Merge remote-tracking branch 'upstream/develop' into feature/cedar-in…

…tegration

Dockerfile

@@ -26,10 +26,8 @@ RUN apk add --no-cache --virtual .run-deps \
     libevent \
     && yarn global add bower
 
-RUN apk add curl
-RUN curl https://bootstrap.pypa.io/pip/3.6/get-pip.py -o get-pip.py
-RUN python3 get-pip.py --force-reinstall pip==21.0
-RUN apk del curl
+RUN python3 -m ensurepip && \
+    pip3 install --upgrade pip==21.0
 
 WORKDIR /code
 

README-docker-compose.md

@@ -229,6 +229,8 @@
 - Populate preprint, registration, and collection providers:
   - After resetting your database or with a new install, the required providers and subjects will be created automatically **when you run migrations.** To create more:
     - `docker-compose run --rm web python3 manage.py populate_fake_providers`
+    - _NOTE: In case, you encounter error with missing data, when running the `'populate_fake_providers'` command. Fix this with 'update_taxonomies' command:_
+      - `docker-compose run --rm web python3 -m scripts.update_taxonomies`
 - Populate citation styles
   - Needed for api v2 citation style rendering.
     - `docker-compose run --rm web python3 -m scripts.parse_citation_styles`

addons/wiki/models.py

@@ -203,11 +203,7 @@ def check_spam(self):
         )
 
     def _get_spam_content(self, node):
-        content = []
-        content.append(self.raw_text(node))
-        if not content:
-            return None
-        return ' '.join(content)
+        return self.content or None
 
     def clone_version(self, wiki_page, user):
         """Clone a node wiki page.

admin/collection_providers/forms.py

@@ -15,6 +15,8 @@ class CollectionProviderForm(forms.ModelForm):
     program_area_choices = forms.CharField(widget=forms.HiddenInput(), required=False)
     school_type_choices = forms.CharField(widget=forms.HiddenInput(), required=False)
     study_design_choices = forms.CharField(widget=forms.HiddenInput(), required=False)
+    data_type_choices = forms.CharField(widget=forms.HiddenInput(), required=False)
+    disease_choices = forms.CharField(widget=forms.HiddenInput(), required=False)
     _id = forms.SlugField(
         required=True,
         help_text='URL Slug',
@@ -268,3 +270,63 @@ def clean_study_design_choices(self):
             if choices:
                 added_choices = json.loads(choices)
         return {'added': added_choices, 'removed': removed_choices}
+
+    def clean_disease_choices(self):
+        if not self.data.get('disease_choices'):
+            return {'added': [], 'removed': []}
+
+        collection_provider = self.instance
+        primary_collection = collection_provider.primary_collection
+        if primary_collection:  # Modifying an existing CollectionProvider
+            old_choices = {c.strip(' ') for c in primary_collection.disease_choices}
+            updated_choices = {c.strip(' ') for c in json.loads(self.data.get('disease_choices'))}
+            added_choices = updated_choices - old_choices
+            removed_choices = old_choices - updated_choices
+
+            active_removed_choices = set(
+                primary_collection.collectionsubmission_set.filter(
+                    disease__in=removed_choices
+                ).values_list('disease', flat=True)
+            )
+            if active_removed_choices:
+                raise forms.ValidationError(
+                    'Cannot remove the following choices for "disease", as they are '
+                    f'currently in use: {active_removed_choices}'
+                )
+        else:  # Creating a new CollectionProvider
+            added_choices = set()
+            removed_choices = set()
+            choices = self.data.get('disease_choices')
+            if choices:
+                added_choices = json.loads(choices)
+        return {'added': added_choices, 'removed': removed_choices}
+
+    def clean_data_type_choices(self):
+        if not self.data.get('data_type_choices'):
+            return {'added': [], 'removed': []}
+
+        collection_provider = self.instance
+        primary_collection = collection_provider.primary_collection
+        if primary_collection:  # Modifying an existing CollectionProvider
+            old_choices = {c.strip(' ') for c in primary_collection.data_type_choices}
+            updated_choices = {c.strip(' ') for c in json.loads(self.data.get('data_type_choices'))}
+            added_choices = updated_choices - old_choices
+            removed_choices = old_choices - updated_choices
+
+            active_removed_choices = set(
+                primary_collection.collectionsubmission_set.filter(
+                    data_type__in=removed_choices
+                ).values_list('data_type', flat=True)
+            )
+            if active_removed_choices:
+                raise forms.ValidationError(
+                    'Cannot remove the following choices for "data_type", as they are '
+                    f'currently in use: {active_removed_choices}'
+                )
+        else:  # Creating a new CollectionProvider
+            added_choices = set()
+            removed_choices = set()
+            choices = self.data.get('data_type_choices')
+            if choices:
+                added_choices = json.loads(choices)
+        return {'added': added_choices, 'removed': removed_choices}

admin/collection_providers/views.py

@@ -21,6 +21,17 @@
 from admin.providers.views import AddAdminOrModerator, RemoveAdminsAndModerators
 
