Merge feat/owner and feat@type #39 #38

biolab-unige · Sep 29, 2017 · 8d753e0 · 8d753e0
2 parents 852f553 + c041cfd
commit 8d753e0
Show file tree

Hide file tree

Showing 96 changed files with 3,736 additions and 14,814 deletions.
diff --git a/api/controllers/AddressInformationController.js b/api/controllers/AddressInformationController.js
@@ -0,0 +1,10 @@
+/**
+ * AddressInformationController
+ *
+ * @description :: Server-side logic for managing contactinformations
+ * @help        :: See http://links.sailsjs.org/docs/controllers
+ */
+
+module.exports = {
+
+};
diff --git a/api/controllers/AuthController.js b/api/controllers/AuthController.js
@@ -92,8 +92,8 @@ let AuthController = {
             return res.ok("User successfully logged out.");
         })
 
-        .catch(function(err) {
-            // console.log(err);
+        .catch(/* istanbul ignore next */ function(err) {
+            sails.log.error(err);
             return res.serverError("Caught some error while disconnecting the user");
         });
     }

diff --git a/api/controllers/DataController.js b/api/controllers/DataController.js
@@ -5,7 +5,7 @@
  * @help        :: See http://links.sailsjs.org/docs/controllers
  */
 /* jshint node: true */
-/* globals _, sails, Data, DataType, DataService, DataTypeService, SubjectService, SampleService, QueryService, TokenService, DataTypePrivileges */
+/* globals _, sails, Data, DataType, DataService, DataTypeService, SubjectService, OperatorService, SampleService, QueryService, TokenService, DataTypePrivileges */
 "use strict";
 
 const BluebirdPromise = require('bluebird');
@@ -38,8 +38,8 @@ const coroutines = {
             throw new PrivilegesError(`Authenticated user has not edit privileges on the data type ${data.type}`);
         }
         DataService.simplify(data);
-        const dataType = yield DataType.findOne(data.type);
-        const validationRes = DataService.validate(data, true, dataType);
+        const dataType = yield DataType.findOne(data.type).populate('superType');
+        const validationRes = yield DataService.validate(data, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -103,6 +103,7 @@ const coroutines = {
         const operator = TokenService.getToken(req);
 
         let result = yield DataService.hasDataSensitive(data.id, DATA);
+        console.log(result,operator);
         if (result.hasDataSensitive && !operator.canAccessSensitiveData) {
             throw new PrivilegesError("Authenticated user is not allowed to modify sensitive data");
         }
@@ -114,8 +115,8 @@ const coroutines = {
         }
         DataService.simplify(data);
 
-        const dataType = yield DataType.findOne(idDataType);
-        const validationRes = DataService.validate(data, true, dataType);
+        const dataType = yield DataType.findOne(idDataType).populate('superType');
+        const validationRes = yield DataService.validate(data, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -175,6 +176,8 @@ const coroutines = {
         if (_.isEmpty(payload.dataTypes)){ throw new PrivilegesError(`Authenticated user has not edit privileges on any data type`); }
 
         if (payload.data){
+            let operators = yield OperatorService.getOwners(payload.data);
+            payload.operators = operators;
           // if operator has not access to Sensitive Data and dataType has sensitive data, then return forbidden
             const sensitiveRes = yield DataService.hasDataSensitive(payload.data.id, DATA);
             if (sensitiveRes && ((sensitiveRes.hasDataSensitive && !operator.canAccessSensitiveData))) {
@@ -221,7 +224,7 @@ module.exports = {
     findOne: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.findOne(req, res)
-        .catch(error => {
+        .catch(/* istanbul ignore next */ function(error) {
             sails.log.error("DataController.findOne: " + error.message);
             return co.error(error);
         });
@@ -239,8 +242,8 @@ module.exports = {
     find: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.find(req,res)
-        .catch( function(err) {
-            sails.log.error(err);
+        .catch( /* istanbul ignore next */ function(err) {
+            sails.log(err);
             return co.error(err);
         });
     },

diff --git a/api/controllers/DataTypeController.js b/api/controllers/DataTypeController.js
@@ -5,7 +5,7 @@
 * @help        :: See http://links.sailsjs.org/docs/controllers
 */
 /* jshint node: true */
-/* globals _, sails, DataType, DataTypeService, TokenService, Group, Project */
+/* globals _, sails, DataType, DataTypeService, TokenService, Group, Project, SuperTypeService */
 "use strict";
 const ControllerOut = require("xtens-utils").ControllerOut, ValidationError = require('xtens-utils').Errors.ValidationError;
 const PrivilegesError = require('xtens-utils').Errors.PrivilegesError;
@@ -33,7 +33,7 @@ const coroutines = {
             query.limit(1000);  // default limit for dataTypes
         }
         if (!req.param('populate')) {
-            query.populate('parents');  // by default populate only with 'parents' dataTypes
+            query.populate(['parents', 'superType']);  // by default populate only with 'parents' dataTypes and 'superType'
         }
         else {
             query = actionUtil.populateRequest(query, req);
@@ -150,12 +150,20 @@ const coroutines = {
     edit: BluebirdPromise.coroutine(function *(req, res) {
         const operator = TokenService.getToken(req);
         const params = req.allParams();
+        let isMultiProject, resObject = {};
         sails.log.info("DataTypeController.edit - Decoded ID is: " + operator.id);
 
         const projects = yield Project.find().sort('id ASC');
 
