Merge branch 'Ren22-master' (PR #6): optical images deletion, fdrCoun…

…ts resolver
Ren22 · Mar 16, 2018 · cb97991 · cb97991
1 parent b0a1674
commit cb97991
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Showing 3 changed files with 71 additions and 17 deletions.
diff --git a/esConnector.js b/esConnector.js
@@ -147,11 +147,10 @@ module.exports.esSearchResults = function(args, docType) {
     from: args.offset,
     size: args.limit
   };
-  logger.info(JSON.stringify(body));
-  console.time('esQuery');
+  // console.time('esQuery');
 
   return es.search(request).then((resp) => {
-    console.timeEnd('esQuery');
+    // console.timeEnd('esQuery');
     return resp.hits.hits;
   }).catch((e) => {
     logger.error(e);

diff --git a/resolvers.js b/resolvers.js
@@ -77,6 +77,14 @@ function baseDatasetQuery() {
   });
 }
 
+function checkFetchRes(resp) {
+  if (resp.ok) {
+    return resp
+  } else {
+    throw new Error(`An error occurred during fetch request - status ${resp.status}`);
+  }
+}
+
 const Resolvers = {
   Person: {
     name(obj) { return obj.First_Name; },
@@ -159,17 +167,17 @@ const Resolvers = {
     opticalImageUrl(_, {datasetId, zoom}) {
       const intZoom = zoom <= 1.5 ? 1 : (zoom <= 3 ? 2 : (zoom <= 6 ? 4 : 8));
       return pg.select().from('optical_image')
-               .where('ds_id', '=', datasetId)
-               .where('zoom', '=', intZoom)
-               .then(records => {
-                 if (records.length > 0)
-                   return '/optical_images/' + records[0].id;
-                 else
-                   return null;
-               })
-               .catch((e) => {
-                 logger.error(e);
-               })
+          .where('ds_id', '=', datasetId)
+          .where('zoom', '=', intZoom)
+          .then(records => {
+              if (records.length > 0)
+                  return '/optical_images/' + records[0].id;
+              else
+                  return null;
+          })
+          .catch((e) => {
+              logger.error(e);
+          })
     },
 
     rawOpticalImage(_, {datasetId}) {
@@ -255,6 +263,26 @@ const Resolvers = {
 
     uploadDateTime(ds) {
       return ds._source.ds_upload_dt;
+    },
+
+    fdrCounts(ds, {inpFdrLvls}) {
+      let outFdrLvls = [], outFdrCounts = [];
+      if(ds._source.annotation_counts && ds._source.ds_status === 'FINISHED') {
+        let inpAllLvlCounts = ds._source.annotation_counts[0].counts;
+        inpFdrLvls.forEach(lvl => {
+          let findRes = inpAllLvlCounts.find(lvlCount => {
+            return lvlCount.level === lvl
+          });
+          if (findRes) {
+            outFdrLvls.push(findRes.level);
+            outFdrCounts.push(findRes.n);
+          }
+        });
+      }
+      return {
+        'levels': outFdrLvls,
+        'counts': outFdrCounts
+      }
     }
   },
 
@@ -501,6 +529,7 @@ const Resolvers = {
 
     async addOpticalImage(_, {input}) {
       let {datasetId, imageUrl, transform} = input;
+      const basePath = `http://localhost:${config.img_storage_port}`;
       if (imageUrl[0] == '/') {
         // imageUrl comes from the web application and should not include host/port.
         //
@@ -509,18 +538,36 @@ const Resolvers = {
         // if internal network is used.
         //
         // TODO support image storage running on a separate host
-        imageUrl = 'http://localhost:' + config.img_storage_port + imageUrl;
+        imageUrl = basePath + imageUrl;
       }
       const payload = jwt.decode(input.jwt, config.jwt.secret);
       try {
-        logger.info(input);
         await checkPermissions(datasetId, payload);
         const url = `http://${config.services.sm_engine_api_host}/v1/datasets/${datasetId}/add-optical-image`;
         const body = {url: imageUrl, transform};
-        await fetch(url, {
+        let processOptImage = await fetch(url, {
           method: 'POST',
           body: JSON.stringify(body),
           headers: {'Content-Type': 'application/json'}});
+        checkFetchRes(processOptImage);
+        return 'success';
+      } catch (e) {
+        logger.error(e.message);
+        return e.message;
+      }
+    },
+
+    async deleteOpticalImage(_, args) {
+      let {datasetId} = args;
+      const payload = jwt.decode(args.jwt, config.jwt.secret);
+      const url = `http://${config.services.sm_engine_api_host}/v1/datasets/${datasetId}/del-optical-image`;
+      try {
+        await checkPermissions(datasetId, payload);
+        let dbDelFetch = await fetch(url, {
+          method: 'POST',
+          body: JSON.stringify({datasetId}),
+          headers: {'Content-Type': 'application/json'}});
+        checkFetchRes(dbDelFetch);
         return 'success';
       } catch (e) {
         logger.error(e.message);

diff --git a/schema.graphql b/schema.graphql
@@ -44,6 +44,11 @@ enum JobStatus {
   FAILED
 }
 
+type FdrCounts {
+  levels: [Float!]!
+  counts: [Float!]!
+}
+
 type Dataset {
   id: String!
   name: String!
@@ -70,6 +75,7 @@ type Dataset {
   status: JobStatus
   inputPath: String
   uploadDateTime: String
+  fdrCounts(inpFdrLvls: [Float!]!): FdrCounts!
 }
 
 # fields of categorical type
@@ -280,6 +286,8 @@ type Mutation {
     delRawData: Boolean, sync: Boolean=true): String
 
   addOpticalImage(input: AddOpticalImageInput!): String
+
+  deleteOpticalImage(jwt: String!, datasetId: String!): String!
 }
 
 type DatasetStatusUpdate {