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-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py6
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py18
-rw-r--r--wqflask/wqflask/ctl/gn3_ctl_analysis.py9
-rw-r--r--wqflask/wqflask/do_search.py1
-rw-r--r--wqflask/wqflask/gsearch.py10
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py16
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py5
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py1
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py26
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py5
-rw-r--r--wqflask/wqflask/top_level_routes.py5
-rw-r--r--wqflask/wqflask/views.py42
-rw-r--r--wqflask/wqflask/wgcna/gn3_wgcna.py5
13 files changed, 77 insertions, 72 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 64a17548..2553249f 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -3,7 +3,9 @@ import json
import time
from functools import wraps
-from utility.tools import SQL_URI
+from flask import current_app as app
+
+from utility.configuration import get_setting
from wqflask.correlation import correlation_functions
from base import data_set
@@ -146,7 +148,7 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait):
geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if
trait_lists.get(trait_name)}
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting(app, "SQL_URI")) as conn:
correlation_results = compute_all_lit_correlation(
conn=conn, trait_lists=list(geneid_dict.items()),
species=species, gene_id=this_trait_geneid)
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index 41dd77a1..cd3af26f 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -2,7 +2,9 @@
import json
from functools import reduce
-from utility.tools import SQL_URI
+from flask import current_app as app
+
+from utility.configuration import get_setting
from utility.db_tools import mescape
from utility.db_tools import create_in_clause
from wqflask.correlation.correlation_functions\
@@ -30,7 +32,7 @@ def query_probes_metadata(dataset, trait_list):
if not bool(trait_list) or dataset.type != "ProbeSet":
return []
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
with conn.cursor() as cursor:
query = """
@@ -106,7 +108,7 @@ def chunk_dataset(dataset, steps, name):
ProbeSetXRef.ProbeSetId = ProbeSet.Id
""".format(name)
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
with conn.cursor() as curr:
curr.execute(query)
traits_name_dict = dict(curr.fetchall())
@@ -130,7 +132,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
sample_data=json.loads(samples_vals),
dataset_samples=dataset.group.all_samples_ordered())
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
with conn.cursor() as curr:
curr.execute(
"""
@@ -148,7 +150,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
if len(trait_list) == 0:
return {}
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
with conn.cursor() as curr:
# fetching strain data in bulk
query = (
@@ -184,7 +186,7 @@ def compute_top_n_lit(corr_results, target_dataset, this_trait) -> dict:
geneid_dict = {trait_name: geneid for (trait_name, geneid)
in geneid_dict.items() if
corr_results.get(trait_name)}
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
return reduce(
lambda acc, corr: {**acc, **corr},
compute_all_lit_correlation(
@@ -258,7 +260,7 @@ def __compute_sample_corr__(
return {}
if target_dataset.type == "ProbeSet" and start_vars.get("use_cache") == "true":
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
file_path = fetch_text_file(target_dataset.name, conn)
if file_path:
(sample_vals, target_data) = read_text_file(
@@ -339,7 +341,7 @@ def __compute_lit_corr__(
(this_trait_geneid, geneid_dict, species) = do_lit_correlation(
this_trait, target_dataset)
- with database_connection(SQL_URI) as conn:
+ with database_connection(get_setting("SQL_URI")) as conn:
return reduce(
lambda acc, lit: {**acc, **lit},
compute_all_lit_correlation(
diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/wqflask/wqflask/ctl/gn3_ctl_analysis.py
index 8f790597..ca363f49 100644
--- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py
+++ b/wqflask/wqflask/ctl/gn3_ctl_analysis.py
@@ -1,9 +1,10 @@
import requests
import itertools
+from flask import current_app as app
+
from utility import genofile_parser
-from utility.tools import GN3_LOCAL_URL
-from utility.tools import locate
+from utility.configuration import locate, get_setting