 
+def _process_collection_choices(provider, choices_name, form):
+    collection = provider.primary_collection
+    choices_name_attr = f'{choices_name}_choices'
+    choices_added = form.cleaned_data[choices_name_attr]['added']
+    choices_removed = form.cleaned_data[choices_name_attr]['removed']
+
+    getattr(collection, choices_name_attr).extend(choices_added)
+    for item in choices_removed:
+        getattr(collection, choices_name_attr).remove(item)
+
+
 class CreateCollectionProvider(PermissionRequiredMixin, CreateView):
     raise_exception = True
     permission_required = 'osf.change_collectionprovider'
@@ -47,6 +58,10 @@ def form_valid(self, form):
             self.object.primary_collection.school_type_choices.append(item)
         for item in form.cleaned_data['study_design_choices']['added']:
             self.object.primary_collection.study_design_choices.append(item)
+        for item in form.cleaned_data['data_type_choices']['added']:
+            self.object.primary_collection.data_type_choices.append(item)
+        for item in form.cleaned_data['disease_choices']['added']:
+            self.object.primary_collection.disease_choices.append(item)
         self.object.primary_collection.save()
         return super().form_valid(form)
 
@@ -163,6 +178,16 @@ def get_context_data(self, *args, **kwargs):
         ))
         kwargs['study_design_choices'] = study_design_choices_html
 
+        disease_choices_html = '<ul>{choices}</ul>'.format(choices=''.join(
+            f'<li>{choice}</li>' for choice in primary_collection.disease_choices
+        ))
+        kwargs['disease_choices'] = disease_choices_html
+
+        data_type_choices_html = '<ul>{choices}</ul>'.format(choices=''.join(
+            f'<li>{choice}</li>' for choice in primary_collection.data_type_choices
+        ))
+        kwargs['data_type_choices'] = data_type_choices_html
+
         # get a dict of model fields so that we can set the initial value for the update form
         fields = model_to_dict(collection_provider)
         fields['collected_type_choices'] = json.dumps(primary_collection.collected_type_choices)
@@ -175,6 +200,8 @@ def get_context_data(self, *args, **kwargs):
 
         fields['school_type_choices'] = json.dumps(primary_collection.school_type_choices)
         fields['study_design_choices'] = json.dumps(primary_collection.study_design_choices)
+        fields['data_type_choices'] = json.dumps(primary_collection.data_type_choices)
+        fields['disease_choices'] = json.dumps(primary_collection.disease_choices)
 
         # compile html list of collected_type_choices
         if collection_provider.primary_collection:
@@ -235,34 +262,8 @@ class CollectionProviderChangeForm(PermissionRequiredMixin, UpdateView):
 
     def form_valid(self, form):
         if self.object.primary_collection:
-            self.object.primary_collection.collected_type_choices.extend(form.cleaned_data['collected_type_choices']['added'])
-            for item in form.cleaned_data['collected_type_choices']['removed']:
-                self.object.primary_collection.collected_type_choices.remove(item)
-
-            self.object.primary_collection.status_choices.extend(form.cleaned_data['status_choices']['added'])
-            for item in form.cleaned_data['status_choices']['removed']:
-                self.object.primary_collection.status_choices.remove(item)
-
-            self.object.primary_collection.issue_choices.extend(form.cleaned_data['issue_choices']['added'])
-            for item in form.cleaned_data['issue_choices']['removed']:
-                self.object.primary_collection.issue_choices.remove(item)
-
-            self.object.primary_collection.volume_choices.extend(form.cleaned_data['volume_choices']['added'])
-            for item in form.cleaned_data['volume_choices']['removed']:
-                self.object.primary_collection.volume_choices.remove(item)
-
-            self.object.primary_collection.program_area_choices.extend(form.cleaned_data['program_area_choices']['added'])
-            for item in form.cleaned_data['program_area_choices']['removed']:
-                self.object.primary_collection.program_area_choices.remove(item)
-
-        self.object.primary_collection.school_type_choices.extend(form.cleaned_data['school_type_choices']['added'])
-        for item in form.cleaned_data['school_type_choices']['removed']:
-            self.object.primary_collection.school_type_choices.remove(item)
-
-        self.object.primary_collection.study_design_choices.extend(form.cleaned_data['study_design_choices']['added'])
-        for item in form.cleaned_data['study_design_choices']['removed']:
-            self.object.primary_collection.study_design_choices.remove(item)
-
+            for choices_name in ['collected_type', 'status', 'issue', 'volume', 'program_area', 'school_type', 'study_design', 'data_type', 'disease']:
+                _process_collection_choices(self.object, choices_name, form)
         self.object.primary_collection.save()
         return super().form_valid(form)
 
