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@iemam
iemam committed Jul 15, 2019
2 parents abbe846 + 3a2f5ee commit a535da0
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Showing 222 changed files with 50,075 additions and 38,465 deletions.
21 changes: 10 additions & 11 deletions app/admin/activities/activityConfig-controller.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
*/

'use strict';
function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout,SweetAlert,toaster,$q) {
function ActivityConfigCtrl($scope,$state, $stateParams, ActivityConfigService,$timeout,SweetAlert,toaster,$q) {
var vm = this;
vm.projectId = $stateParams.projectId;

Expand All @@ -12,6 +12,8 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
vm.showFieldInfo = false;
vm.creatingCfield = false;

$scope.$parent.vm.stateName = "Define Activity";

vm.dataTypes = ['STRING','INTEGER','DOUBLE','DATETIME'];
vm.varTypes = ['SUBMITTED','DERIVED'];
vm.roleTypes = ['Observation Qualifier','Finding about observation']
Expand Down Expand Up @@ -88,7 +90,6 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
activity.isNew = false;

vm.activity = activity;
console.log(vm.activity.datasets.length)

$timeout(function(){
//console.log($('#ds_template_tbl'))
Expand Down Expand Up @@ -144,7 +145,7 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
vm.cField.expressionList = vm.expressionList
console.log(vm.cField)

if(vm.cField.varType == 'DERIVED')
if(vm.cField.varType === 'DERIVED')
vm.cField.isComputed = true;
vm.activity.datasets[0].variables.push(vm.cField)
toaster.pop('success', "SUCCESS", vm.cField.name+" has been added to dataset template successfully.",8000);
Expand All @@ -159,8 +160,6 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
};




/**
* Called when a variable is being dragged to prepare the equivalent expression element to be
* added to the expression
Expand Down Expand Up @@ -329,12 +328,12 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
};

vm.saveActivity = function() {
if (vm.activity.name != null && vm.activity.name != ''){
if (vm.activity.name != null && vm.activity.name !== ''){

if (vm.activity.isNew) {
vm.activity.$save(function (response) {
toaster.pop('success', "SUCCESS", vm.activity.name," was successfully CREATED.",8000);
$state.transitionTo('admin.project', $stateParams, {
$state.transitionTo('project.manager.main', $stateParams, {
reload: true,
inherit: false,
notify: true
Expand All @@ -344,7 +343,7 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
else {
vm.activity.$update(function (response) {
toaster.pop('success', "SUCCESS", vm.activity.name," was successfully UPDATED.",8000);
$state.transitionTo('admin.project', $stateParams, {
$state.transitionTo('project.manager.main', $stateParams, {
reload: true,
inherit: false,
notify: true
Expand All @@ -357,7 +356,7 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout

vm.dontSaveActivity = function(){
vm.activity = {}
$state.go('admin.project',{
$state.go('project.manager.main',{
projectId: vm.projectId}
);
}
Expand Down Expand Up @@ -410,7 +409,7 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
var pos;
for(var i=0; i< vm.activity.datasets.length;i++) {
console.log(i)
if(vm.currDS.id == vm.activity.datasets[i].id){
if(vm.currDS.id === vm.activity.datasets[i].id){
console.log(i, 'for',vm.currDS.name)
pos = i;
break;
Expand All @@ -426,4 +425,4 @@ function ActivityConfigCtrl($state, $stateParams, ActivityConfigService,$timeout
}

angular.module('bioSpeak.config')
.controller('ActivityConfigCtrl',['$state','$stateParams','ActivityConfigService','$timeout','SweetAlert','toaster','$q',ActivityConfigCtrl]);
.controller('ActivityConfigCtrl',['$scope','$state','$stateParams','ActivityConfigService','$timeout','SweetAlert','toaster','$q',ActivityConfigCtrl]);
7 changes: 1 addition & 6 deletions app/admin/activities/activityConfig-service.js
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,7 @@ function ActivityConfigService($resource, ngAppConfig) {
update:{
method: 'PUT',
params: {activityId: '@id'}
}/*,
getProjectActivities:{
method: 'GET',
url : serviceBase+'projects/:projectId/activities',
isArray : true
}*/
}
});

