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-rw-r--r--wqflask/base/data_set/__init__.py10
-rw-r--r--wqflask/base/data_set/datasetgroup.py22
-rw-r--r--wqflask/base/data_set/datasettype.py7
-rw-r--r--wqflask/base/data_set/markers.py10
-rw-r--r--wqflask/base/data_set/utils.py10
-rw-r--r--wqflask/base/trait.py20
-rw-r--r--wqflask/base/webqtlCaseData.py5
-rw-r--r--wqflask/base/webqtlConfig.py90
8 files changed, 97 insertions, 77 deletions
diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py
index e49c6a93..ad51e47e 100644
--- a/wqflask/base/data_set/__init__.py
+++ b/wqflask/base/data_set/__init__.py
@@ -6,11 +6,14 @@ import pickle as pickle
# 3rd-party imports
from redis import Redis
+from flask import current_app as app
# local imports
-from .dataset import DataSet
from base import webqtlConfig
-from utility.tools import USE_REDIS
+from wqflask.database import database_connection
+from utility.configuration import get_setting_bool
+
+from .dataset import DataSet
from .datasettype import DatasetType
from .tempdataset import TempDataSet
from .datasetgroup import DatasetGroup
@@ -18,7 +21,6 @@ from .utils import query_table_timestamp
from .genotypedataset import GenotypeDataSet
from .phenotypedataset import PhenotypeDataSet
from .mrnaassaydataset import MrnaAssayDataSet
-from wqflask.database import database_connection
# Used by create_database to instantiate objects
# Each subclass will add to this
@@ -113,7 +115,7 @@ def datasets(group_name, this_group=None, redis_conn=Redis()):
dataset_menu.append(dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
- if USE_REDIS:
+ if get_setting_bool("USE_REDIS"):
redis_conn.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
redis_conn.expire(key, 60 * 5)
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py
index 72577f38..90c59a1e 100644
--- a/wqflask/base/data_set/datasetgroup.py
+++ b/wqflask/base/data_set/datasetgroup.py
@@ -3,6 +3,7 @@
import os
import json
+from flask import current_app as app
from base import webqtlConfig
from .markers import Markers, HumanMarkers
@@ -11,11 +12,11 @@ from utility import gen_geno_ob
from db import webqtlDatabaseFunction
from maintenance import get_group_samplelists
from wqflask.database import database_connection
-from utility.tools import (
+from utility.configuration import (
locate,
- USE_REDIS,
flat_files,
flat_file_exists,
+ get_setting_bool,
locate_ignore_error)
class DatasetGroup:
@@ -87,8 +88,8 @@ class DatasetGroup:
def get_markers(self):
def check_plink_gemma():
- if flat_file_exists("mapping"):
- MAPPING_PATH = flat_files("mapping") + "/"
+ if flat_file_exists(app, "mapping"):
+ MAPPING_PATH = flat_files(app, "mapping") + "/"
if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
return True
return False
@@ -117,6 +118,7 @@ class DatasetGroup:
def get_study_samplelists(self):
study_sample_file = locate_ignore_error(
+ app,
self.name + ".json", 'study_sample_lists')
try:
f = open(study_sample_file)
@@ -137,13 +139,15 @@ class DatasetGroup:
def get_samplelist(self, redis_conn):
result = None
key = "samplelist:v3:" + self.name
+ USE_REDIS = get_setting_bool(app, "USE_REDIS")
if USE_REDIS:
result = redis_conn.get(key)
if result is not None:
self.samplelist = json.loads(result)
else:
- genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
+ genotype_fn = locate_ignore_error(
+ app, self.name + ".geno", 'genotype')
if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist(
"geno", genotype_fn)
@@ -168,12 +172,12 @@ class DatasetGroup:
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
- full_filename = str(
- locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+ full_filename = str(locate(
+ app, self.genofile.split(".")[0] + ".geno", 'genotype'))
else:
- full_filename = str(locate(self.genofile, 'genotype'))
+ full_filename = str(locate(app, self.genofile, 'genotype'))
else:
- full_filename = str(locate(self.name + '.geno', 'genotype'))
+ full_filename = str(locate(app, self.name + '.geno', 'genotype'))
genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
diff --git a/wqflask/base/data_set/datasettype.py b/wqflask/base/data_set/datasettype.py
index 05f0f564..ab36a797 100644
--- a/wqflask/base/data_set/datasettype.py
+++ b/wqflask/base/data_set/datasettype.py
@@ -4,11 +4,10 @@ import json
import requests
from typing import Optional, Dict
-
from redis import Redis