@@ -399,6 +400,8 @@ def create_or_update_provider(self, provider_data):
             provider.primary_collection.program_area_choices = primary_collection['fields']['program_area_choices']
             provider.primary_collection.school_type_choices = primary_collection['fields']['school_type_choices']
             provider.primary_collection.study_design_choices = primary_collection['fields']['study_design_choices']
+            provider.primary_collection.disease_choices = primary_collection['fields']['disease_choices']
+            provider.primary_collection.data_type_choices = primary_collection['fields']['data_type_choices']
             provider.primary_collection.save()
         if licenses:
             provider.licenses_acceptable.set(licenses)

admin/static/js/pages/collection-provider-page.js

@@ -57,6 +57,22 @@ $('#tags-input-study-design').on('itemRemoved', function(event) {
     $('#id_study_design_choices').val(JSON.stringify($('#tags-input-study-design').tagsinput('items')));
 });
 
+$('#tags-input-data-type').on('itemAdded', function(event) {
+    $('#id_data_type_choices').val(JSON.stringify($('#tags-input-data-type').tagsinput('items')));
+});
+
+$('#tags-input-data-type').on('itemRemoved', function(event) {
+    $('#id_data_type_choices').val(JSON.stringify($('#tags-input-data-type').tagsinput('items')));
+});
+
+$('#tags-input-disease').on('itemAdded', function(event) {
+    $('#id_disease_choices').val(JSON.stringify($('#tags-input-disease').tagsinput('items')));
+});
+
+$('#tags-input-disease').on('itemRemoved', function(event) {
+    $('#id_disease_choices').val(JSON.stringify($('#tags-input-disease').tagsinput('items')));
+});
+
 
 $(document).ready(function() {
    var collectedTypeItems = JSON.parse($('#id_collected_type_choices').val());
@@ -93,4 +109,14 @@ $(document).ready(function() {
    studyDesignItems.forEach(function(element){
        $('#tags-input-study-design').tagsinput('add', element)
    });
+
+   var diseaseItems = JSON.parse($('#id_disease_choices').val());
+   diseaseItems.forEach(function(element){
+       $('#tags-input-disease').tagsinput('add', element)
+   });
+
+   var dataTypeItems = JSON.parse($('#id_data_type_choices').val());
+   dataTypeItems.forEach(function(element){
+       $('#tags-input-data-type').tagsinput('add', element)
+   });
 });

admin/templates/collection_providers/detail.html

@@ -66,6 +66,14 @@ <h2>{{ collection_provider.name }}</h2>
 						<th>study_design_choices</th>
 						<td>{{ study_design_choices | safe}}</td>
 					</tr>
+					<tr>
+						<th>disease_choices</th>
+						<td>{{ disease_choices | safe}}</td>
+					</tr>
+					<tr>
+						<th>data_type_choices</th>
+						<td>{{ data_type_choices | safe}}</td>
+					</tr>
                 </table>
             </div>
         </div>

admin/templates/collection_providers/update_collection_provider_form.html

@@ -98,6 +98,18 @@
 					<input id="tags-input-study-design" type="text" data-role="tagsinput"/>
 				</div>
 			</div>
+			<div>
+				<label>Disease choices:</label>
+				<div class=#bootstrap-tagsinput">
+					<input id="tags-input-disease" type="text" data-role="tagsinput"/>
+				</div>
+			</div>
+			<div>
+				<label>Data Type choices:</label>
+				<div class=#bootstrap-tagsinput">
+					<input id="tags-input-data-type" type="text" data-role="tagsinput"/>
+				</div>
+			</div>
             <input class="form-button" type="submit" value="Save" />
         </form>
     </div>

api/actions/views.py

@@ -159,7 +159,7 @@ class ReviewActionListCreate(JSONAPIBaseView, generics.ListCreateAPIView, ListFi
     )
 
     required_read_scopes = [CoreScopes.ACTIONS_READ]
-    required_write_scopes = [CoreScopes.NULL]
+    required_write_scopes = [CoreScopes.ACTIONS_WRITE]
 
