    if (dynamicCohort) {
+                        throw new AnalysisException("Missing cohort or samples. "
+                                + "Use cohort " + StudyEntry.DEFAULT_COHORT + " to compute stats for all indexed samples");
+                    } else {
+                        throw new AnalysisException("Unable to compute variant stats for cohorts " + emptyCohorts);
+                    }
                 }
 
                 // check read permission

diff --git a/...p/src/main/java/org/opencb/opencga/app/cli/internal/executors/VariantCommandExecutor.java b/...p/src/main/java/org/opencb/opencga/app/cli/internal/executors/VariantCommandExecutor.java
@@ -385,7 +385,7 @@ private void stats() throws AnalysisException {
 
         options.putAll(cliOptions.commonOptions.params);
 
-        List<String> cohorts = cliOptions.cohorts;
+        List<String> cohorts = cliOptions.cohort;
         List<String> samples = cliOptions.samples;
         variantManager.stats(cliOptions.study, cohorts, samples, cliOptions.outdir, cliOptions.index, options, sessionId);
     }

diff --git a/...-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java b/...-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
@@ -547,12 +547,12 @@ public class VariantStatsCommandOptions extends GeneralCliOptions.StudyOption {
         @ParametersDelegate
         public GeneralCliOptions.CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"--cohorts"}, description = "Cohort Ids for the cohorts to be calculated.")
-        public List<String> cohorts;
+        @Parameter(names = {"--cohort"}, description = "Cohort Ids for the cohorts to be calculated.")
+        public List<String> cohort;
 
         @Parameter(names = {"--cohort-ids"}, hidden = true)
         public void setCohortIds(List<String> cohortIds) {
-            this.cohorts = cohortIds;
+            this.cohort = cohortIds;
         }
 
         @Parameter(names = {"-o", "--outdir"}, description = "Output directory outside catalog boundaries.", required = false, arity = 1)

diff --git a/.../main/java/org/opencb/opencga/app/cli/main/executors/analysis/VariantCommandExecutor.java b/.../main/java/org/opencb/opencga/app/cli/main/executors/analysis/VariantCommandExecutor.java
@@ -133,7 +133,7 @@ public void execute() throws Exception {
 
     private DataResponse stats() throws IOException {
         ObjectMap params = new VariantAnalysisWSService.StatsRunParams(
-                variantCommandOptions.statsVariantCommandOptions.cohorts,
+                variantCommandOptions.statsVariantCommandOptions.cohort,
                 variantCommandOptions.statsVariantCommandOptions.samples,
                 variantCommandOptions.statsVariantCommandOptions.index,
                 variantCommandOptions.statsVariantCommandOptions.outdir,

diff --git a/...erver/src/main/java/org/opencb/opencga/server/rest/analysis/VariantAnalysisWSService.java b/...erver/src/main/java/org/opencb/opencga/server/rest/analysis/VariantAnalysisWSService.java
@@ -577,10 +577,10 @@ public Response getAnnotationMetadata(@ApiParam(value = "Annotation identifier")
     public static class StatsRunParams extends RestBodyParams {
         public StatsRunParams() {
         }
-        public StatsRunParams(List<String> cohorts, List<String> samples, boolean index, String outdir, String outputFileName,
+        public StatsRunParams(List<String> cohort, List<String> samples, boolean index, String outdir, String outputFileName,
                               String region, boolean overwriteStats, boolean updateStats, boolean resume, Aggregation aggregated,
                               String aggregationMappingFile) {
-            this.cohorts = cohorts;
+            this.cohort = cohort;
             this.samples = samples;
             this.index = index;
             this.outdir = outdir;
@@ -593,7 +593,7 @@ public StatsRunParams(List<String> cohorts, List<String> samples, boolean index,
             this.aggregationMappingFile = aggregationMappingFile;
         }
 
-        public List<String> cohorts;
+        public List<String> cohort;
         public List<String> samples;
         public boolean index;
         public String region;