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Remove sendEmail method (#155)
* Remove sendEmail method Use sentry to capture exception instead.
1 parent 8810dd9 commit 3c771fc

15 files changed

Lines changed: 34 additions & 672 deletions

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‎README.md‎

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@@ -49,12 +49,6 @@ For example, if concokb-core runs at `http://localhost:8888/oncokb`, you should
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...
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```
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## Testing
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For front-end, we use Karma and Jasmin to run unit test cases.
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1. Install karma-cli (globally).
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2. Copy /app/data/config.json to **OncoKB.config** in /app/scripts/app.spec.js.
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3. Run **karma start** at root folder.
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## FAQs
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#### Can’t getAllUsers() because of the different rules set in Firebase. It still shows 'don’t have access...' after logging in successfully.
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Add rules to the database.

‎app/index.html‎

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@@ -199,7 +199,6 @@
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<script src="scripts/factories/TreeFactory.js"></script>
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<script src="scripts/factories/VariantFactory.js"></script>
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<script src="scripts/controllers/VariantCtrl.js"></script>
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<script src="scripts/controllers/emailDialogCtrl.js"></script>
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<script src="scripts/controllers/VUSCtrl.js"></script>
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<script src="scripts/filters/Filter.js"></script>
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<script src="scripts/directives/regularview.js"></script>

‎app/scripts/app.spec.js‎

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This file was deleted.

‎app/scripts/controllers/drugs.js‎

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@@ -114,7 +114,6 @@ angular.module('oncokbApp')
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}, function(reason) {
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// something goes wrong then the data in database should not be updated.
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});
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mainUtils.sendEmailtoMultipulUsers(['kundrar@mskcc.org', 'chakravd@mskcc.org', 'nissanm@mskcc.org'], 'Reminder: A therapy preferred name changed.', content);
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}
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}
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};

‎app/scripts/controllers/emailDialogCtrl.js‎

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This file was deleted.

‎app/scripts/controllers/gene.js‎

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Original file line numberDiff line numberDiff line change
@@ -3387,18 +3387,7 @@ angular.module('oncokbApp')
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}, function (error) {
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// Something goes wrong, this needs to be stored into meta file for future update.
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console.log('Failed to update priority.');
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DatabaseConnector.sendEmail({
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sendTo: 'dev.oncokb@gmail.com',
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subject: 'Error when updating treatments\' priority',
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content: JSON.stringify(postData)
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},
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function (result) {
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deferred.rejected(error);
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},
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function (error) {
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deferred.rejected(error);
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}
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);
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Sentry.captureException(new Exception('Error when updating treatments\' priority. Data: ' + JSON.stringify(postData)));
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});
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} else {
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deferred.resolve();

‎app/scripts/controllers/genes.js‎

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@@ -140,7 +140,6 @@ angular.module('oncokbApp')
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rendering: true,
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queueRendering: true
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};
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$scope.adminEmails = [];
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$scope.oncoTree = {
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mainTypes: {}
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};

‎app/scripts/controllers/nav.js‎

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@@ -62,8 +62,7 @@ angular.module('oncokbApp')
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$location.url('/genes');
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}
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}, function(error) {
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mainUtils.sendEmail('dev.oncokb@gmail.com', 'Failed to set user role.',
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'Content: \n' + JSON.stringify(firebaseUser) + '\n\nError: \n' + JSON.stringify(error));
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Sentry.captureException(new Exception('Failed to set user role. Content: \n' + JSON.stringify(firebaseUser) + '\n\nError: \n' + JSON.stringify(error)));
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});
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} else {
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console.log('not logged in yet');

‎app/scripts/directives/createnewdrug.js‎

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@@ -36,7 +36,6 @@ angular.module('oncokbApp')
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$scope.addDrugErrorMessage = 'Failed to create the drug ' + drugName + '! Please contact developers.';
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deferred.reject(error);
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});
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mainUtils.sendEmailtoMultipulUsers(['kundrar@mskcc.org', 'chakravd@mskcc.org', 'nissanm@mskcc.org'], 'Reminder: A therapy has been added.', content);
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}
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else {
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$scope.addDrugErrorMessage = "Sorry, same drug exists.";