     parser_classes = (JSONAPIMultipleRelationshipsParser, JSONAPIMultipleRelationshipsParserForRegularJSON,)
     serializer_class = ReviewActionSerializer

api/base/serializers.py

@@ -924,6 +924,9 @@ def to_representation(self, value):
                             or related_class.view_name == 'registration-citation':
                         related_id = resolved_url.kwargs['node_id']
                         related_type = 'citation'
+                    elif related_class.view_name == 'preprint-citation':
+                        related_id = resolved_url.kwargs['preprint_id']
+                        related_type = 'citation'
                     elif related_type in ('preprint_providers', 'preprint-providers', 'registration-providers'):
                         related_id = resolved_url.kwargs['provider_id']
                     elif related_type in ('registrations', 'draft_nodes'):

api/collections/serializers.py

@@ -68,6 +68,14 @@ class CollectionSerializer(JSONAPISerializer):
         child=ser.CharField(max_length=127),
         default=list(),
     )
+    data_type_choices = ser.ListField(
+        child=ser.CharField(max_length=127),
+        default=list(),
+    )
+    disease_choices = ser.ListField(
+        child=ser.CharField(max_length=127),
+        default=list(),
+    )
 
     links = LinksField({})
 
@@ -241,6 +249,8 @@ def subjects_view_kwargs(self):
     program_area = ser.CharField(required=False)
     school_type = ser.CharField(required=False)
     study_design = ser.CharField(required=False)
+    data_type = ser.CharField(required=False)
+    disease = ser.CharField(required=False)
 
     def get_absolute_url(self, obj):
         return absolute_reverse(
@@ -272,6 +282,10 @@ def update(self, obj, validated_data):
             obj.school_Type = validated_data.pop('school_type')
         if 'study_design' in validated_data:
             obj.study_design = validated_data.pop('study_design')
+        if 'data_type' in validated_data:
+            obj.data_type = validated_data.pop('data_type')
+        if 'disease' in validated_data:
+            obj.disease = validated_data.pop('disease')
 
         obj.save()
         return obj
@@ -337,6 +351,8 @@ def subjects_view_kwargs(self):
     program_area = ser.CharField(required=False)
     school_type = ser.CharField(required=False)
     study_design = ser.CharField(required=False)
+    date_type = ser.CharField(required=False)
+    disease = ser.CharField(required=False)
 
     def get_absolute_url(self, obj):
         return absolute_reverse(
@@ -368,6 +384,10 @@ def update(self, obj, validated_data):
             obj.school_Type = validated_data.pop('school_type')
         if 'study_design' in validated_data:
             obj.study_design = validated_data.pop('study_design')
+        if 'data_type' in validated_data:
+            obj.data_type = validated_data.pop('data_type')
+        if 'disease' in validated_data:
+            obj.disease = validated_data.pop('disease')
 
         obj.save()
         return obj

api/nodes/serializers.py

@@ -542,6 +542,12 @@ class NodeSerializer(TaxonomizableSerializerMixin, JSONAPISerializer):
         related_view_kwargs={'node_id': '<_id>'},
     )
 
+    subjects_acceptable = HideIfRegistration(RelationshipField(
+        related_view='subjects:subject-list',
+        related_view_kwargs={},
+        read_only=True,
+    ))
+
     @property
     def subjects_related_view(self):
         # Overrides TaxonomizableSerializerMixin
@@ -1562,12 +1568,6 @@ class DraftRegistrationLegacySerializer(JSONAPISerializer):
         'html': 'get_absolute_url',
     })
 
-    affiliate_user_institutions = ser.BooleanField(
-        required=False,
-        default=True,
-        help_text='Specify whether user institution affiliations should be copied over to the draft registration.',
-    )
-
     def get_absolute_url(self, obj):
         return obj.absolute_url
 
@@ -1608,7 +1608,6 @@ def create(self, validated_data):
         registration_responses = validated_data.pop('registration_responses', None)
         schema = validated_data.pop('registration_schema')
         provider = validated_data.pop('provider', None)
-        affiliate_user_institutions = validated_data.pop('affiliate_user_institutions', True)
 
         self.enforce_metadata_or_registration_responses(metadata, registration_responses)
 
@@ -1623,9 +1622,6 @@ def create(self, validated_data):
         if registration_responses:
             self.update_registration_responses(draft, registration_responses)
 
-        if affiliate_user_institutions and draft.branched_from_type == DraftNode:
-            draft.affiliated_institutions.set(draft.creator.affiliated_institutions.all())
-
         return draft
 
     class Meta: