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-rw-r--r--README.md21
-rw-r--r--containers/db-container.scm38
-rwxr-xr-xcontainers/db-container.sh12
-rw-r--r--etc/default_settings.py3
-rw-r--r--test/requests/correlation_tests.py70
-rw-r--r--test/requests/link_checker.py5
-rw-r--r--test/requests/main_web_functionality.py10
-rwxr-xr-xtest/requests/test-website.py15
-rw-r--r--wqflask/base/data_set.py156
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py4
-rw-r--r--wqflask/base/webqtlCaseData.py3
-rw-r--r--wqflask/db/call.py79
-rw-r--r--wqflask/db/gn_server.py10
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py16
-rw-r--r--wqflask/maintenance/set_resource_defaults.py2
-rw-r--r--wqflask/runserver.py2
-rw-r--r--wqflask/scripts/__init__.py0
-rw-r--r--wqflask/scripts/profile_corrs.py78
-rw-r--r--wqflask/tests/unit/wqflask/api/test_mapping.py13
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py8
-rw-r--r--wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py140
-rw-r--r--wqflask/utility/Plot.py4
-rw-r--r--wqflask/utility/benchmark.py52
-rw-r--r--wqflask/utility/gen_geno_ob.py4
-rw-r--r--wqflask/utility/helper_functions.py3
-rw-r--r--wqflask/utility/logger.py1
-rw-r--r--wqflask/utility/pillow_utils.py3
-rw-r--r--wqflask/utility/redis_tools.py2
-rw-r--r--wqflask/utility/startup_config.py3
-rw-r--r--wqflask/utility/tools.py2
-rw-r--r--wqflask/wqflask/api/gen_menu.py4
-rw-r--r--wqflask/wqflask/api/mapping.py105
-rw-r--r--wqflask/wqflask/api/router.py4
-rw-r--r--wqflask/wqflask/collect.py4
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py3
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py85
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py329
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py13
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py3
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py26
-rw-r--r--wqflask/wqflask/database.py30
-rw-r--r--wqflask/wqflask/db_info.py3
-rw-r--r--wqflask/wqflask/do_search.py26
-rw-r--r--wqflask/wqflask/docs.py3
-rw-r--r--wqflask/wqflask/export_traits.py2
-rw-r--r--wqflask/wqflask/external_tools/send_to_bnw.py3
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py3
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py3
-rw-r--r--wqflask/wqflask/gsearch.py287
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py3
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py13
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py4
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py5
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py5
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py3
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py68
-rw-r--r--wqflask/wqflask/metadata_edits.py83
-rw-r--r--wqflask/wqflask/parser.py5
-rw-r--r--wqflask/wqflask/partial_correlations_views.py1
-rw-r--r--wqflask/wqflask/search_results.py48
-rw-r--r--wqflask/wqflask/show_trait/export_trait_data.py56
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py22
-rw-r--r--wqflask/wqflask/static/new/javascript/scatterplot.js5
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js27
-rw-r--r--wqflask/wqflask/submit_bnw.py10
-rw-r--r--wqflask/wqflask/templates/bnw_page.html2
-rw-r--r--wqflask/wqflask/templates/collections/view.html13
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html11
-rw-r--r--wqflask/wqflask/templates/edit_history.html2
-rw-r--r--wqflask/wqflask/templates/edit_phenotype.html47
-rw-r--r--wqflask/wqflask/templates/edit_probeset.html395
-rwxr-xr-xwqflask/wqflask/templates/index_page.html6
-rw-r--r--wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html14
-rw-r--r--wqflask/wqflask/templates/pca_scree_plot.html17
-rw-r--r--wqflask/wqflask/templates/search_result_page.html97
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html4
-rw-r--r--wqflask/wqflask/templates/tool_buttons.html4
-rw-r--r--wqflask/wqflask/update_search_results.py39
-rw-r--r--wqflask/wqflask/user_login.py12
-rw-r--r--wqflask/wqflask/user_session.py3
-rw-r--r--wqflask/wqflask/views.py232
81 files changed, 1496 insertions, 1455 deletions
diff --git a/README.md b/README.md
index c5172f8b..78652f50 100644
--- a/README.md
+++ b/README.md
@@ -84,7 +84,7 @@ use `GN3_PYTHONPATH` environment that gets injected in
the ./bin/genenetwork2 startup.
A continuously deployed instance of genenetwork2 is available at
-[https://gn2dev.genenetwork.org/](https://gn2dev.genenetwork.org/). This
+[https://cd.genenetwork.org/](https://cd.genenetwork.org/). This
instance is redeployed on every commit provided that the [continuous
integration tests](https://ci.genenetwork.org/jobs/genenetwork2) pass.
@@ -173,6 +173,25 @@ check the logs. If there is ERROR 1054 (42S22): Unknown column
'InbredSet.Family' in 'field list' it may be you are trying the small
database.
+### Run Scripts
+
+As part of the profiling effort, some scripts are added to run specific parts of the system under a profiler without running the entire web-server - as such, to run the script, you could do something like:
+
+```
+env HOME=/home/frederick \
+ GN2_PROFILE=~/opt/gn2-latest \
+ GN3_DEV_REPO_PATH=~/genenetwork/genenetwork3 \
+ SQL_URI="mysql://username:password@host-ip:host-port/db_webqtl" \
+ SERVER_PORT=5001 \
+ bin/genenetwork2 ../gn2_settings.py \
+ -cli python3 -m scripts.profile_corrs \
+ ../performance_$(date +"%Y%m%dT%H:%M:%S").profile
+```
+
+and you can find the performance metrics at the file specified, in this case, a file starting with `performance_` with the date and time of the run, and ending with `.profile`.
+
+Please replace the environment variables in the sample command above with the appropriate values for your environment.
+
## Documentation
User documentation can be found
diff --git a/containers/db-container.scm b/containers/db-container.scm
new file mode 100644
index 00000000..848b6a2e
--- /dev/null
+++ b/containers/db-container.scm
@@ -0,0 +1,38 @@
+;;; This file describes a Guix system container to run the database
+;;; services required by genenetwork2 locally on your own
+;;; machine. This is to allow a purely offline development setup for
+;;; hacking on genenetwork2. To build and run the container, use
+;;; db-container.sh.
+
+(use-modules (gnu)
+ (gnu packages databases)
+ (gnu services databases))
+
+(define %mariadb-state-directory
+ "/var/lib/mysql")
+
+(define set-permissions-gexp
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+
+ ;; Set ownership of mariadb state directory.
+ (let ((user (getpw "mysql")))
+ (for-each (lambda (file)
+ (chown file (passwd:uid user) (passwd:gid user)))
+ (find-files #$%mariadb-state-directory #:directories? #t))))))
+
+(operating-system
+ (host-name "genenetwork2")
+ (timezone "Etc/UTC")
+ (locale "en_US.utf8")
+ (bootloader (bootloader-configuration
+ (bootloader grub-bootloader)
+ (targets (list "does-not-matter"))))
+ (file-systems %base-file-systems)
+ (services (cons* (service mysql-service-type)
+ (service redis-service-type)
+ (simple-service 'set-permissions
+ activation-service-type
+ set-permissions-gexp)
+ %base-services)))
diff --git a/containers/db-container.sh b/containers/db-container.sh
new file mode 100755
index 00000000..bbe0247a
--- /dev/null
+++ b/containers/db-container.sh
@@ -0,0 +1,12 @@
+#! /bin/sh -e
+
+# Find path to containers directory.
+containers=$(dirname $0)
+
+# Create mariadb state directory if it does not exist.
+mkdir -p $containers/mariadb-state
+
+# Build the container.
+guix system container --network \
+ --share=$containers/mariadb-state=/var/lib/mysql \
+ $containers/db-container.scm
diff --git a/etc/default_settings.py b/etc/default_settings.py
index a0d01de0..ff84f021 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -33,6 +33,9 @@ REDIS_URL = "redis://:@localhost:6379/0"
# gn2-proxy
GN2_PROXY = "http://localhost:8080"
+# GN PROXY
+GN_PROXY_URL="https://genenetwork.org/gn3-proxy/"
+
# ---- MySQL
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py
new file mode 100644
index 00000000..abb5794a
--- /dev/null
+++ b/test/requests/correlation_tests.py
@@ -0,0 +1,70 @@
+import requests
+from lxml.html import parse
+from link_checker import check_page
+
+def sample_vals():
+ return '{"C57BL/6J":"10.835","DBA/2J":"11.142","B6D2F1":"11.126","D2B6F1":"11.143","BXD1":"10.811","BXD2":"11.503","BXD5":"10.766","BXD6":"10.986","BXD8":"11.050","BXD9":"10.822","BXD11":"10.670","BXD12":"10.946","BXD13":"10.890","BXD14":"x","BXD15":"10.884","BXD16":"11.222","BXD18":"x","BXD19":"10.968","BXD20":"10.962","BXD21":"10.906","BXD22":"11.080","BXD23":"11.046","BXD24":"11.146","BXD24a":"x","BXD25":"x","BXD27":"11.078","BXD28":"11.034","BXD29":"10.808","BXD30":"x","BXD31":"11.087","BXD32":"11.029","BXD33":"10.662","BXD34":"11.482","BXD35":"x","BXD36":"x","BXD37":"x","BXD38":"10.836","BXD39":"10.926","BXD40":"10.638","BXD41":"x","BXD42":"10.974","BXD43":"10.828","BXD44":"10.900","BXD45":"11.358","BXD48":"11.042","BXD48a":"10.975","BXD49":"x","BXD50":"11.228","BXD51":"11.126","BXD52":"x","BXD53":"x","BXD54":"x","BXD55":"11.580","BXD56":"x","BXD59":"x","BXD60":"10.829","BXD61":"11.152","BXD62":"11.156","BXD63":"10.942","BXD64":"10.506","BXD65":"11.126","BXD65a":"11.272","BXD65b":"11.157","BXD66":"11.071","BXD67":"11.080","BXD68":"10.997","BXD69":"11.096","BXD70":"11.152","BXD71":"x","BXD72":"x","BXD73":"11.262","BXD73a":"11.444","BXD73b":"x","BXD74":"10.974","BXD75":"11.150","BXD76":"10.920","BXD77":"10.928","BXD78":"x","BXD79":"11.371","BXD81":"x","BXD83":"10.946","BXD84":"11.181","BXD85":"10.992","BXD86":"10.770","BXD87":"11.200","BXD88":"x","BXD89":"10.930","BXD90":"11.183","BXD91":"x","BXD93":"11.056","BXD94":"10.737","BXD95":"x","BXD98":"10.986","BXD99":"10.892","BXD100":"x","BXD101":"x","BXD102":"x","BXD104":"x","BXD105":"x","BXD106":"x","BXD107":"x","BXD108":"x","BXD109":"x","BXD110":"x","BXD111":"x","BXD112":"x","BXD113":"x","BXD114":"x","BXD115":"x","BXD116":"x","BXD117":"x","BXD119":"x","BXD120":"x","BXD121":"x","BXD122":"x","BXD123":"x","BXD124":"x","BXD125":"x","BXD126":"x","BXD127":"x","BXD128":"x","BXD128a":"x","BXD130":"x","BXD131":"x","BXD132":"x","BXD133":"x","BXD134":"x","BXD135":"x","BXD136":"x","BXD137":"x","BXD138":"x","BXD139":"x","BXD141":"x","BXD142":"x","BXD144":"x","BXD145":"x","BXD146":"x","BXD147":"x","BXD148":"x","BXD149":"x","BXD150":"x","BXD151":"x","BXD152":"x","BXD153":"x","BXD154":"x","BXD155":"x","BXD156":"x","BXD157":"x","BXD160":"x","BXD161":"x","BXD162":"x","BXD165":"x","BXD168":"x","BXD169":"x","BXD170":"x","BXD171":"x","BXD172":"x","BXD173":"x","BXD174":"x","BXD175":"x","BXD176":"x","BXD177":"x","BXD178":"x","BXD180":"x","BXD181":"x","BXD183":"x","BXD184":"x","BXD186":"x","BXD187":"x","BXD188":"x","BXD189":"x","BXD190":"x","BXD191":"x","BXD192":"x","BXD193":"x","BXD194":"x","BXD195":"x","BXD196":"x","BXD197":"x","BXD198":"x","BXD199":"x","BXD200":"x","BXD201":"x","BXD202":"x","BXD203":"x","BXD204":"x","BXD205":"x","BXD206":"x","BXD207":"x","BXD208":"x","BXD209":"x","BXD210":"x","BXD211":"x","BXD212":"x","BXD213":"x","BXD214":"x","BXD215":"x","BXD216":"x","BXD217":"x","BXD218":"x","BXD219":"x","BXD220":"x"}'
+
+def do_request(url, data):
+ return requests.post(
+ url,
+ data={
+ "dataset": "HC_M2_0606_P",
+ "trait_id": "1435464_at",
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_sample_method": "pearson",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",
+ "sample_vals": sample_vals(),
+ **data,
+ })
+
+def check_sample_correlations(baseurl):
+ data = {
+ "corr_type": "sample",
+ "corr_sample_method": "pearson",
+ "location_type": "gene",
+ "corr_return_results": "200"
+ }
+ top_n_message = "The top 200 correlations ranked by the Genetic Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_tissue_correlations(baseurl):
+ data = {
+ "corr_type": "tissue",
+ "location_type": "gene",
+ }
+ top_n_message = "The top 100 correlations ranked by the Tissue Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_lit_correlations(baseurl):
+ data = {
+ "corr_type": "lit",
+ "corr_return_results": "200"
+ }
+ top_n_message = "The top 200 correlations ranked by the Literature Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_correlations(args_obj, parser):
+ print("")
+ print("Checking the correlations...")