var _datasetResource = $resource(serviceBase+'templates/clinical/:datasetId',{},{
Expand Down
60 changes: 21 additions & 39 deletions app/admin/activities/activityConfig.html
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Original file line number Diff line number Diff line change
@@ -1,33 +1,15 @@
<div class="row wrapper border-bottom white-bg page-heading">
<div class="col-sm-4">
<h2>{{vm.activity.isNew ? 'New Activity' :'Define Activity'}}</h2>
<ol class="breadcrumb">
<li>
<a ui-sref="home.dashboard">Home</a>
</li>
<li>
<a ui-sref="admin.project({projectId:vm.projectId})">{{vm.projectId}}</a>
</li>
<li class="active">
<a>{{vm.activity.isNew ? 'New Activity' : vm.activity.name}}</a>
</li>
</ol>
</div>
<div class="col-sm-8">
<div class="title-action">
<a ng-click="vm.saveActivity()" class="btn btn-primary">Save</a>
<a ng-click="vm.dontSaveActivity()" class="btn btn-primary">Go Back</a>

<div has-permission="can-manage" project="vm.projectId" class="title-action" style="display: none">
<a ng-click="vm.saveActivity()" class="btn btn-primary">Save</a>
</div>
</div>
</div>

<div class="row">
<div class="col-md-12">
<div class="wrapper wrapper-content animated fadeInRight">
<div class="ibox">

<div class="">
<div class="ibox-content">
<div class="row">
<div class="col-md-12">
<div class="col-md-12 m-t-md">
<dl class="dl-horizontal">
<dt>Activity Title</dt>
<dd>
Expand All @@ -43,10 +25,10 @@ <h2>{{vm.activity.isNew ? 'New Activity' :'Define Activity'}}</h2>

<div>
<div class="ibox-title panel-header">
<span>Define Templates</span>
<span>Dataset Descriptor</span>
<span style="font-size:16px;margin-top:-5px;" class="pull-right">
<i class="p-xs fa fa-eye"> </i><i class="p-xs fa fa-download"> </i>
<a ng-click="vm.deleteDS()"><i class="p-xs fa fa-trash"> </i></a>
<a has-permission="can-manage" project="vm.projectId" ng-click="vm.deleteDS()"><i class="p-xs fa fa-trash"> </i></a>
| <a ng-init="vm.creatingNewDS = false" ng-click="vm.creatingNewDS = !vm.creatingNewDS"><i uib-tooltip="Add Dataset Template" class="p-xs fa fa-plus"></i></a>
</span>
</div>
Expand All @@ -55,16 +37,16 @@ <h2>{{vm.activity.isNew ? 'New Activity' :'Define Activity'}}</h2>
<form role="form">
<div class="row">
<div class="col-md-11">
<h3>Define New Template</h3>
<h3>Select a dataset descriptor</h3>
</div>
<div class="col-md-1"> <span class="pull-right"><a ng-click="vm.creatingNewDS=false" class="btn btn-white btn-lg"><i class="fa fa-times"></i></a> </span></div>

</div>
<div class="row">
<div class="col-md-7">
<div class="row m-b-sm m-t-sm">

<div class="col-md-12">
<div class="h5">Standard Dataset Descriptors</div>
<div class="">
<input ng-model="searchTemplate" type="text" placeholder="Search"
class="input-sm form-control"></div>
Expand Down Expand Up @@ -109,8 +91,8 @@ <h3>Define New Template</h3>

