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-rw-r--r--wqflask/base/trait.py6
-rw-r--r--wqflask/gn2_main.py67
-rw-r--r--wqflask/wqflask/__init__.py193
-rw-r--r--wqflask/wqflask/api/__init__.py5
-rw-r--r--wqflask/wqflask/api/router.py74
-rw-r--r--wqflask/wqflask/collect.py23
-rw-r--r--wqflask/wqflask/partial_correlations_views.py7
-rw-r--r--wqflask/wqflask/templates/base.html18
-rw-r--r--wqflask/wqflask/templates/correlation_error_page.html8
-rw-r--r--wqflask/wqflask/templates/correlation_page.html28
-rw-r--r--wqflask/wqflask/templates/loading.html6
-rw-r--r--wqflask/wqflask/templates/loading_corrs.html6
-rw-r--r--wqflask/wqflask/templates/search_result_page.html24
-rw-r--r--wqflask/wqflask/templates/show_trait.html30
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html4
-rw-r--r--wqflask/wqflask/templates/tool_buttons.html2
-rw-r--r--wqflask/wqflask/user_login.py29
-rw-r--r--wqflask/wqflask/user_session.py9
-rw-r--r--wqflask/wqflask/views.py133
19 files changed, 322 insertions, 350 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 3a52e889..eb043769 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,8 +1,9 @@
import requests
import simplejson as json
-from flask import g, request, url_for, Blueprint, current_app as app
+from flask import g, request, url_for
+from wqflask import app
import utility.hmac as hmac
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
@@ -15,7 +16,6 @@ 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(
@@ -256,7 +256,7 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
return trait
-@trait_bp.route("/trait/get_sample_data")
+@app.route("/trait/get_sample_data")
def get_sample_data():
params = request.args
trait = params['trait']
diff --git a/wqflask/gn2_main.py b/wqflask/gn2_main.py
index 923a35d3..3fd18b6d 100644
--- a/wqflask/gn2_main.py
+++ b/wqflask/gn2_main.py
@@ -1,60 +1,11 @@
-"""Main app creation module"""
-import time
+"""Application entry-point module"""
-from flask import g, session, request
+from wqflask import app
-from wqflask import create_app
-from wqflask.user_session import UserSession
-from gn3.authentication import DataRole, AdminRole
-
-app = create_app()
-
-@app.before_request
-def before_request():
- g.request_start_time = time.time()
- g.request_time = lambda: "%.5fs" % (time.time() - g.request_start_time)
-
- token = session.get("oauth2_token", False)
- if token and not bool(session.get("user_details", False)):
- config = current_app.config
- client = OAuth2Session(
- config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"],
- token=token)
- resp = client.get(
- urljoin(config["GN_SERVER_URL"], "oauth2/user"))
- user_details = resp.json()
- session["user_details"] = user_details
-
- if user_details.get("error") == "invalid_token":
- flash(user_details["error_description"], "alert-danger")
- flash("You are now logged out.", "alert-info")
- session.pop("user_details", None)
- session.pop("oauth2_token", None)
-
-@app.context_processor
-def include_admin_role_class():
- return {'AdminRole': AdminRole}
-
-
-@app.context_processor
-def include_data_role_class():
- return {'DataRole': DataRole}
-
-@app.before_request
-def get_user_session():
- g.user_session = UserSession()
- # I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired
- if not g.user_session:
- response = make_response(redirect(url_for('login')))
- response.set_cookie('session_id_v2', '', expires=0)
- return response
-
-@app.after_request
-def set_user_session(response):
- if hasattr(g, 'user_session'):
- if not request.cookies.get(g.user_session.cookie_name):
- response.set_cookie(g.user_session.cookie_name,
- g.user_session.cookie)
- else:
- response.set_cookie('session_id_v2', '', expires=0)
- return response
+from base import trait
+from wqflask import views
+from wqflask import collect
+from wqflask.api import router
+from wqflask import user_login
+from wqflask import user_session
+from wqflask import partial_correlations_views
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index b9ad5c84..fab66e60 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -9,7 +9,10 @@ import jinja2
import werkzeug
from flask_session import Session
from authlib.integrations.requests_client import OAuth2Session
-from flask import g, Flask, flash, session, url_for, redirect, current_app
+from flask import (
+ g, Flask, flash, session, request, url_for, redirect, current_app)
+
+from gn3.authentication import DataRole, AdminRole
from base import webqtlConfig
from utility import formatting
@@ -18,19 +21,10 @@ from utility.hmac import data_hmac, url_for_hmac
from utility.configuration import tempdir, override_from_envvars
from wqflask.database import parse_db_url
-from wqflask.user_session import UserSession
from wqflask.group_manager import group_management
from wqflask.resource_manager import resource_management
from wqflask.metadata_edits import metadata_edit
-from base.trait import trait_bp
-from wqflask.api import api_bp
-from wqflask.views import main_views
-from wqflask.user_login import ulogin_bp
-from wqflask.user_session import usession_bp
-from wqflask.collect import collections_bp
-from wqflask.partial_correlations_views import pcorrs_bp
-
from wqflask.api.markdown import glossary_blueprint
from wqflask.api.markdown import references_blueprint
from wqflask.api.markdown import links_blueprint
@@ -47,6 +41,118 @@ from wqflask.oauth2.request_utils import user_details, authserver_authorise_uri
from wqflask.jupyter_notebooks import jupyter_notebooks
+
+app = Flask(__name__)
+
+
+# See http://flask.pocoo.org/docs/config/#configuring-from-files
+# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
+app.config.from_envvar('GN2_SETTINGS')
+
+DB_HOST, DB_USER, DB_PASS, DB_NAME, DB_PORT = parse_db_url(app.config.get('SQL_URI'))
+app.config["DB_HOST"] = DB_HOST
+app.config["DB_USER"] = DB_USER
+app.config["DB_PASS"] = DB_PASS
+app.config["DB_NAME"] = DB_NAME
+app.config["DB_PORT"] = DB_PORT
+
+app.jinja_env.globals.update(
+ undefined=jinja2.StrictUndefined,
+ numify=formatting.numify,
+ logged_in=user_logged_in,
+ authserver_authorise_uri=authserver_authorise_uri,
+ user_details=user_details,
+ num_collections=num_collections,
+ url_for_hmac=url_for_hmac,