+ corr_type_fns = {
+ "sample": check_sample_correlations,
+ "tissue": check_tissue_correlations,
+ "lit": check_lit_correlations
+ }
+ host = args_obj.host
+ for corr_type, corr_type_fn in corr_type_fns.items():
+ print(f"\tChecking {corr_type} correlations...", end="")
+ corr_type_fn(host)
+ print(" ok")
+ print("OK")
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index feae6526..86222254 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -1,6 +1,6 @@
import re
import requests
-from lxml.html import parse
+from lxml.html import document_fromstring
from requests.exceptions import ConnectionError
DO_FAIL=False # fail on error
@@ -66,7 +66,8 @@ def verify_static_file(link):
def check_page(host, start_url):
print("")
print("Checking links host "+host+" in page `"+start_url+"`")
- doc = parse(start_url).getroot()
+ req = requests.get(start_url)
+ doc = document_fromstring(start_url)
links = get_links(doc)
in_page_links = list(filter(is_in_page_link, links))
internal_links = list(filter(is_internal_link, links))
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index 28033ad5..79f37bb4 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -1,10 +1,11 @@
import requests
-from lxml.html import parse
+from lxml.html import document_fromstring
from link_checker import check_page
def check_home(url):
- doc = parse(url).getroot()
+ results = requests.get(url)
+ doc = document_fromstring(results.text)
search_button = doc.cssselect("#btsearch")
assert(search_button[0].value == "Search")
print("OK")
@@ -18,7 +19,7 @@ def check_search_page(host):
search_terms_or="",
search_terms_and="MEAN=(15 16) LRS=(23 46)")
result = requests.get(host+"/search", params=data)
- found = result.text.find("records were found")
+ found = result.text.find("records found")
assert(found >= 0)
assert(result.status_code == 200)
print("OK")
@@ -27,7 +28,8 @@ def check_search_page(host):
def check_traits_page(host, traits_url):
- doc = parse(host+traits_url).getroot()
+ results = requests.get(host+traits_url)
+ doc = document_fromstring(results.text)
traits_form = doc.forms[1]
assert(traits_form.fields["corr_dataset"] == "HC_M2_0606_P")
print("OK")
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 71055fca..c0b36182 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -9,6 +9,7 @@ from link_checker import check_links
from link_checker import check_packaged_js_files
from mapping_tests import check_mapping
from navigation_tests import check_navigation
+from correlation_tests import check_correlations
from main_web_functionality import check_main_web_functionality
import link_checker
import sys
@@ -18,16 +19,30 @@ from unittest import TestSuite, TextTestRunner, TestLoader
print("Mechanical Rob firing up...")
+def host_is_online(host):
+ import time
+ import requests
+ for count in range(1, 5):
+ try:
+ time.sleep(count)
+ requests.get(host)
+ return True
+ except Exception as cre:
+ print(f"Retrying in {count + 1} seconds ...")
+
+ return False
def run_all(args_obj, parser):
print("")
print("Running all tests.")
print(args_obj)
+ assert host_is_online(args_obj.host), f"Could not connect to {host}"
link_checker.DO_FAIL = args_obj.fail
check_main_web_functionality(args_obj, parser)
check_links(args_obj, parser)
check_packaged_js_files(args_obj, parser)
check_mapping(args_obj, parser)
+ check_correlations(args_obj, parser)
# TODO: Add other functions as they are created.
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a7811a30..f66bf186 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -21,10 +21,7 @@ from dataclasses import dataclass
from dataclasses import field
from dataclasses import InitVar
from typing import Optional, Dict, List
-from db.call import fetchall, fetchone, fetch1
-from utility.logger import getLogger
from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
-from db.gn_server import menu_main
from pprint import pformat as pf
from utility.db_tools import escape
from utility.db_tools import mescape
@@ -33,7 +30,6 @@ from maintenance import get_group_samplelists
from utility.tools import locate, locate_ignore_error, flat_files
from utility import gen_geno_ob
from utility import chunks
-from utility.benchmark import Bench
from utility import webqtlUtil
from db import webqtlDatabaseFunction
from base import species
@@ -42,6 +38,7 @@ from flask import Flask, g
from base.webqtlConfig import TMPDIR
from urllib.parse import urlparse
from utility.tools import SQL_URI
+from wqflask.database import database_connection
import os
import math
import string
@@ -60,8 +57,6 @@ from redis import Redis
r = Redis()
-logger = getLogger(__name__)
-
# Used by create_database to instantiate objects
# Each subclass will add to this
DS_NAME_MAP = {}
@@ -200,26 +195,23 @@ def create_datasets_list():
result = r.get(key)
if result:
- logger.debug("Redis cache hit")
datasets = pickle.loads(result)
if result is None:
datasets = list()
- with Bench("Creating DataSets object"):
- type_dict = {'Publish': 'PublishFreeze',
- 'ProbeSet': 'ProbeSetFreeze',
- 'Geno': 'GenoFreeze'}
-
- for dataset_type in type_dict:
- query = "SELECT Name FROM {}".format(type_dict[dataset_type])
- for result in fetchall(query):
- # The query at the beginning of this function isn't
- # necessary here, but still would rather just reuse
- # it logger.debug("type: {}\tname:
- # {}".format(dataset_type, result.Name))
- dataset = create_dataset(result.Name, dataset_type)
- datasets.append(dataset)
-
+ type_dict = {'Publish': 'PublishFreeze',
+ 'ProbeSet': 'ProbeSetFreeze',
+ 'Geno': 'GenoFreeze'}
+
+ for dataset_type in type_dict:
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute("SELECT Name FROM %s",
+ (type_dict[dataset_type],))
+ results = cursor.fetchall(query)
+ if results:
+ for result in results:
+ datasets.append(
+ create_dataset(result.Name, dataset_type))
if USE_REDIS:
r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
r.expire(key, 60 * 60)
@@ -259,9 +251,6 @@ class Markers:
self.markers = markers
def add_pvalues(self, p_values):
- logger.debug("length of self.markers:", len(self.markers))
- logger.debug("length of p_values:", len(p_values))
-
if isinstance(p_values, list):
# THIS IS only needed for the case when we are limiting the number of p-values calculated
# if len(self.markers) > len(p_values):
@@ -332,12 +321,16 @@ class DatasetGroup:
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
- if name == None:
- self.name, self.id, self.genetic_type, self.code = fetchone(
- dataset.query_for_group)
- else:
- self.name, self.id, self.genetic_type, self.code = fetchone(
- "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet where Name='%s'" % name)
+ query = """SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType,
+ InbredSet.InbredSetCode FROM InbredSet where Name=%s
+ """
+ if not name:
+ query, name = dataset.query_for_group, dataset.name
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute(query, (name,))
+ results = cursor.fetchone()
+ if results:
+ self.name, self.id, self.genetic_type, self.code = results
if self.name == 'BXD300':
self.name = "BXD"
@@ -633,39 +626,33 @@ class DataSet:
"""
try:
+ query = ""
+ _vars = None
+ query_args = (self.name, self.name, self.name)
if self.type == "ProbeSet":
- query_args = tuple(escape(x) for x in (
- self.name,
- self.name,
- self.name))
-
- self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
- SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
- FROM ProbeSetFreeze, ProbeFreeze, Tissue
- WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
- AND ProbeFreeze.TissueId = Tissue.Id
- AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
- """ % (query_args), "/dataset/" + self.name + ".json",
- lambda r: (r["id"], r["name"], r["full_name"],
- r["short_name"], r["data_scale"], r["tissue"])
- )
+ query = (
+ "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+ "ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, "
+ "ProbeSetFreeze.DataScale, Tissue.Name "
+ "FROM ProbeSetFreeze, ProbeFreeze, Tissue "
+ "WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ "AND ProbeFreeze.TissueId = Tissue.Id "
+ "AND (ProbeSetFreeze.Name = %s OR ProbeSetFreeze.FullName = %s OR ProbeSetFreeze.ShortName = %s)")
else:
- query_args = tuple(escape(x) for x in (
- (self.type + "Freeze"),
- self.name,
- self.name,
- self.name))
-
+ query = (
+ "SELECT Id, Name, FullName, ShortName "
+ f"FROM {self.type}Freeze "
+ "WHERE (Name = %s OR FullName = %s OR ShortName = %s)")
self.tissue = "N/A"
- self.id, self.name, self.fullname, self.shortname = fetchone("""
- SELECT Id, Name, FullName, ShortName
- FROM %s
- WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args))
-
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute(query, query_args)
+ _vars = cursor.fetchone()
+ if self.type == "ProbeSet":
+ (self.id, self.name, self.fullname, self.shortname,
+ self.data_scale, self.tissue) = _vars
+ else:
+ self.id, self.name, self.fullname, self.shortname = _vars
except TypeError:
- logger.debug(
- "Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def chunk_dataset(self, dataset, n):
@@ -863,16 +850,8 @@ class PhenotypeDataSet(DataSet):
'Additive Effect']
self.type = 'Publish'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
- FROM
- InbredSet, PublishFreeze
- WHERE
- PublishFreeze.InbredSetId = InbredSet.Id AND
- PublishFreeze.Name = "%s"
- ''' % escape(self.name)
+ self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id AND PublishFreeze.Name = %s"""
def check_confidentiality(self):
# (Urgently?) Need to write this
@@ -979,16 +958,10 @@ class GenotypeDataSet(DataSet):
# Todo: Obsolete or rename this field
self.type = 'Geno'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
- FROM
- InbredSet, GenoFreeze
- WHERE
- GenoFreeze.InbredSetId = InbredSet.Id AND
- GenoFreeze.Name = "%s"
- ''' % escape(self.name)
+ self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
+FROM InbredSet, GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id AND
+GenoFreeze.Name = %s"""
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
@@ -1022,6 +995,14 @@ class GenotypeDataSet(DataSet):
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
+
+ if self.group.name in webqtlUtil.ParInfo:
+ f1_1, f1_2, ref, nonref = webqtlUtil.ParInfo[self.group.name]
+ results.append([f1_1, 0, None, "N/A", f1_1])
+ results.append([f1_2, 0, None, "N/A", f1_2])
+ results.append([ref, -1, None, "N/A", ref])
+ results.append([nonref, 1, None, "N/A", nonref])
+
return results
