Merge branch 'develop' into feature/DEVSU-2457-update-kbmatches-multi…

…ple-variants-per-statement
bcgsc · Oct 21, 2024 · b254bee · b254bee
2 parents b4be7ff + a664414
commit b254bee
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Showing 8 changed files with 125 additions and 17 deletions.
diff --git a/app/api/graphkb.js b/app/api/graphkb.js
@@ -25,7 +25,7 @@ const graphkbAutocomplete = async (targetType, graphkbToken, keyword = null) =>
   if (targetType === 'context') {
     query.target = 'Vocabulary';
     query.queryType = 'ancestors';
-    query.filters = {name: 'therapeutic efficacy'};
+    query.filters = {name: 'therapeutic indicator'};
   } else {
     if (targetType === 'evidenceLevel') {
       query.target = 'EvidenceLevel';
@@ -49,7 +49,7 @@ const graphkbAutocomplete = async (targetType, graphkbToken, keyword = null) =>
     }
   }
 
-  return request({
+  const res = await request({
     url: `${uri}/query`,
     method: 'POST',
     body: JSON.stringify(query),
@@ -59,6 +59,19 @@ const graphkbAutocomplete = async (targetType, graphkbToken, keyword = null) =>
       'Content-Type': 'application/json',
     },
   });
+
+  // DEVSU-2344; Filtering results for context route
+  // Needs to be done after the query since cannot be combined with ancestors as a subquery
+  if (targetType === 'context') {
+    res.result = res.result.filter((term) => {
+      return [
+        'resistance', 'sensitivity', 'toxicity',
+      ].includes(term.displayName);
+    });
+    res.metadata.records = res.result.length;
+  }
+
+  return res;
 };
 
 /* Get IPR evidence level descriptions from GraphKB

diff --git a/app/libs/email.js b/app/libs/email.js
@@ -57,15 +57,16 @@ const getEmailList = async (triggers) => {
 const notifyUsers = async (subject, text, triggers) => {
   const emailList = await getEmailList(triggers);
 
-  emailList.forEach(({toEmail, notifId, eventType}) => {
+  for (const emailItem of emailList) {
+    const {toEmail, notifId, eventType} = emailItem;
     const mailOptions = {
       from: `${email}${domain}`,
       to: toEmail,
       subject,
       text,
     };
-    addJobToEmailQueue({mailOptions, notifId, eventType});
-  });
+    await addJobToEmailQueue({mailOptions, notifId, eventType});
+  }
 };
 
 module.exports = {sendEmail, getEmailList, notifyUsers};
diff --git a/app/models/notification/notificationTrack.js b/app/models/notification/notificationTrack.js
@@ -16,6 +16,13 @@ module.exports = (sequelize, Sq) => {
         },
         allowNull: false,
       },
+      jobId: {
+        name: 'jobId',
+        field: 'job_id',
+        unique: false,
+        type: Sq.INTEGER,
+        allowNull: false,
+      },
       recipient: {
         name: 'recipient',
         field: 'recipient',

diff --git a/app/queue.js b/app/queue.js
@@ -41,7 +41,20 @@ const EMAIL_REMOVE_CONFIG = {
 const addJobToEmailQueue = async (data) => {
   if (emailQueue) {
     logger.info('adding email to queue: ', data);
-    return emailQueue.add('job', data, EMAIL_REMOVE_CONFIG);
+    const job = await emailQueue.add('job', data, EMAIL_REMOVE_CONFIG);
+    try {
+      await db.models.notificationTrack.create({
+        notificationId: data.notifId,
+        jobId: job.id,
+        recipient: data.mailOptions.to,
+        reason: data.eventType,
+        outcome: 'created',
+      });
+    } catch (error) {
+      logger.error(`Unable to create notification track ${error}`);
+      throw new Error(error);
+    }
+    return job;
   }
   return null;
 };
@@ -84,10 +97,13 @@ const setUpEmailWorker = (emailJobProcessor) => {
 
 const onEmailWorkderCompleted = async (job) => {
   try {
-    await db.models.notificationTrack.create({
-      notificationId: job.data.notifId,
-      recipient: job.data.mailOptions.to,
-      reason: job.data.eventType,
+    const notification = await db.models.notificationTrack.findOne({
+      where: {
+        notificationId: job.data.notifId,
+        jobId: job.id,
+      },
+    });
+    await notification.update({
       outcome: 'completed',
     });
   } catch (error) {
@@ -98,11 +114,14 @@ const onEmailWorkderCompleted = async (job) => {
 
 const onEmailWorkderFailed = async (job) => {
   try {
-    await db.models.notificationTrack.create({
-      notificationId: job.data.notifId,
-      recipient: job.data.mailOptions.to,
-      reason: job.data.eventType,
-      outcome: 'Failed',
+    const notification = await db.models.notificationTrack.findOne({
+      where: {
+        notificationId: job.data.notifId,
+        jobId: job.id,
+      },
+    });
+    await notification.update({
+      outcome: 'failed',
     });
   } catch (error) {
     logger.error(`Unable to create notification track ${error}`);
@@ -124,6 +143,20 @@ const emailProcessor = async (job) => {
   });
 