+ data_hmac=data_hmac)
+
+app.config["SESSION_REDIS"] = redis.from_url(app.config["REDIS_URL"])
+
+# Override settings
+app = override_from_envvars(app)
+app = set_mandatory_settings(app)
+app = webqtlConfig.init_app(app)
+
+# Registering blueprints
+app.register_blueprint(glossary_blueprint, url_prefix="/glossary")
+app.register_blueprint(references_blueprint, url_prefix="/references")
+app.register_blueprint(links_blueprint, url_prefix="/links")
+app.register_blueprint(policies_blueprint, url_prefix="/policies")
+app.register_blueprint(environments_blueprint, url_prefix="/environments")
+app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
+app.register_blueprint(blogs_blueprint, url_prefix="/blogs")
+app.register_blueprint(news_blueprint, url_prefix="/news")
+app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks")
+
+app.register_blueprint(resource_management, url_prefix="/resource-management")
+app.register_blueprint(metadata_edit, url_prefix="/datasets/")
+app.register_blueprint(group_management, url_prefix="/group-management")
+app.register_blueprint(jobs_bp, url_prefix="/jobs")
+app.register_blueprint(oauth2, url_prefix="/oauth2")
+
+from wqflask.decorators import AuthorisationError
+from wqflask.app_errors import (
+ handle_generic_exceptions, handle_authorisation_error)
+app.register_error_handler(Exception, handle_generic_exceptions)
+app.register_error_handler(AuthorisationError, handle_authorisation_error)
+
+server_session = Session(app)
+
+@app.before_request
+def before_request():
+ g.request_start_time = time.time()
+ g.request_time = lambda: "%.5fs" % (time.time() - g.request_start_time)
+
+ token = session.get("oauth2_token", False)
+ if token and not bool(session.get("user_details", False)):
+ config = current_app.config
+ client = OAuth2Session(
+ config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"],
+ token=token)
+ resp = client.get(
+ urljoin(config["GN_SERVER_URL"], "oauth2/user"))
+ user_details = resp.json()
+ session["user_details"] = user_details
+
+ if user_details.get("error") == "invalid_token":
+ flash(user_details["error_description"], "alert-danger")
+ flash("You are now logged out.", "alert-info")
+ session.pop("user_details", None)
+ session.pop("oauth2_token", None)
+
+@app.context_processor
+def include_admin_role_class():
+ return {'AdminRole': AdminRole}
+
+
+@app.context_processor
+def include_data_role_class():
+ return {'DataRole': DataRole}
+
+@app.before_request
+def get_user_session():
+ # import here to prevent circular import issues
+ from wqflask.user_session import UserSession
+ g.user_session = UserSession()
+ # I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired
+ if not g.user_session:
+ response = make_response(redirect(url_for('login')))
+ response.set_cookie('session_id_v2', '', expires=0)
+ return response
+
+@app.after_request
+def set_user_session(response):
+ if hasattr(g, 'user_session'):
+ if not request.cookies.get(g.user_session.cookie_name):
+ response.set_cookie(g.user_session.cookie_name,
+ g.user_session.cookie)
+ else:
+ response.set_cookie('session_id_v2', '', expires=0)
+ return response
+
+
+
+
from wqflask import group_manager
from wqflask import resource_manager
from wqflask import search_results
@@ -55,70 +161,3 @@ from wqflask import gsearch
from wqflask import update_search_results
from wqflask import docs
from wqflask import db_info
-
-def create_app():
- """Create the application object."""
- app = Flask(__name__)
-
-
- # See http://flask.pocoo.org/docs/config/#configuring-from-files
- # Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
- app.config.from_envvar('GN2_SETTINGS')
-
- DB_HOST, DB_USER, DB_PASS, DB_NAME, DB_PORT = parse_db_url(app.config.get('SQL_URI'))
- app.config["DB_HOST"] = DB_HOST
- app.config["DB_USER"] = DB_USER
- app.config["DB_PASS"] = DB_PASS
- app.config["DB_NAME"] = DB_NAME
- app.config["DB_PORT"] = DB_PORT
-
- app.jinja_env.globals.update(
- undefined=jinja2.StrictUndefined,
- numify=formatting.numify,
- logged_in=user_logged_in,
- authserver_authorise_uri=authserver_authorise_uri,
- user_details=user_details,
- num_collections=num_collections,
- url_for_hmac=url_for_hmac,
- data_hmac=data_hmac)
-
- app.config["SESSION_REDIS"] = redis.from_url(app.config["REDIS_URL"])
-
- # Override settings
- app = override_from_envvars(app)
- app = set_mandatory_settings(app)
- app = webqtlConfig.init_app(app)
-
- # Registering blueprints
- app.register_blueprint(trait_bp)
- app.register_blueprint(pcorrs_bp)
- app.register_blueprint(ulogin_bp)
- app.register_blueprint(main_views)
- app.register_blueprint(usession_bp)
- app.register_blueprint(collections_bp)
- app.register_blueprint(api_bp, url_prefix="/api")
-
- app.register_blueprint(glossary_blueprint, url_prefix="/glossary")
- app.register_blueprint(references_blueprint, url_prefix="/references")
- app.register_blueprint(links_blueprint, url_prefix="/links")
- app.register_blueprint(policies_blueprint, url_prefix="/policies")
- app.register_blueprint(environments_blueprint, url_prefix="/environments")
- app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
- app.register_blueprint(blogs_blueprint, url_prefix="/blogs")
- app.register_blueprint(news_blueprint, url_prefix="/news")
- app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks")
-
- app.register_blueprint(resource_management, url_prefix="/resource-management")
- app.register_blueprint(metadata_edit, url_prefix="/datasets/")
- app.register_blueprint(group_management, url_prefix="/group-management")
- app.register_blueprint(jobs_bp, url_prefix="/jobs")
- app.register_blueprint(oauth2, url_prefix="/oauth2")
-
- from wqflask.decorators import AuthorisationError
- from wqflask.app_errors import (
- handle_generic_exceptions, handle_authorisation_error)
- app.register_error_handler(Exception, handle_generic_exceptions)
- app.register_error_handler(AuthorisationError, handle_authorisation_error)
-
- server_session = Session(app)
- return app
diff --git a/wqflask/wqflask/api/__init__.py b/wqflask/wqflask/api/__init__.py
index abeb6e56..4f6e348c 100644
--- a/wqflask/wqflask/api/__init__.py
+++ b/wqflask/wqflask/api/__init__.py
@@ -1,9 +1,4 @@
"""
Set up the package's top-level objects.