@@ -1079,17 +1060,10 @@ class MrnaAssayDataSet(DataSet):
# Todo: Obsolete or rename this field
self.type = 'ProbeSet'
-
- self.query_for_group = '''
- SELECT
- InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
- FROM
- InbredSet, ProbeSetFreeze, ProbeFreeze
- WHERE
- ProbeFreeze.InbredSetId = InbredSet.Id AND
- ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
- ProbeSetFreeze.Name = "%s"
- ''' % escape(self.name)
+ self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
+FROM InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id AND
+ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s"""
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 8f8e2b0a..d7e747aa 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -9,10 +9,6 @@ from utility.db_tools import escape
from gn3.db_utils import database_connector
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
class MrnaAssayTissueData:
def __init__(self, gene_symbols=None):
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 25b6cb8a..dd6fad04 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -21,9 +21,6 @@
# Created by GeneNetwork Core Team 2010/08/10
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
import utility.tools
utility.tools.show_settings()
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
deleted file mode 100644
index 1fe0772b..00000000
--- a/wqflask/db/call.py
+++ /dev/null
@@ -1,79 +0,0 @@
-# Module for calling the backend
-
-from flask import g
-
-import string
-try: # Python2 support
- import urllib.request
- import urllib.error
- import urllib.parse
-except:
- import urllib2
-import json
-from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL
-from utility.benchmark import Bench
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-# from inspect import stack
-
-
-def fetch1(query, path=None, func=None):
- """Fetch one result as a Tuple using either a SQL query or the URI
-path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
-GN_SERVER result when set (which should return a Tuple)
-
- """
- if USE_GN_SERVER and path:
- result = gn_server(path)
- if func != None:
- res2 = func(result)
- else:
- res2 = result,
- if LOG_SQL:
- logger.debug("Replaced SQL call", query)
- logger.debug(path, res2)
- return res2
- else:
- return fetchone(query)
-
-
-def fetchone(query):
- """Return tuple containing one row by calling SQL directly (the
-original fetchone, but with logging)
-
- """
- with Bench("SQL", LOG_SQL):
- def helper(query):
- res = g.db.execute(query)
- return res.fetchone()
- return logger.sql(query, helper)
-
-
-def fetchall(query):
- """Return row iterator by calling SQL directly (the
-original fetchall, but with logging)
-
- """
- with Bench("SQL", LOG_SQL):
- def helper(query):
- res = g.db.execute(query)
- return res.fetchall()
- return logger.sql(query, helper)
-
-
-def gn_server(path):
- """Return JSON record by calling GN_SERVER
-
- """
- with Bench("GN_SERVER", LOG_SQL):
- res = ()
- try:
- res = urllib.request.urlopen(GN_SERVER_URL + path)
- except:
- res = urllib2.urlopen(GN_SERVER_URL + path)
- rest = res.read()
- res2 = json.loads(rest)
- logger.debug(res2)
- return res2
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
deleted file mode 100644
index f9b01658..00000000
--- a/wqflask/db/gn_server.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Backend query functions (logic)
-
-from db.call import gn_server
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
-def menu_main():
- return gn_server("/int/menu/main.json")
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 9ec650a4..122c546f 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -20,19 +20,23 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from db.call import fetch1
+from wqflask.database import database_connection
def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
- result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
- group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT Species.Name FROM Species, InbredSet WHERE InbredSet.Name = %s AND InbredSet.SpeciesId = Species.Id",
+ (group,))
+ return cursor.fetchone()[0]
return result
def retrieve_species_id(group):
- result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
- group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
- return result
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute("SELECT SpeciesId FROM InbredSet WHERE Name = %s",
+ (group,))
+ return cursor.fetchone()[0]
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 22d73ba3..0d9372ff 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -33,8 +33,6 @@ Redis = get_redis_conn()
import urllib.parse
from wqflask.database import database_connection
-from utility.logger import getLogger
-logger = getLogger(__name__)
def parse_db_uri():
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 8198b921..fee29be1 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -23,9 +23,7 @@ app_config()
werkzeug_logger = logging.getLogger('werkzeug')
if WEBSERVER_MODE == 'DEBUG':
- from flask_debugtoolbar import DebugToolbarExtension
app.debug = True
- toolbar = DebugToolbarExtension(app)
app.run(host='0.0.0.0',
port=SERVER_PORT,
debug=True,
diff --git a/wqflask/scripts/__init__.py b/wqflask/scripts/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/scripts/__init__.py
diff --git a/wqflask/scripts/profile_corrs.py b/wqflask/scripts/profile_corrs.py
new file mode 100644
index 00000000..7c43b8c7
--- /dev/null
+++ b/wqflask/scripts/profile_corrs.py
@@ -0,0 +1,78 @@
+import io
+import sys
+import pstats
+import cProfile
+
+import sqlalchemy
+from flask import g, request
+
+from utility.startup_config import app_config
+
+from wqflask import app
+from wqflask.user_session import UserSession
+from wqflask.views import connect_db, shutdown_session
+from wqflask.correlation.correlation_gn3_api import compute_correlation
+
+def sample_vals():
+ return '{"C57BL/6J":"10.835","DBA/2J":"11.142","B6D2F1":"11.126","D2B6F1":"11.143","BXD1":"10.811","BXD2":"11.503","BXD5":"10.766","BXD6":"10.986","BXD8":"11.050","BXD9":"10.822","BXD11":"10.670","BXD12":"10.946","BXD13":"10.890","BXD14":"x","BXD15":"10.884","BXD16":"11.222","BXD18":"x","BXD19":"10.968","BXD20":"10.962","BXD21":"10.906","BXD22":"11.080","BXD23":"11.046","BXD24":"11.146","BXD24a":"x","BXD25":"x","BXD27":"11.078","BXD28":"11.034","BXD29":"10.808","BXD30":"x","BXD31":"11.087","BXD32":"11.029","BXD33":"10.662","BXD34":"11.482","BXD35":"x","BXD36":"x","BXD37":"x","BXD38":"10.836","BXD39":"10.926","BXD40":"10.638","BXD41":"x","BXD42":"10.974","BXD43":"10.828","BXD44":"10.900","BXD45":"11.358","BXD48":"11.042","BXD48a":"10.975","BXD49":"x","BXD50":"11.228","BXD51":"11.126","BXD52":"x","BXD53":"x","BXD54":"x","BXD55":"11.580","BXD56":"x","BXD59":"x","BXD60":"10.829","BXD61":"11.152","BXD62":"11.156","BXD63":"10.942","BXD64":"10.506","BXD65":"11.126","BXD65a":"11.272","BXD65b":"11.157","BXD66":"11.071","BXD67":"11.080","BXD68":"10.997","BXD69":"11.096","BXD70":"11.152","BXD71":"x","BXD72":"x","BXD73":"11.262","BXD73a":"11.444","BXD73b":"x","BXD74":"10.974","BXD75":"11.150","BXD76":"10.920","BXD77":"10.928","BXD78":"x","BXD79":"11.371","BXD81":"x","BXD83":"10.946","BXD84":"11.181","BXD85":"10.992","BXD86":"10.770","BXD87":"11.200","BXD88":"x","BXD89":"10.930","BXD90":"11.183","BXD91":"x","BXD93":"11.056","BXD94":"10.737","BXD95":"x","BXD98":"10.986","BXD99":"10.892","BXD100":"x","BXD101":"x","BXD102":"x","BXD104":"x","BXD105":"x","BXD106":"x","BXD107":"x","BXD108":"x","BXD109":"x","BXD110":"x","BXD111":"x","BXD112":"x","BXD113":"x","BXD114":"x","BXD115":"x","BXD116":"x","BXD117":"x","BXD119":"x","BXD120":"x","BXD121":"x","BXD122":"x","BXD123":"x","BXD124":"x","BXD125":"x","BXD126":"x","BXD127":"x","BXD128":"x","BXD128a":"x","BXD130":"x","BXD131":"x","BXD132":"x","BXD133":"x","BXD134":"x","BXD135":"x","BXD136":"x","BXD137":"x","BXD138":"x","BXD139":"x","BXD141":"x","BXD142":"x","BXD144":"x","BXD145":"x","BXD146":"x","BXD147":"x","BXD148":"x","BXD149":"x","BXD150":"x","BXD151":"x","BXD152":"x","BXD153":"x","BXD154":"x","BXD155":"x","BXD156":"x","BXD157":"x","BXD160":"x","BXD161":"x","BXD162":"x","BXD165":"x","BXD168":"x","BXD169":"x","BXD170":"x","BXD171":"x","BXD172":"x","BXD173":"x","BXD174":"x","BXD175":"x","BXD176":"x","BXD177":"x","BXD178":"x","BXD180":"x","BXD181":"x","BXD183":"x","BXD184":"x","BXD186":"x","BXD187":"x","BXD188":"x","BXD189":"x","BXD190":"x","BXD191":"x","BXD192":"x","BXD193":"x","BXD194":"x","BXD195":"x","BXD196":"x","BXD197":"x","BXD198":"x","BXD199":"x","BXD200":"x","BXD201":"x","BXD202":"x","BXD203":"x","BXD204":"x","BXD205":"x","BXD206":"x","BXD207":"x","BXD208":"x","BXD209":"x","BXD210":"x","BXD211":"x","BXD212":"x","BXD213":"x","BXD214":"x","BXD215":"x","BXD216":"x","BXD217":"x","BXD218":"x","BXD219":"x","BXD220":"x"}'
+
+def simulated_form(corr_type: str = "sample"):
+ assert corr_type in ("sample", "tissue", "lit")
+ return {
+ "dataset": "HC_M2_0606_P",
+ "trait_id": "1435464_at",
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_sample_method": "pearson",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",
+ "sample_vals": sample_vals(),
+ "corr_type": corr_type,
+ "corr_sample_method": "pearson",
+ "location_type": "gene",
+ "corr_return_results": "20000"
+ }
+
+def profile_corrs():
+ "Profile tho correlations"
+ profiler = cProfile.Profile()
+ # compute_correlation(simulated_form(), compute_all=True)
+ profiler.enable()
+ correlation_results = compute_correlation(request.form, compute_all=True)
+ # correlation_results = set_template_vars(request.form, correlation_results)
+ profiler.disable()
+
+ return profiler
+
+def dump_stats(profiler):
+ iostr = io.StringIO()
+ sort_by = pstats.SortKey.CUMULATIVE
+ ps = pstats.Stats(profiler, stream=iostr).sort_stats(sort_by)
+ ps.print_stats()
+
+ cli_args = sys.argv
+ if len(cli_args) > 1:
+ with open(cli_args[1], "w+", encoding="utf-8") as output_file:
+ print(iostr.getvalue(), file=output_file)
+
+ return 0
+
+ print(iostr.getvalue())
+ return 0
+
+
+if __name__ == "__main__":
+ def main():
+ "Entry point for profiler script"
+ return dump_stats(profile_corrs())
+
+ app_config()
+ with app.app_context():
+ with app.test_request_context("/corr_compute", data=simulated_form()):
+ g.db = sqlalchemy.create_engine( ## Setup global db connection
+ app.config.get('SQL_URI'), encoding="latin1")
+ g.user_session = UserSession()
+ # g.user_session.user_id = 0
+ main()
+ ## dispose global db connection
+ g.db.dispose()
+ g.db.close()
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index 159c982b..006e9826 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -25,7 +25,9 @@ class TestMapping(unittest.TestCase):
"maf": 0.01,
"use_loco": True,
"num_perm": 0,
- "perm_check": False
+ "perm_check": False,
+ "transform": False,
+ "genofile": False
}
results = initialize_parameters(
@@ -40,8 +42,9 @@ class TestMapping(unittest.TestCase):
"pair_scan": "true",
"interval_mapping": "true",
"use_loco": "true",
- "num_perm": "14"
-
+ "num_perm": "14",
+ "transform": "qnorm",
+ "genofile": "BXD.8.geno"
}
results_2 = initialize_parameters(
@@ -53,7 +56,9 @@ class TestMapping(unittest.TestCase):
"maf": 0.01,
"use_loco": True,
"num_perm": 14,
- "perm_check": "ON"
+ "perm_check": "ON",
+ "transform": "qnorm",
+ "genofile": "BXD.8.geno"
}
self.assertEqual(results_2, expected_results)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 611c0d70..53d96d7f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -165,12 +165,12 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
this_dataset={}, gwa_output_filename=".xw/")
expected_results = [
{'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
- 'additive': -23.3, 'lod_score': 0.07058107428570727},
+ 'additive': -11.65, 'lod_score': 0.07058107428570727},
{'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
- 'additive': -24.0, 'lod_score': 0.3010299956639812},
+ 'additive': -12.0, 'lod_score': 0.3010299956639812},
{'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
- 'additive': -11.6, 'lod_score': 0.1549019599857432},
- {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -21.1, 'lod_score': 0.22184874961635637}]
+ 'additive': -5.8, 'lod_score': 0.1549019599857432},
+ {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -10.55, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
diff --git a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
index 41761944..fbe39f13 100644
--- a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
+++ b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -1,3 +1,4 @@
+import datetime
import unittest
from unittest import mock
from wqflask.show_trait.export_trait_data import dict_to_sorted_list
@@ -13,116 +14,53 @@ class AttributesSetter:
class TestExportTraits(unittest.TestCase):
- """Test methods related to converting dict to sortedlist"""
- @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
- @mock.patch("wqflask.show_trait.export_trait_data.data_set")
- def test_get_export_metadata_no_publish(self, mock_dataset, mock_trait):
- """test for exporting metadata with no publish"""
- mock_dataset_attributes = AttributesSetter(
- {"type": "no_publish", "dataset_name": "Temp", "name": "Temp"})
-
- mock_nested_attributes = AttributesSetter({"name": "name"})
- mock_dataset_attributes.group = mock_nested_attributes
- mock_dataset.create_dataset.return_value = mock_dataset_attributes
- mock_trait.return_value = AttributesSetter({"symbol": "", "description_display": "Description",
- "title": "research1", "journal": "", "authors": ""})
-
- results = get_export_metadata("random_id", "Temp")
- expected = [["Record ID: random_id"],
- ["Trait URL: http://genenetwork.org/show_trait?trait_id=random_id&dataset=Temp"],
- ["Dataset: Temp"],
- ["Group: name"], []]
-
- mock_dataset.create_dataset.assert_called_with("Temp")
- mock_trait.assert_called_with(
- dataset=mock_dataset_attributes, name="random_id", cellid=None, get_qtl_info=False)
- self.assertEqual(results, expected)
+ """Test methods for exporting traits and metadata"""
+ @mock.patch("wqflask.show_trait.export_trait_data.datetime")
@mock.patch("wqflask.show_trait.export_trait_data.create_trait")
@mock.patch("wqflask.show_trait.export_trait_data.data_set")
- def test_get_export_metadata_with_publish(self, data_mock, trait_mock):
+ def test_get_export_metadata(self, data_mock, trait_mock, date_mock):
"""test for exporting metadata with dataset.type=Publish"""
- mock_dataset_attributes = AttributesSetter({"type": "Publish", "dataset_name": "Temp",
- "name": "Temp", "description_display": "Description goes here"})
-
- mock_nested_attributes = AttributesSetter({"name": "name"})
- mock_dataset_attributes.group = mock_nested_attributes
- data_mock.create_dataset.return_value = mock_dataset_attributes
- trait_instance = AttributesSetter({"symbol": "", "description_display": "Description",
- "title": "research1", "journal": "", "authors": ""})
- trait_mock.return_value = trait_instance
+ mock_dataset = AttributesSetter({"type": "Publish",
+ "name": "HC_M2_0606_P",
+ "dataset_name": "HC_M2_0606_P"})
- results = get_export_metadata(
- "29ae0615-0d77-4814-97c7-c9e91f6bfd7b", "Temp")
+ mock_dataset.group = AttributesSetter({"name": "C"})
+ data_mock.create_dataset.return_value = mock_dataset
- expected = [['Phenotype ID: 29ae0615-0d77-4814-97c7-c9e91f6bfd7b'],
- ['Phenotype URL: http://genenetwork.org/show_trait?trait_id=29ae0615-0d77-4814-97c7-c9e91f6bfd7b&dataset=Temp'], [
- 'Group: name'], ['Phenotype: Description'],
- ['Authors: N/A'], ['Title: research1'],
- ['Journal: N/A'], ['Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Temp'], []]
+ trait_data = {
+ "symbol": "Nr3c1",
+ "description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR",
+ "title": "Trait_1 title",
- self.assertEqual(results, expected)
+ "authors": "XL_1",
+ "journal": ""
- @mock.patch("wqflask.show_trait.export_trait_data.dict_to_sorted_list")
- @mock.patch("wqflask.show_trait.export_trait_data.get_export_metadata")
- def test_export_sample_table(self, exp_metadata, dict_list):
- """test for exporting sample table"""
- targs_obj = {
- "export_data": """{
- "primary_samples": [
- {
- "other": "germanotta",
- "name": "Sauroniops",
- "se":{
- "name":"S2"
- },
- "num_cases":{
- "k1":"value"
-
- }
- }
- ],
- "other_samples": [
- {
- "se": 1,
- "num_cases": 4,
- "value": 6,
- "name": 3
- }
- ]
- }""",
- "trait_display_name": "Hair_color",
- "trait_id": "23177fdc-312e-4084-ad0c-f3eae785fff5",
- "dataset": {
- }
}
- exp_metadata.return_value = [
- ["Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f"], ['Group:gp1'],
- ["Phenotype:p1"], [
- "Authors:N/A"],
- ["Title:research1"],
- ["Journal:N/A"],
- ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1"], []]
- expected = ('Hair_color',
- [['Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f'],
- ['Group:gp1'],
- ['Phenotype:p1'],
- ['Authors:N/A'],
- ['Title:research1'],
- ['Journal:N/A'],
- ['Dataset Link: '
- 'http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1'],
- [],
- ['Name', 'Value', 'SE', 'N'],
- ['Sauroniops', 'germanotta'],
- [3, 6, 1, 4]])
-
- dict_list.side_effect = [['Sauroniops', 'germanotta'], [3, 6, 1, 4]]
-
- self.assertEqual(export_sample_table(targs_obj), expected)
- exp_metadata.assert_called_with(
- "23177fdc-312e-4084-ad0c-f3eae785fff5", {})
- self.assertEqual(dict_list.call_count, 2)
+
+ date_mock.datetime.now.return_value = datetime.datetime(
+ 2022, 8, 8, 19, 2, 31, 628813)
+ trait_mock.return_value = AttributesSetter(trait_data)
+
+ results = get_export_metadata({
+ "trait_id": "1460303_at",
+ "trait_display_name": "1460303_at",
+ "dataset": "HC_M2_0606_P"
+ })
+
+ expected = [["Phenotype ID:", "1460303_at"],
+ ["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"],
+ ["Group: ", "C"],
+ ["Phenotype: ",
+ 'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'],
+ ["Authors: ", "XL_1"],
+ ["Title: ", "Trait_1 title"],
+ ["Journal: ", "N/A"],
+ ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"],
+ ["Export Date: ", "August 08, 2022"],
+ ["Export Time: ", "19:02 GMT"]]
+
+ self.assertEqual(results, expected)
def test_dict_to_sortedlist(self):
"""test for conversion of dict to sorted list"""
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d4256a46..df7156b4 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -33,8 +33,7 @@ from math import *
import utility.corestats as corestats
from base import webqtlConfig
from utility.pillow_utils import draw_rotated_text
-import utility.logger
-logger = utility.logger.getLogger(__name__)
+
# ---- Define common colours ---- #
BLUE = ImageColor.getrgb("blue")
@@ -105,7 +104,6 @@ def find_outliers(vals):
"""
if vals:
- #logger.debug("vals is:", pf(vals))
stats = corestats.Stats(vals)
low_hinge = stats.percentile(25)
up_hinge = stats.percentile(75)
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
deleted file mode 100644
index 6ece2f21..00000000
--- a/wqflask/utility/benchmark.py
+++ /dev/null
@@ -1,52 +0,0 @@
-import collections
-import inspect
-import time
-from utility.tools import LOG_BENCH
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
-class Bench:
- entries = collections.OrderedDict()
-
- def __init__(self, name=None, write_output=LOG_BENCH):
- self.name = name
- self.write_output = write_output
-
- def __enter__(self):
- if self.write_output:
- if self.name:
- logger.debug("Starting benchmark: %s" % (self.name))
- else:
- logger.debug("Starting benchmark at: %s [%i]" % (
- inspect.stack()[1][3], inspect.stack()[1][2]))
- self.start_time = time.time()
-
- def __exit__(self, type, value, traceback):
- time_taken = time.time() - self.start_time
- if self.write_output:
- if self.name:
- name = self.name
- else:
- name = "That"
-
- logger.info(" %s took: %f seconds" % (name, (time_taken)))
-
- if self.name:
- Bench.entries[self.name] = Bench.entries.get(
- self.name, 0) + time_taken
-
- @classmethod
- def report(cls):
- total_time = sum(
- (time_taken for time_taken in list(cls.entries.values())))
- print("\nTiming report\n")
- for name, time_taken in list(cls.entries.items()):
- percent = int(round((time_taken / total_time) * 100))
- print("[{}%] {}: {}".format(percent, name, time_taken))
- print()
-
- def reset(cls):
- """Reset the entries"""
- cls.entries = collections.OrderedDict()
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index e619b7b6..c7a1ea59 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,3 @@
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
-
class genotype:
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 27dd0729..4229a91f 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -6,9 +6,6 @@ from utility import hmac
from flask import g
-import logging
-logger = logging.getLogger(__name__)
-
def get_species_dataset_trait(self, start_vars):
if "temp_trait" in list(start_vars.keys()):
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index d706e32a..65f2f1ee 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -27,7 +27,6 @@
