Merge pull request #562 from salimkanoun/dev

0.6.2
salimkanoun · May 12, 2021 · bc5f15b · bc5f15b
2 parents d454865 + 890fd6f
commit bc5f15b
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Showing 33 changed files with 323 additions and 326 deletions.
diff --git a/BackEnd/adapter/bullAdapter.js b/BackEnd/adapter/bullAdapter.js
@@ -8,7 +8,7 @@ const REDIS_OPTIONS = {
 }
 
 const queues = [];
-const CLEAN_GRACE = 50;
+const CLEAN_GRACE = 0;
 const DEFAULT_POOL_SIZE = 10;
 
 class Queue extends event.EventEmitter {
@@ -49,6 +49,10 @@ class Queue extends event.EventEmitter {
             }
             this.emit('error', err);
         });
+        this._queue.on('failed', (job, err) => {
+            console.log(err);
+            this.emit('failed', job, err);
+        });
         queues.push(this);
     }
 
@@ -122,7 +126,14 @@ class Queue extends event.EventEmitter {
      * Remove all jobs of the queue
      * @returns {Promise<>} Promise resolved when the clean is done
      */
-    clean = () => Promise.all(Object.values(Queue._JOB_STATES_CLEAN).map(x => this._queue.clean(CLEAN_GRACE, x)));
+    clean = async () => {
+        await Promise.all(Object.values(Queue._JOB_STATES_CLEAN).map(x => this._queue.clean(CLEAN_GRACE, x)))
+
+        await this._queue.getActive().then(
+            jobs => Promise.all(jobs.map(job => job.releaseLock().then(
+                () => job.remove()))));
+
+    };
 
     /**
      * Returns a promise completed when the queue is ready
@@ -146,16 +157,17 @@ class Queue extends event.EventEmitter {
 
     static _batch_processor(processor) {
         return async (job, done) => {
+            job.progress(new Array(job.data.jobs.length).fill(null));
             let subJobs = job.data.jobs.map((j, i) => {
                 return {
                     data: j,
                     progress: async (progress = null) => {
-                        let prog = await job.progress() || [];
+                        let prog = await job.progress();
                         if (progress) {
                             prog[i] = progress;
                             await job.progress(prog);
                         }
-                        return prog;
+                        return prog[i];
                     }
                 }
             });
@@ -216,6 +228,10 @@ class Job {
     update(data) {
         return this._bullJob.update(data);
     }
+
+    remove() {
+        return this._bullJob.remove()
+    }
 }
 
 Queue.Job = Job;
@@ -256,6 +272,7 @@ class BatchedJob extends Job {
         this._bullJob.data.jobs[this._i] = data;
         return this._bullJob.update(this._bullJob.data);
     }
+
 }
 
 Queue.JOB_STATES = {

diff --git a/BackEnd/controllers/task.js b/BackEnd/controllers/task.js
@@ -43,8 +43,8 @@ const addDeleteTask = async (req, res) => {
  */
 const addRetrieveTask = async (req, res) => {
 
-    let answers = req.body.retrieveArray
-    let id = await RetrieveTask.createTask(req.roles.username, req.body.projectName, answers);
+    let retrieveArray = req.body.retrieveArray
+    let id = await RetrieveTask.createTask(req.roles.username, req.body.projectName, retrieveArray);
     res.send(id)
 }
 

diff --git a/BackEnd/model/Ldap.js b/BackEnd/model/Ldap.js
@@ -55,6 +55,7 @@ const Ldap = {
 
     getAllCorrespondences: async () => {
         const correspondances = await DistantUser.getAllLocalRoleAndLdapGroup()
+        let results = []
         correspondances.forEach( (correspondance) => {
             results.push({ localRole: correspondance.local_role, ldapGroup: correspondance.ldap_group })
         });

diff --git a/BackEnd/model/Orthanc.js b/BackEnd/model/Orthanc.js
@@ -473,7 +473,7 @@ class Orthanc {
     }
 
