Commit 419d50c0 authored by Hervé  MENAGER's avatar Hervé MENAGER
Browse files

Merge branch 'master' into 'release'

prepare for v1.0.5

See merge request !22
parents e8aeca08 0c15a78b
Pipeline #43964 failed with stages
in 11 minutes and 33 seconds
# 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(),
)
)
)
......@@ -3,6 +3,7 @@ iPPI-DB unit tests
"""
import json
import re
from requests.exceptions import SSLError
from django.contrib.auth import get_user_model
from django.core.management import call_command
......@@ -768,9 +769,12 @@ class TestConvertSMILESToIUPAC(TestCase):
def test_valid(self):
smiles_to_iupacs = {"CCC": "propane"}
for smiles, expected_iupac in smiles_to_iupacs.items():
self.assertEqual(
convert_smiles_to_iupac(smiles).lower(), expected_iupac.lower()
)
try:
self.assertEqual(
convert_smiles_to_iupac(smiles).lower(), expected_iupac.lower()
)
except SSLError:
self.skipTest("SSL connection issue with the CACTUS WS, skipping")
class DuplicateGeneNameTestCase(TestCase):
......
"""
iPPI-DB contribution module tests
"""
from requests.exceptions import HTTPError
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Permission
from django.contrib.contenttypes.models import ContentType
......@@ -22,7 +24,10 @@ class BibliographyIDTestCase(TestCase):
b = models.Bibliography()
b.source = "DO"
b.id_source = "10.1016/j.bmcl.2013.03.013"
b.save(autofill=True)
try:
b.save(autofill=True)
except HTTPError:
self.skipTest("Connection error, skipping test")
class ContributionViewsAccessTestCase(TestCase):
......
......@@ -536,3 +536,13 @@ def get_ligand_id(smiles: str) -> str:
raise EntryNotFoundError(
smiles, msg=str(f"ligand for smiles {smiles} not found in PDB Ligand")
)
def get_orcid_user_details(orcid: str) -> str:
endpoint = f"https://pub.orcid.org/v3.0/{orcid}/person"
resp = requests.get(endpoint, headers={"Accept": "application/json"},)
data = resp.json()
return {
"first": data["name"]["given-names"]["value"],
"last": data["name"]["family-name"]["value"],
}
......@@ -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"
......@@ -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"
......@@ -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
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