Merge pull request #423 from elixir-luxembourg/422-is-published-property

#422-is-published-property

core/management/commands/load_initial_data.py

@@ -159,7 +159,7 @@ def create_elu_institutions():
             data = json.load(handler)
             for partner in data:
                 _current = {k: v for k, v in partner.items()}
-                _current.update({'is_published': True})
+                _current.update({'_is_published': True})
                 if 'external_id' in _current:
                     _current['elu_accession'] = _current['external_id']
                     _current.pop('external_id')

core/migrations/0034_auto_20230515_1353.py

@@ -0,0 +1,32 @@
+# Generated by Django 3.2.19 on 2023-05-15 11:53
+
+import core.models.utils
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0033_auto_20230515_1147'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='cohort',
+            old_name='is_published',
+            new_name='_is_published',
+        ),
+        migrations.RenameField(
+            model_name='partner',
+            old_name='is_published',
+            new_name='_is_published',
+        ),
+        migrations.RemoveField(
+            model_name='dataset',
+            name='is_published',
+        ),
+        migrations.RemoveField(
+            model_name='project',
+            name='is_published',
+        ),
+    ]

core/models/access.py

@@ -3,7 +3,7 @@
 
 from django.core.exceptions import ValidationError
 from django.db import models
-from django.db.models import Q, ObjectDoesNotExist
+from django.db.models import Q, ObjectDoesNotExist, Count
 
 from enumchoicefield import EnumChoiceField, ChoiceEnum
 
@@ -13,7 +13,6 @@
 from auditlog.models import AuditlogHistoryField
 
 
-
 class StatusChoices(ChoiceEnum):
     precreated = "Pre-created"
     active = "Active"
@@ -145,7 +144,7 @@ def __str__(self):
             else:
                 return f"Access ({self.status}) to dataset {self.dataset.title} given to a user: {self.user}/{self.access_notes}"
         except ObjectDoesNotExist as e:
-                return f"Access ({self.status}) to dataset {self.dataset.title} given to a deleted contact or user: {self.access_notes}"
+            return f"Access ({self.status}) to dataset {self.dataset.title} given to a deleted contact or user: {self.access_notes}"
 
     def delete(self, force: bool = False):
         self.status = StatusChoices.terminated
@@ -159,12 +158,12 @@ def display_locations(self):
 
     @classmethod
     def find_for_user(cls, user) -> List[str]:
-        accesses = cls.objects.filter(user=user, dataset__is_published=True)
+        accesses = cls.objects.annotate(c=Count("dataset__exposures")).filter(user=user, c__gt=0)
         return cls._filter_expired(accesses)
 
     @classmethod
     def find_for_contact(cls, contact) -> List[str]:
-        accesses = cls.objects.filter(contact=contact, dataset__is_published=True)
+        accesses = cls.objects.annotate(c=Count("dataset__exposures")).filter(contact=contact, c__gt=0)
         return cls._filter_expired(accesses)
 
     @staticmethod

core/models/cohort.py

@@ -1,10 +1,10 @@
 from django.db import models
 from django.conf import settings
 
-from .utils import CoreTrackedModel, TextFieldWithInputWidget
+from .utils import CoreTrackedDBModel, TextFieldWithInputWidget
 
 
-class Cohort(CoreTrackedModel):
+class Cohort(CoreTrackedDBModel):
     class Meta:
         app_label = 'core'
         get_latest_by = "added"

core/models/dataset.py

@@ -3,6 +3,8 @@
 from django.conf import settings
 from django.db import models
 from django.urls import reverse
+from django.utils.module_loading import import_string
+
 from guardian.models import GroupObjectPermissionBase, UserObjectPermissionBase
 from core import constants
 from core.permissions.mapping import PERMISSION_MAPPING
@@ -60,6 +62,11 @@ class AppMeta:
                                     verbose_name='Sensitivity class',
                                     help_text='Sensitivity denotes the security classification of this dataset.')
 
+    @property
+    def is_published(self):
+        exposures_list = self.exposures.all()
+        return len(exposures_list) > 0
+
     @property
     def data_types(self):
         all_data_types = set()
@@ -163,13 +170,15 @@ def serialize_to_export(self):
         return d
 
     def publish(self, save=True):
-        if self.project:
-            self.project.publish()
-
+        generate_id_function_path = getattr(settings, 'IDSERVICE_FUNCTION')
+        generate_id_function = import_string(generate_id_function_path)
+        if not self.elu_accession:
+            self.elu_accession = generate_id_function(self)
+        if save:
+            self.save(update_fields=['elu_accession'])
+
         for data_declaration in self.data_declarations.all():
             data_declaration.publish_subentities()
-
-        super().publish()
 