# We'll add more overrides soon.
import logging
-import string
from inspect import isfunction
from pprint import pformat as pf
from inspect import stack
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 5713e155..e302df18 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -2,9 +2,6 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont
from utility.tools import TEMPDIR
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
BLACK = ImageColor.getrgb("black")
WHITE = ImageColor.getrgb("white")
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 641d973e..945efbbd 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -5,8 +5,6 @@ import datetime
import redis # used for collections
from utility.hmac import hmac_creation
-from utility.logger import getLogger
-logger = getLogger(__name__)
def get_redis_conn():
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 778fb64d..59923fa1 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -23,12 +23,9 @@ def app_config():
if mode in ["DEV", "DEBUG"]:
app.config['TEMPLATES_AUTO_RELOAD'] = True
if mode == "DEBUG":
- from flask_debugtoolbar import DebugToolbarExtension
app.debug = True
- toolbar = DebugToolbarExtension(app)
print("==========================================")
-
show_settings()
port = get_setting_int("SERVER_PORT")
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index db0b4320..19bf686b 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -50,7 +50,7 @@ def get_setting(command_id, guess=None):
app_set(command_id, command)
return command
else:
- return None
+ return app.config.get(command_id)
# ---- Check whether environment exists
# print("Looking for "+command_id+"\n")
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 5d239343..45d5739e 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,8 +1,5 @@
from gn3.db.species import get_all_species
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
def gen_dropdown_json(conn):
"""Generates and outputs (as json file) the data for the main dropdown menus on
the home page
@@ -31,7 +28,6 @@ def get_groups(species, conn):
"InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
"InbredSet.FullName) ASC, InbredSet.FullName ASC, "
"InbredSet.MenuOrderId ASC").format(species_name)
- # logger.debug(query)
cursor.execute(query)
results = cursor.fetchall()
for result in results:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index d1cc368e..5eacc83a 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -1,19 +1,12 @@
-import string
-
from base import data_set
-from base import webqtlConfig
from base.trait import create_trait, retrieve_sample_data
-from utility import helper_functions
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
-
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
+from wqflask.marker_regression import gemma_mapping, rqtl_mapping
+from wqflask.show_trait.show_trait import normf
def do_mapping_for_api(start_vars):
- assert('db' in start_vars)
- assert('trait_id' in start_vars)
+ if ('db' not in start_vars) or ("trait_id" not in start_vars):
+ raise ValueError("Mapping: db and trait_id are not in start_vars")
dataset = data_set.create_dataset(dataset_name=start_vars['db'])
dataset.group.get_markers()
@@ -23,33 +16,67 @@ def do_mapping_for_api(start_vars):
samples = []
vals = []
- for sample in dataset.group.samplelist:
- in_trait_data = False
- for item in this_trait.data:
- if this_trait.data[item].name == sample:
- value = str(this_trait.data[item].value)
- samples.append(item)
- vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- vals.append("x")
-
mapping_params = initialize_parameters(start_vars, dataset, this_trait)
- # ZS: It seems to take an empty string as default. This should probably be changed.
+ genofile_samplelist = []
+ if mapping_params.get('genofile'):
+ dataset.group.genofile = mapping_params['genofile']
+ genofile_samplelist = get_genofile_samplelist(dataset)
+
+ if (len(genofile_samplelist) > 0):
+ samplelist = genofile_samplelist
+ for sample in samplelist:
+ in_trait_data = False
+ for item in this_trait.data:
+ if this_trait.data[item].name == sample:
+ value = str(this_trait.data[item].value)
+ samples.append(item)
+ vals.append(value)
+ in_trait_data = True
+ break
+ if not in_trait_data:
+ vals.append("x")
+ else:
+ samplelist = dataset.group.samplelist
+ for sample in samplelist:
+ in_trait_data = False
+ for item in this_trait.data:
+ if this_trait.data[item].name == sample:
+ value = str(this_trait.data[item].value)
+ samples.append(item)
+ vals.append(value)
+ in_trait_data = True
+ break
+ if not in_trait_data:
+ vals.append("x")
+
+ if mapping_params.get('transform') == "qnorm":
+ vals_minus_x = [float(val) for val in vals if val != "x"]
+ qnorm_vals = normf(vals_minus_x)
+ qnorm_vals_with_x = []
+ counter = 0
+ for val in vals:
+ if val == "x":
+ qnorm_vals_with_x.append("x")
+ else:
+ qnorm_vals_with_x.append(qnorm_vals[counter])
+ counter += 1
+
+ vals = qnorm_vals_with_x
+
+ # It seems to take an empty string as default. This should probably be changed.
covariates = ""
- if mapping_params['mapping_method'] == "gemma":
+ if mapping_params.get('mapping_method') == "gemma":
header_row = ["name", "chr", "Mb", "lod_score", "p_value"]
- # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
- if mapping_params['use_loco'] == "True":
+ # gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
+ if mapping_params.get('use_loco') == "True":
result_markers = gemma_mapping.run_gemma(
this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
else:
result_markers = gemma_mapping.run_gemma(
this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
- elif mapping_params['mapping_method'] == "rqtl":
+ elif mapping_params.get('mapping_method') == "rqtl":
header_row = ["name", "chr", "cM", "lod_score"]
if mapping_params['num_perm'] > 0:
_sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'],
@@ -62,10 +89,10 @@ def do_mapping_for_api(start_vars):
mapping_params['do_control'], mapping_params['control_marker'],
mapping_params['manhattan_plot'], None)
- if mapping_params['limit_to']:
+ if mapping_params.get('limit_to'):
result_markers = result_markers[:mapping_params['limit_to']]
- if mapping_params['format'] == "csv":
+ if mapping_params.get('format') == "csv":
output_rows = []
output_rows.append(header_row)
for marker in result_markers:
@@ -138,4 +165,22 @@ def initialize_parameters(start_vars, dataset, this_trait):
except:
mapping_params['perm_check'] = False
+ mapping_params['transform'] = False
+ if 'transform' in start_vars:
+ mapping_params['transform'] = start_vars['transform']
+
+ mapping_params['genofile'] = False
+ if 'genofile' in start_vars:
+ mapping_params['genofile'] = start_vars['genofile']
+
return mapping_params
+
+def get_genofile_samplelist(dataset):
+ genofile_samplelist = []
+
+ genofile_json = dataset.group.get_genofiles()
+ for genofile in genofile_json:
+ if genofile['location'] == dataset.group.genofile and 'sample_list' in genofile:
+ genofile_samplelist = genofile['sample_list']
+
+ return genofile_samplelist
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 3d33cc87..95cd2953 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -25,8 +25,6 @@ from utility.tools import flat_files
from wqflask.database import database_connection
-import utility.logger
-logger = utility.logger.getLogger(__name__)
version = "pre1"
@@ -275,8 +273,6 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
InbredSet.Name = "{0}" AND PublishXRef.Id = "{1}"
""".format(group_name, dataset_name)
- logger.debug("QUERY:", pheno_query)
-
pheno_results = g.db.execute(pheno_query)
dataset = pheno_results.fetchone()
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index b46e1859..09ab2b60 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -21,9 +21,7 @@ from base.trait import retrieve_trait_info
from base.trait import jsonable
from base.data_set import create_dataset
-from utility.logger import getLogger
-logger = getLogger(__name__)
Redis = get_redis_conn()
@@ -48,8 +46,6 @@ def report_change(len_before, len_now):
if new_length:
flash("We've added {} to your collection.".format(
numify(new_length, 'new trait', 'new traits')))
- else:
- logger.debug("No new traits were added.")
@app.route("/collections/store_trait_list", methods=('POST',))
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index cafb9265..5df28c45 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -8,9 +8,6 @@ from utility import corr_result_helpers
from scipy import stats
import numpy as np
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index caa9b619..1a375501 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -11,12 +11,12 @@ from base import data_set
from base.trait import create_trait
from base.trait import retrieve_sample_data
-from gn3.computations.correlations import compute_all_sample_correlation
-from gn3.computations.correlations import fast_compute_all_sample_correlation
+from gn3.db_utils import database_connector
+from gn3.commands import run_sample_corr_cmd
from gn3.computations.correlations import map_shared_keys_to_values
from gn3.computations.correlations import compute_all_lit_correlation
from gn3.computations.correlations import compute_tissue_correlation
-from gn3.db_utils import database_connector
+from gn3.computations.correlations import fast_compute_all_sample_correlation
def create_target_this_trait(start_vars):
@@ -108,9 +108,9 @@ def sample_for_trait_lists(corr_results, target_dataset,
(this_trait_data, target_dataset) = fetch_sample_data(
start_vars, this_trait, this_dataset, target_dataset)
- correlation_results = compute_all_sample_correlation(corr_method="pearson",
- this_trait=this_trait_data,
- target_dataset=target_dataset)
+ correlation_results = run_sample_corr_cmd(
+ corr_method="pearson", this_trait=this_trait_data,
+ target_dataset=target_dataset)
return correlation_results
@@ -194,78 +194,13 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
method -- Correlation method to be used (pearson, spearman, or bicor)
compute_all -- Include sample, tissue, and literature correlations (when applicable)
"""
- # pylint: disable-msg=too-many-locals
+ from wqflask.correlation.rust_correlation import compute_correlation_rust
corr_type = start_vars['corr_type']
-
- (this_dataset, this_trait, target_dataset,
- sample_data) = create_target_this_trait(start_vars)
-
- target_dataset_type = target_dataset.type
- this_dataset_type = this_dataset.type
-
method = start_vars['corr_sample_method']
corr_return_results = int(start_vars.get("corr_return_results", 100))
- corr_input_data = {}
-
- if corr_type == "sample":
- (this_trait_data, target_dataset_data) = fetch_sample_data(
- start_vars, this_trait, this_dataset, target_dataset)
-
- correlation_results = compute_all_sample_correlation(
- corr_method=method, this_trait=this_trait_data, target_dataset=target_dataset_data)
-
- elif corr_type == "tissue":
- trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
- tissue_input = get_tissue_correlation_input(
- this_trait, trait_symbol_dict)
-
- if tissue_input is not None:
- (primary_tissue_data, target_tissue_data) = tissue_input
-
- corr_input_data = {
- "primary_tissue": primary_tissue_data,
- "target_tissues_dict": target_tissue_data
- }
- correlation_results = compute_tissue_correlation(
- primary_tissue_dict=corr_input_data["primary_tissue"],
- target_tissues_data=corr_input_data[
- "target_tissues_dict"],
- corr_method=method
-
- )
- else:
- return {"correlation_results": [],
- "this_trait": this_trait.name,
- "target_dataset": start_vars['corr_dataset'],
- "return_results": corr_return_results}
-
- elif corr_type == "lit":
- (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
- this_trait, this_dataset)
-
- conn = database_connector()
- with conn:
- correlation_results = compute_all_lit_correlation(
- conn=conn, trait_lists=list(geneid_dict.items()),
- species=species, gene_id=this_trait_geneid)
-
- correlation_results = correlation_results[0:corr_return_results]
-
- if (compute_all):
- correlation_results = compute_corr_for_top_results(start_vars,
- correlation_results,
- this_trait,
- this_dataset,
- target_dataset,
- corr_type)
-
- correlation_data = {"correlation_results": correlation_results,
- "this_trait": this_trait.name,
- "target_dataset": start_vars['corr_dataset'],
- "return_results": corr_return_results}
-
- return correlation_data
+ return compute_correlation_rust(
+ start_vars, corr_type, method, corr_return_results, compute_all)
def compute_corr_for_top_results(start_vars,
@@ -275,12 +210,10 @@ def compute_corr_for_top_results(start_vars,
target_dataset,
corr_type):
if corr_type != "tissue" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet":
-
tissue_result = tissue_for_trait_lists(
correlation_results, this_dataset, this_trait)
if tissue_result:
-
correlation_results = merge_correlation_results(
correlation_results, tissue_result)
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
new file mode 100644
index 00000000..cfa360d0
--- /dev/null
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -0,0 +1,329 @@
+"""module contains integration code for rust-gn3"""
+import json
+from functools import reduce
+from utility.db_tools import mescape
+from utility.db_tools import create_in_clause
+from wqflask.correlation.correlation_functions\
+ import get_trait_symbol_and_tissue_values
+from wqflask.correlation.correlation_gn3_api import create_target_this_trait
+from wqflask.correlation.correlation_gn3_api import lit_for_trait_list
+from wqflask.correlation.correlation_gn3_api import do_lit_correlation
+from gn3.computations.correlations import compute_all_lit_correlation
+from gn3.computations.rust_correlation import run_correlation
+from gn3.computations.rust_correlation import get_sample_corr_data
+from gn3.computations.rust_correlation import parse_tissue_corr_data
+from gn3.db_utils import database_connector
+
+
+def query_probes_metadata(dataset, trait_list):
+ """query traits metadata in bulk for probeset"""
+
+ with database_connector() as conn:
+ with conn.cursor() as cursor:
+
+ query = """
+ SELECT ProbeSet.Name,ProbeSet.Chr,ProbeSet.Mb,
+ ProbeSet.Symbol,ProbeSetXRef.mean,ProbeSet.description,
+ ProbeSetXRef.additive,ProbeSetXRef.LRS,Geno.Chr, Geno.Mb
+ FROM ProbeSet INNER JOIN ProbeSetXRef
+ ON ProbeSet.Id=ProbeSetXRef.ProbeSetId
+ INNER JOIN Geno
+ ON ProbeSetXRef.Locus = Geno.Name
+ INNER JOIN Species
+ ON Geno.SpeciesId = Species.Id
+ WHERE ProbeSet.Name in ({}) AND
+ Species.Name = %s AND
+ ProbeSetXRef.ProbeSetFreezeId IN (
+ SELECT ProbeSetFreeze.Id
+ FROM ProbeSetFreeze WHERE ProbeSetFreeze.Name = %s)
+ """.format(", ".join(["%s"] * len(trait_list)))
+
+ cursor.execute(query,
+ (tuple(trait_list) +
+ (dataset.group.species,) + (dataset.name,))
+ )
+
+ return cursor.fetchall()
+
+
+def get_metadata(dataset, traits):
+ """Retrieve the metadata"""
+ def __location__(probe_chr, probe_mb):
+ if probe_mb:
+ return f"Chr{probe_chr}: {probe_mb:.6f}"
+ return f"Chr{probe_chr}: ???"
