Merge branch 'master' of https://github.com/BD2KGenomics/brca-website

acthp · acthp · commit 84a32e2ad9d7 · 2016-08-01T12:27:08.000-07:00
diff --git a/content/researchWarning.md b/content/researchWarning.md
@@ -1,3 +1,3 @@
-You are leaving the BRCA Exchange Expert Reviewed portal and entering the portal to view all variant data. This portal contains a much larger set of variant data than the Expert Reviewed portal, and includes variants that have not yet been subject to expert review by the ENIGMA consortium. Pathogenicity assignments are from the original submitters.
+You are leaving the BRCA Exchange Expert Reviewed portal and entering the portal to view all public variant data. This portal contains a much larger set of variant data than the Expert Reviewed portal, and includes variants that have not yet been subject to expert review by the ENIGMA consortium. Pathogenicity assignments are from the original submitters.
 
-Are you sure you want to leave the Expert Reviewed portal to view all variant data?
+Are you sure you want to leave the Expert Reviewed portal to view all public variant data?
diff --git a/content/variantsResearch.md b/content/variantsResearch.md
@@ -1 +1 @@
-This is all BRCA Exchange variant data. It contains information drawn from multiple databases which have been intelligently merged together, one row per variant. It is intended to provide researchers with a set of BRCA variations and annotations which is as comprehensive as possible.
+This is all BRCA Exchange public variant data. It contains information drawn from multiple databases which have been intelligently merged together, one row per variant. It is intended to provide researchers with a set of BRCA variations and annotations which is as comprehensive as possible.
diff --git a/django/brca/settings.py b/django/brca/settings.py
@@ -70,11 +70,6 @@
     'brca-website.cloudapp.net'
 )
 
-
-EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
-
-DEFAULT_FROM_EMAIL = "no-reply@brcaexchange.org"
-
 ROOT_URLCONF = 'brca.urls'
 
 TEMPLATES = [
@@ -132,8 +127,8 @@
 SITE_ID = 1
 
 EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
-EMAIL_PORT = 25
-EMAIL_USE_TLS = True
+EMAIL_PORT = 465
+EMAIL_USE_SSL = True
 DEFAULT_FROM_EMAIL = 'noreply@brcaexchange.org'
 
 AUTH_USER_MODEL = 'users.MyUser'
diff --git a/django/users/urls.py b/django/users/urls.py
@@ -11,6 +11,7 @@
     url(r'^update/$', views.update, name="update"),
     url(r'^password_reset/$', views.password_reset, name="password_reset"),
     url(r'^confirm/(?P<activation_key>\w+)/$', views.confirm, name="confirm"),
+    url(r'^resend-activation/$', views.resend_activation, name="resend_activation"),
     url(r'^update_password/(?P<password_reset_token>\w+)/$', views.update_password, name="update_password"),
     url(r'^check_password_token/(?P<password_reset_token>\w+)/$', views.check_password_token, name="check_password_token"),
 ]
diff --git a/django/users/views.py b/django/users/views.py
@@ -114,6 +114,30 @@ def register(request):
 
     return JsonResponse({'success': True})
 
+def resend_activation(request):
+    email = request.POST.get('email', '')
+    user = MyUser.objects.filter(email = email)
+    if not user:
+        response = JsonResponse({'success': False, 'error': 'Email not found'})
+        response['Access-Control-Allow-Origin'] = '*'
+        return response;
+    user = user[0]
+
+    # resend activation email
+    url = "{0}confirm/{1}".format(site_settings.URL_FRONTEND, user.activation_key)
+    plaintext_email = get_template(os.path.join(settings.BASE_DIR, 'users', 'templates', 'registration_email.txt'))
+    html_email = get_template(os.path.join(settings.BASE_DIR, 'users', 'templates', 'registration_email.html'))
+
+    d = Context({'firstname': user.firstName, 'url': url})
+
+    subject, from_email, to = 'BRCAExchange account confirmation', 'noreply@brcaexchange.org', user.email
+    text_content = plaintext_email.render(d)
+    html_content = html_email.render(d)
+    msg = EmailMultiAlternatives(subject, text_content, from_email, [to])
+    msg.attach_alternative(html_content, "text/html")
+    msg.send()
+
+    return JsonResponse({'success': True})
 