     async makeAnon(level, orthancID, profile, newAccessionNumber, newPatientID, newPatientName, newStudyDescription, synchronous) {
-        let postData = this.buildAnonQuery(profile, newAccessionNumber, newPatientID, newPatientName, newStudyDescription, synchronous);
+        let postData = this.buildAnonQuery(profile, newAccessionNumber, newPatientID, newPatientName, newStudyDescription, synchronous)
         const answer = await ReverseProxy.getAnswer('/' + level + '/' + orthancID + '/anonymize', 'POST', postData)
         return answer
     }

diff --git a/BackEnd/model/Users.js b/BackEnd/model/Users.js
@@ -151,7 +151,7 @@ class Users {
     async getLDAPUserRight() {
 
         //Get Ldap Group having a local role correspondance
-        const ldapMatches = await DistantUser.getAllDistantUser()
+        const ldapMatches = await DistantUser.getAllLocalRoleAndLdapGroup()
 
         //Flatten known LdapGroup in Array
         let knownLdapGroups = ldapMatches.map((match) => {

diff --git a/BackEnd/model/tasks/AnonTask.js b/BackEnd/model/tasks/AnonTask.js
@@ -1,8 +1,8 @@
-const {OTJSForbiddenException} = require("../../Exceptions/OTJSErrors");
+const { OTJSForbiddenException } = require("../../Exceptions/OTJSErrors");
 const TaskType = require("../TaskType");
 const Queue = require('../../adapter/bullAdapter');
 const Orthanc = require('../Orthanc');
-const {v4: uuid} = require('uuid');
+const { v4: uuid } = require('uuid');
 
 let orthanc = new Orthanc();
 const JOBS_TTL = 5;
@@ -159,7 +159,7 @@ class AnonTask {
      */
     static async delete(taskId) {
         let anonJobs = await AnonTask._getJobs(taskId);
-        anonJobs.forEach(job => job.remove()); //Delete jobs of the task
+        anonJobs.forEach(job => { job.remove() }); //Delete jobs of the task
     }
 
     /**
@@ -198,7 +198,13 @@ class AnonTask {
         let item = job.data.item
 
         //Requesting orthanc API to anonymize a study
-        let anonAnswer = await orthanc.makeAnon('studies', item.orthancStudyID, item.profile, item.newAccessionNumber, item.newPatientID, item.newPatientName, item.newStudyDescription, false);
+
+
+        let anonAnswer = await orthanc.makeAnon('studies', item.orthancStudyID, item.profile, item.newAccessionNumber, item.newPatientID, item.newPatientName, item.newStudyDescription, false).catch((err) => {
+            console.error(item)
+            console.error(err);
+            done(err);
+        })
 
         //Monitor orthanc job
         orthanc.monitorJob(anonAnswer.Path, (response) => {

diff --git a/BackEnd/model/tasks/ExportTask.js b/BackEnd/model/tasks/ExportTask.js
@@ -98,8 +98,8 @@ class ExportTask {
      * Remove all jobs for export
      */
     static async flush() {
-        await Promise.all(JOBS_STATUS.map(x => archiveQueue.clean()));
-        await Promise.all(JOBS_STATUS.map(x => exporter.sendQueue.clean(1, x)));
+         archiveQueue.clean()
+         exporter.sendQueue.clean()
     }
 
     /**

diff --git a/BackEnd/model/tasks/RetrieveTask.js b/BackEnd/model/tasks/RetrieveTask.js
@@ -1,9 +1,9 @@
-const {OTJSForbiddenException, OTJSNotFoundException} = require("../../Exceptions/OTJSErrors");
+const { OTJSForbiddenException, OTJSNotFoundException, OTJSBadRequestException } = require("../../Exceptions/OTJSErrors");
 const Orthanc = require("../Orthanc");
 const TaskType = require("../TaskType");
 const Queue = require("../../adapter/bullAdapter");
 const OrthancQueryAnswer = require("../OrthancData/queries-answer/OrthancQueryAnswer");
-const {v4: uuid} = require('uuid');
+const { v4: uuid } = require('uuid');
 const schedule = require('node-schedule');
 const Options = require('../Options');
 const time = require('../../utils/time');
@@ -29,8 +29,10 @@ class RetrieveTask {
 
