Merge pull request #244 from CBIIT/EVSSIP-308

Evssip 308

Author: fmanuelos

server/components/elasticsearch.js

@@ -209,9 +209,9 @@ const helper_gdc = (fileJson, syns) => {
       });
     }
 
-    if (entry.deprecated_enum) {
-      values = _.differenceWith(values, entry.deprecated_enum, _.isEqual);
-    }
+    // if (entry.deprecated_enum) {
+    //   values = _.differenceWith(values, entry.deprecated_enum, _.isEqual);
+    // }
 
     //generate p.enum
     if(values.length > 0){

server/data_files/GDC/model-2.6.5/_terms_enum.yaml

@@ -28470,8 +28470,8 @@ bcell_lymphoma_unclassifiable_with_features_intermediate_between_diffuse_large_b
       term_id: C80291
       term_version: 20.05a
 
-? bcell_lymphoma_unclassifiable_with_features_intermediate_between_diffuse_large_bcell_lymphoma_and_classical_hodgkin_lymphoma
-: common:
+bcell_lymphoma_unclassifiable_with_features_intermediate_between_diffuse_large_bcell_lymphoma_and_classical_hodgkin_lymphoma:
+  common:
     description: >-
       A group of lymphomas displaying molecular, morphologic, immunophenotypic, and
       clinical overlap between classic Hodgkin lymphoma and diffuse large B-cell lymphoma.  This

server/data_files/GDC/model-2.6.5/diagnosis.yaml

@@ -10709,9 +10709,8 @@ properties:
       B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma:
         $ref:
           - "_terms_enum.yaml#/bcell_lymphoma_unclassifiable_with_features_intermediate_between_diffuse_large_bcell_lymphoma_and_burkitt_lymphoma/common"
-      ? B-cell lymphoma, unclassifiable, with features intermediate between diffuse
-        large B-cell lymphoma and classical Hodgkin lymphoma
-      : $ref:
+      B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and classical Hodgkin lymphoma:
+        $ref:
           - "_terms_enum.yaml#/bcell_lymphoma_unclassifiable_with_features_intermediate_between_diffuse_large_bcell_lymphoma_and_classical_hodgkin_lymphoma/common"
       Balloon cell melanoma:
         $ref:

server/data_files/GDC/model-2.6.5/molecular_test.yaml

@@ -3761,8 +3761,7 @@ properties:
     $ref:
       - "_terms.yaml#/locus/common"
     type: string
-    pattern: "^(AC_|NC_|NG_|NT_|NW_|NZ_b|NM_|NR_|XM_c|XR_c|AP_|NP_|YP_c|XP_c|WP_)[0-9]+(\\\
-      .(0|[1-9][0-9]{0,3}))?$"
+    pattern: "^(AC_|NC_|NG_|NT_|NW_|NZ_b|NM_|NR_|XM_c|XR_c|AP_|NP_|YP_c|XP_c|WP_)[0-9]+(\\.(0|[1-9][0-9]{0,3}))?$"
 
   mismatch_repair_mutation:
     $ref:

server/lib/Property.js

@@ -45,6 +45,9 @@ const Property = class {
       if (schema.hasOwnProperty('enum')) {
         this._type = 'enum';
         this._values = schema.enum;
+        if (schema.deprecated_enum) {
+          this._values = schema.enum.filter(value => !schema.deprecated_enum.includes(value));
+        }
       } else if (schema.hasOwnProperty('oneOf')) {
         const types = [];