 
 # faster lookup for permissions

core/models/partner.py

@@ -3,7 +3,7 @@
 from django_countries.fields import CountryField
 
 from model_utils import Choices
-from .utils import CoreTrackedModel, TextFieldWithInputWidget
+from .utils import CoreTrackedDBModel, TextFieldWithInputWidget
 
 from elixir_daisy import settings
 
@@ -21,7 +21,7 @@
 )
 
 
-class Partner(CoreTrackedModel):
+class Partner(CoreTrackedDBModel):
     """
     Represents a partner.
       {

core/models/project.py

@@ -151,7 +151,9 @@ def __str__(self):
         return self.acronym or self.title or "undefined"
 
 
-
+    @property
+    def is_published(self):
+        return any(dataset.is_published for dataset in self.datasets.all())
 
     def to_dict(self):
         contact_dicts = []
@@ -217,6 +219,9 @@ def serialize_to_export(self):
         d['publications'] = ','.join(publications)
         return d
 
+    def publish(self):
+        pass
+
 # faster lookup for permissions
 # https://django-guardian.readthedocs.io/en/stable/userguide/performance.html#direct-foreign-keys
 class ProjectUserObjectPermission(UserObjectPermissionBase):

core/models/utils.py

@@ -1,3 +1,4 @@
+from abc import abstractmethod
 from json import loads
 from json.decoder import JSONDecodeError
 
@@ -11,19 +12,21 @@
 
 COMPANY = getattr(settings, "COMPANY", 'Company')
 
+
 def validate_json(value):
     if len(value) == 0:
         return value
 
     try:
         loads(value)
         if '{' not in value:  # Very inaccurate, but should do the trick when the user tries to save e.g. '123'
-            raise ValidationError(f'`scientific_metadata` field must be a valid JSON containing a dictionary!')    
+            raise ValidationError(f'`scientific_metadata` field must be a valid JSON containing a dictionary!')
         return value
     except JSONDecodeError as ex:
         msg = str(ex)
         raise ValidationError(f'`scientific_metadata` field must contain a valid JSON! ({msg})')
 
+
 class classproperty(property):
     def __get__(self, cls, owner):
         return self.fget.__get__(None, owner)()
@@ -43,11 +46,6 @@ class CoreTrackedModel(CoreModel):
         blank=True,
         null=True,
         max_length=20)
-
-    is_published = models.BooleanField(
-        default=False,
-        blank=False,
-        verbose_name='Is published?')
 
     scientific_metadata = models.TextField(
         default='{}',
@@ -56,26 +54,17 @@ class CoreTrackedModel(CoreModel):
         verbose_name='Additional scientific metadata (in JSON format)',
         validators=[validate_json]  # This will work in ModelForm only
     )
+
     class Meta:
         abstract = True
 
-    def publish(self, save=True):
-        generate_id_function_path = getattr(settings, 'IDSERVICE_FUNCTION')
-        generate_id_function = import_string(generate_id_function_path)
-        if not self.is_published:
-            self.is_published = True
-            if not self.elu_accession:
-                self.elu_accession = generate_id_function(self)
-        if save:
-            self.save(update_fields=['is_published', 'elu_accession'])
+    @abstractmethod
+    def is_published(self):
+        pass
 
-    def generate_elu_accession(self, save=True):
-        generate_id_function_path = getattr(settings, 'IDSERVICE_FUNCTION')
-        generate_id_function = import_string(generate_id_function_path)
-        if not self.elu_accession:
-            self.elu_accession = generate_id_function(self)
-        if save:
-            self.save(update_fields=['elu_accession'])
+    @abstractmethod
+    def publish(self):
+        pass
 
     def clean(self):
         cleaned_data = super().clean()
@@ -87,6 +76,36 @@ def save(self, *args, **kwargs):
         super().save(*args, **kwargs)
 
 
+class CoreTrackedDBModel(CoreTrackedModel):
+    _is_published = models.BooleanField(
+        default=False,
+        blank=False,
+        verbose_name='Is published?')
+
+    class Meta:
+        abstract = True
+
+    def publish(self, save=True):
+        generate_id_function_path = getattr(settings, 'IDSERVICE_FUNCTION')
+        generate_id_function = import_string(generate_id_function_path)
+        if not self.is_published:
+            self.is_published = True
+            if not self.elu_accession:
+                self.elu_accession = generate_id_function(self)
+        if save:
+            self.save(update_fields=['_is_published', 'elu_accession'])
+
+    @property
+    def is_published(self):
+        # Getter method
+        return self._is_published
+
+    @is_published.setter
+    def is_published(self, value):
+        # Setter method
+        self._is_published = value
+
+
 class TextFieldWithInputWidget(TextField):
 