"""
-from flask import Blueprint
-from . import router as router
-
-api_bp = Blueprint("api", __name__)
-api_bp.register_blueprint(router.pre1_router)
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index afa150dc..f180527d 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -12,26 +12,24 @@ from zipfile import ZipFile, ZIP_DEFLATED
import flask
from flask import request
-from flask import Blueprint
from flask import send_file
from flask import make_response
-from flask import current_app as app
from utility.configuration import flat_files
+from wqflask import app
from wqflask.database import database_connection
from wqflask.api import correlation, mapping, gen_menu
version = "pre1"
-pre1_router = Blueprint("pre1_router", __name__)
-@pre1_router.route("/v_{}/".format(version))
+@app.route("/v_{}/".format(version))
def hello_world():
return flask.jsonify({"hello": "world"})
-@pre1_router.route("/v_{}/species".format(version))
+@app.route("/v_{}/species".format(version))
def get_species_list():
species_list = []
with database_connection() as conn, conn.cursor() as cursor:
@@ -49,8 +47,8 @@ def get_species_list():
return flask.jsonify(species_list)
-@pre1_router.route("/v_{}/species/<path:species_name>".format(version))
-@pre1_router.route("/v_{}/species/<path:species_name>.<path:file_format>".format(version))
+@app.route("/v_{}/species/<path:species_name>".format(version))
+@app.route("/v_{}/species/<path:species_name>.<path:file_format>".format(version))
def get_species_info(species_name, file_format="json"):
with database_connection() as conn, conn.cursor() as cursor:
cursor.execute(
@@ -68,8 +66,8 @@ def get_species_info(species_name, file_format="json"):
return flask.jsonify(species_dict)
-@pre1_router.route("/v_{}/groups".format(version))
-@pre1_router.route("/v_{}/groups/<path:species_name>".format(version))
+@app.route("/v_{}/groups".format(version))
+@app.route("/v_{}/groups/<path:species_name>".format(version))
def get_groups_list(species_name=None):
_groups = ()
with database_connection() as conn, conn.cursor() as cursor:
@@ -114,10 +112,10 @@ def get_groups_list(species_name=None):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/group/<path:group_name>".format(version))
-@pre1_router.route("/v_{}/group/<path:group_name>.<path:file_format>".format(version))
-@pre1_router.route("/v_{}/group/<path:species_name>/<path:group_name>".format(version))
-@pre1_router.route("/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".format(version))
+@app.route("/v_{}/group/<path:group_name>".format(version))
+@app.route("/v_{}/group/<path:group_name>.<path:file_format>".format(version))
+@app.route("/v_{}/group/<path:species_name>/<path:group_name>".format(version))
+@app.route("/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".format(version))
def get_group_info(group_name, species_name=None, file_format="json"):
group = ()
with database_connection() as conn, conn.cursor() as cursor:
@@ -169,8 +167,8 @@ def get_group_info(group_name, species_name=None, file_format="json"):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/datasets/<path:group_name>".format(version))
-@pre1_router.route("/v_{}/datasets/<path:species_name>/<path:group_name>".format(version))
+@app.route("/v_{}/datasets/<path:group_name>".format(version))
+@app.route("/v_{}/datasets/<path:species_name>/<path:group_name>".format(version))
def get_datasets_for_group(group_name, species_name=None):
_datasets = ()
with database_connection() as conn, conn.cursor() as cursor:
@@ -234,10 +232,10 @@ def get_datasets_for_group(group_name, species_name=None):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/dataset/<path:dataset_name>".format(version))
-@pre1_router.route("/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version))
-@pre1_router.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
-@pre1_router.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".format(version))
+@app.route("/v_{}/dataset/<path:dataset_name>".format(version))
+@app.route("/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version))
+@app.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
+@app.route("/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".format(version))
def get_dataset_info(dataset_name, group_name=None, file_format="json"):
# ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets
@@ -340,8 +338,8 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
-@pre1_router.route("/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
+@app.route("/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
+@app.route("/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
def fetch_traits(dataset_name, file_format="json"):
trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
dataset_name, request.args)
@@ -489,8 +487,8 @@ def fetch_traits(dataset_name, file_format="json"):
details="")
-@pre1_router.route("/v_{}/sample_data/<path:dataset_name>".format(version))
-@pre1_router.route("/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
+@app.route("/v_{}/sample_data/<path:dataset_name>".format(version))
+@app.route("/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
def all_sample_data(dataset_name, file_format="csv"):
trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
dataset_name, request.args)
@@ -598,8 +596,8 @@ def all_sample_data(dataset_name, file_format="csv"):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version))
-@pre1_router.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+@app.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
def trait_sample_data(dataset_name, trait_name, file_format="json"):
with database_connection() as conn, conn.cursor() as cursor:
cursor.execute(
@@ -685,10 +683,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
-@pre1_router.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
-@pre1_router.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
-@pre1_router.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+@app.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
+@app.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
+@app.route("/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
def get_trait_info(dataset_name, trait_name, file_format="json"):
with database_connection() as conn, conn.cursor() as cursor:
cursor.execute(
@@ -750,7 +748,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/correlation".format(version), methods=("GET",))
+@app.route("/v_{}/correlation".format(version), methods=("GET",))
def get_corr_results():
results = correlation.do_correlation(request.args)
@@ -761,7 +759,7 @@ def get_corr_results():
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/mapping".format(version), methods=("GET",))
+@app.route("/v_{}/mapping".format(version), methods=("GET",))
def get_mapping_results():
results, format = mapping.do_mapping_for_api(request.args)
@@ -785,18 +783,18 @@ def get_mapping_results():
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@pre1_router.route("/v_{}/genotypes/view/<string:group_name>".format(version))
+@app.route("/v_{}/genotypes/view/<string:group_name>".format(version))
def view_genotype_files(group_name):
if os.path.isfile("{0}/{1}.json".format(flat_files(app, "genotype"), group_name)):
with open("{0}/{1}.json".format(flat_files(app, "genotype"), group_name)) as geno_json:
return flask.jsonify(json.load(geno_json))
-@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
-@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
-@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
-@pre1_router.route("/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version))
-@pre1_router.route("/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version))
+@app.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
+@app.route("/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
+@app.route("/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
+@app.route("/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version))
+@app.route("/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version))
def get_genotypes(group_name, file_format="csv", dataset_name=None):
limit_num = None
if 'limit_to' in request.args:
@@ -887,7 +885,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
return output
-@pre1_router.route("/v_{}/gen_dropdown".format(version), methods=("GET",))
+@app.route("/v_{}/gen_dropdown".format(version), methods=("GET",))
def gen_dropdown_menu():
with database_connection() as conn:
results = gen_menu.gen_dropdown_json(conn)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index dd3f3330..5c97b69c 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -11,7 +11,6 @@ from flask import url_for
from flask import request
from flask import redirect
from flask import flash
-from flask import Blueprint
from flask import current_app
from utility import hmac
@@ -23,6 +22,7 @@ from base.trait import retrieve_trait_info
from base.trait import jsonable
from base.data_set import create_dataset
+from wqflask import app
from wqflask.oauth2 import client
from wqflask.oauth2 import session
from wqflask.oauth2.session import session_info
@@ -34,7 +34,6 @@ from wqflask.oauth2.client import (
Redis = get_redis_conn()
-collections_bp = Blueprint("collections", __name__)
def process_traits(unprocessed_traits):
if isinstance(unprocessed_traits, bytes):
@@ -59,7 +58,7 @@ def report_change(len_before, len_now):
numify(new_length, 'new trait', 'new traits')))
-@collections_bp.route("/collections/store_trait_list", methods=('POST',))
+@app.route("/collections/store_trait_list", methods=('POST',))
def store_traits_list():
params = request.form
@@ -71,7 +70,7 @@ def store_traits_list():
return hash
-@collections_bp.route("/collections/add", methods=["POST"])
+@app.route("/collections/add", methods=["POST"])
def collections_add():
anon_id = session_info()["anon_id"]
traits = request.args.get("traits", request.form.get("traits"))
@@ -114,7 +113,7 @@ def __compute_traits__(params):
unprocessed_traits = params['traits']
return process_traits(unprocessed_traits)
-@collections_bp.route("/collections/new")
+@app.route("/collections/new")
def collections_new():
params = request.args
anon_id = session_info()["anon_id"]
@@ -179,7 +178,7 @@ def create_new(collection_name):
return redirect(url_for('view_collection', uc_id=uc_id))
-@collections_bp.route("/collections/list")
+@app.route("/collections/list")
def list_collections():
params = request.args
anon_id = session.session_info()["anon_id"]
@@ -199,7 +198,7 @@ def list_collections():
**user_collections,
**anon_collections)
-@collections_bp.route("/collections/handle_anonymous", methods=["POST"])
+@app.route("/collections/handle_anonymous", methods=["POST"])
def handle_anonymous_collections():
"""Handle any anonymous collection on logging in."""