+
+ return {trait_name: {
+ "name": trait_name,
+ "view": True,
+ "symbol": symbol,
+ "dataset": dataset.name,
+ "dataset_name": dataset.shortname,
+ "mean": mean,
+ "description": description,
+ "additive": additive,
+ "lrs_score": f"{lrs:3.1f}",
+ "location": __location__(probe_chr, probe_mb),
+ "lrs_location": f"Chr{chr_score}: {mb:.6f}"
+
+ } for trait_name, probe_chr, probe_mb, symbol, mean, description,
+ additive, lrs, chr_score, mb
+ in query_probes_metadata(dataset, traits)}
+
+
+def chunk_dataset(dataset, steps, name):
+
+ results = []
+
+ query = """
+ SELECT ProbeSetXRef.DataId,ProbeSet.Name
+ FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
+ WHERE ProbeSetFreeze.Name = '{}' AND
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id
+ """.format(name)
+
+ with database_connector() as conn:
+ with conn.cursor() as curr:
+ curr.execute(query)
+ traits_name_dict = dict(curr.fetchall())
+
+ for i in range(0, len(dataset), steps):
+ matrix = list(dataset[i:i + steps])
+ trait_name = traits_name_dict[matrix[0][0]]
+
+ strains = [trait_name] + [str(value)
+ for (trait_name, strain, value) in matrix]
+ results.append(",".join(strains))
+
+ return results
+
+
+def compute_top_n_sample(start_vars, dataset, trait_list):
+ """check if dataset is of type probeset"""
+
+ if dataset.type.lower() != "probeset":
+ return {}
+
+ def __fetch_sample_ids__(samples_vals, samples_group):
+ all_samples = json.loads(samples_vals)
+ sample_data = get_sample_corr_data(
+ sample_type=samples_group, all_samples=all_samples,
+ dataset_samples=dataset.group.all_samples_ordered())
+
+ with database_connector() as conn:
+ with conn.cursor() as curr:
+ curr.execute(
+ """
+ SELECT Strain.Name, Strain.Id FROM Strain, Species
+ WHERE Strain.Name IN {}
+ and Strain.SpeciesId=Species.Id
+ and Species.name = '{}'
+ """.format(create_in_clause(list(sample_data.keys())),
+ *mescape(dataset.group.species)))
+ return (sample_data, dict(curr.fetchall()))
+
+ (sample_data, sample_ids) = __fetch_sample_ids__(
+ start_vars["sample_vals"], start_vars["corr_samples_group"])
+
+ with database_connector() as conn:
+ with conn.cursor() as curr:
+ # fetching strain data in bulk
+ curr.execute(
+ """
+ SELECT * from ProbeSetData
+ where StrainID in {}
+ and id in (SELECT ProbeSetXRef.DataId
+ FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSetFreeze.Name = '{}'
+ and ProbeSet.Name in {}
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId)
+ """.format(
+ create_in_clause(list(sample_ids.values())),
+ dataset.name,
+ create_in_clause(trait_list)))
+
+ corr_data = chunk_dataset(
+ list(curr.fetchall()), len(sample_ids.values()), dataset.name)
+
+ return run_correlation(
+ corr_data, list(sample_data.values()), "pearson", ",")
+
+
+def compute_top_n_lit(corr_results, this_dataset, this_trait) -> dict:
+ (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
+ this_trait, this_dataset)
+
+ geneid_dict = {trait_name: geneid for (trait_name, geneid)
+ in geneid_dict.items() if
+ corr_results.get(trait_name)}
+ with database_connector() as conn:
+ return reduce(
+ lambda acc, corr: {**acc, **corr},
+ compute_all_lit_correlation(
+ conn=conn, trait_lists=list(geneid_dict.items()),
+ species=species, gene_id=this_trait_geneid),
+ {})
+
+ return {}
+
+
+def compute_top_n_tissue(this_dataset, this_trait, traits, method):
+
+ # refactor lots of rpt
+
+ trait_symbol_dict = dict({
+ trait_name: symbol
+ for (trait_name, symbol)
+ in this_dataset.retrieve_genes("Symbol").items()
+ if traits.get(trait_name)})
+
+ corr_result_tissue_vals_dict = get_trait_symbol_and_tissue_values(
+ symbol_list=list(trait_symbol_dict.values()))
+
+ data = parse_tissue_corr_data(symbol_name=this_trait.symbol,
+ symbol_dict=get_trait_symbol_and_tissue_values(
+ symbol_list=[this_trait.symbol]),
+ dataset_symbols=trait_symbol_dict,
+ dataset_vals=corr_result_tissue_vals_dict)
+
+ if data:
+ return run_correlation(
+ data[1], data[0], method, ",", "tissue")
+
+ return {}
+
+
+def merge_results(dict_a: dict, dict_b: dict, dict_c: dict) -> list[dict]:
+ """code to merge diff corr into individual dicts
+ a"""
+
+ def __merge__(trait_name, trait_corrs):
+ return {
+ trait_name: {
+ **trait_corrs,
+ **dict_b.get(trait_name, {}),
+ **dict_c.get(trait_name, {})
+ }
+ }
+ return [__merge__(tname, tcorrs) for tname, tcorrs in dict_a.items()]
+
+
+def __compute_sample_corr__(
+ start_vars: dict, corr_type: str, method: str, n_top: int,
+ target_trait_info: tuple):
+ """Compute the sample correlations"""
+ (this_dataset, this_trait, target_dataset, sample_data) = target_trait_info
+ all_samples = json.loads(start_vars["sample_vals"])
+ sample_data = get_sample_corr_data(
+ sample_type=start_vars["corr_samples_group"], all_samples=all_samples,
+ dataset_samples=this_dataset.group.all_samples_ordered())
+ target_dataset.get_trait_data(list(sample_data.keys()))
+
+ target_data = []
+ for (key, val) in target_dataset.trait_data.items():
+ lts = [key] + [str(x) for x in val]
+ r = ",".join(lts)
+ target_data.append(r)
+
+ return run_correlation(
+ target_data, list(sample_data.values()), method, ",", corr_type,
+ n_top)
+
+
+def __compute_tissue_corr__(
+ start_vars: dict, corr_type: str, method: str, n_top: int,
+ target_trait_info: tuple):
+ """Compute the tissue correlations"""
+ (this_dataset, this_trait, target_dataset, sample_data) = target_trait_info
+ trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
+ corr_result_tissue_vals_dict = get_trait_symbol_and_tissue_values(
+ symbol_list=list(trait_symbol_dict.values()))
+
+ data = parse_tissue_corr_data(
+ symbol_name=this_trait.symbol,
+ symbol_dict=get_trait_symbol_and_tissue_values(
+ symbol_list=[this_trait.symbol]),
+ dataset_symbols=trait_symbol_dict,
+ dataset_vals=corr_result_tissue_vals_dict)
+
+ if data:
+ return run_correlation(data[1], data[0], method, ",", "tissue")
+ return {}
+
+
+def __compute_lit_corr__(
+ start_vars: dict, corr_type: str, method: str, n_top: int,
+ target_trait_info: tuple):
+ """Compute the literature correlations"""
+ (this_dataset, this_trait, target_dataset, sample_data) = target_trait_info
+ target_dataset_type = target_dataset.type
+ this_dataset_type = this_dataset.type
+ (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
+ this_trait, target_dataset)
+
+ with database_connector() as conn:
+ return reduce(
+ lambda acc, lit: {**acc, **lit},
+ compute_all_lit_correlation(
+ conn=conn, trait_lists=list(geneid_dict.items()),
+ species=species, gene_id=this_trait_geneid)[:n_top],
+ {})
+ return {}
+
+
+def compute_correlation_rust(
+ start_vars: dict, corr_type: str, method: str = "pearson",
+ n_top: int = 500, should_compute_all: bool = False):
+ """function to compute correlation"""
+ target_trait_info = create_target_this_trait(start_vars)
+ (this_dataset, this_trait, target_dataset, sample_data) = (
+ target_trait_info)
+
+ # Replace this with `match ...` once we hit Python 3.10
+ corr_type_fns = {
+ "sample": __compute_sample_corr__,
+ "tissue": __compute_tissue_corr__,
+ "lit": __compute_lit_corr__
+ }
+ results = corr_type_fns[corr_type](
+ start_vars, corr_type, method, n_top, target_trait_info)
+
+ # END: Replace this with `match ...` once we hit Python 3.10
+
+ top_a = top_b = {}
+
+ if should_compute_all:
+
+ if corr_type == "sample":
+
+ top_a = compute_top_n_tissue(
+ this_dataset, this_trait, results, method)
+
+ top_b = compute_top_n_lit(results, this_dataset, this_trait)
+
+ elif corr_type == "lit":
+
+ # currently fails for lit
+
+ top_a = compute_top_n_sample(
+ start_vars, target_dataset, list(results.keys()))
+ top_b = compute_top_n_tissue(
+ this_dataset, this_trait, results, method)
+
+ else:
+
+ top_a = compute_top_n_sample(
+ start_vars, target_dataset, list(results.keys()))
+
+ top_b = compute_top_n_lit(results, this_dataset, this_trait)
+
+ return {
+ "correlation_results": merge_results(
+ results, top_a, top_b),
+ "this_trait": this_trait.name,
+ "target_dataset": start_vars['corr_dataset'],
+ "traits_metadata": get_metadata(target_dataset, list(results.keys())),
+ "return_results": n_top
+ }
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 1c391386..4910b0e0 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -93,8 +93,7 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
new_traits_metadata = {}
- (file_path, dataset_metadata) = fetch_all_cached_metadata(
- target_dataset['name'])
+ dataset_metadata = correlation_data["traits_metadata"]
for i, trait_dict in enumerate(corr_results):
trait_name = list(trait_dict.keys())[0]
@@ -121,9 +120,9 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
results_dict['dataset'] = target_dataset['name']
results_dict['hmac'] = hmac.data_hmac(
'{}:{}'.format(target_trait['name'], target_dataset['name']))
- results_dict['sample_r'] = f"{float(trait['corr_coefficient']):.3f}"
- results_dict['num_overlap'] = trait['num_overlap']
- results_dict['sample_p'] = f"{float(trait['p_value']):.3e}"
+ results_dict['sample_r'] = f"{float(trait.get('corr_coefficient',0.0)):.3f}"
+ results_dict['num_overlap'] = trait.get('num_overlap',0)
+ results_dict['sample_p'] = f"{float(trait.get('p_value',0)):.3e}"
if target_dataset['type'] == "ProbeSet":
results_dict['symbol'] = target_trait['symbol']
results_dict['description'] = "N/A"
@@ -187,10 +186,6 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
results_list.append(results_dict)
- cache_new_traits_metadata(dataset_metadata,
- new_traits_metadata,
- file_path)
-
return json.dumps(results_list)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index cf37b9e9..17c174b1 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -77,7 +77,7 @@ class CorrelationMatrix:
self.sample_data.append(this_trait_vals)
# Shouldn't do PCA if there are more traits than observations/samples
- if len(this_trait_vals) < len(self.trait_list):
+ if len(this_trait_vals) < len(self.trait_list) or len(self.trait_list) < 3:
self.do_PCA = False
# ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
@@ -85,6 +85,7 @@ class CorrelationMatrix:
self.corr_results = []
self.pca_corr_results = []
+ self.scree_data = []
self.shared_samples_list = self.all_sample_list
for trait_db in self.trait_list:
this_trait = trait_db[0]
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index bb928ec5..96a47eb8 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -24,8 +24,6 @@ from utility.tools import locate, GN2_BRANCH_URL
from rpy2.robjects.packages import importr
-import utility.logger
-logger = utility.logger.getLogger(__name__)
# Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
@@ -42,14 +40,9 @@ r_as_numeric = ro.r["as.numeric"] # Map the write.table function
class CTL:
def __init__(self):
- logger.info("Initialization of CTL")
- #log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
- # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
- #r_sink(log, type = "message")
# Load CTL - Should only be done once, since it is quite expensive
r_library("ctl")
r_options(stringsAsFactors=False)
- logger.info("Initialization of CTL done, package loaded in R session")
# Map the CTLscan function
self.r_CTLscan = ro.r["CTLscan"]
# Map the CTLsignificant function
@@ -60,7 +53,6 @@ class CTL:
self.r_plotCTLobject = ro.r["plot.CTLobject"]
self.nodes_list = []
self.edges_list = []
- logger.info("Obtained pointers to CTL functions")
self.gn2_url = GN2_BRANCH_URL
@@ -85,21 +77,12 @@ class CTL:
self.edges_list.append(edge_dict)
def run_analysis(self, requestform):
- logger.info("Starting CTL analysis on dataset")
self.trait_db_list = [trait.strip()
for trait in requestform['trait_list'].split(',')]
self.trait_db_list = [x for x in self.trait_db_list if x]
-
- logger.debug("strategy:", requestform.get("strategy"))
strategy = requestform.get("strategy")
-
- logger.debug("nperm:", requestform.get("nperm"))
nperm = int(requestform.get("nperm"))
-
- logger.debug("parametric:", requestform.get("parametric"))
parametric = bool(requestform.get("parametric"))
-
- logger.debug("significance:", requestform.get("significance"))
significance = float(requestform.get("significance"))
# Get the name of the .geno file belonging to the first phenotype
@@ -109,7 +92,6 @@ class CTL:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
parser = genofile_parser.ConvertGenoFile(genofilelocation)
parser.process_csv()
- logger.debug("dataset group: ", dataset.group)
# Create a genotype matrix
individuals = parser.individuals
markers = []
@@ -119,8 +101,6 @@ class CTL:
markers.append(marker["genotypes"])
genotypes = list(itertools.chain(*markers))
- logger.debug(len(genotypes) / len(individuals),
- "==", len(parser.markers))
rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(
individuals), dimnames=r_list(markernames, individuals), byrow=True))
@@ -128,7 +108,6 @@ class CTL:
# Create a phenotype matrix
traits = []
for trait in self.trait_db_list:
- logger.debug("retrieving data for", trait)
if trait != "":
ts = trait.split(':')
gt = create_trait(name=ts[0], dataset_name=ts[1])
@@ -142,8 +121,6 @@ class CTL:
rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(
individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
- logger.debug(rPheno)
-
# Use a data frame to store the objects
rPheno = r_data_frame(rPheno, check_names=False)
rGeno = r_data_frame(rGeno, check_names=False)
@@ -195,8 +172,6 @@ class CTL:
# Create the interactive graph for cytoscape visualization (Nodes and Edges)
if not isinstance(significant, ri.RNULLType):
for x in range(len(significant[0])):
- logger.debug(significant[0][x], significant[1]
- [x], significant[2][x]) # Debug to console
# Source
tsS = significant[0][x].split(':')
# Target
@@ -231,7 +206,6 @@ class CTL:
n = n + 1
def process_results(self, results):
- logger.info("Processing CTL output")
template_vars = {}
template_vars["results"] = self.results
template_vars["elements"] = self.elements
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index f0ce0a77..ec616d07 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -1,16 +1,13 @@
# Module to initialize sqlalchemy with flask
import os
import sys
-from string import Template
from typing import Tuple
from urllib.parse import urlparse
import importlib
+import contextlib
import MySQLdb
-from sqlalchemy import create_engine
-from sqlalchemy.orm import scoped_session, sessionmaker
-from sqlalchemy.ext.declarative import declarative_base
def read_from_pyfile(pyfile, setting):
orig_sys_path = sys.path[:]
@@ -19,6 +16,7 @@ def read_from_pyfile(pyfile, setting):
sys.path = orig_sys_path[:]
return module.__dict__.get(setting)
+
def sql_uri():
"""Read the SQL_URI from the environment or settings file."""
return os.environ.get(
@@ -37,8 +35,26 @@ def parse_db_url(sql_uri: str) -> Tuple:
parsed_db.hostname, parsed_db.username, parsed_db.password,
parsed_db.path[1:], parsed_db.port)
+
+@contextlib.contextmanager
def database_connection():
- """Returns a database connection"""
+ """Provide a context manager for opening, closing, and rolling
+ back - if supported - a database connection. Should an error occur,
+ and if the table supports transactions, the connection will be
+ rolled back.
+
+ """
host, user, passwd, db_name, port = parse_db_url(sql_uri())
- return MySQLdb.connect(
- db=db_name, user=user, passwd=passwd, host=host, port=port)
+ connection = MySQLdb.connect(
+ db=db_name, user=user, passwd=passwd or '', host=host, port=port,
+ autocommit=False # Required for roll-backs
+ )
+ try:
+ yield connection
+ except Exception:
+ connection.rollback()
+ raise
+ else:
+ connection.commit()
+ finally:
+ connection.close()
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 938c453e..f52c30e4 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -6,9 +6,6 @@ import re
from flask import Flask, g
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
class InfoPage:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b0756361..97143486 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -13,10 +13,6 @@ import sys
from db import webqtlDatabaseFunction
from utility.tools import GN2_BASE_URL
-import logging
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
class DoSearch:
"""Parent class containing parameters/functions used for all searches"""
@@ -41,7 +37,6 @@ class DoSearch:
def execute(self, query):
"""Executes query and returns results"""
query = self.normalize_spaces(query)
- logger.sql(query)
results = g.db.execute(query, no_parameters=True).fetchall()
return results
@@ -55,7 +50,6 @@ class DoSearch:
def mescape(self, *items):
"""Multiple escape"""
escaped = [escape(str(item)) for item in items]
- logger.debug("escaped is:", escaped)
return tuple(escaped)
def normalize_spaces(self, stringy):
@@ -69,8 +63,6 @@ class DoSearch:
if 'key' in search_type and search_type['key'] != None:
search_type_string += '_' + search_type['key']
- logger.debug("search_type_string is:", search_type_string)
-
if search_type_string in cls.search_types:
return cls.search_types[search_type_string]
else:
@@ -177,8 +169,6 @@ class MrnaAssaySearch(DoSearch):
def run_combined(self, from_clause='', where_clause=''):
"""Generates and runs a combined search of an mRNA expression dataset"""
-
- logger.debug("Running ProbeSetSearch")
#query = self.base_query + from_clause + " WHERE " + where_clause
from_clause = self.normalize_spaces(from_clause)
@@ -197,11 +187,8 @@ class MrnaAssaySearch(DoSearch):
def run(self):
"""Generates and runs a simple search of an mRNA expression dataset"""
-
- logger.debug("Running ProbeSetSearch")
where_clause = self.get_where_clause()
query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC"
-
return self.execute(query)
@@ -310,9 +297,6 @@ class PhenotypeSearch(DoSearch):
def run_combined(self, from_clause, where_clause):
"""Generates and runs a combined search of an phenotype dataset"""
-
- logger.debug("Running PhenotypeSearch")
-
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
@@ -370,7 +354,6 @@ class GenotypeSearch(DoSearch):
where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
field),
self.search_term))
- logger.debug("hello ;where_clause is:", pf(where_clause))
where_clause = "(%s) " % ' OR '.join(where_clause)
return where_clause
@@ -559,7 +542,6 @@ class LrsSearch(DoSearch):
self.species_id)
else:
# Deal with >, <, >=, and <=
- logger.debug("self.search_term is:", self.search_term)
lrs_val = self.search_term[0]
if self.search_type == "LOD":
lrs_val = lrs_val * 4.61
@@ -794,7 +776,6 @@ class MeanSearch(MrnaAssaySearch):
def run(self):
self.where_clause = self.get_where_clause()
- logger.debug("where_clause is:", pf(self.where_clause))
self.query = self.compile_final_query(where_clause=self.where_clause)
@@ -824,9 +805,6 @@ class RangeSearch(MrnaAssaySearch):
FROM ProbeSetData
WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
""" % (escape(self.search_term[0]))
-
- logger.debug("where_clause is:", pf(where_clause))
-
return where_clause
def run(self):
@@ -932,11 +910,7 @@ class PvalueSearch(MrnaAssaySearch):
self.search_operator,
self.search_term[0])
- logger.debug("where_clause is:", pf(self.where_clause))
-
self.query = self.compile_final_query(where_clause=self.where_clause)
-
- logger.sql(self.query)
return self.execute(self.query)
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 0a1a597d..9d58162e 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -2,9 +2,6 @@ import codecs
from flask import g
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
class Docs:
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 0c80e9a4..4b37c7f7 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -14,8 +14,6 @@ from gn3.computations.gemma import generate_hash_of_string
from base.trait import create_trait, retrieve_trait_info
-from utility.logger import getLogger
-logger = getLogger(__name__)
def export_traits(targs, export_type):
if export_type == "collection":