<!--FIELD INFO-->
<div ng-show="vm.showDS" style="border-left: white 1px solid;" class=" m-b-sm m-t-sm col-md-5">
<div class="ibox-title"><strong>{{vm.showDS.name}} Template Columns</strong>
<span class="pull-right"><a ng-click="vm.selectTemplate(vm.showDS);vm.creatingNewDS=false" class="btn btn-xs btn-primary">Add Dataset</a></span>
<div class="ibox-title"><strong>{{vm.showDS.name}} descriptor fields</strong>
<span class="pull-right"><a ng-click="vm.selectTemplate(vm.showDS);vm.creatingNewDS=false" class="btn btn-xs btn-primary">Use this descriptor</a></span>
</div>
<div class="ibox-content" style="height: 350px">
<div class="activities-list" full-scroll>
Expand Down Expand Up @@ -177,7 +159,7 @@ <h4>No associated templates set for this activity. Pleae click on the '+' icon a

<div class="ibox-title">
<div class="ibox-tools">
<a class="btn btn-primary btn-xs" ng-init="vm.creatingCfield = false" ng-click="vm.creatingCfield = !vm.creatingCfield;vm.createNewCfield()">New Template Variable</a>
<a class="btn btn-primary btn-xs" ng-init="vm.creatingCfield = false" ng-click="vm.creatingCfield = !vm.creatingCfield;vm.createNewCfield()">New Descriptor field</a>
<!--<a href="" class="btn btn-primary btn-xs">Preview Template</a>
<a href="" class="btn btn-primary btn-xs">Download Template</a>-->
</div>
Expand Down Expand Up @@ -587,10 +569,10 @@ <h3>Select columns to include in this template</h3>
<th>Variable Name</th>
<th>Include</th>
<th data-hide="phone">Mandatory</th>
<th data-hide="all">Description</th>
<th data-hide="all">Controlled Vocabulary</th>
<th data-hide="all">Order</th>
<th data-hide="all">Key Sequence</th>
<th data-hide="phone">Description</th>
<th data-hide="phone">Controlled Vocabulary</th>
<!--<th data-hide="all">Order</th>
<th data-hide="all">Key Sequence</th>-->
</tr>
</thead>
<tbody>
Expand All @@ -616,12 +598,12 @@ <h3>Select columns to include in this template</h3>
<td>
{{var.dictionaryName}}
</td>
<td>
<a href="#" e-ng-model="var.order" editable-text="var.order" buttons="no" blur="submit">{{var.order || "Undefined"}}</a>
<!-- <td>
<a href="#" e-ng-model="var.orderNumber" editable-text="var.orderNumber" buttons="no" blur="submit">{{var.orderNumber || "Undefined"}}</a>
</td>
<td>
<a href="#" e-ng-model="var.sequence" editable-text="var.sequence" buttons="no" blur="submit">{{var.sequence || "Undefined"}}</a>
</td>
<a href="#" e-ng-model="var.keySequence" editable-text="var.sequence" buttons="no" blur="submit">{{var.keySequence || "Undefined"}}</a>
</td>-->
</tr>
</tbody>
<tfoot>
Expand Down
64 changes: 41 additions & 23 deletions app/admin/activities/assayConfig-controller.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,10 @@
* Created by iemam on 17/05/2016.
*/
'use strict'
function AssayConfigCtrl($scope, $state, $stateParams, AssayConfigService, toaster){
function AssayConfigCtrl($scope, $state, $stateParams, AssayConfigService, toaster, SweetAlert){
var vm = this;
vm.projectId = $stateParams.projectId
vm.assayId = $stateParams.assayId;
console.log($stateParams.projectId)

vm.templates={}
vm.loaded = true;
Expand All @@ -17,7 +16,7 @@ function AssayConfigCtrl($scope, $state, $stateParams, AssayConfigService, toast

vm.newField= {};


$scope.$parent.vm.stateName = "Define Assay";

