Merge main into sweep/add-readme-dev-docs

.vscode/settings.json

@@ -16,5 +16,17 @@
     "**/.git/objects/**": true,
     "**/.git/subtree-cache/**": true,
     "**/node_modules/*/**": true
-  }
+  },
+  "sqltools.connections": [
+    {
+      "previewLimit": 50,
+      "server": "10.10.0.3",
+      "port": 5432,
+      "driver": "PostgreSQL",
+      "name": "CP",
+      "password": "postgres",
+      "database": "postgres",
+      "username": "postgres"
+    }
+  ]
 }

convertPheno_client/src/code/views/conversion/ components/clinicalData/components/dataGrid/CopyOnClick.jsx

@@ -50,6 +50,16 @@ const getValue = (props) => {
       ? data[field]["values"]
       : [];
 
+  const urls =
+    data[field] && Array.isArray(data[field]["urls"])
+      ? data[field]["urls"]
+      : [];
+
+  const ontology_ids =
+    data[field] && Array.isArray(data[field]["ontology_ids"])
+      ? data[field]["ontology_ids"]
+      : [];
+
   return checkKeyExists(data[field], "count") ? (
     <a
       href={`#${location.pathname}`}
@@ -61,15 +71,20 @@ const getValue = (props) => {
       }}
     >
       {values.map((value, index) => (
-        <ValueWithTooltip key={index} value={value} />
+        <ValueWithTooltip
+          key={index}
+          value={value}
+          ontology_id={ontology_ids[index]}
+          url={urls[index]}
+        />
       ))}
     </a>
   ) : (
     data[field]
   );
 };
 
-const ValueWithTooltip = ({ value }) => {
+const ValueWithTooltip = ({ value, ontology_id, url }) => {
   const [isTooltipOpen, setIsTooltipOpen] = useState(false);
   const tooltipTimeout = useRef({ current: null });
 
@@ -86,7 +101,7 @@ const ValueWithTooltip = ({ value }) => {
 
   const handleLinkClick = () => {
     clearTimeout(tooltipTimeout.current);
-    window.open(`https://google.com`, "_blank");
+    window.open(url, "_blank");
   };
 
   return (
@@ -96,12 +111,12 @@ const ValueWithTooltip = ({ value }) => {
         <span>
           Click to open{" "}
           <a
-            href={`https://google.com`}
+            href={url}
             target="_blank"
             rel="noopener noreferrer"
             onClick={handleLinkClick}
           >
-            {value} link
+            {ontology_id}
           </a>
         </span>
       }

convertPheno_server/server/apis/clinical.py

@@ -170,29 +170,57 @@ def recursive_search(dictionary, key):
     return None
 
 
+def generate_url(ontology_id):
+    if (
+        ontology_id is not None
+        and "NCIT" in ontology_id
+        and ontology_id != "NCIT:NA0000"
+    ):
+        ont_query = ontology_id.split(":")[1]
+
+        # TODO
+        # The NCIT base url should be in a config file
+
+        ncit_base = "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp"
+        ncit_query = f"?dictionary=NCI_Thesaurus&code={ont_query}"
+        ncit_url = f"{ncit_base}{ncit_query}"
+
+        return ncit_url
+
+    return "NA"
+
+
 def parse_meta_info(meta, field):
     """
     Parse the meta info from the json array
     """
     data = []
     nested_info = ["value", "status"]
     values = []
+    ontology_ids = []
+    urls = []
     for meta_data in meta:
         meta_row = {}
         for key in meta_data:
             if isinstance(meta_data[key], dict):
                 value = recursive_search(meta_data[key], "label")
+                ontology_id = recursive_search(meta_data[key], "id")
+                ncit_url = generate_url(ontology_id)
+
                 meta_row[key] = value
                 if key == field[0] or key in field[0]:
                     values.append(value)
+                    ontology_ids.append(ontology_id)
+                    urls.append(ncit_url)
+
                 for info in nested_info:
                     nested_info_val = recursive_search(meta_data[key], info)
                     if nested_info_val is not None:
                         meta_row[f"{key}_{info}"] = nested_info_val
             else:
                 meta_row[key] = meta_data[key]
         data.append(meta_row)
-    return data, values
+    return data, values, ontology_ids, urls
 
 
 def catch_errors(func):
@@ -231,8 +259,14 @@ def get_basic_row(row, key, selected_fields):
         row_data[key] = row[key]
         return row_data
 
-    data, values = parse_meta_info(row[key], selected_fields[key])
-    row_data[key] = {"data": data, "count": len(row[key]), "values": values}
+    data, values, ontology_ids, urls = parse_meta_info(row[key], selected_fields[key])
+    row_data[key] = {
+        "data": data,
+        "count": len(row[key]),
+        "values": values,
+        "ontology_ids": ontology_ids,
+        "urls": urls,
+    }
     return row_data
 
 
@@ -559,6 +593,7 @@ def post(self, userid):
             "shownColumns": selected_cols,
             "nodeToSelected": node_to_selected,
         }
+        # print(response)
         return make_response(response)