choice = request.form.get("anon_choice")
@@ -220,7 +219,7 @@ def handle_anonymous_collections():
"anon_id": str(session_info()["anon_id"])
}).either(__impdel_error__, __impdel_success__)
-@collections_bp.route("/collections/remove", methods=('POST',))
+@app.route("/collections/remove", methods=('POST',))
def remove_traits():
params = request.form
uc_id = params['uc_id']
@@ -234,7 +233,7 @@ def remove_traits():
}).either(with_flash_error(resp), with_flash_success(resp))
-@collections_bp.route("/collections/delete", methods=('POST',))
+@app.route("/collections/delete", methods=('POST',))
def delete_collection():
def __error__(err):
error = process_error(err)
@@ -303,7 +302,7 @@ def trait_info_str(trait):
trait.name, trait.dataset.name, __trait_desc(trait), __symbol(trait),
__location(trait), __mean(trait), __lrs(trait), __lrs_location(trait))
-@collections_bp.route("/collections/import", methods=('POST',))
+@app.route("/collections/import", methods=('POST',))
def import_collection():
import_file = request.files['import_file']
if import_file.filename != '':
@@ -319,7 +318,7 @@ def import_collection():
return render_template(
"collections/list.html")
-@collections_bp.route("/collections/view")
+@app.route("/collections/view")
def view_collection():
params = request.args
@@ -382,7 +381,7 @@ def view_collection():
return coll.either(__error__, __view__)
-@collections_bp.route("/collections/change_name", methods=('POST',))
+@app.route("/collections/change_name", methods=('POST',))
def change_collection_name():
collection_id = request.form['collection_id']
resp = redirect(url_for("view_collection", uc_id=collection_id))
diff --git a/wqflask/wqflask/partial_correlations_views.py b/wqflask/wqflask/partial_correlations_views.py
index f5f88147..5911860d 100644
--- a/wqflask/wqflask/partial_correlations_views.py
+++ b/wqflask/wqflask/partial_correlations_views.py
@@ -14,12 +14,11 @@ from flask import (
current_app,
render_template)
+from wqflask import app
from utility.configuration import get_setting
from wqflask.database import database_connection
from gn3.db.partial_correlations import traits_info
-pcorrs_bp = Blueprint("partial_correlations", __name__)
-
def publish_target_databases(conn, groups, threshold):
query = (
"SELECT PublishFreeze.FullName,PublishFreeze.Name "
@@ -268,7 +267,7 @@ def handle_response(response):
message = response_error_message(response))
return handle_200_response(response.json())
-@pcorrs_bp.route("/partial_correlations", methods=["POST"])
+@app.route("/partial_correlations", methods=["POST"])
def partial_correlations():
form = request.form
traits = tuple(
@@ -349,7 +348,7 @@ def process_pcorrs_command_output(result):
return render_error(
f"({result['error_type']}: {result['message']})")
-@pcorrs_bp.route("/partial_correlations/<command_id>", methods=["GET"])
+@app.route("/partial_correlations/<command_id>", methods=["GET"])
def poll_partial_correlation_results(command_id):
response = requests.get(
url=urljoin(get_setting(current_app, "GN_SERVER_URL"),
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 7cda4bab..1328d229 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -12,7 +12,7 @@
</script>
<link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
<link rel="apple-touch-icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
- <link REL="stylesheet" TYPE="text/css" href="{{ url_for('main_views.css', filename='bootstrap/css/bootstrap.css') }}" />
+ <link REL="stylesheet" TYPE="text/css" href="{{ url_for('css', filename='bootstrap/css/bootstrap.css') }}" />
<link REL="stylesheet" TYPE="text/css" href="/static/new/css/bootstrap-custom.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/new/css/non-responsive.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/new/css/docs.css" />
@@ -30,10 +30,10 @@
border-radius: 1rem;
}
table.dataTable thead .sorting_asc {
- background-image: url({{ url_for("main_views.js", filename="DataTables/images/sort_asc_disabled.png") }});
+ background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
}
table.dataTable thead .sorting_desc {
- background-image: url({{ url_for("main_views.js", filename="DataTables/images/sort_desc_disabled.png") }});
+ background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
}
@@ -336,8 +336,8 @@
<!-- <button class="btn btn-primary">Save changes</button>-->
<!--</div>-->
</div>
- <script src="{{ url_for('main_views.js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
- <script src="{{ url_for('main_views.js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
<script src="/static/new/javascript/search_autocomplete.js"></script>
<script>
//http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
@@ -389,11 +389,11 @@
});
</script>
- <script src="{{ url_for('main_views.js', filename='jquery-cookie/jquery.cookie.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='jquery-cookie/jquery.cookie.js') }}" type="text/javascript"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
- <!-- <script src="{{ url_for('main_views.js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script> -->
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/parsley.min.js') }}"></script>
+ <!-- <script src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script> -->
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
{% block js %}
{% endblock %}
<script type="text/javascript">
diff --git a/wqflask/wqflask/templates/correlation_error_page.html b/wqflask/wqflask/templates/correlation_error_page.html
index be3da15a..7d11daf0 100644
--- a/wqflask/wqflask/templates/correlation_error_page.html
+++ b/wqflask/wqflask/templates/correlation_error_page.html
@@ -2,10 +2,10 @@
{%block title%}Correlation Results{%endblock%}
{%block css%}
-<link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('main_views.js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('main_views.js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
-<link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='fontawesome/css/all.min.css') }}"/>
+<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/>
<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{%endblock%}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 853a6c0a..84fa4648 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,10 +1,10 @@
{% extends "base.html" %}
{% block title %}Correlation Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='fontawesome/css/all.min.css') }}"/>
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/>
<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
@@ -131,16 +131,16 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/md5.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/underscore.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='jszip/jszip.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/underscore.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='fontawesome/js/all.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='fontawesome/js/all.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script type="text/javascript" src="/static/new/javascript/table_functions.js"></script>
<script type="text/javascript" src="/static/new/javascript/create_datatable.js"></script>
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 3d4c4643..a6d9ae5e 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,5 +1,5 @@
<title>Loading {{ start_vars.tool_used }} Results</title>
-<link REL="stylesheet" TYPE="text/css" href="{{ url_for('main_views.css', filename='bootstrap/css/bootstrap.css') }}" />