+from flask import current_app as app
-
-from utility.tools import GN2_BASE_URL
+from utility.configuration import get_setting
from wqflask.database import database_connection
@@ -41,7 +40,7 @@ class DatasetType:
# emptied
try:
data = json.loads(requests.get(
- GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
+ get_setting(app, "GN2_BASE_URL") + "/api/v_pre1/gen_dropdown",
timeout=5).content)
for _species in data['datasets']:
for group in data['datasets'][_species]:
diff --git a/wqflask/base/data_set/markers.py b/wqflask/base/data_set/markers.py
index 6f56445e..2fa7cce0 100644
--- a/wqflask/base/data_set/markers.py
+++ b/wqflask/base/data_set/markers.py
@@ -2,16 +2,18 @@
import math
-from utility.tools import locate, flat_files
+from flask import current_app as app
+
+from utility.configuration import locate, flat_files
class Markers:
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
- json_data_fh = open(locate(name + ".json", 'genotype/json'))
+ json_data_fh = open(locate(app, name + ".json", 'genotype/json'))
markers = []
- with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
+ with open("%s/%s_snps.txt" % (flat_files(app, 'genotype/bimbam'), name), 'r') as bimbam_fh:
if len(bimbam_fh.readline().split(", ")) > 2:
delimiter = ", "
elif len(bimbam_fh.readline().split(",")) > 2:
@@ -73,7 +75,7 @@ class HumanMarkers(Markers):
"Markers for humans ..."
def __init__(self, name, specified_markers=[]):
- marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
+ marker_data_fh = open(flat_files(app, 'mapping') + '/' + name + '.bim')
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 703fee04..465538af 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -6,9 +6,9 @@ import json
import hashlib
from typing import List
+from flask import current_app as app
-from utility.tools import SQL_URI
-from base.webqtlConfig import TMPDIR
+from utility.configuration import get_setting
from wqflask.database import parse_db_url, database_connection
def geno_mrna_confidentiality(ob):
@@ -27,7 +27,7 @@ def query_table_timestamp(dataset_type: str):
# computation data and actions
with database_connection() as conn, conn.cursor() as cursor:
- fetch_db_name = parse_db_url(SQL_URI)
+ fetch_db_name = parse_db_url(get_setting("SQL_URI"))
cursor.execute(
"SELECT UPDATE_TIME FROM "
"information_schema.tables "
@@ -57,7 +57,7 @@ def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List
samplelist_as_str = ",".join(samplelist)
file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
- file_path = os.path.join(TMPDIR, f"{file_name}.json")
+ file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
with open(file_path, "w") as file_handler:
json.dump(query_results, file_handler)
@@ -70,7 +70,7 @@ def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List)
samplelist_as_str = ",".join(samplelist)
file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
- file_path = os.path.join(TMPDIR, f"{file_name}.json")
+ file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
try:
with open(file_path, "r") as file_handler:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 37085448..70afa2cc 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,22 +1,21 @@
import requests
import simplejson as json
-from wqflask import app
+
+from flask import g, request, url_for, Blueprint, current_app as app
import utility.hmac as hmac
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
+from utility.configuration import get_setting
from utility.redis_tools import get_redis_conn, get_resource_id
-from flask import g, request, url_for
-
from wqflask.database import database_connection
Redis = get_redis_conn()
-
+trait_bp = Blueprint("trait", __name__)
def create_trait(**kw):
assert bool(kw.get('dataset')) != bool(
@@ -173,11 +172,14 @@ class GeneralTrait:
alias = 'Not available'
if self.symbol:
human_response = requests.get(
- GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+ get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+ self.symbol.upper())
mouse_response = requests.get(
- GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+ get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+ self.symbol.capitalize())
other_response = requests.get(
- GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+ get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+ self.symbol.lower())
