diff options
| -rw-r--r-- | wqflask/wqflask/database.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 17 |
2 files changed, 9 insertions, 16 deletions
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index d2929488..663e2ebf 100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -1,7 +1,6 @@ # Module to initialize sqlalchemy with flask import os import sys -from SPARQLWrapper import JSON, SPARQLWrapper from typing import Tuple, Protocol, Any, Iterator from urllib.parse import urlparse import importlib @@ -61,10 +60,3 @@ def database_connection() -> Iterator[Connection]: yield connection finally: connection.close() - - -def sparql_connection(): - """Create a sparql objection that is used to query RDF""" - return SPARQLWrapper( - get_setting("SPARQL_ENDPOINT") - ) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 1b34e2f8..91a04c62 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -11,6 +11,7 @@ import numpy as np import os import pickle as pickle import random +import requests import sys import traceback import uuid @@ -21,6 +22,8 @@ from zipfile import ZIP_DEFLATED from uuid import UUID +from urllib.parse import urljoin + from wqflask import app from gn3.computations.gemma import generate_hash_of_string @@ -76,6 +79,7 @@ from utility.tools import TEMPDIR from utility.tools import USE_REDIS from utility.tools import REDIS_URL from utility.tools import GN_SERVER_URL +from utility.tools import GN3_LOCAL_URL from utility.tools import GN_VERSION from utility.tools import JS_TWITTER_POST_FETCHER_PATH from utility.tools import JS_GUIX_PATH @@ -83,14 +87,11 @@ from utility.helper_functions import get_species_groups from utility.redis_tools import get_redis_conn import utility.hmac as hmac -from gn3.db.rdf import get_dataset_metadata - from base.webqtlConfig import TMPDIR from base.webqtlConfig import GENERATED_IMAGE_DIR from wqflask.database import database_connection -from wqflask.database import sparql_connection import jobs.jobs as jobs @@ -492,13 +493,13 @@ def show_trait_page(): metadata = ( template_vars.dataset.accession_id .bind( - lambda idx: get_dataset_metadata( - sparql_connection(), - f"GN{idx}" + lambda idx: requests.get( + urljoin( + GN3_LOCAL_URL, + f"/api/metadata/dataset/GN{idx}") ) ) - ).data - + ).json() return render_template("show_trait.html", metadata=metadata, **template_vars.__dict__) |