Merge pull request #58 from omics-datascience/gonza

- Fixed font icons and biomarkers can be shared

Author: Genarito

Diff for: src/biomarkers/migrations/0019_biomarker_is_public.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-11-21 18:10
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('biomarkers', '0018_alter_biomarker_state'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='biomarker',
+            name='is_public',
+            field=models.BooleanField(default=False),
+        ),
+    ]

Diff for: src/biomarkers/migrations/0020_biomarker_shared_institutions.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.2.15 on 2024-11-21 18:36
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('institutions', '0004_auto_20220923_2322'),
+        ('biomarkers', '0019_biomarker_is_public'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='biomarker',
+            name='shared_institutions',
+            field=models.ManyToManyField(blank=True, related_name='biomarkers', to='institutions.institution'),
+        ),
+    ]

Diff for: src/biomarkers/models.py

@@ -3,6 +3,8 @@
 from django.db import models
 from django.db.models import QuerySet
 from queryset_sequence import QuerySetSequence
+
+from institutions.models import Institution
 from tags.models import Tag
 from api_service.websocket_functions import send_update_biomarkers_command
 from user_files.models_choices import MoleculeType
@@ -60,14 +62,15 @@ class Biomarker(models.Model):
     cnas: QuerySet['CNAIdentifier']
     mirnas: QuerySet['MiRNAIdentifier']
     mrnas: QuerySet['MRNAIdentifier']
-
+    is_public = models.BooleanField(blank=False, null=False, default=False)
     name: str = models.CharField(max_length=300)
     description: Optional[str] = models.TextField(null=True, blank=True)
     tag: Optional[Tag] = models.ForeignKey(Tag, on_delete=models.SET_NULL, default=None, blank=True, null=True)
     upload_date: Optional[models.DateTimeField] = models.DateTimeField(auto_now_add=True, blank=False, null=True)
     origin: int = models.IntegerField(choices=BiomarkerOrigin.choices)
     state: int = models.IntegerField(choices=BiomarkerState.choices)
     user = models.ForeignKey(get_user_model(), on_delete=models.CASCADE)
+    shared_institutions = models.ManyToManyField(Institution, related_name='biomarkers', blank=True)
 
     def __str__(self) -> str:
         return self.name

Diff for: src/biomarkers/views.py

@@ -16,15 +16,18 @@
     BiomarkerSimpleSerializer, BiomarkerSimpleUpdateSerializer
 from common.pagination import StandardResultsSetPagination
 from common.response import generate_json_response_or_404
-from django.db.models import QuerySet
+from django.db.models import QuerySet, Q
 
 
 class BiomarkerList(generics.ListAPIView):
     """REST endpoint: list for Biomarker model"""
 
     def get_queryset(self):
+        user = self.request.user
         only_successful = self.request.GET.get('onlySuccessful') == 'true'
-        biomarkers = Biomarker.objects.filter(user=self.request.user)
+        biomarkers = Biomarker.objects.filter(
+            Q(is_public=True) | Q(user=user) | Q(shared_institutions__institutionadministration__user=user)).distinct()
+
         if only_successful:
             # FIXME: this is VERY slow. Taking more than 20secs in production. Must parametrize the DB, maybe
             # FIXME: autovacuum settings could help
@@ -112,7 +115,6 @@ def get(self, request: Request, pk: int):
             self.__copy_molecules_instances(biomarker_copy, biomarker.cnas.all())
             self.__copy_molecules_instances(biomarker_copy, biomarker.methylations.all())
 
-
         return Response({'ok': True})
 
 
@@ -142,6 +144,7 @@ def get_gene_aliases(genes_ids: List[str]) -> Optional[Dict]:
         method='post'
     )
 
+
 def find_genes_from_request(request: Request) -> List[Dict]:
     """
     Generates the structure for the frontend for a list of genes. The needed structure is a list of dicts with