[ALS-5979] AIM-AHEAD PIC-SURE: Downloaded dataset seems incorrect (#161)

* Refactor FENCEAuthenticationService to customize query fields Different fields for queryTemplateText are set based on the idp_provider in FENCEAuthenticationService. The "?fields" parameter of the query is now conditionally filled, with it being set to the parentAccessionField if idp_provider equals "fence", and empty otherwise. This change provides more flexibility for FENCE authentication depending on the provider setting. * Remove empty string for fields * Flip equals to avoid npe
hms-dbmi · Mar 26, 2024 · 95d0ad6 · 95d0ad6
1 parent 174913e
commit 95d0ad6
Showing 1 changed file with 10 additions and 3 deletions.
diff --git a/...main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java b/...main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java
@@ -514,11 +514,18 @@ private Privilege upsertClinicalPrivilege(String studyIdentifier, String project
                     +"\":[\""
                     +studyIdentifierField
                     +"\"]},"
-                    +"\"numericFilters\":{},\"requiredFields\":[],"
-                    +"\"fields\":[\"" + parentAccessionField + "\"],"
-                    +"\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],"
+                    +"\"numericFilters\":{},\"requiredFields\":[],";
+
+                    if("fence".equalsIgnoreCase(JAXRSConfiguration.idp_provider)) {
+                    	queryTemplateText += "\"fields\":[\"" + parentAccessionField + "\"],";
+                    } else {
+                        queryTemplateText += "\"fields\":[],";
+                    }
+
+                    queryTemplateText+="\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],"
                     +"\"expectedResultType\": \"COUNT\""
                     +"}";
+
             priv.setQueryTemplate(queryTemplateText);
             if(isHarmonized) {
             	priv.setQueryScope("[\"" + conceptPath + "\",\"_\",\"" + fence_harmonized_concept_path + "\"]");