from base.trait import create_trait
from base.trait import retrieve_sample_data
@@ -33,7 +34,7 @@ def parse_geno_data(dataset_group_name) -> dict:
@returns : dict with keys genotypes,markernames & individuals
"""
- genofile_location = locate(dataset_group_name + ".geno", "genotype")
+ genofile_location = locate(app, dataset_group_name + ".geno", "genotype")
parser = genofile_parser.ConvertGenoFile(genofile_location)
parser.process_csv()
markers = []
@@ -100,7 +101,7 @@ def parse_form_data(form_data: dict):
def run_ctl(requestform):
"""function to make an api call
to gn3 and run ctl"""
- ctl_api = f"{GN3_LOCAL_URL}/api/ctl/run_ctl"
+ ctl_api = f"{get_setting(app, 'GN3_LOCAL_URL')}/api/ctl/run_ctl"
form_data = parse_form_data(requestform.to_dict())
trait_db_list = form_data["trait_db_list"]
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index fbeb7a49..b5ddb1dc 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -11,7 +11,6 @@ from pprint import pformat as pf
import sys
from db import webqtlDatabaseFunction
-from utility.tools import GN2_BASE_URL
class DoSearch:
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 72c55153..e0e79900 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -3,10 +3,11 @@ from urllib.parse import urlencode, urljoin
from pymonad.maybe import Just, Maybe
from pymonad.tools import curry
import requests
+from flask import current_app as app
from gn3.monads import MonadicDict
from utility.hmac import hmac_creation
-from utility.tools import GN3_LOCAL_URL
+from utility.configuration import get_setting
from base import webqtlConfig
# KLUDGE: Due to the lack of pagination, we hard-limit the maximum
@@ -29,9 +30,10 @@ class GSearch:
convert_lod = lambda x: x / 4.61
self.trait_list = []
for i, trait in enumerate(requests.get(
- urljoin(GN3_LOCAL_URL, "/api/search?" + urlencode({"query": self.terms,
- "type": self.type,
- "per_page": MAX_SEARCH_RESULTS}))).json()):
+ urljoin(get_setting(app, "GN3_LOCAL_URL"),
+ "/api/search?" + urlencode({"query": self.terms,
+ "type": self.type,
+ "per_page": MAX_SEARCH_RESULTS}))).json()):
trait = MonadicDict(trait)
trait["index"] = Just(i)
trait["location_repr"] = (Maybe.apply(chr_mb)
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 8ef85d3c..727fdaf8 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -1,13 +1,15 @@
-import string
import os
+import string
import random
+
+from redis import Redis
+from flask import g, Flask, current_app as app
+
from base import species
from base import webqtlConfig
from utility import helper_functions
-from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
-from redis import Redis
-from flask import Flask, g
+from utility.configuration import flat_files, get_setting
from wqflask.database import database_connection
@@ -119,9 +121,9 @@ class Heatmap:
''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
- reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'),
+ reaper_command = get_setting(app, "REAPER_COMMAND") + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files(app, 'genotype'),
genofile_name,
- TEMPDIR,
+ get_setting(app, "TEMPDIR"),
trait_filename,
webqtlConfig.GENERATED_IMAGE_DIR,
output_filename)
@@ -145,7 +147,7 @@ class Heatmap:
def gen_pheno_txt_file(samples, vals, filename):
"""Generates phenotype file for GEMMA"""
- with open("{0}/gn2/{1}.txt".format(TEMPDIR, filename), "w") as outfile:
+ with open("{0}/gn2/{1}.txt".format(get_setting(app, "TEMPDIR"), filename), "w") as outfile:
outfile.write("Trait\t")
filtered_sample_list = []
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 5e3e9c9d..c194ad24 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -1,12 +1,13 @@
import string
+from flask import current_app as app
from wqflask.database import database_connection
-from utility.tools import flat_files
+from utility.configuration import flat_files
def load_homology(chr_name, start_mb, end_mb, source_file):
homology_list = []
- with open(flat_files("homology/") + source_file) as h_file:
+ with open(flat_files(app, "homology/") + source_file) as h_file:
current_chr = 0
for line in h_file:
line_items = line.split()
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index b7a296b7..a86e2919 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -5,7 +5,6 @@ from flask import current_app as app
from utility import webqtlUtil
from utility.configuration import flat_files, get_setting