if human_response and mouse_response and other_response:
alias_list = json.loads(human_response.content) + json.loads(
@@ -254,7 +256,7 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
return trait
-@app.route("/trait/get_sample_data")
+@trait_bp.route("/trait/get_sample_data")
def get_sample_data():
params = request.args
trait = params['trait']
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index dd6fad04..d144a342 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -21,11 +21,6 @@
# Created by GeneNetwork Core Team 2010/08/10
-import utility.tools
-
-utility.tools.show_settings()
-
-
class webqtlCaseData:
"""one case data in one trait"""
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index a7dbed3d..296bd314 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -8,7 +8,14 @@
#
#########################################
import os
-from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
+from functools import partial
+
+from utility.configuration import (
+ mk_dir,
+ valid_path,
+ flat_files,
+ assert_dir,
+ assert_writable_dir)
# Debug Level
# 1 for debug, mod python will reload import each time
@@ -69,39 +76,48 @@ PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&gen
RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
-# Temporary storage (note that this TMPDIR can be set as an
-# environment variable - use utility.tools.TEMPDIR when you
-# want to reach this base dir
-assert_writable_dir(TEMPDIR)
-
-TMPDIR = mk_dir(TEMPDIR + '/gn2/')
-assert_writable_dir(TMPDIR)
-
-CACHEDIR = mk_dir(TMPDIR + '/cache/')
-# We can no longer write into the git tree:
-GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/')
-GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/')
-
-# Make sure we have permissions to access these
-assert_writable_dir(CACHEDIR)
-assert_writable_dir(GENERATED_IMAGE_DIR)
-assert_writable_dir(GENERATED_TEXT_DIR)
-
-# Flat file directories
-GENODIR = flat_files('genotype') + '/'
-assert_dir(GENODIR)
-# assert_dir(GENODIR+'bimbam') # for gemma
-
-# JSON genotypes are OBSOLETE
-JSON_GENODIR = flat_files('genotype/json') + '/'
-if not valid_path(JSON_GENODIR):
- # fall back on old location (move the dir, FIXME)
- JSON_GENODIR = flat_files('json')
-
-
-TEXTDIR = os.path.join(os.environ.get(
- "GNSHARE", "/gnshare/gn/"), "web/ProbeSetFreeze_DataMatrix")
-# Are we using the following...?
-PORTADDR = "http://50.16.251.170"
-INFOPAGEHREF = '/dbdoc/%s.html'
-CGIDIR = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+def mkdir_with_assert_writable(parent_dir, child_dir):
+ """
+ Make a directory `child_dir` as a child of `parent_dir` asserting that they
+ are both writable."""
+ return assert_writable_dir(mk_dir(
+ assert_writable_dir(parent_dir) + child_dir))
+
+def init_app(app):
+ """Initialise the application with configurations for webqtl."""
+ # Temporary storage (note that this TMPDIR can be set as an
+ # environment variable - use utility.tools.TEMPDIR when you
+ # want to reach this base dir)
+ TEMPDIR = app.config["TEMPDIR"]
+ mkdir_with_temp_dir = lambda child: mkdir_with_assert_writable(
+ TEMPDIR, child)
+ WEBQTL_TMPDIR = mkdir_with_temp_dir("/gn2/")
+ app.config["WEBQTL_TMPDIR"] = WEBQTL_TMPDIR
+ app.config["WEBQTL_CACHEDIR"] = mkdir_with_temp_dir(
+ f"{WEBQTL_TMPDIR}cache/")
+
+ # We can no longer write into the git tree:
+ app.config["WEBQTL_GENERATED_IMAGE_DIR"] = mkdir_with_temp_dir(
+ f"{WEBQTL_TMPDIR}generated/")
+ app.config["WEBQTL_GENERATED_TEXT_DIR"] = mkdir_with_temp_dir(
+ f"{WEBQTL_TMPDIR}generated_text/")
+
+ # Flat file directories
+ app.config["WEBQTL_GENODIR"] = flat_files(app, 'genotype/')
+
+ # JSON genotypes are OBSOLETE
+ WEBQTL_JSON_GENODIR = flat_files(app, 'genotype/json/')
+ if not valid_path(WEBQTL_JSON_GENODIR):
+ # fall back on old location (move the dir, FIXME)
+ WEBQTL_JSON_GENODIR = flat_files('json')
+ app.config["WEBQTL_JSON_GENODIR"] = WEBQTL_JSON_GENODIR
+
+
+ app.config["WEBQTL_TEXTDIR"] = os.path.join(
+ app.config.get("GNSHARE", "/gnshare/gn/"),
+ "web/ProbeSetFreeze_DataMatrix")
+ # Are we using the following...?
+ app.config["WEBQTL_PORTADDR"] = "http://50.16.251.170"
+ app.config["WEBQTL_INFOPAGEHREF"] = '/dbdoc/%s.html'
+ app.config["WEBQTL_CGIDIR"] = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+ return app
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 17:54:29 +0000