From f702e461324f6bf4d436be70b1f9a416f998463c Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 18 Nov 2022 19:14:32 +0100
Subject: [PATCH] updated open nedrex_v2 api route; circumvented nedrex version
issue
Former-commit-id: f16b9235462ccf40d066c649bed17e60df252cde [formerly 2dfe4bcf4c3b6c98665a1e94b505e3ecfe7f286a]
Former-commit-id: 06b576083ffb36e638805640341553f0281a9c5a
---
drugstone/management/commands/populate_db.py | 14 +++++++-------
drugstone/management/includes/DatasetLoader.py | 6 ++++--
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 94f64ce..5d5e859 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -86,8 +86,8 @@ class Command(BaseCommand):
def populate(kwargs):
- nedrex_api_url_unlicenced= "https://nedrex-api-open.zbh.uni-hamburg.de/"
- nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/"
+ nedrex_api_url_open= "https://api.nedrex.net/open"
+ nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/licensed"
data_dir = kwargs['data_dir']
@@ -102,7 +102,7 @@ def populate(kwargs):
cache = NodeCache()
update = True if kwargs['update'] else False
- importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_unlicenced, cache)
+ importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_open, cache)
populator = DataPopulator(cache)
total_n = 0
@@ -152,7 +152,7 @@ def populate(kwargs):
if kwargs['protein_drug']:
print('Importing PDIs from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
- DatasetLoader.get_drug_target_nedrex(nedrex_api_url_unlicenced, False),
+ DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PDIs from unlicenced NeDRexDB')
@@ -179,7 +179,7 @@ def populate(kwargs):
print('Importing PDis from unlicenced NeDRexDB...')
n = NedrexImporter.import_protein_disorder_associations(importer,
DatasetLoader.get_protein_disorder_nedrex(
- nedrex_api_url_unlicenced, False),
+ nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PDis from unlicenced NeDRexDB')
@@ -196,7 +196,7 @@ def populate(kwargs):
if kwargs['drug_disorder']:
print('Importing DrDis from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_disorder_indications(importer,
- DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_unlicenced, False),
+ DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} DrDis from unlicenced NeDRexDB')
@@ -217,7 +217,7 @@ def populate(kwargs):
if kwargs['protein_protein']:
print('Importing PPIs from unlicenced NeDRexDB...')
n = NedrexImporter.import_protein_protein_interactions(importer,
- DatasetLoader.get_ppi_nedrex(nedrex_api_url_unlicenced, False),
+ DatasetLoader.get_ppi_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PPIs from unlicended NeDRexDB')
diff --git a/drugstone/management/includes/DatasetLoader.py b/drugstone/management/includes/DatasetLoader.py
index 804a3df..4ec2538 100644
--- a/drugstone/management/includes/DatasetLoader.py
+++ b/drugstone/management/includes/DatasetLoader.py
@@ -39,7 +39,9 @@ def get_ppi_biogrid():
def get_nedrex_version():
version = get_today_version()
try:
- version = get_metadata()['version']
+ real_version = get_metadata()['version']
+ if real_version != "0.0.0":
+ version = real_version
except RetryError:
pass
return version
@@ -50,7 +52,7 @@ def get_nedrex_source_version(source):
# TODO remove once fixed in nedrex db
if 'drug_central' in metadata:
metadata['drugcentral'] = metadata['drug_central']
-
+
return metadata[source]['date']
--
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