Merge pull request #64 from PDXFinder/beta

Beta
PDCMFinder · Apr 2, 2019 · 2be96a9 · 2be96a9
2 parents 123568a + d63a62e
commit 2be96a9
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Showing 4 changed files with 24 additions and 8 deletions.
diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java b/data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
@@ -152,7 +152,7 @@ public static String getSampleID(JSONObject data,String ds) throws Exception {
             sampleID = data.getString("Sample ID");
         }
 
-        if (ds.equals(irccCrc) || ds.equals(mdAnderson) || ds.equals(jax) || ds.equals(pdmr)){
+        if (ds.equals(irccCrc) || ds.equals(mdAnderson) || ds.equals(jax) || ds.equals(pdmr) || ds.equals(wustl)){
             sampleID = data.getString("Model ID");
         }
 

diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java b/data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
@@ -571,7 +571,6 @@ public Set<ModelForQuery> search(Map<SearchFacetName, List<String>> filters){
                     result = breastCancerMarkersSearch.search(filters.get(SearchFacetName.breast_cancer_markers), result, ModelForQuery::addBreastCancerMarkers);
                     break;
 
-
                 default:
                     //undexpected filter option
                     log.warn("Unrecognised facet {} passed to search, skipping", facet.getName());
@@ -696,6 +695,13 @@ private void initializeModels() {
 
                 }
 
+                if(j.has("accessModalities")){
+                    mfq.setAccessModalities(j.getString("accessModalities"));
+                }
+                else{
+                    mfq.setAccessModalities("");
+                }
+
 
                 this.models.add(mfq);
             }

diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java b/data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
@@ -20,7 +20,8 @@ public enum SearchFacetName {
     drug,
     project,
     data_available,
-    breast_cancer_markers;
+    breast_cancer_markers,
+    access_modalities;
 
     public String getName() {
         return name();

diff --git a/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java b/data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
@@ -12,6 +12,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.security.spec.ECField;
 import java.util.ArrayList;
 
 /**
@@ -82,12 +83,20 @@ public static String getAge(String age){
 
     public static String getValue(String name, JSONObject j){
         String value = NOT_SPECIFIED;
-        try{
-            value = j.getString(name);
-            if(value.trim().length()==0){
-                value = NOT_SPECIFIED;
+
+        if(j.has(name)){
+            try {
+                value = j.getString(name);
+                if(value.trim().length()==0) {
+                    value = NOT_SPECIFIED;
+                }
+            }
+            catch (Exception e){
+                e.printStackTrace();
             }
-        }catch(Exception e){}
+
+        }
+
         return value;
     }