   try {
+    try {
+      const notification = await db.models.notificationTrack.findOne({
+        where: {
+          notificationId: job.data.notifId,
+          jobId: job.id,
+        },
+      });
+      await notification.update({
+        outcome: 'processing',
+      });
+    } catch (error) {
+      logger.error(`Unable to add process notification track ${error}`);
+      throw new Error(error);
+    }
     await transporter.sendMail(job.data.mailOptions);
   } catch (err) {
     logger.error(JSON.stringify(job.data.mailOptions));

diff --git a/app/routes/report/report.js b/app/routes/report/report.js
@@ -175,8 +175,8 @@ router.route('/')
         ...((keyVariant && matchingThreshold) ? {
           '$genomicAlterationsIdentified.geneVariant$': {
             [Op.in]: literal(
-              `(SELECT "geneVariant" 
-              FROM (SELECT "geneVariant", word_similarity('${keyVariant}', "geneVariant") FROM reports_summary_genomic_alterations_identified) AS subquery 
+              `(SELECT "geneVariant"
+              FROM (SELECT "geneVariant", word_similarity('${keyVariant}', "geneVariant") FROM reports_summary_genomic_alterations_identified) AS subquery
               WHERE word_similarity >= ${matchingThreshold})`,
             ),
           },
@@ -372,6 +372,15 @@ router.route('/')
         projectIdArray.push(project.project_id);
       });
 
+      await db.models.notification.findOrCreate({
+        where: {
+          userId: req.user.id,
+          eventType: NOTIFICATION_EVENT.REPORT_CREATED,
+          templateId: report.templateId,
+          projectId: report.projects[0].project_id,
+        },
+      });
+
       await email.notifyUsers(
         `Report Created: ${req.body.patientId} ${req.body.template}`,
         `New report:

diff --git a/app/routes/report/reportUser.js b/app/routes/report/reportUser.js
@@ -130,6 +130,17 @@ router.route('/')
         addedBy_id: req.user.id,
       });
 
+      const report = await db.models.report.findOne({where: {id: req.report.id}});
+      const reportProject = await db.models.reportProject.findOne({where: {report_id: req.report.id}});
+      const notif = await db.models.notification.findOrCreate({
+        where: {
+          userId: req.user.id,
+          eventType: NOTIFICATION_EVENT.USER_BOUND,
+          templateId: report.templateId,
+          projectId: reportProject.project_id,
+        },
+      });
+
       // Try sending email
       try {
         await email.notifyUsers(
@@ -140,8 +151,11 @@ router.route('/')
             templateId: req.report.templateId,
           },
         );
+
+        await notif[0].update({status: 'Success'}, {userId: req.user.id});
         logger.info('Email sent successfully');
       } catch (error) {
+        await notif[0].update({status: 'Unsuccess'}, {userId: req.user.id});
         logger.error(`Email not sent successfully: ${error}`);
       }
 

diff --git a/migrations/20240918231722-DEVSU-2449-add-job-id-to-notification-track-table.js b/migrations/20240918231722-DEVSU-2449-add-job-id-to-notification-track-table.js
@@ -0,0 +1,20 @@
+const TABLE = 'notifications_tracks';
+
+module.exports = {
+  up: async (queryInterface, Sq) => {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      await queryInterface.addColumn(
+        TABLE,
+        'job_id',
+        {
+          type: Sq.INTEGER,
+        },
+        {transaction},
+      );
+    });
+  },
+
+  down: async () => {
+    throw new Error('Not Implemented!');
+  },
+};
diff --git a/test/routes/report/reportUser.test.js b/test/routes/report/reportUser.test.js
@@ -61,6 +61,8 @@ beforeAll(async () => {
 describe('/reports/{REPORTID}/user', () => {
   let user;
   let report;
+  let project;
+  let reportProject;
   let createUser;
   let userReportBinding;
 
@@ -77,6 +79,13 @@ describe('/reports/{REPORTID}/user', () => {
       createdBy_id: user.id,
     });
 
+    project = await db.models.project.create({name: 'test'});
+
+    reportProject = await db.models.reportProject.create({
+      reportId: report.id,
+      project_id: project.id,
+    });
+
     createUser = await db.models.user.create({
       username: uuidv4(),
       type: 'bcgsc',
@@ -316,6 +325,8 @@ describe('/reports/{REPORTID}/user', () => {
     // delete newly created report and all of it's components
     // indirectly by hard deleting newly created patient
     await db.models.report.destroy({where: {ident: report.ident}});
+    await db.models.project.destroy({where: {ident: project.ident}});
+    await db.models.reportProject.destroy({where: {id: reportProject.id}});
   });
 });