     def formfield(self, **kwargs):
@@ -105,11 +124,10 @@ class HashedField(models.CharField):
     A custom field that will store a hash of the provided value.
     """
     description = "Keeps the hash of the string in the DB"
-    
+
     def pre_save(self, model_instance, add):
         """
         This function is called when the value is about to be saved to the DB. We hash the value and return it.
         """
         value = getattr(model_instance, self.attname)
         return make_password(value, salt=settings.SECRET_KEY)
-

core/tests/test_lcsb.py

@@ -10,7 +10,7 @@
 from core.lcsb.rems import create_rems_entitlement
 from core.models.access import Access
 from core.models.contact import Contact
-from test.factories import ContactFactory, DatasetFactory, UserFactory
+from test.factories import ContactFactory, DatasetFactory, UserFactory, ExposureFactory, EndpointFactory
 from web.views.utils import get_user_or_contact_by_oidc_id
 
 
@@ -120,7 +120,9 @@ def test_permissions():
     contact = ContactFactory()
     contact.save()
 
-    dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession='123', is_published=True)
+    dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession='123')
+    endpoint = EndpointFactory()
+    _ = ExposureFactory(dataset=dataset, endpoint=endpoint)
     dataset.save()
 
     access = Access(access_notes='Access contact', contact=contact, dataset=dataset, status=StatusChoices.active)

elixir_daisy/settings.py

@@ -282,6 +282,7 @@
         'consent_status',
         'data_types',
         'deidentification_method',
+        'is_published',
     ),
     'contract': (
         'contacts',

web/templates/projects/project.html

@@ -7,11 +7,6 @@
 {% block content %}
     <div class="row mt-4">
         <div class="jumbotron col">
-            {% if project.is_published %}
-                <div class="ribbon ribbon-green"><span>Published</span></div>
-            {% else %}
-                <div class="ribbon ribbon-orange"><span>Not Published</span></div>
-            {% endif %}
             <span style="color: #8D8F8F;">Project</span>
             <h1>{{ project.acronym }} </h1>
             <div class="row">
@@ -78,24 +73,6 @@ <h1>{{ project.acronym }} </h1>
                             </a>
                         </p>
                     {% endif %}
-                    {% if request.user.can_publish %}
-                        {% if not project.is_published %}
-                            <a href="{% url 'project_publish' pk=project.pk %}"
-                               id="publish"
-                               title="Publish project"
-                               class="btn btn-default bmd-btn-fab float-right">
-                               <i class="material-icons">publish</i>
-                            </a>
-                        {% else %}
-                            <a href="{% url 'project_unpublish' pk=project.pk %}"
-                               id="unpublish"
-                               title="Unpublish project"
-                               data-confirm="Are you sure to unpublish the project? The changes won't be propagated to other systems!"
-                               class="btn btn-default bmd-btn-fab float-right">
-                                <i class="material-icons">undo</i>
-                            </a>
-                        {% endif %}
-                    {% endif %}
                     {% if is_admin %}
                         <a class="btn btn-default bmd-btn-fab float-right"
                            title="Manage project permissions"
@@ -227,6 +204,10 @@ <h2 class="card-title"><span><i class="material-icons">folder</i></span> Data of
                     {% for dataset in project.datasets.all %}
                     <li class="list-group-item">
                         <a href="{% url 'dataset' pk=dataset.id %}">{{ dataset }}</a>
+                        {% if dataset.is_published %}
+                        <span class="badge badge-success">Publicly Available</span>
+                        {% endif %}
+
                     </li>
                     {% endfor %}
                 </ul>

web/templates/search/_items/datasets.html

@@ -6,6 +6,7 @@ <h2 class="card-title">
                   <a href="{% url 'dataset' pk=dataset.pk %}">{{ dataset.title }}</a>
                 </h2>
                 <ul class="card-text">
+                    <li><strong>Published:</strong> {{ dataset.is_published | yesno }}</li>
                     <li><strong>Datatypes:</strong>
                         {% for datatype in dataset.data_types %}
                             <span class="badge badge-pill badge-secondary">{{ datatype }}</span>

web/tests/views/test_project_views.py

@@ -150,7 +150,7 @@ def test_project_edit_protected_documents(permissions, group):
     os.remove(document.content.name)
 
 @pytest.mark.parametrize('group', [VIPGroup, DataStewardGroup, LegalGroup, AuditorGroup])
-@pytest.mark.parametrize('url_name', ['project_publish', 'project_unpublish', 'projects_export'])
+@pytest.mark.parametrize('url_name', ['projects_export'])
 def test_projects_publications_and_export(permissions, group, url_name):
     user = UserFactory(groups=[group()])
     kwargs = {}