         let retrieve = 0;
         for (const job of retrieveJobs) {
-            retrieve += await job.progress();
+            let jobProgress = await job.progress()
+            if (jobProgress != null) retrieve += jobProgress
         }
+
         retrieve /= (retrieveJobs.length === 0 ? 1 : retrieveJobs.length);
         return {
             validation,
@@ -110,17 +112,18 @@ class RetrieveTask {
      */
     static async validateTask(id) {
         let task = await RetrieveTask.getTask(id);
-        if (task === null) throw new OTJSNotFoundException("No task of this kind");
 
-        let jobs = await validationQueue.getJobs();
+        if (task === null) throw new OTJSNotFoundException("No task of this kind");
+        if (task.progress.validation != 100 ) throw OTJSBadRequestException("Items validation still in progress")
+        let jobs = await validationQueue.getJobs()
 
         let jobsData = [];
         for (const job of jobs) {
             jobsData.push(
                 {
                     data: job.data
-                });
-            if (!await job.finished()) return;
+                }
+            );
         }
         await retrieveQueue.addJobs(jobsData);
     }
@@ -138,15 +141,14 @@ class RetrieveTask {
         let progress = await RetrieveTask.getProgress(validationJobs, retrieveJobs);
 
         //Making state
-        let state = null;
-        if (progress.validation === 0) {
-            state = 'waiting validation';
-        } else if (progress.validation < 100) {
-            state = 'validation';
+        let state = null
+
+        if (progress.validation < 100) {
+            state = 'validating robot';
         } else if (progress.validation === 100 && progress.retrieve === 0 && retrieveJobs.length === 0) {
-            state = 'waiting retireve'
+            state = 'waiting admin validation'
         } else if (progress.validation === 100 && progress.retrieve < 100 && retrieveJobs.length !== 0) {
-            state = 'retrieve';
+            state = 'retrieving';
         } else if (progress.validation === 100 && progress.retrieve === 100 && retrieveJobs.length !== 0) {
             state = 'completed';
             for (const job of validationJobs) {

diff --git a/FrontEnd/package.json b/FrontEnd/package.json
@@ -1,6 +1,6 @@
 {
   "name": "orthanctoolsjsfront",
-  "version": "0.1.0",
+  "version": "0.6.2",
   "proxy": "http://localhost:4000",
   "private": true,
   "dependencies": {

diff --git a/FrontEnd/src/assets/styles/orthancToolsJs.css b/FrontEnd/src/assets/styles/orthancToolsJs.css
@@ -436,6 +436,5 @@ button > p {
 }
 
 .table-responsive {
-    overflow-x: visible;
-
+    overflow-x: auto;
 }
diff --git a/FrontEnd/src/components/Admin/Endpoints/EndpointsOptions.js b/FrontEnd/src/components/Admin/Endpoints/EndpointsOptions.js
@@ -75,7 +75,7 @@ export default class EndpointsOptions extends Component{
     render = () => {
         return (
             <div>
-                <h2>Endpoint Options</h2>
+                <h2>Export Transcoding </h2>
                 <div className='grid-form-group'>
                     <label htmlFor="export_transcoding">Transfer Syntax : </label>
                     <Select single options={TRANSCODING_OPTIONS} name='export_transcoding' value={this.getSelectedObject(TRANSCODING_OPTIONS, this.state.export_transcoding)} onChange={this.handleChangeSelect} />

diff --git a/FrontEnd/src/components/Admin/Labels/LabelRootPanel.js b/FrontEnd/src/components/Admin/Labels/LabelRootPanel.js
@@ -9,7 +9,8 @@ class LabelRootPanel extends Component {
     state = {
         userManagement: null,
         labels: [],
-        search: ''
+        search: '',
+        createLabel:''
     }
 