+<link REL="stylesheet" TYPE="text/css" href="{{ url_for('css', filename='bootstrap/css/bootstrap.css') }}" />
<link REL="stylesheet" TYPE="text/css" href="/static/new/css/bootstrap-custom.css" />
<form method="post" action="" name="loading_form" id="loading_form" class="form-horizontal">
{% for key, value in start_vars.items() %}
@@ -100,8 +100,8 @@
</div>
</div>
</form>
-<script src="{{ url_for('main_views.js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
-<script src="{{ url_for('main_views.js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+<script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
<script type="text/javascript">
$('#show_full_diff').click(function() {
if ($('#diff_table_container').is(':visible')){
diff --git a/wqflask/wqflask/templates/loading_corrs.html b/wqflask/wqflask/templates/loading_corrs.html
index bfcbcf57..8abd5464 100644
--- a/wqflask/wqflask/templates/loading_corrs.html
+++ b/wqflask/wqflask/templates/loading_corrs.html
@@ -8,7 +8,7 @@
<meta http-equiv="refresh" content="5">
<link rel="stylesheet" type="text/css"
- href="{{url_for('main_views.css', filename='bootstrap/css/bootstrap.css')}}" />
+ href="{{url_for('css', filename='bootstrap/css/bootstrap.css')}}" />
<link rel="stylesheet" type="text/css"
href="/static/new/css/bootstrap-custom.css" />
</head>
@@ -21,8 +21,8 @@
</div>
</div>
- <script src="{{ url_for('main_views.js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
- <script src="{{ url_for('main_views.js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
</body>
</html>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 15ec75d7..495c5669 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -1,10 +1,10 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='fontawesome/css/font-awesome.min.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='fontawesome/css/all.min.css') }}"/>
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/all.min.css') }}"/>
<link href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" rel="stylesheet" type="text/css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" />
@@ -153,14 +153,14 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/md5.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='jszip/jszip.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='fontawesome/js/all.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='fontawesome/js/all.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/table_functions.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 414a6ec0..84231d34 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -8,9 +8,9 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='d3-tip/d3-tip.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('main_views.css', filename='nouislider/nouislider.min.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" />
<link href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" rel="stylesheet" type="text/css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -139,13 +139,13 @@
$('.collapse').collapse()
</script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='d3js/d3.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/underscore.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='underscore-string/underscore.string.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='d3-tip/d3-tip.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='js_alt/jstat.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='shapiro-wilk/shapiro-wilk.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='plotly/plotly.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='shapiro-wilk/shapiro-wilk.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/stats.js"></script>
@@ -154,11 +154,11 @@
<script language="javascript" type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('main_views.js', filename='nouislider/nouislider.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/table_functions.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/create_datatable.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 795267dd..c745fce8 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -63,7 +63,7 @@
{{ dataset.fullname }}
</a>
<br/>
- <a href="{{ url_for('main_views.get_dataset', name=dataset.name) }}" target="_blank">
+ <a href="{{ url_for('get_dataset', name=dataset.name) }}" target="_blank">
GN2 Link: {{ dataset.fullname }}
</a>
</td>
@@ -229,7 +229,7 @@
{% endif %}
{% if this_trait.symbol != None %}
<button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">(GN1) GeneWiki</button>
- <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('{{ url_for('main_views.display_generif_page', symbol=this_trait.symbol) }}', '_blank')">(GN2) GeneWiki</button>
+ <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('{{ url_for('display_generif_page', symbol=this_trait.symbol) }}', '_blank')">(GN2) GeneWiki</button>
{% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
<button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
{% endif %}
diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html
index 50e26486..c6d1476c 100644
--- a/wqflask/wqflask/templates/tool_buttons.html
+++ b/wqflask/wqflask/templates/tool_buttons.html
@@ -32,7 +32,7 @@
<button id="partial-correlations"
class="btn btn-primary submit_special"
- data-url="{{url_for('partial_correlations.partial_correlations')}}"
+ data-url="{{url_for('partial_correlations')}}"
title="Run partial correlations with the selected traits">
Partial Correlations
</button>
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 69ae9e10..4d9cc021 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -17,11 +17,10 @@ from flask import (
url_for,
request,
redirect,
- Blueprint,
make_response,
- render_template,
- current_app as app)
+ render_template)
+from wqflask import app
from wqflask import pbkdf2
from wqflask.user_session import UserSession
@@ -33,8 +32,6 @@ Redis = get_redis_conn()
THREE_DAYS = 60 * 60 * 24 * 3
-ulogin_bp = Blueprint("user_login", __name__)
-
def timestamp():
return datetime.datetime.utcnow().isoformat()
@@ -160,7 +157,7 @@ def send_invitation_email(user_email, temp_password, template_name="email/user_i
return {"recipient": recipient, "subject": subject, "body": body}
-@ulogin_bp.route("/manage/verify_email")
+@app.route("/manage/verify_email")
def verify_email():
if 'code' in request.args:
user_details = check_verification_code(request.args['code'])
@@ -180,7 +177,7 @@ def verify_email():
"Invalid code: Password reset code does not exist or might have expired!", "error")
-@ulogin_bp.route("/n/login", methods=('GET', 'POST'))
+@app.route("/n/login", methods=('GET', 'POST'))
def login():
params = request.form if request.form else request.args
if not params: # ZS: If coming to page for first time
@@ -260,7 +257,7 @@ def login():
return response
-@ulogin_bp.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
code = request.args.get("code")
@@ -303,7 +300,7 @@ def get_github_user_details(access_token):
return json.loads(result)
-@ulogin_bp.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
def orcid_oauth2():
from uuid import uuid4
from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
@@ -350,7 +347,7 @@ def get_github_user_details(access_token):
return json.loads(result)
-@ulogin_bp.route("/n/logout")
+@app.route("/n/logout")
def logout():
UserSession().delete_session()
flash("You are now logged out. We hope you come back soon!")
