add collection metadata options for ibdgc

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_choices__in=removed_choices
+                ).values_list('disease', flat=True)
+            )
+            if active_removed_choices:
+                raise forms.ValidationError(
+                    'Cannot remove the following choices for "study_design", 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(
+                    disease_choices__in=removed_choices
+                ).values_list('data_type_choices', flat=True)
+            )
+            if active_removed_choices:
+                raise forms.ValidationError(
+                    'Cannot remove the following choices for "data_type_choices", 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

@@ -47,6 +47,10 @@ 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.study_design_choices.append(item)
+        for item in form.cleaned_data['disease_choices']['added']:
+            self.object.primary_collection.study_design_choices.append(item)
         self.object.primary_collection.save()
         return super().form_valid(form)
 
@@ -162,6 +166,20 @@ def get_context_data(self, *args, **kwargs):
             f'<li>{choice}</li>' for choice in primary_collection.study_design_choices
         ))
         kwargs['study_design_choices'] = study_design_choices_html
+        study_design_choices_html = '<ul>{choices}</ul>'.format(choices=''.join(
+            f'<li>{choice}</li>' for choice in primary_collection.study_design_choices
+        ))
+        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)
@@ -175,6 +193,8 @@ 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:
@@ -233,36 +253,19 @@ class CollectionProviderChangeForm(PermissionRequiredMixin, UpdateView):
     model = CollectionProvider
     form_class = CollectionProviderForm
 
-    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)
+    def process_choices(self, choices_name, form):
+        collection = self.object.primary_collection
+        choices_added = form.cleaned_data[f'{choices_name}_choices']['added']
+        choices_removed = form.cleaned_data[f'{choices_name}_choices']['removed']
 
-            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)
+        getattr(collection, f'{choices_name}_choices').extend(choices_added)
+        for item in choices_removed:
+            getattr(collection, f'{choices_name}_choices').remove(item)
 
+    def form_valid(self, form):
+        if self.object.primary_collection:
+            for choices_name in ['collected_type', 'status', 'issue', 'volume', 'program_area', 'school_type', 'study_design', 'data_type', 'disease']:
+                self.process_choices(choices_name, form)
         self.object.primary_collection.save()
         return super().form_valid(form)
 
@@ -399,6 +402,8 @@ 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/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.study_design = validated_data.pop('data_type')
+        if 'disease' in validated_data:
+            obj.study_design = 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

osf/migrations/0017_auto_20231207_1407.py

@@ -0,0 +1,34 @@
+# Generated by Django 3.2.17 on 2023-12-07 14:07
+
+import django.contrib.postgres.fields
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('osf', '0016_auto_20230828_1810'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='collection',
+            name='data_type_choices',
+            field=django.contrib.postgres.fields.ArrayField(base_field=models.CharField(max_length=127), blank=True, default=list, size=None),
+        ),
+        migrations.AddField(
+            model_name='collection',
+            name='disease_choices',
+            field=django.contrib.postgres.fields.ArrayField(base_field=models.CharField(max_length=127), blank=True, default=list, size=None),
+        ),
+        migrations.AddField(
+            model_name='collectionsubmission',
+            name='data_type',
+            field=models.CharField(blank=True, help_text='This field was added for use by Inflammatory Bowel Disease Genetics Consortium', max_length=500),
+        ),
+        migrations.AddField(
+            model_name='collectionsubmission',
+            name='disease',
+            field=models.CharField(blank=True, help_text='This field was added for use by Inflammatory Bowel Disease Genetics Consortium', max_length=500),
+        ),
+    ]

osf/models/collection.py

@@ -55,6 +55,8 @@ class Meta:
     program_area_choices = ArrayField(models.CharField(max_length=127), blank=True, default=list)
     school_type_choices = ArrayField(models.CharField(max_length=127), blank=True, default=list)
     study_design_choices = ArrayField(models.CharField(max_length=127), blank=True, default=list)
+    disease_choices = ArrayField(models.CharField(max_length=127), blank=True, default=list)
+    data_type_choices = ArrayField(models.CharField(max_length=127), blank=True, default=list)
     is_public = models.BooleanField(default=False, db_index=True)
     is_promoted = models.BooleanField(default=False, db_index=True)
     is_bookmark_collection = models.BooleanField(default=False, db_index=True)
@@ -160,7 +162,7 @@ def has_permission(self, user, perm):
 
     def collect_object(
             self, obj, collector, collected_type=None, status=None, volume=None, issue=None,
-            program_area=None, school_type=None, study_design=None):
+            program_area=None, school_type=None, study_design=None, data_type=None, disease=None):
         """ Adds object to collection, creates CollectionSubmission reference
             Performs type / metadata validation. User permissions checked in view.
 
@@ -177,6 +179,9 @@ def collect_object(
         program_area = program_area or ''
         school_type = school_type or ''
         study_design = study_design or ''
+        data_type = data_type or ''
+        study_design = study_design or ''
+        disease = disease or ''
 
         if not self.collected_type_choices and collected_type:
             raise ValidationError('May not specify "type" for this collection')
@@ -220,6 +225,18 @@ def collect_object(
             elif study_design not in self.study_design_choices:
                 raise ValidationError(f'"{study_design}" is not an acceptable "study_design" for this collection')
 
+        if disease:
+            if not self.disease_choices:
+                raise ValidationError('May not specify "disease" for this collection')
+            elif disease not in self.disease_choices:
+                raise ValidationError(f'"{disease}" is not an acceptable "disease" for this collection')
+
+        if data_type:
+            if not self.data_type_choices:
+                raise ValidationError('May not specify "data_type" for this collection')
+            elif data_type not in self.data_type_choices:
+                raise ValidationError(f'"{data_type}" is not an acceptable "data_type" for this collection')
+
         if not any([isinstance(obj, t.model_class()) for t in self.collected_types.all()]):
             # Not all objects have a content_type_pk, have to look the other way.
             # Ideally, all objects would, and we could do:
@@ -248,6 +265,8 @@ def collect_object(
             collection_submission.program_area = program_area
             collection_submission.school_type = school_type
             collection_submission.study_design = study_design
+            collection_submission.data_type = data_type
+            collection_submission.disease = disease
             collection_submission.save()
 
             return collection_submission