-        const dataTypes= yield DataType.find({ project:_.map(projects,'id') }).populate(['project','parents']).sort('id ASC');
-        return res.json({params: params, dataTypes: dataTypes});
+        const dataTypes= yield DataType.find({ project:_.map(projects,'id') }).populate(['project','parents','superType']).sort('id ASC');
+        if (params.id) {
+            const dataType = _.find(dataTypes,{'id': parseInt(params.id)});
+            isMultiProject = yield SuperTypeService.isMultiProject(dataType.superType);
+            resObject.isMultiProject = isMultiProject;
+        }
+        resObject.params = params;
+        resObject.dataTypes = dataTypes;
+        return res.json(resObject);
     }),
 
     destroy: BluebirdPromise.coroutine(function *(req, res, co) {
@@ -194,7 +202,7 @@ const DataTypeController = {
     find: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.find(req, res)
-        .catch(err => {
+        .catch(/* istanbul ignore next */ function(err) {
             sails.log.error(err);
             return co.error(err);
         });
@@ -237,7 +245,7 @@ const DataTypeController = {
 
         let co = new ControllerOut(res);
         coroutines.destroy(req,res,co)
-        .catch(function(err) {
+        .catch(/* istanbul ignore next */ function(err) {
             sails.log(err);
             return co.error(err);
         });
@@ -252,7 +260,7 @@ const DataTypeController = {
     edit: function(req, res) {
         let co = new ControllerOut(res);
         coroutines.edit(req,res)
-        .catch(function(err) {
+        .catch(/* istanbul ignore next */ function(err) {
             sails.log(err);
             return co.error(err);
         });

diff --git a/api/controllers/DataTypePrivilegesController.js b/api/controllers/DataTypePrivilegesController.js
@@ -40,7 +40,7 @@ let DataTypePrivilegesController = {
             return res.json(201, result);
         })
 
-        .catch(function(err) {
+        .catch(/* istanbul ignore next */ function(err) {
             sails.log.error("DataTypePrivilegesController.create - got some error while creating new data type privileges");
             return co.error(err);
         });
@@ -62,12 +62,13 @@ let DataTypePrivilegesController = {
         query = actionUtil.populateRequest(query, req);
 
         query.then(function(result) {
-          
+
             return res.json(result);
         })
 
-        .catch(function(error) {
-            return co.error(error);
+        .catch(/* istanbul ignore next */ function(err) {
+            sails.log.error(err);
+            return co.error(err);
         });
 
     },
@@ -145,7 +146,8 @@ let DataTypePrivilegesController = {
             return res.json({deleted: results && results.length});
         })
 
-        .catch(function(err) {
+        .catch(/* istanbul ignore next */ function(err) {
+            sails.log.error(err);
             return co.error(err);
         });
 
@@ -177,8 +179,8 @@ let DataTypePrivilegesController = {
             return res.json(result);
         })
 
-        .catch(function(err) {
-            sails.log(err);
+        .catch(/* istanbul ignore next */ function(err) {
+            sails.log.error(err);
             return co.error(err);
         });
 

diff --git a/api/controllers/ProjectController.js b/api/controllers/ProjectController.js
@@ -66,7 +66,7 @@ module.exports = {
     find: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.find(req, res)
-            .catch(err => {
+            .catch(/* istanbul ignore next */ function(err) {
                 sails.log.error(err);
                 return co.error(err);
             });
@@ -81,7 +81,7 @@ module.exports = {
     edit: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.edit(req, res)
-            .catch(err => {
+            .catch(/* istanbul ignore next */ function(err) {
                 sails.log.error(err);
                 return co.error(err);
             });

diff --git a/api/controllers/QueryController.js b/api/controllers/QueryController.js
@@ -46,7 +46,7 @@
 
          })
 