@@ -360,7 +357,7 @@ def logout():
return response
-@ulogin_bp.route("/n/forgot_password", methods=['GET'])
+@app.route("/n/forgot_password", methods=['GET'])
def forgot_password():
"""Entry point for forgotten password"""
print("ARGS: ", request.args)
@@ -402,7 +399,7 @@ def send_forgot_password_email(verification_email):
return subject
-@ulogin_bp.route("/n/forgot_password_submit", methods=('POST',))
+@app.route("/n/forgot_password_submit", methods=('POST',))
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
params = request.form
@@ -426,7 +423,7 @@ def forgot_password_submit():
return redirect(url_for("forgot_password"))
-@ulogin_bp.route("/n/password_reset", methods=['GET'])
+@app.route("/n/password_reset", methods=['GET'])
def password_reset():
"""Entry point after user clicks link in E-mail"""
verification_code = request.args.get('code')
@@ -445,7 +442,7 @@ def password_reset():
return redirect(url_for("login"))
-@ulogin_bp.route("/n/password_reset_step2", methods=('POST',))
+@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
errors = []
@@ -507,7 +504,7 @@ def register_user(params):
return errors
-@ulogin_bp.route("/n/register", methods=('GET', 'POST'))
+@app.route("/n/register", methods=('GET', 'POST'))
def register():
errors = []
@@ -525,6 +522,6 @@ def register():
return render_template("new_security/register_user.html", values=params, errors=errors)
-@ulogin_bp.errorhandler(401)
+@app.errorhandler(401)
def unauthorized(error):
return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 54bfb609..60125b57 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -12,11 +12,10 @@ from flask import (
url_for,
request,
redirect,
- Blueprint,
make_response,
- render_template,
- current_app as app)
+ render_template)
+from wqflask import app
from utility import hmac
from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
@@ -26,8 +25,6 @@ Redis = get_redis_conn()
THREE_DAYS = 60 * 60 * 24 * 3
THIRTY_DAYS = 60 * 60 * 24 * 30
-usession_bp = Blueprint("user_session", __name__)
-
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
@@ -45,7 +42,7 @@ def create_signed_cookie():
return the_uuid, uuid_signed
-@usession_bp.route("/user/manage", methods=('GET', 'POST'))
+@app.route("/user/manage", methods=('GET', 'POST'))
def manage_user():
params = request.form if request.form else request.args
if 'new_full_name' in params:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3ce7d0cb..de2e803a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -26,7 +26,6 @@ from uuid import UUID
from urllib.parse import urljoin
from gn3.computations.gemma import generate_hash_of_string
-from flask import current_app as app
from flask import g
from flask import Response
from flask import request
@@ -37,10 +36,10 @@ from flask import send_file
from flask import url_for
from flask import flash
from flask import session
-from flask import Blueprint
# Some of these (like collect) might contain endpoints, so they're still used.
# Blueprints should probably be used instead.
+from wqflask import app
from wqflask import search_results
from wqflask import server_side
from base.data_set import create_dataset # Used by YAML in marker_regression
@@ -94,15 +93,13 @@ from wqflask.oauth2.checks import user_logged_in
Redis = get_redis_conn()
-main_views = Blueprint("main_views", __name__)
-
-@main_views.route("/authentication_needed")
+@app.route("/authentication_needed")
def no_access_page():
return render_template("new_security/not_authenticated.html")
-@main_views.route("/")
+@app.route("/")
def index_page():
anon_id = session_info()["anon_id"]
def __render__(colls):
@@ -118,7 +115,7 @@ def index_page():
__render__)
-@main_views.route("/tmp/<img_path>")
+@app.route("/tmp/<img_path>")
def tmp_page(img_path):
initial_start_vars = request.form
imgfile = open(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR") + img_path, 'rb')
@@ -129,7 +126,7 @@ def tmp_page(img_path):
img_base64=bytesarray)
-@main_views.route("/js/<path:filename>")
+@app.route("/js/<path:filename>")
def js(filename):
js_path = get_setting(app, "JS_GUIX_PATH")
name = filename
@@ -139,7 +136,7 @@ def js(filename):
return send_from_directory(js_path, name)
-@main_views.route("/css/<path:filename>")
+@app.route("/css/<path:filename>")
def css(filename):
js_path = get_setting(app, "JS_GUIX_PATH")
name = filename
@@ -149,13 +146,13 @@ def css(filename):
return send_from_directory(js_path, name)
-@main_views.route("/twitter/<path:filename>")
+@app.route("/twitter/<path:filename>")
def twitter(filename):
return send_from_directory(get_setting(app, "JS_TWITTER_POST_FETCHER_PATH"),
filename)
-@main_views.route("/search", methods=('GET',))
+@app.route("/search", methods=('GET',))
def search_page():
result = None
if get_setting(app, "USE_REDIS"):
@@ -176,7 +173,7 @@ def search_page():
return render_template("search_error.html")
-@main_views.route("/search_table", methods=('GET',))
+@app.route("/search_table", methods=('GET',))
def search_page_table():
the_search = search_results.SearchResultPage(request.args)
current_page = server_side.ServerSideTable(
@@ -189,7 +186,7 @@ def search_page_table():
return flask.jsonify(current_page)
-@main_views.route("/gsearch", methods=('GET',))
+@app.route("/gsearch", methods=('GET',))
def gsearchact():
result = GSearch(request.args).__dict__
type = request.args['type']
@@ -199,7 +196,7 @@ def gsearchact():
return render_template("gsearch_pheno.html", **result)
-@main_views.route("/gsearch_table", methods=('GET',))
+@app.route("/gsearch_table", methods=('GET',))
def gsearchtable():
gsearch_table_data = GSearch(request.args)
current_page = server_side.ServerSideTable(
@@ -212,13 +209,13 @@ def gsearchtable():
return flask.jsonify(current_page)
-@main_views.route("/gsearch_updating", methods=('POST',))
+@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
result = UpdateGSearch(request.args).__dict__
return result['results']
-@main_views.route("/docedit")
+@app.route("/docedit")
def docedit():
try:
if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
@@ -230,45 +227,45 @@ def docedit():
return "You shouldn't be here!"
