enable lablinks files generation

fix #266

ippisite/ippidb/management/commands/create_labslink_files.py

+# coding: utf-8
+from django.db.models import CharField, Value as V
+from django.db.models.functions import Concat
+from django.db.models import F, Q, Case, When
+
+from ippidb.models import RefCompoundBiblio
+from biodblinks.lablinks.command import LabsLinkCommand
+
+
+class Command(LabsLinkCommand):
+
+    queryset = (
+        RefCompoundBiblio.objects.exclude(Q(bibliography__source="PT"))
+        .annotate(
+            resource_title=Concat(
+                V("iPPI-DB compound #"), F("compound__id"), output_field=CharField()
+            )
+        )
+        .annotate(
+            resource_url=Concat(
+                V("https://ippidb.pasteur.fr/compounds/"),
+                F("compound__id"),
+                output_field=CharField(),
+            )
+        )
+        .annotate(
+            doi=Case(
+                When(Q(bibliography__source="DO"), then=F("bibliography__id_source")),
+                default=None,
+                output_field=CharField(),
+            )
+        )
+        .annotate(
+            record_id=Case(
+                When(Q(bibliography__source="PM"), then=F("bibliography__id_source")),
+                default=None,
+                output_field=CharField(),
+            )
+        )
+        .annotate(
+            record_source=Case(
+                When(Q(bibliography__source="PM"), then=V("MED")),
+                default=None,
+                output_field=CharField(),
+            )
+        )
+    )

ippisite/ippisite/settings.py

@@ -58,6 +58,7 @@ INSTALLED_APPS = [
     # "allauth.socialaccount.providers.github",
     "allauth.socialaccount.providers.orcid",
     "polymorphic",
+    "biodblinks",
 ]
 
 MIDDLEWARE = [
@@ -191,3 +192,10 @@ GALAXY_COMPOUNDPROPERTIES_WORKFLOWID = None
 CELERY_RESULT_BACKEND = "django-db"
 
 GA_CODE = None
+
+# Django BioDbLinks settings
+LABLINKS_ID_PREFIX = "https://ippidb.pasteur.fr"
+LABLINKS_PROVIDER_ID = "2079"
+LABLINKS_RESOURCE_NAME = "iPPI-DB"
+LABLINKS_RESOURCE_DESCRIPTION = "iPPI-DB : An interactive database of protein-protein interactions modulators"
+LABLINKS_CONTACT_EMAIL = "ippidb@pasteur.fr"
\ No newline at end of file

ippisite/ippisite/settings.template.py

@@ -169,3 +169,10 @@ CRISPY_TEMPLATE_PACK = "bootstrap4"
 
 # celery setting.
 CELERY_RESULT_BACKEND = 'django-db'
+
+# Django BioDbLinks settings
+LABLINKS_ID_PREFIX = "https://ippidb.pasteur.fr"
+LABLINKS_PROVIDER_ID = "2079"
+LABLINKS_RESOURCE_NAME = "iPPI-DB"
+LABLINKS_RESOURCE_DESCRIPTION = "iPPI-DB : An interactive database of protein-protein interactions modulators"
+LABLINKS_CONTACT_EMAIL = "ippidb@pasteur.fr"
\ No newline at end of file

ippisite/requirements-core.txt

@@ -30,3 +30,5 @@ django-crispy-forms
 celery==4.4.7
 django-polymorphic
 boltons
+# django-biodblinks App
+git+https://gitlab.pasteur.fr/hub/django-biodblinks.git#egg=django-biodblinks==0.1