     componentDidMount() {

diff --git a/FrontEnd/src/components/Admin/Labels/UserManagementModal.js b/FrontEnd/src/components/Admin/Labels/UserManagementModal.js
@@ -53,16 +53,18 @@ export default class UserManagementModal
                 <Modal.Body>
                     <Table striped bordered hover>
                         <thead>
-                        <th>Users</th>
+                        <tr><th>Users</th></tr>
                         </thead>
-                        {this.state.userlabels.map(userlabel => <tr
-                            className={'d-flex justify-content-between align-content-center'}>
-                            <p>{this.state.users.filter(user => user.id === userlabel.user_id)[0].username}</p>
-                            <Button variant={"danger"}
-                                    onClick={() => apis.userlabel.deleteUserLabel(userlabel.user_id, this.props.label).then(() => this._refreshUserLabels())}>
-                                {'X'}
-                            </Button>
-                        </tr>)}
+                        <tbody>
+                            {this.state.userlabels.map(userlabel => <tr key={userlabel.user_id}
+                                className={'d-flex justify-content-between align-content-center'}>
+                                <td>{this.state.users.filter(user => user.id === userlabel.user_id)[0].username}</td>
+                                <td><Button  variant={"danger"}
+                                        onClick={() => apis.userlabel.deleteUserLabel(userlabel.user_id, this.props.label).then(() => this._refreshUserLabels())}>
+                                    {'X'}
+                                </Button></td>
+                            </tr>)}
+                        </tbody>
                     </Table>
                     <UserSelect
                         users={this.state.users.filter(user => !this.state.userlabels.map(ul => ul.user_id).includes(user.id))}

diff --git a/FrontEnd/src/components/Admin/Labels/UserSelect.js b/FrontEnd/src/components/Admin/Labels/UserSelect.js
@@ -65,7 +65,7 @@ export default class UserSelect extends Component {
     render() {
         let elements = this.props.users
             .filter(user => user.username.includes(this.state.value))
-            .map(user => <Dropdown.Item eventKey={user.username}>{user.username}</Dropdown.Item>)
+            .map(user => <Dropdown.Item key={user.username} eventKey={user.username}>{user.username}</Dropdown.Item>)
 
         return (
             <Dropdown onSelect={this.handleSelect} show={this.state.show}>

diff --git a/FrontEnd/src/components/Admin/Robots/RobotStatus.js b/FrontEnd/src/components/Admin/Robots/RobotStatus.js
@@ -20,8 +20,11 @@ export default class RobotStatus extends Component {
         dataField: 'queriesNb',
         text: 'Number of Queries'
     }, {
-        dataField: 'progress',
-        text: 'Progress'
+        dataField: 'validation',
+        text: 'Progress Validation'
+    }, {
+        dataField: 'retrieve',
+        text: 'Progress Retrieve'
     }, {
         dataField: 'state',
         text: 'State'
@@ -107,7 +110,8 @@ export default class RobotStatus extends Component {
                     key: Math.random(),
                     name: robotJob.details.projectName,
                     username: robotJob.creator,
-                    progress: (robotJob.progress.retrieve+robotJob.progress.validation)/2,
+                    retrieve: robotJob.progress.retrieve + '%',
+                    validation: robotJob.progress.validation + '%',
                     state: robotJob.state,
                     queriesNb: robotJob.details.items.length,
                     valid: robotJob.details.valid,

diff --git a/FrontEnd/src/components/Admin/UserManagement/CreateMatch.js b/FrontEnd/src/components/Admin/UserManagement/CreateMatch.js
@@ -72,7 +72,7 @@ export default class CreateMatch extends Component {
         let roles = []
         try {
             let existingsRoles = await apis.role.getRoles()
-            existingsRoles.map( (role) => {
+            existingsRoles.forEach( (role) => {
                 roles.push({value : role.name, label : role.name})
             })
         } catch (error) {