‎app/scripts/directives/curationQueue.js‎

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@@ -34,13 +34,11 @@ angular.module('oncokbApp')
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formExpanded: false,
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editing: false,
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hugoVariantMapping: {},
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resendEmail: false,
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queueItemInEditing: '',
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invalidData: false,
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hugoSymbols: [],
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loading: true
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};
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scope.resendEmail = false;
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scope.input = {
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article: '',
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link: '',
@@ -83,7 +81,6 @@ angular.module('oncokbApp')
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});
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}
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scope.data.loading = false;
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scope.secondTimeAutoNotify();
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});
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// The column difference in terms of curation queue location in queues page or gene page it that,
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// gene page has an unique column 'Previously curated in', and queues page has an unique column 'Gene'
@@ -206,9 +203,6 @@ angular.module('oncokbApp')
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currentQueues.push(item);
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$scope.updateQueueInDB(hugoSymbol, currentQueues).then(function(result) {
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$scope.queue.push(item);
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if (item.curator) {
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$scope.sendEmail(item);
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}
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});
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}
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$scope.initialProcess = function(x, type) {
@@ -239,7 +233,6 @@ angular.module('oncokbApp')
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};
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function editCuration(queueItem) {
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$scope.data.resendEmail = false;
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$scope.data.editing = true;
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$scope.data.queueItemInEditing = queueItem;
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$scope.data.modifiedCurator = {};
@@ -334,9 +327,6 @@ angular.module('oncokbApp')
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_.each(_.keys(item), function(key) {
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$scope.data.queueItemInEditing[key] = item[key];
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});
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if ($scope.resendEmail) {
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$scope.sendEmail(queueItem);
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}
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});
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}
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function completeCuration(queueItem) {
@@ -417,60 +407,6 @@ angular.module('oncokbApp')
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console.log('error');
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});
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};
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$scope.sendEmail = function(queueItem) {
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var expiredCuration = false;
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if ($scope.isExpiredCuration(queueItem.dueDay)) {
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expiredCuration = true;
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}
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var email = '';
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for (var i = 0; i < $scope.data.curators.length; i++) {
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if (queueItem.curator === $scope.data.curators[i].name) {
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email = $scope.data.curators[i].email;
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break;
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}
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}
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if (!email) return;
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var content = 'Dear ' + queueItem.curator.split(' ')[0] + ',\n\n';
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if (expiredCuration) {
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content += 'You have not completed curation of the assigned publication: ' + queueItem.article;
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if (queueItem.link) {
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content += '(' + queueItem.link + ')';
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}
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content += ' which was due on ' + $scope.getFormattedDate(queueItem.dueDay) + '. Please complete this assignment as soon as possible and let us know when you have done this. \n\nIf you have already completed this task, please remember to CLICK THE GREEN CHECK BOX BUTTON at the Curation Queue page or the bottom of the gene page (this will let us know the task is complete). If you have any questions or concerns please email or slack us as needed.';
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content += 'Thank you, \nOncoKB Admin';
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} else {
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content += queueItem.addedBy + ' of OncoKB would like you curate the following publications in the indicated alteration, tumor type and section:\n\n';
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var tempArr = [queueItem.article];
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if (queueItem.link) {
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tempArr = tempArr.concat(['(', queueItem.link, ')']);
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}
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if (queueItem.variant) {
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tempArr = tempArr.concat(['Alteration:', queueItem.variant + ',']);
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}
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if (queueItem.subType) {
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tempArr = tempArr.concat(['Tumor type:', queueItem.subType + ',']);
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}
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if (queueItem.section) {
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tempArr = tempArr.concat(['Section:', queueItem.section]);
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}
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content += tempArr.join(' ') + '\n';
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if (queueItem.comment) {
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content += queueItem.comment + '\n';
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}
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content += '\nPlease try to curate this literature before ' + $scope.getFormattedDate(queueItem.dueDay) + ' and remember to log your hours for curating this data.\n\n';
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content += 'IMPORTANT: Please remember to CLICK THE GREEN CHECK BOX BUTTON at the Curation Queue page or the bottom of the gene page (this will let us know the task is complete).\n\n';
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content += 'If you have any questions or concerns please email or slack ' + queueItem.addedBy + '.\n\n';
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content += 'Thank you, \nOncoKB Admin';
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}
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var subject = 'OncoKB Curation Assignment';
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mainUtils.sendEmail(email, subject, content).then(function() {
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if (expiredCuration) {
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setCurationNotified(queueItem);
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}
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}, function(error) {
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dialogs.error('Error', 'Failed to notify curator automatically. Please send curator email manually.');
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});
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};
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var annotationLocation = $scope.specifyAnnotationInGene();
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$scope.getAnnotationLocation = function(x) {
@@ -513,7 +449,6 @@ angular.module('oncokbApp')
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$scope.data.editing = false;
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$scope.predictedArticle = '';
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$scope.validPMID = false;
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$scope.data.resendEmail = false;
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};
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$scope.isExpiredCuration = mainUtils.isExpiredCuration;
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$scope.checkInput = function() {
@@ -526,20 +461,8 @@ angular.module('oncokbApp')
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if ($scope.data.editing && !$scope.data.invalidData) {
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if ($scope.input.curator && queueItem.curator !== $scope.input.curator.name ||
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$scope.input.dueDay && queueItem.dueDay !== new Date($scope.input.dueDay).getTime()) {
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$scope.data.resendEmail = true;
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} else {
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$scope.data.resendEmail = false;
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}
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}
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$scope.resendEmail = $scope.data.resendEmail;
535-
};
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$scope.secondTimeAutoNotify = function() {
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_.each($scope.queue, function (queueItem) {
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var hugoSymbol = queueItem.hugoSymbol;
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if (hugoSymbol && queueItem.curator && !queueItem.curated && mainUtils.isExpiredCuration(queueItem.dueDay) && !queueItem.notified) {
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$scope.sendEmail(queueItem);
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}
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});
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};
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$scope.getQueuesByGene = function(hugoSymbol) {
545468
return $rootScope.firebaseQueues[hugoSymbol] ? angular.copy($rootScope.firebaseQueues[hugoSymbol].queue) : [];

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