Merge pull request #91 from CBIIT/MVS-295

MVS-295
CBIIT · Feb 27, 2023 · 8f6d173 · 8f6d173
2 parents 8100e87 + 9647b6d
commit 8f6d173
Show file tree

Hide file tree

Showing 6 changed files with 28 additions and 22 deletions.
diff --git a/server/components/caDSR.js b/server/components/caDSR.js
@@ -298,7 +298,7 @@ const synchronziedLoadSynonmysfromNCIT = (ncitids, idx, next) => {
 		return;
 	}
 	let syn = [];
-	https.get(config.NCIt_url[4] + ncitids[idx], (rsp) => {
+	https.get(config.NCIt_url[6] + ncitids[idx], (rsp) => {
 		let html = '';
 		rsp.on('data', (dt) => {
 			html += dt;
@@ -309,25 +309,34 @@ const synchronziedLoadSynonmysfromNCIT = (ncitids, idx, next) => {
 				if (d.synonyms !== undefined) {
 					let tmp = {}
 					tmp[ncitids[idx]] = {};
-					tmp[ncitids[idx]].preferredName = d.preferredName;
+					tmp[ncitids[idx]].preferredName = d.name;
 					tmp[ncitids[idx]].code = d.code;
 					tmp[ncitids[idx]].definitions = d.definitions;
 					tmp[ncitids[idx]].synonyms = [];
 					let checker_arr = [];
 					d.synonyms.forEach(data => {
-						if(checker_arr.indexOf((data.termName+"@#$"+data.termGroup+"@#$"+data.termSource).trim().toLowerCase()) !== -1) return;
+						if (checker_arr.indexOf((data.name + "@#$" + data.termType + "@#$" + data.source).trim().toLowerCase()) !== -1) return;
+
 						let obj = {};
-						obj.termName = data.termName;
-						obj.termGroup = data.termGroup;
-						obj.termSource = data.termSource;
-						tmp[ncitids[idx]].synonyms.push(obj);
-						checker_arr.push((data.termName+"@#$"+data.termGroup+"@#$"+data.termSource).trim().toLowerCase());
+						obj.termName = data.name;
+						obj.termGroup = data.termType;
+						obj.termSource = data.source;
+						//only keep NCI synonyms
+						if (obj.termSource == "NCI") {
+							if (obj.termGroup == "PT") {
+								tmp[ncitids[idx]].synonyms.unshift(obj);
+							} else {
+								tmp[ncitids[idx]].synonyms.push(obj);
+							}
+						}
+
+						checker_arr.push((data.name + "@#$" + data.termType + "@#$" + data.source).trim().toLowerCase());
 					});
-					if (d.additionalProperties !== undefined) {
+					if (d.properties !== undefined) {
 						tmp[ncitids[idx]].additionalProperties = [];
-						d.additionalProperties.forEach(data => {
+						d.properties.forEach(data => {
 							let obj = {};
-							obj.name = data.name;
+							obj.name = data.type;
 							obj.value = data.value;
 							tmp[ncitids[idx]].additionalProperties.push(obj);
 						});
@@ -348,9 +357,8 @@ const synchronziedLoadSynonmysfromNCIT = (ncitids, idx, next) => {
 			if (ncitids.length == idx) {
 				return next('Success');
 			} else {
-				return next("NCIT finished number: " + idx + " of " + ncitids.length + "\n");
+				return next("NCIT finished number: " + idx + " of " + ncitids.length + " : " + ncitids[idx] +"\n");
 			}
-
 		});
 
 	}).on('error', (e) => {

diff --git a/server/config/index.js b/server/config/index.js
@@ -51,7 +51,8 @@ const all = {
     'http://nciws-d790.nci.nih.gov:15080/evsrestapi2/api/v1/ctrp/concept/',
     'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=CTCAE&type=synonym&code=',
     'https://evsrestapi.nci.nih.gov/evsrestapi/api/v1/ctrp/concept/',
-    'https://evsrestapi-stage.nci.nih.gov/evsrestapi/api/v1/conceptList?db=weekly&properties=Code,Preferred_Name,FULL_SYN,DEFINITION&concepts='
+    'https://evsrestapi-stage.nci.nih.gov/evsrestapi/api/v1/conceptList?db=weekly&properties=Code,Preferred_Name,FULL_SYN,DEFINITION&concepts=',
+    'https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/'
   ],
 
   // GDC searchable nodes

diff --git a/server/data_files/gdc_values.js b/server/data_files/gdc_values.js
diff --git a/server/data_files/ncit_details.js b/server/data_files/ncit_details.js
diff --git a/server/service/search/report.js b/server/service/search/report.js
@@ -193,7 +193,7 @@ const exportMapping = (req, res) => {
 							tmp_data.t_t = map.term_type;
 						  }
 						  for(let code of map.n_c){
-							tmp_data.ncit_v.push(ncit_details[code] !== undefined ? ncit_details[code].pname : '');
+							tmp_data.ncit_v.push(ncit_details[code] !== undefined ? ncit_details[code].preferredName : '');
 						  }
 						  tmp_data.ncit_v = Array.isArray(tmp_data.ncit_v) ? tmp_data.ncit_v.join('|') : tmp_data.ncit_v;
 						}

diff --git a/server/service/search/search.controller.js b/server/service/search/search.controller.js
@@ -13,6 +13,7 @@ const _ = require('lodash');
 const shared = require('./shared');
 const folderPath = path.join(__dirname, '..', '..', 'data');
 // const git = require('nodegit');
+// const Excel = require('exceljs');
 var cdeData = {};
 var gdcData = {};
 
@@ -785,10 +786,6 @@ const updateSynonumsNcit = (req, res) => {
 
 		res.end('Success!!');
 	});
-
-
-
-
 };
 
 const loadSynonyms_continue = (req, res) => {
@@ -1329,7 +1326,7 @@ const updateGDCDataMappings = async (req, res) => {
 					} else {
 						entry.i_c_s = "";
 					}
-					entry.term_type = "PT";
+					entry.term_type = "";
 					current_mappings[prop_id].push(entry);
 				}
 			}