-@main_views.route('/generated/<filename>')
+@app.route('/generated/<filename>')
def generated_file(filename):
return send_from_directory(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR"), filename)
-@main_views.route("/help")
+@app.route("/help")
def help():
doc = Docs("help", request.args)
return render_template("docs.html", **doc.__dict__)
-@main_views.route("/wgcna_setup", methods=('POST',))
+@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
# We are going to get additional user input for the analysis
# Display them using the template
return render_template("wgcna_setup.html", **request.form)
-@main_views.route("/wgcna_results", methods=('POST',))
+@app.route("/wgcna_results", methods=('POST',))
def wcgna_results():
"""call the gn3 api to get wgcna response data"""
results = run_wgcna(dict(request.form))
return render_template("gn3_wgcna_results.html", **results)
-@main_views.route("/ctl_setup", methods=('POST',))
+@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
# We are going to get additional user input for the analysis
# Display them using the template
return render_template("ctl_setup.html", **request.form)
-@main_views.route("/ctl_results", methods=["POST"])
+@app.route("/ctl_results", methods=["POST"])
def ctl_results():
ctl_results = run_ctl(request.form)
return render_template("gn3_ctl_results.html", **ctl_results)
-@main_views.route("/ctl_network_files/<file_name>/<file_type>")
+@app.route("/ctl_network_files/<file_name>/<file_type>")
def fetch_network_files(file_name, file_type):
file_path = f"{file_name}.{file_type}"
@@ -277,30 +274,30 @@ def fetch_network_files(file_name, file_type):
return send_file(file_path)
-@main_views.route("/intro")
+@app.route("/intro")
def intro():
doc = Docs("intro", request.args)
return render_template("docs.html", **doc.__dict__)
-@main_views.route("/tutorials")
+@app.route("/tutorials")
def tutorials():
return render_template("tutorials.html")
-@main_views.route("/credits")
+@app.route("/credits")
def credits():
return render_template("credits.html")
-@main_views.route("/update_text", methods=('POST',))
+@app.route("/update_text", methods=('POST',))
def update_page():
update_text(request.form)
doc = Docs(request.form['entry_type'], request.form)
return render_template("docs.html", **doc.__dict__)
-@main_views.route("/submit_trait")
+@app.route("/submit_trait")
def submit_trait_form():
species_and_groups = get_species_groups()
return render_template(
@@ -310,13 +307,13 @@ def submit_trait_form():
version=get_setting(app, "GN_VERSION"))
-@main_views.route("/create_temp_trait", methods=('POST',))
+@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
doc = Docs("links")
return render_template("links.html", **doc.__dict__)
-@main_views.route('/export_trait_excel', methods=('POST',))
+@app.route('/export_trait_excel', methods=('POST',))
def export_trait_excel():
"""Excel file consisting of the sample data from the trait data and analysis page"""
trait_name, sample_data = export_trait_data.export_sample_table(
@@ -337,7 +334,7 @@ def export_trait_excel():
headers={"Content-Disposition": "attachment;filename=" + trait_name + ".xlsx"})
-@main_views.route('/export_trait_csv', methods=('POST',))
+@app.route('/export_trait_csv', methods=('POST',))
def export_trait_csv():
"""CSV file consisting of the sample data from the trait data and analysis page"""
trait_name, sample_data = export_trait_data.export_sample_table(
@@ -355,7 +352,7 @@ def export_trait_csv():
headers={"Content-Disposition": "attachment;filename=" + trait_name + ".csv"})
-@main_views.route('/export_traits_csv', methods=('POST',))
+@app.route('/export_traits_csv', methods=('POST',))
def export_traits_csv():
"""CSV file consisting of the traits from the search result page"""
file_list = export_traits(request.form, "metadata")
@@ -378,7 +375,7 @@ def export_traits_csv():
headers={"Content-Disposition": "attachment;filename=" + file_list[0][0]})
-@main_views.route('/export_collection', methods=('POST',))
+@app.route('/export_collection', methods=('POST',))
def export_collection_csv():
"""CSV file consisting of trait list so collections can be exported/shared"""
out_file = export_traits(request.form, "collection")
@@ -387,7 +384,7 @@ def export_collection_csv():
headers={"Content-Disposition": "attachment;filename=" + out_file[0] + ".csv"})
-@main_views.route('/export_perm_data', methods=('POST',))
+@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():
"""CSV file consisting of the permutation data for the mapping results"""
perm_info = json.loads(request.form['perm_info'])
@@ -434,7 +431,7 @@ def export_perm_data():
headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"})
-@main_views.route("/show_temp_trait", methods=('POST',))
+@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
with database_connection() as conn, conn.cursor() as cursor:
user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
@@ -448,7 +445,7 @@ def show_temp_trait_page():
return render_template("show_trait.html", **template_vars.__dict__)
-@main_views.route("/show_trait")
+@app.route("/show_trait")
def show_trait_page():
def __show_trait__(privileges_data):
assert len(privileges_data) == 1
@@ -486,7 +483,7 @@ def show_trait_page():
}).either(__failure__, __show_trait__)
-@main_views.route("/heatmap", methods=('POST',))
+@app.route("/heatmap", methods=('POST',))
def heatmap_page():
start_vars = request.form
temp_uuid = uuid.uuid4()
@@ -522,7 +519,7 @@ def heatmap_page():
return rendered_template
-@main_views.route("/bnw_page", methods=('POST',))
+@app.route("/bnw_page", methods=('POST',))
def bnw_page():
start_vars = request.form
@@ -539,7 +536,7 @@ def bnw_page():
return rendered_template
-@main_views.route("/webgestalt_page", methods=('POST',))
+@app.route("/webgestalt_page", methods=('POST',))
def webgestalt_page():
start_vars = request.form
@@ -556,7 +553,7 @@ def webgestalt_page():
return rendered_template
-@main_views.route("/geneweaver_page", methods=('POST',))
+@app.route("/geneweaver_page", methods=('POST',))
def geneweaver_page():
start_vars = request.form
@@ -573,7 +570,7 @@ def geneweaver_page():
return rendered_template
-@main_views.route("/comparison_bar_chart", methods=('POST',))
+@app.route("/comparison_bar_chart", methods=('POST',))
def comp_bar_chart_page():
start_vars = request.form
@@ -594,12 +591,12 @@ def comp_bar_chart_page():
return rendered_template
-@main_views.route("/mapping_results_container")
+@app.route("/mapping_results_container")
def mapping_results_container_page():
return render_template("mapping_results_container.html")
-@main_views.route("/loading", methods=('POST',))