-from utility.tools import PLINK_COMMAND
def run_plink(this_trait, dataset, species, vals, maf):
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 4d5db2ee..1cf32f2c 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -5,10 +5,12 @@ import random
import json
import re
+from flask import current_app as app
+
from base import webqtlConfig
from base.trait import GeneralTrait
from base.data_set import create_dataset
-from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
+from utility.configuration import flat_files
def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
@@ -54,16 +56,16 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
if manhattan_plot != True:
opt_list.append("--interval 1")
- reaper_command = (REAPER_COMMAND +
- ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
-
- genofile_name,
- TEMPDIR,
- trait_filename,
- " ".join(
- opt_list),
- webqtlConfig.GENERATED_IMAGE_DIR,
- output_filename))
+ reaper_command = (
+ get_setting(app, REAPER_COMMAND) +
+ ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(
+ flat_files(app, 'genotype'),
+ genofile_name,
+ get_setting(app, 'TEMPDIR'),
+ trait_filename,
+ " ".join(opt_list),
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ output_filename))
os.system(reaper_command)
else:
output_filename, permu_filename, bootstrap_filename = output_files
@@ -84,7 +86,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
def gen_pheno_txt_file(samples, vals, trait_filename):
"""Generates phenotype file for GEMMA"""
- with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile:
+ with open(f"{get_setting(app, 'TEMPDIR')}/gn2/{trait_filename}.txt", "w") as outfile:
outfile.write("Trait\t")
filtered_sample_list = []
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 9b70f03d..7b09d516 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -20,12 +20,13 @@
import scipy
import simplejson as json
+from flask import current_app as app
from base.trait import create_trait
from base import data_set
from utility import helper_functions
from utility import corr_result_helpers
-from utility.tools import GN2_BRANCH_URL
+from utility.configuration import get_setting
class NetworkGraph:
@@ -173,7 +174,7 @@ class NetworkGraph:
self.nodes_list.append(node_dict)
self.elements = json.dumps(self.nodes_list + self.edges_list)
- self.gn2_url = GN2_BRANCH_URL
+ self.gn2_url = get_setting(app, "GN2_BRANCH_URL")
groups = []
for sample in self.all_sample_list:
diff --git a/wqflask/wqflask/top_level_routes.py b/wqflask/wqflask/top_level_routes.py
index a1f26725..b733d955 100644
--- a/wqflask/wqflask/top_level_routes.py
+++ b/wqflask/wqflask/top_level_routes.py
@@ -2,7 +2,7 @@
from flask import Blueprint
from .api import api_bp
-# from .views import main_views
+from .views import main_views
from base.trait import trait_bp
from .user_login import ulogin_bp
from .user_session import usession_bp
@@ -16,8 +16,7 @@ toplevel = Blueprint("toplevel", __name__)
toplevel.register_blueprint(trait_bp)
toplevel.register_blueprint(pcorrs_bp)
toplevel.register_blueprint(ulogin_bp)
-# toplevel.register_blueprint(main_views)
+toplevel.register_blueprint(main_views)
toplevel.register_blueprint(usession_bp)
toplevel.register_blueprint(collections_bp)
-
toplevel.register_blueprint(api_bp, url_prefix="/api")
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index bb0e408f..ebd273af 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -80,14 +80,7 @@ from wqflask.oauth2.client import no_token_get
from wqflask.oauth2.request_utils import process_error
from utility import temp_data
-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
+from utility.configuration import get_setting
from utility.helper_functions import get_species_groups
from utility.redis_tools import get_redis_conn
@@ -114,8 +107,8 @@ def no_access_page():
def index_page():
anon_id = session_info()["anon_id"]
def __render__(colls):
- return render_template("index_page.html", version=GN_VERSION,
- gn_server_url=GN_SERVER_URL,
+ return render_template("index_page.html", version=get_setting(app, "GN_VERSION"),
+ gn_server_url=get_setting(app, "GN_SERVER_URL"),
anon_collections=(
colls if user_logged_in() else []),
anon_id=anon_id)
@@ -139,7 +132,7 @@ def tmp_page(img_path):
@main_views.route("/js/<path:filename>")
def js(filename):
- js_path = JS_GUIX_PATH
+ js_path = get_setting(app, "JS_GUIX_PATH")
name = filename