AssayConfigService.getAssayTerms().then(function(data){
vm.assayTypes = data.terms;
Expand All @@ -34,7 +33,7 @@ function AssayConfigCtrl($scope, $state, $stateParams, AssayConfigService, toast
//console.log(selAssayType)
for(var i=0; i<vm.assayTypes.length; i++){
var type = vm.assayTypes[i]
if(type.assayTypeTerm.id == selAssayType){
if(type.assayTypeTerm.id === selAssayType){
vm.assayTechTerms = type.assayTechTerms;
vm.assayPlatTerms = type.assayPlatTerms;
}
Expand All @@ -59,11 +58,11 @@ var assay;
}

else if($stateParams.assayId){
console.log(AssayConfigService.getAssayResource);
//console.log(AssayConfigService.getAssayResource);
AssayConfigService.getAssayResource.get({assayId:$stateParams.assayId},function(response){
vm.assay = response;
vm.assay.isNew = false;
console.log("Retrieved Assay",vm.assay.id);
//console.log("Retrieved Assay",vm.assay.id);


vm.selectedDatasets['sample'] = vm.assay.samplesDataset;
Expand Down Expand Up @@ -160,30 +159,18 @@ var assay;
vm.assay.$save(function(response) {
//console.log("Assay created",response)
toaster.pop('success', "SUCCESS", vm.assay.name," was successfully CREATED.",8000);
$state.transitionTo('admin.project', $stateParams, {
$state.transitionTo('project.manager.main', $stateParams, {
reload: true,
inherit: false,
notify: true
});
});
}
else{
console.log("Assay Edited")
console.log(vm.selectedDatasets)
//vm.assay.samplesDataset = vm.selectedDatasets['sample'];
//vm.assay.featuresDataset = vm.selectedDatasets['feature'];
//vm.assay.observationsDataset = vm.selectedDatasets['data'];

//TODO: REPEATED SAVE AFTER FAILING FIRST tIME WILL KEEP PUSHING TO DAtASETS
//NEED TO REMOVE BEFORE PUSH

//vm.assay.datasets.push(vm.selectedDatasets['sample'])
//vm.assay.datasets.push(vm.selectedDatasets['feature'])
//vm.assay.datasets.push(vm.selectedDatasets['data'])

vm.assay.$update(function(response) {
toaster.pop('success', "SUCCESS", vm.assay.name," was successfully UPDATED.",8000);
$state.transitionTo('admin.project', $stateParams, {
$state.transitionTo('project.manager.main', $stateParams, {
reload: true,
inherit: false,
notify: true
Expand All @@ -199,12 +186,43 @@ var assay;
}

vm.dontSaveAssay = function(){
vm.assay = {}
$state.go('admin.project',{
vm.assay = {};
$state.go('project.manager.main',{
projectId: vm.projectId}
);
}

vm.deleteDS = function(dataset){

SweetAlert.swal({
title: "Are you sure you want to delete "+dataset.name+" dataset ?",
text: "All associated data files will be deleted and all loaded data attached to this dataset will be permanently deleted! ",
type: "warning",
showCancelButton: true,
confirmButtonColor: "#DD6B55",
confirmButtonText: "Yes, delete it!",
cancelButtonText: "No, cancel plx!",
closeOnConfirm: false,
closeOnCancel: false },
function (isConfirm) {
if (isConfirm) {
var pos;
for(var i=0; i< vm.activity.datasets.length;i++) {
console.log(i)
if(vm.currDS.id === vm.activity.datasets[i].id){
console.log(i, 'for',vm.currDS.name)
pos = i;
break;
}
}
vm.activity.datasets.splice(pos,1)
SweetAlert.swal("Deleted!", "Dataset "+vm.currDS.name+" has been deleted.", "success");
} else {
SweetAlert.swal("Cancelled", "", "error");
}
});
}
}

angular.module('bioSpeak.config')
.controller('AssayConfigCtrl',['$scope', '$state','$stateParams','AssayConfigService','toaster',AssayConfigCtrl])
.controller('AssayConfigCtrl',['$scope', '$state','$stateParams','AssayConfigService','toaster','SweetAlert',AssayConfigCtrl])
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