+@app.route("/loading", methods=('POST',))
def loading_page():
initial_start_vars = request.form
start_vars_container = {}
@@ -656,7 +653,7 @@ def loading_page():
return rendered_template
-@main_views.route("/run_mapping", methods=('POST','GET'))
+@app.route("/run_mapping", methods=('POST','GET'))
def mapping_results_page():
if request.method == "GET" and (hash_of_inputs := request.args.get("hash")):
hash_of_inputs = request.args.get("hash")
@@ -781,7 +778,7 @@ def mapping_results_page():
return rendered_template
-@main_views.route("/cache_mapping_inputs", methods=('POST',))
+@app.route("/cache_mapping_inputs", methods=('POST',))
def cache_mapping_inputs():
ONE_MONTH = 60 * 60 * 24 * 30
cache_id = request.form.get("inputs_hash")
@@ -790,7 +787,7 @@ def cache_mapping_inputs():
return "Success"
-@main_views.route("/export_mapping_results", methods=('POST',))
+@app.route("/export_mapping_results", methods=('POST',))
def export_mapping_results():
file_path = request.form.get("results_path")
results_csv = open(file_path, "r").read()
@@ -801,7 +798,7 @@ def export_mapping_results():
return response
-@main_views.route("/export_corr_matrix", methods=('POST',))
+@app.route("/export_corr_matrix", methods=('POST',))
def export_corr_matrix():
file_path = request.form.get("export_filepath")
file_name = request.form.get("export_filename")
@@ -813,7 +810,7 @@ def export_corr_matrix():
return response
-@main_views.route("/export", methods=('POST',))
+@app.route("/export", methods=('POST',))
def export():
svg_xml = request.form.get("data", "Invalid data")
filename = request.form.get("filename", "manhattan_plot_snp")
@@ -822,7 +819,7 @@ def export():
return response
-@main_views.route("/export_pdf", methods=('POST',))
+@app.route("/export_pdf", methods=('POST',))
def export_pdf():
import cairosvg
svg_xml = request.form.get("data", "Invalid data")
@@ -833,7 +830,7 @@ def export_pdf():
return response
-@main_views.route("/network_graph", methods=('POST',))
+@app.route("/network_graph", methods=('POST',))
def network_graph_page():
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -857,7 +854,7 @@ def __handle_correlation_error__(exc):
"error-message": exc.args[0]
})
-@main_views.route("/corr_compute", methods=('POST', 'GET'))
+@app.route("/corr_compute", methods=('POST', 'GET'))
def corr_compute_page():
with Redis.from_url(get_setting(app, "REDIS_URL"), decode_responses=True) as rconn:
if request.method == "POST":
@@ -876,7 +873,7 @@ def corr_compute_page():
})
jobs.run(job_id, get_setting(app, "REDIS_URL"))
- return redirect(url_for("main_views.corr_compute_page", job_id=str(job_id)))
+ return redirect(url_for("corr_compute_page", job_id=str(job_id)))
job = jobs.job(
rconn, UUID(request.args.get("job_id"))).maybe(
@@ -902,7 +899,7 @@ def corr_compute_page():
return render_template("loading_corrs.html")
-@main_views.route("/corr_matrix", methods=('POST',))
+@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -917,7 +914,7 @@ def corr_matrix_page():
return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})
-@main_views.route("/corr_scatter_plot")
+@app.route("/corr_scatter_plot")
def corr_scatter_plot_page():
template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -926,21 +923,21 @@ def corr_scatter_plot_page():
return render_template("corr_scatterplot.html", **template_vars.__dict__)
-@main_views.route("/snp_browser", methods=('GET',))
+@app.route("/snp_browser", methods=('GET',))
def snp_browser_page():
with database_connection() as conn, conn.cursor() as cursor:
template_vars = snp_browser.SnpBrowser(cursor, request.args)
return render_template("snp_browser.html", **template_vars.__dict__)
-@main_views.route("/db_info", methods=('GET',))
+@app.route("/db_info", methods=('GET',))
def db_info_page():
template_vars = InfoPage(request.args)
return render_template("info_page.html", **template_vars.__dict__)
-@main_views.route("/snp_browser_table", methods=('GET',))
+@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
with database_connection() as conn, conn.cursor() as cursor:
snp_table_data = snp_browser.SnpBrowser(cursor, request.args)
@@ -954,32 +951,32 @@ def snp_browser_table():
return flask.jsonify(current_page)
-@main_views.route("/tutorial/WebQTLTour", methods=('GET',))
+@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
# ZS: Currently just links to GN1
return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
-@main_views.route("/tutorial/security", methods=('GET',))
+@app.route("/tutorial/security", methods=('GET',))
def security_tutorial_page():
# ZS: Currently just links to GN1
return render_template("admin/security_help.html")
-@main_views.route("/submit_bnw", methods=('POST',))
+@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})
# Take this out or secure it before putting into production
-@main_views.route("/get_temp_data")
+@app.route("/get_temp_data")
def get_temp_data():
temp_uuid = request.args['key']
return flask.jsonify(temp_data.TempData(temp_uuid).get_all())
-@main_views.route("/browser_input", methods=('GET',))
+@app.route("/browser_input", methods=('GET',))
def browser_inputs():
""" Returns JSON from tmp directory for the purescript genome browser"""
@@ -1007,7 +1004,7 @@ def json_default_handler(obj):
type(obj), repr(obj)))
-@main_views.route("/admin/data-sample/diffs/")
+@app.route("/admin/data-sample/diffs/")
@edit_access_required
def display_diffs_admin():
TMPDIR = app.config.get("TMPDIR")
@@ -1021,7 +1018,7 @@ def display_diffs_admin():
files=files)
-@main_views.route("/user/data-sample/diffs/")
+@app.route("/user/data-sample/diffs/")
def display_diffs_users():
TMPDIR = app.config.get("TMPDIR")
DIFF_DIR = f"{TMPDIR}/sample-data/diffs"
@@ -1036,7 +1033,7 @@ def display_diffs_users():
files=files)
-@main_views.route("/genewiki/<symbol>")
+@app.route("/genewiki/<symbol>")
def display_generif_page(symbol):
"""Fetch GeneRIF metadata from GN3 and display it"""
entries = requests.get(
@@ -1052,7 +1049,7 @@ def display_generif_page(symbol):
)
-@main_views.route("/dataset/<name>", methods=('GET',))
+@app.route("/dataset/<name>", methods=('GET',))
def get_dataset(name):
metadata = requests.get(
urljoin(
@@ -1075,7 +1072,7 @@ def get_dataset(name):
)
-@main_views.route("/publication/<name>", methods=('GET',))
+@app.route("/publication/<name>", methods=('GET',))
def get_publication(name):
metadata = requests.get(
urljoin(
@@ -1088,7 +1085,7 @@ def get_publication(name):
)
-@main_views.route("/phenotype/<name>", methods=('GET',))
+@app.route("/phenotype/<name>", methods=('GET',))
def get_phenotype(name):
metadata = requests.get(
urljoin(
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 03:07:10 +0000