-         .catch(error => {
+         .catch(/* istanbul ignore next */ function(error) {
              sails.log.error(error);
              res.serverError(error.message);
          });

diff --git a/api/controllers/SampleController.js b/api/controllers/SampleController.js
@@ -5,7 +5,7 @@
  * @help        :: See http://links.sailsjs.org/docs/controllers
  */
 /* jshint node: true */
-/* globals _, sails, Sample, DataType, SubjectService, BiobankService, SampleService, DataTypePrivileges, TokenService, QueryService, DataService, DataTypeService */
+/* globals _, sails, Sample, DataType, SubjectService, BiobankService, OperatorService, SampleService, DataTypePrivileges, TokenService, QueryService, DataService, DataTypeService */
 "use strict";
 
 const BluebirdPromise = require('bluebird');
@@ -38,7 +38,8 @@ const coroutines = {
         }
         SampleService.simplify(sample);
         const dataType = yield DataType.findOne(sample.type);
-        const validationRes = SampleService.validate(sample, true, dataType);
+
+        const validationRes = yield SampleService.validate(sample, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -114,7 +115,7 @@ const coroutines = {
         SampleService.simplify(sample);
 
         const dataType = yield DataType.findOne(idSampleType);
-        const validationRes = SampleService.validate(sample, true, dataType);
+        const validationRes = yield SampleService.validate(sample, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -176,6 +177,9 @@ const coroutines = {
 
 
         if (payload.sample){
+
+            let operators = yield OperatorService.getOwners(payload.sample);
+            payload.operators = operators;
           // if operator has not access to Sensitive Data and dataType has sensitive data, then return forbidden
             const sensitiveRes = yield DataService.hasDataSensitive(payload.sample.id, SAMPLE);
             if (sensitiveRes && ((sensitiveRes.hasDataSensitive && !operator.canAccessSensitiveData))) {
@@ -220,8 +224,9 @@ module.exports = {
     findOne: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.findOne(req,res)
-        .catch(error => {
-            return co.error(error);
+        .catch(/* istanbul ignore next */ function(err) {
+            sails.log.error(err);
+            return co.error(err);
         });
 
     },
@@ -237,7 +242,7 @@ module.exports = {
     find: function(req, res) {
         const co = new ControllerOut(res);
         coroutines.find(req,res)
-        .catch(err => {
+        .catch(/* istanbul ignore next */ function(err) {
             sails.log.error(err);
             return co.error(err);
         });

diff --git a/api/controllers/SubjectController.js b/api/controllers/SubjectController.js
@@ -5,7 +5,7 @@
  * @help        :: See http://links.sailsjs.org/docs/controllers
  */
 /* jshint node: true */
-/* globals _, sails, DataTypePrivileges, Subject, DataType, SubjectService, TokenService, QueryService, DataService, DataTypeService */
+/* globals _, sails, DataTypePrivileges, Subject, DataType, SubjectService, OperatorService, TokenService, QueryService, DataService, DataTypeService */
 "use strict";
 
 const ControllerOut = require("xtens-utils").ControllerOut;
@@ -39,7 +39,7 @@ const coroutines = {
         SubjectService.simplify(subject);
         const dataType = yield DataType.findOne(subject.type);
 
-        const validationRes = SubjectService.validate(subject, true, dataType);
+        const validationRes = yield SubjectService.validate(subject, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -123,7 +123,7 @@ const coroutines = {
         SubjectService.simplify(subject);
 
         const dataType = yield DataType.findOne(idSubjectType);
-        const validationRes = SubjectService.validate(subject, true, dataType);
+        const validationRes = yield SubjectService.validate(subject, true, dataType);
         if (validationRes.error !== null) {
             throw new ValidationError(validationRes.error);
         }
@@ -178,6 +178,8 @@ const coroutines = {
         if (_.isEmpty(payload.dataTypes)){ throw new PrivilegesError(`Authenticated user has not edit privileges on any subject type`); }
 
         if (payload.subject){
+            let operators = yield OperatorService.getOwners(payload.subject);
+            payload.operators = operators;
           // if operator has not access to Sensitive Data and dataType has sensitive data, then return forbidden
             const sensitiveRes = yield DataService.hasDataSensitive(payload.subject.id, SUBJECT);
             if (sensitiveRes && ((sensitiveRes.hasDataSensitive && !operator.canAccessSensitiveData))) {

diff --git a/api/controllers/SuperTypeController.js b/api/controllers/SuperTypeController.js
@@ -0,0 +1,31 @@
+/**
+* SuperTypeController
+*
+* @description :: Server-side logic for managing supertypes
+* @help        :: See http://links.sailsjs.org/docs/controllers
+*/
+/* jshint node: true */
+/* globals _, sails, SuperType, SuperTypeService, TokenService, Group, Project */
+"use strict";
+
+const ControllerOut = require("xtens-utils").ControllerOut, ValidationError = require('xtens-utils').Errors.ValidationError;
+const PrivilegesError = require('xtens-utils').Errors.PrivilegesError;
+const crudManager = sails.hooks.persistence.crudManager;
+const actionUtil = require('sails/lib/hooks/blueprints/actionUtil');
+const BluebirdPromise = require('bluebird');
+
+const coroutines = {
+
+
+};
+
+
+
+const SuperTypeController = {
+
+
+
+
+};
+
+module.exports = SuperTypeController;