 def confirm(request, activation_key):
     user = MyUser.objects.filter(activation_key=activation_key)
diff --git a/js/NavBarNew.js b/js/NavBarNew.js
@@ -58,7 +58,7 @@ var NavBarNew = React.createClass({
                     <span className="BRCA">BRCA</span>
                     <span className="exchange"> Exchange</span>
                 </h1>
-                {this.props.mode === 'research_mode' && <span id="research-label" className="label label-info">All Data</span>}
+                {this.props.mode === 'research_mode' && <span id="research-label" className="label label-info">All Public Data</span>}
                 {this.props.mode === 'default' && <span id="research-label" className="label label-info">Expert Reviewed</span>}
             </a>);
         return (
diff --git a/js/Signin.js b/js/Signin.js
@@ -133,7 +133,8 @@ var Signin = React.createClass({
     getInitialState: function () {
         return {
             submitted: null,
-            success: null
+            success: null,
+            successMessage: null
         }
     },
     render: function () {
@@ -142,6 +143,10 @@ var Signin = React.createClass({
             message = <div className="alert alert-danger">
                 <p>{this.state.error}</p>
             </div>
+        } else if (this.state.success && this.state.successMessage != null) {
+            message = <div className="alert alert-success">
+                <p>{this.state.successMessage}</p>
+            </div>
         }
         return (
             <Grid id="main-grid">
@@ -171,15 +176,42 @@ var Signin = React.createClass({
     handleSubmit: function () {
         if (this.refs.contactForm.isValid()) {
             var formData = this.refs.contactForm.getFormData();
-            auth.login(formData.email, formData.password, (loggedIn) => {
+            auth.login(formData.email, formData.password, (loggedIn, error) => {
                 if (loggedIn) {
                     var target = this.getQuery()["target"];
                     if (target == null) {
                         target = '/profile';
                     }
                     this.transitionTo(target)
                 } else {
-                    this.setState({error: "Please try again"});
+                    if (error.non_field_errors == 'User account is disabled.') {
+                        var showSuccess = (() => {this.setState({success: true, successMessage: "Activation email sent."})});
+                        var showFailure = (msg => {this.setState({error: msg})});
+                        var resend_activation = function() {
+                            $.post({
+                                url: config.backend_url + "/accounts/resend-activation/",
+                                data: {email: formData.email},
+                                success: function (data) {
+                                    showFailure(data.error);
+                                    if (data.success) {
+                                        showSuccess()
+                                    }
+                                },
+                                error: function (xhr, ajaxOptions, thrownError) {
+                                    showFailure('Could not complete this action');
+                                }.bind(this)
+                            });
+                        };
+                        var activation_message =
+                            <span>
+                                This account has not yet been activated. Please check your email for an activation link, or <a href="#" onClick={resend_activation}>resend activation</a>.
+                            </span>
+                        this.setState({error: activation_message});
+                    } else if (error.non_field_errors == 'Unable to login with provided credentials.') {
+                        this.setState({error: "Incorrect email/password"});
+                    } else {
+                        this.setState({error: error.non_field_errors});
+                    }
                 }
             });
         } else {
diff --git a/js/VariantTable.js b/js/VariantTable.js
@@ -102,7 +102,7 @@ var research_mode_columns = [
 
     {title: 'Gene Symbol', prop: 'Gene_Symbol'},
     {title: 'Genome (GRCh36)', prop: 'Genomic_Coordinate_hg36'},
-    {title: 'Genome (GRCh37)', prop: 'Genomic_Coordinaty1e_hg37'},
+    {title: 'Genome (GRCh37)', prop: 'Genomic_Coordinate_hg37'},
     {title: 'Genome (GRCh38)', prop: 'Genomic_Coordinate_hg38'},
 