if 'js_alt/' in filename:
js_path = js_path.replace('genenetwork2/javascript', 'javascript')
@@ -149,7 +142,7 @@ def js(filename):
@main_views.route("/css/<path:filename>")
def css(filename):
- js_path = JS_GUIX_PATH
+ js_path = get_setting(app, "JS_GUIX_PATH")
name = filename
if 'js_alt/' in filename:
js_path = js_path.replace('genenetwork2/javascript', 'javascript')
@@ -159,13 +152,14 @@ def css(filename):
@main_views.route("/twitter/<path:filename>")
def twitter(filename):
- return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)
+ return send_from_directory(get_setting(app, "JS_TWITTER_POST_FETCHER_PATH"),
+ filename)
@main_views.route("/search", methods=('GET',))
def search_page():
result = None
- if USE_REDIS:
+ if get_setting(app, "USE_REDIS"):
key = "search_results:v1:" + \
json.dumps(request.args, sort_keys=True)
result = Redis.get(key)
@@ -173,7 +167,7 @@ def search_page():
result = pickle.loads(result)
result = SearchResultPage(request.args).__dict__
valid_search = result['search_term_exists']
- if USE_REDIS and valid_search:
+ if get_setting(app, "USE_REDIS") and valid_search:
# Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60 * 60)
@@ -313,8 +307,8 @@ def submit_trait_form():
return render_template(
"submit_trait.html",
species_and_groups=species_and_groups,
- gn_server_url=GN_SERVER_URL,
- version=GN_VERSION)
+ gn_server_url=get_setting(app, "GN_SERVER_URL"),
+ version=get_setting(app, "GN_VERSION"))
@main_views.route("/create_temp_trait", methods=('POST',))
@@ -866,7 +860,7 @@ def __handle_correlation_error__(exc):
@main_views.route("/corr_compute", methods=('POST', 'GET'))
def corr_compute_page():
- with Redis.from_url(REDIS_URL, decode_responses=True) as rconn:
+ with Redis.from_url(get_setting(app, "REDIS_URL"), decode_responses=True) as rconn:
if request.method == "POST":
request_received = datetime.datetime.utcnow()
filename=hmac.hmac_creation(f"request_form_{request_received.isoformat()}")
@@ -881,7 +875,7 @@ def corr_compute_page():
"request_received_time": request_received.isoformat(),
"status": "queued"
})
- jobs.run(job_id, REDIS_URL)
+ jobs.run(job_id, get_setting(app, "REDIS_URL"))
return redirect(url_for("corr_compute_page", job_id=str(job_id)))
@@ -992,7 +986,7 @@ def browser_inputs():
filename = request.args['filename']
- with open("{}/gn2/".format(TEMPDIR) + filename + ".json", "r") as the_file:
+ with open("{}/gn2/".format(get_setting(app, "TEMPDIR")) + filename + ".json", "r") as the_file:
file_contents = json.load(the_file)
return flask.jsonify(file_contents)
@@ -1048,7 +1042,7 @@ def display_generif_page(symbol):
"""Fetch GeneRIF metadata from GN3 and display it"""
entries = requests.get(
urljoin(
- GN3_LOCAL_URL,
+ get_setting(app, "GN3_LOCAL_URL"),
f"/api/metadata/genewiki/{symbol}"
)
).json()
@@ -1063,7 +1057,7 @@ def display_generif_page(symbol):
def get_dataset(name):
metadata = requests.get(
urljoin(
- GN3_LOCAL_URL,
+ get_setting(app, "GN3_LOCAL_URL"),
f"/api/metadata/dataset/{name}")
).json()
float_p = ""
@@ -1086,7 +1080,7 @@ def get_dataset(name):
def get_publication(name):
metadata = requests.get(
urljoin(
- GN3_LOCAL_URL,
+ get_setting(app, "GN3_LOCAL_URL"),
f"/api/metadata/publication/{name}")
).json()
return render_template(
@@ -1099,7 +1093,7 @@ def get_publication(name):
def get_phenotype(name):
metadata = requests.get(
urljoin(
- GN3_LOCAL_URL,
+ get_setting(app, "GN3_LOCAL_URL"),
f"/api/metadata/phenotype/{name}")
).json()
return render_template(
diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/wqflask/wqflask/wgcna/gn3_wgcna.py
index ab7fe46c..ec35ccc9 100644
--- a/wqflask/wqflask/wgcna/gn3_wgcna.py
+++ b/wqflask/wqflask/wgcna/gn3_wgcna.py
@@ -4,9 +4,10 @@ and process data to be rendered by datatables
import requests
from types import SimpleNamespace
+from flask import current_app as app
from utility.helper_functions import get_trait_db_obs
-from utility.tools import GN3_LOCAL_URL
+from utility.configuration import get_setting
def fetch_trait_data(requestform):
@@ -74,7 +75,7 @@ def process_image(response):
def run_wgcna(form_data):
"""function to run wgcna"""
- wgcna_api = f"{GN3_LOCAL_URL}/api/wgcna/run_wgcna"
+ wgcna_api = f"{get_setting(app, 'GN3_LOCAL_URL')}/api/wgcna/run_wgcna"
trait_dataset = fetch_trait_data(form_data)
form_data["minModuleSize"] = int(form_data["MinModuleSize"])
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 22:47:05 +0000