Code review

Author: bbimber

ehr/resources/pipeline/kinship/populateKinship.r

@@ -42,12 +42,6 @@ for (species in unique(allPed$Species)){
         next
     }
 
-    pctMissingSex <- sum(allRecordsForSpecies$Gender > 2) / nrow(allRecordsForSpecies)
-    if (pctMissingSex > 0.25) {
-        paste0('More than 25% of this species group are missing sex and cannot be processed by fixParents(), skipping')
-        next
-    }
-
     # Add missing parents for accurate kinship calculations
     fixedRecords <- with(allRecordsForSpecies, fixParents(id = Id, dadid = Sire, momid = Dam, sex = Gender))
 

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java

@@ -153,7 +153,7 @@ public RecordedActionSet run() throws PipelineJobException
             processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
             processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
 
-            if (Boolean.parseBoolean(getJob().getParameters().get("kinshipValidation")))
+            if (GeneticCalculationsJob.isKinshipValidation())
             {
                 validateKinship();
             }