     {title: 'Mutation category (BIC)', prop: 'Mutation_type_BIC'},
@@ -494,7 +494,7 @@ var ResearchVariantTableSupplier = function (Component) {
 };
 
 var VariantTableSupplier = function (Component) {
-    var ResearchVariantTableComponent = React.createClass({
+    var VariantTableComponent = React.createClass({
         mixins: [PureRenderMixin],
         getColumns: function () {
             return columns;
@@ -518,7 +518,7 @@ var VariantTableSupplier = function (Component) {
             );
         }
     });
-    return ResearchVariantTableComponent;
+    return VariantTableComponent;
 };
 
 
diff --git a/js/auth.js b/js/auth.js
@@ -14,7 +14,7 @@ module.exports = {
                 localStorage.token = res.token;
                 if (cb) cb(true)
             } else {
-                if (cb) cb(false)
+                if (cb) cb(false, res.error)
             }
         })
     },
@@ -48,9 +48,10 @@ module.exports = {
                     token: res.token
                 })
             },
-            error: function () {
+            error: function (res) {
                 cb({
-                    authenticated: false
+                    authenticated: false,
+                    error: res.responseJSON
                 })
             }
         });
diff --git a/js/config.js b/js/config.js
@@ -1,6 +1,7 @@
 'use strict';
 
 module.exports = {
-    captcha_key: '6LdwNBwTAAAAACFRvttQc08debhGzAzNY0xWQhxw',
+    captcha_key: '6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI',
+    //backend_url: 'http://brcaexchange.cloudapp.net/backend'
     backend_url: 'http://localhost:8000'
-};
+};
diff --git a/js/d3Lollipop.js b/js/d3Lollipop.js
@@ -58,7 +58,8 @@ var D3Lollipop = React.createClass({
     filterAttributes: function (obj) {
         var oldObj = _(obj).pick('Genomic_Coordinate_hg38', 'Pathogenicity_default');
         var parts = oldObj.Genomic_Coordinate_hg38.split(':');
-        var chrCoordinate = parseInt(oldObj.Genomic_Coordinate_hg38.split(':')[parts.length - 2]);
+        // new format for genomic coordinates, now includes "g.", trim first two characters
+        var chrCoordinate = parseInt(parts[1].substr(2));
         var alleleChange = _.last(parts);
         var refAllele = alleleChange.split('>')[0];
         var altAllele = alleleChange.split('>')[1];
diff --git a/js/index.js b/js/index.js
@@ -307,6 +307,7 @@ var Database = React.createClass({
                 onRowClick={this.showVariant}/>
             message = this.renderMessage(content.pages.variantsResearch)
         } else {
+            params.columnSelection = {};
             table = <VariantTable
                 ref='table'
                 initialState={params}
@@ -337,7 +338,7 @@ var Database = React.createClass({
                         </Button>}
                         {this.props.mode === 'default' &&
                         <Button className="btn-small" onClick={() =>this.setState({showModal: true})}>
-                            Show All Data
+                            Show All Public Data
                         </Button>}
                         {this.props.mode === 'default' && this.state.showModal &&
                         <Modal onRequestHide={() => this.setState({ showModal: false })}>
@@ -458,7 +459,7 @@ var VariantDetail = React.createClass({
                 </Row>
                 <Row>
                     <Col md={8} mdOffset={2}>
-                        <DisclaimerModal buttonModal onToggleMode={this.onChildToggleMode} text="Show All Data on this Variant"/>
+                        <DisclaimerModal buttonModal onToggleMode={this.onChildToggleMode} text="Show All Public Data on this Variant"/>
                     </Col>
                 </Row>
             </Grid>

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-This is all BRCA Exchange variant data. It contains information drawn from multiple databases which have been intelligently merged together, one row per variant. It is intended to provide researchers with a set of BRCA variations and annotations which is as comprehensive as possible.`
	`1`	`+This is all BRCA Exchange public variant data. It contains information drawn from multiple databases which have been intelligently merged together, one row per variant. It is intended to provide researchers with a set of BRCA variations and annotations which is as comprehensive as possible.`
Original file line number	Diff line number	Diff line change
`@@ -11,6 +11,7 @@`
`11`	`11`	`url(r'^update/$', views.update, name="update"),`
`12`	`12`	`url(r'^password_reset/$', views.password_reset, name="password_reset"),`
`13`	`13`	`url(r'^confirm/(?P<activation_key>\w+)/$', views.confirm, name="confirm"),`
	`14`	`+ url(r'^resend-activation/$', views.resend_activation, name="resend_activation"),`
`14`	`15`	`url(r'^update_password/(?P<password_reset_token>\w+)/$', views.update_password, name="update_password"),`
`15`	`16`	`url(r'^check_password_token/(?P<password_reset_token>\w+)/$', views.check_password_token, name="check_password_token"),`
`16`	`17`	`]`