Merge pull request #157 from camicroscope/develop

Develop

Dockerfile

@@ -1,11 +1,12 @@
 FROM node:14-alpine
+RUN apk add --no-cache git
+RUN apk add --no-cache openssl
 RUN mkdir /src
 COPY . /src
 WORKDIR /src
 RUN npm install
 ARG viewer
 ARG fork
-RUN apk add --no-cache git
 RUN git clone https://github.com/${fork:-camicroscope}/camicroscope.git --branch=${viewer:-master}
 EXPOSE 4010
 

caracal.js

@@ -21,6 +21,7 @@ const permissionHandler = require('./handlers/permssionHandler.js');
 const dataHandlers = require('./handlers/dataHandlers.js');
 const fileHandlers = require('./handlers/fileHandlers.js');
 const sanitizeBody = require('./handlers/sanitizeHandler.js');
+const envEcho = require("./handlers/envEcho.js");
 const DataTransformationHandler = require('./handlers/dataTransformationHandler.js');
 
 
@@ -34,7 +35,7 @@ var MONGO_URI = process.env.MONGO_URI || 'mongodb://localhost';
 
 var DISABLE_CSP = process.env.DISABLE_CSP || false;
 
-var RUN_INDEXER = process.env.RUN_INDEXER || true;
+var RUN_INDEXER = process.env.RUN_INDEXER || false;
 
 const app = express();
 app.use(cookieParser());
@@ -82,6 +83,7 @@ var HANDLERS = {
   "permissionHandler": permissionHandler,
   "editHandler": auth.editHandler,
   "proxyHandler": proxyHandler,
+  "envEcho": envEcho,
   "writeFile": fileHandlers.writeFile,
   "iipHandler": function() {
     return iipHandlers.iipHandler;
@@ -98,6 +100,9 @@ var HANDLERS = {
   "markSpatial": function() {
     return dataHandlers.Mark.spatial;
   },
+  "markSegmentationCount": function() {
+    return dataHandlers.Mark.segmentationCountByExecid;
+  },
   "findMarkTypes": function() {
     return dataHandlers.Mark.findMarkTypes;
   },

handlers/authHandlers.js

@@ -149,7 +149,7 @@ function tokenTrade(checkKey, signKey, userFunction) {
                 'err': 'User Unauthorized',
               });
             } else {
-              data = x;
+              let data = x;
               delete data['exp'];
               // sign using the mounted key
               var token = jwt.sign(data, signKey, {

handlers/dataHandlers.js

@@ -168,7 +168,42 @@ Mark.spatial = function(req, res, next) {
     next();
   }).catch((e) => next(e));
 };
+Mark.segmentationCountByExecid = async function(req, res, next) {
+  var query = req.query;
+  delete query.token;
 
+  // handle  x0, y0, x1, y1
+  if (req.query.x0 && req.query.x1) {
+    query.x = {
+      '$gt': parseFloat(req.query.x0),
+      '$lt': parseFloat(req.query.x1),
+    };
+  }
+  delete query.x0;
+  delete query.x1;
+  if (req.query.y0 && req.query.y1) {
+    query.y = {
+      '$gt': parseFloat(req.query.y0),
+      '$lt': parseFloat(req.query.y1),
+    };
+  }
+  delete query.y0;
+  delete query.y1;
+  try {
+    // {"$match": {"provenance.image.slide": {"$in": sids}}},
+    const data = await mongoDB.aggregate('camic', 'mark',
+        [
+          {"$match": query},
+          {"$group": {_id: "$provenance.analysis.execution_id", count: {$sum: 1}}},
+        ]);
+    console.log(data);
+    req.data = data;
+    next();
+  } catch (error) {
+    req.data = {error};
+    next();
+  }
+};
 Mark.multi = function(req, res, next) {
   var query = {};
 
@@ -211,7 +246,6 @@ Mark.multi = function(req, res, next) {
       '$gt': parseFloat(postQuery.footprint),
     };
   }
-
   mongoDB.find('camic', 'mark', query).then((x) => {
     req.data = x;
     next();

handlers/envEcho.js

@@ -0,0 +1,10 @@
+// echo enviornment variables
+function envEcho() {
+  return function(req, res, next) {
+    req.data = process.env;
+    next();
+  };
+}
+
+
+module.exports = envEcho;

idx_mongo.js

@@ -5,7 +5,7 @@ const mongodb = require("./service/database");
 
 function quietMongoAdd(db, collection, data, x) {
   try {
-    mongodb.add(db, collection, data, x);
+    mongodb.add(db, collection, data, x).catch((e)=>console.error(e));
   } catch (err) {
     console.error(err);
   }