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index c1b14ede..dfb59c63 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -21,9 +21,6 @@
from base.trait import GeneralTrait
from utility import helper_functions, corr_result_helpers
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
class SendToBNW:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 9a4f7150..a8066b43 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -26,9 +26,6 @@ from base.trait import GeneralTrait, retrieve_trait_info
from base.species import TheSpecies
from utility import helper_functions, corr_result_helpers
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
class SendToGeneWeaver:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 6e74f4fe..4de684b0 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -26,9 +26,6 @@ from base.trait import GeneralTrait, retrieve_trait_info
from base.species import TheSpecies
from utility import helper_functions, corr_result_helpers
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
class SendToWebGestalt:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9df7b2e1..56877524 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -11,13 +11,9 @@ from base import webqtlConfig
from utility import hmac
-from utility.benchmark import Bench
from utility.authentication_tools import check_resource_availability
from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
class GSearch:
@@ -64,75 +60,72 @@ class GSearch:
ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
LIMIT 6000
""" % (self.terms)
- with Bench("Running query"):
- logger.sql(sql)
- re = g.db.execute(sql).fetchall()
+ re = g.db.execute(sql).fetchall()
trait_list = []
dataset_to_permissions = {}
- with Bench("Creating trait objects"):
- for i, line in enumerate(re):
- trait_dict = {}
- trait_dict['index'] = i + 1
- trait_dict['name'] = line[5]
- trait_dict['dataset'] = line[3]
- trait_dict['dataset_fullname'] = line[4]
- trait_dict['hmac'] = hmac.data_hmac(
- '{}:{}'.format(line[5], line[3]))
- trait_dict['species'] = line[0]
- trait_dict['group'] = line[1]
- trait_dict['tissue'] = line[2]
- trait_dict['symbol'] = "N/A"
- if line[6]:
- trait_dict['symbol'] = line[6]
- trait_dict['description'] = "N/A"
- if line[7]:
- trait_dict['description'] = line[7].decode(
- 'utf-8', 'replace')
- trait_dict['location_repr'] = "N/A"
- if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
- trait_dict['location_repr'] = 'Chr%s: %.6f' % (
- line[8], float(line[9]))
-
- trait_dict['LRS_score_repr'] = "N/A"
- trait_dict['additive'] = "N/A"
- trait_dict['mean'] = "N/A"
-
- if line[11] != "" and line[11] != None:
- trait_dict['LRS_score_repr'] = f"{line[11]:.3f}"
- if line[14] != "" and line[14] != None:
- trait_dict['additive'] = f"{line[14]:.3f}"
- if line[10] != "" and line[10] != None:
- trait_dict['mean'] = f"{line[10]:.3f}"
-
- locus_chr = line[16]
- locus_mb = line[17]
-
- max_lrs_text = "N/A"
- if locus_chr and locus_mb:
- max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
- trait_dict['max_lrs_text'] = max_lrs_text
-
- trait_dict['additive'] = "N/A"
- if line[14] != "" and line[14] != None:
- trait_dict['additive'] = '%.3f' % line[14]
- trait_dict['dataset_id'] = line[15]
-
- dataset_ob = SimpleNamespace(
- id=trait_dict["dataset_id"], type="ProbeSet", name=trait_dict["dataset"], species=trait_dict["species"])
- if dataset_ob.id not in dataset_to_permissions:
- permissions = check_resource_availability(dataset_ob)
- dataset_to_permissions[dataset_ob.id] = permissions
- else:
- pemissions = dataset_to_permissions[dataset_ob.id]
- if type(permissions['data']) is list:
- if "view" not in permissions['data']:
- continue
- else:
- if permissions['data'] == 'no-access':
- continue
-
- trait_list.append(trait_dict)
+ for i, line in enumerate(re):
+ this_trait = {}
+ this_trait['index'] = i + 1
+ this_trait['name'] = line[5]
+ this_trait['dataset'] = line[3]
+ this_trait['dataset_fullname'] = line[4]
+ this_trait['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(line[5], line[3]))
+ this_trait['species'] = line[0]
+ this_trait['group'] = line[1]
+ this_trait['tissue'] = line[2]
+ this_trait['symbol'] = "N/A"
+ if line[6]:
+ this_trait['symbol'] = line[6]
+ this_trait['description'] = "N/A"
+ if line[7]:
+ this_trait['description'] = line[7].decode(
+ 'utf-8', 'replace')
+ this_trait['location_repr'] = "N/A"
+ if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
+ this_trait['location_repr'] = 'Chr%s: %.6f' % (
+ line[8], float(line[9]))
+
+ this_trait['LRS_score_repr'] = "N/A"
+ this_trait['additive'] = "N/A"
+ this_trait['mean'] = "N/A"
+
+ if line[11] != "" and line[11] != None:
+ this_trait['LRS_score_repr'] = f"{line[11]:.3f}"
+ if line[14] != "" and line[14] != None:
+ this_trait['additive'] = f"{line[14]:.3f}"
+ if line[10] != "" and line[10] != None:
+ this_trait['mean'] = f"{line[10]:.3f}"
+
+ locus_chr = line[16]
+ locus_mb = line[17]
+
+ max_lrs_text = "N/A"
+ if locus_chr and locus_mb:
+ max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
+ this_trait['max_lrs_text'] = max_lrs_text
+
+ this_trait['additive'] = "N/A"
+ if line[14] != "" and line[14] != None:
+ this_trait['additive'] = '%.3f' % line[14]
+ this_trait['dataset_id'] = line[15]
+
+ dataset_ob = SimpleNamespace(
+ id=this_trait["dataset_id"], type="ProbeSet", name=this_trait["dataset"], species=this_trait["species"])
+ if dataset_ob.id not in dataset_to_permissions:
+ permissions = check_resource_availability(dataset_ob)
+ dataset_to_permissions[dataset_ob.id] = permissions
+ else:
+ pemissions = dataset_to_permissions[dataset_ob.id]
+ if type(permissions['data']) is list:
+ if "view" not in permissions['data']:
+ continue
+ else:
+ if permissions['data'] == 'no-access':
+ continue
+
+ trait_list.append(this_trait)
self.trait_count = len(trait_list)
self.trait_list = trait_list
@@ -210,86 +203,84 @@ class GSearch:
ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
LIMIT 6000
""".format(group_clause, search_term)
- logger.sql(sql)
re = g.db.execute(sql).fetchall()
trait_list = []
- with Bench("Creating trait objects"):
- for i, line in enumerate(re):
- trait_dict = {}
- trait_dict['index'] = i + 1
- trait_dict['name'] = str(line[4])
- if len(str(line[12])) == 3:
- trait_dict['display_name'] = str(
- line[12]) + "_" + trait_dict['name']
- else:
- trait_dict['display_name'] = trait_dict['name']
- trait_dict['dataset'] = line[2]
- trait_dict['dataset_fullname'] = line[3]
- trait_dict['hmac'] = hmac.data_hmac(
- '{}:{}'.format(line[4], line[2]))
- trait_dict['species'] = line[0]
- trait_dict['group'] = line[1]
- if line[9] != None and line[6] != None:
- trait_dict['description'] = line[6].decode(
- 'utf-8', 'replace')
- elif line[5] != None:
- trait_dict['description'] = line[5].decode(
- 'utf-8', 'replace')
- else:
- trait_dict['description'] = "N/A"
- trait_dict['dataset_id'] = line[14]
-
- trait_dict['LRS_score_repr'] = "N/A"
- trait_dict['additive'] = "N/A"
- trait_dict['mean'] = "N/A"
-
- if line[10] != "" and line[10] != None:
- trait_dict['LRS_score_repr'] = f"{line[10]:.3f}"
- # Some Max LRS values in the DB are wrongly listed as 0.000, but shouldn't be displayed
- if trait_dict['LRS_score_repr'] == "0.000":
- trait_dict['LRS_score_repr'] = "N/A"
- if line[11] != "" and line[11] != None:
- trait_dict['additive'] = f"{line[11]:.3f}"
- if line[13] != "" and line[13] != None:
- trait_dict['mean'] = f"{line[13]:.3f}"
-
- locus_chr = line[15]
- locus_mb = line[16]
-
- max_lrs_text = "N/A"
- if locus_chr and locus_mb:
- max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
- trait_dict['max_lrs_text'] = max_lrs_text
-
- trait_dict['authors'] = line[7]
-
- trait_dict['authors'] = line[7]
- trait_dict['authors_display'] = trait_dict['authors']
- author_list = trait_dict['authors'].split(",")
- if len(author_list) >= 2:
- trait_dict['authors_display'] = (",").join(author_list[:2]) + ", et al."
-
- trait_dict['year'] = line[8]
- trait_dict['pubmed_text'] = "N/A"
- trait_dict['pubmed_link'] = "N/A"
- if trait_dict['year'].isdigit():
- trait_dict['pubmed_text'] = trait_dict['year']
- if line[9] != "" and line[9] != None:
- trait_dict['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
- if line[12]:
- trait_dict['display_name'] = line[12] + \
- "_" + str(trait_dict['name'])
-
- dataset_ob = SimpleNamespace(id=trait_dict["dataset_id"], type="Publish", species=trait_dict["species"])
- permissions = check_resource_availability(dataset_ob, trait_dict['name'])
- if type(permissions['data']) is list:
- if "view" not in permissions['data']:
- continue
- else:
- if permissions['data'] == 'no-access':
- continue
-
- trait_list.append(trait_dict)
+ for i, line in enumerate(re):
+ trait_dict = {}
+ trait_dict['index'] = i + 1
+ trait_dict['name'] = str(line[4])
+ if len(str(line[12])) == 3:
+ trait_dict['display_name'] = str(
+ line[12]) + "_" + trait_dict['name']
+ else:
+ trait_dict['display_name'] = trait_dict['name']
+ trait_dict['dataset'] = line[2]
+ trait_dict['dataset_fullname'] = line[3]
+ trait_dict['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(line[4], line[2]))
+ trait_dict['species'] = line[0]
+ trait_dict['group'] = line[1]
+ if line[9] != None and line[6] != None:
+ trait_dict['description'] = line[6].decode(
+ 'utf-8', 'replace')
+ elif line[5] != None:
+ trait_dict['description'] = line[5].decode(
+ 'utf-8', 'replace')
+ else:
+ trait_dict['description'] = "N/A"
+ trait_dict['dataset_id'] = line[14]
+
+ trait_dict['LRS_score_repr'] = "N/A"
+ trait_dict['additive'] = "N/A"
+ trait_dict['mean'] = "N/A"
+
+ if line[10] != "" and line[10] != None:
+ trait_dict['LRS_score_repr'] = f"{line[10]:.3f}"
+ # Some Max LRS values in the DB are wrongly listed as 0.000, but shouldn't be displayed
+ if trait_dict['LRS_score_repr'] == "0.000":
+ trait_dict['LRS_score_repr'] = "N/A"
+ if line[11] != "" and line[11] != None:
+ trait_dict['additive'] = f"{line[11]:.3f}"
+ if line[13] != "" and line[13] != None:
+ trait_dict['mean'] = f"{line[13]:.3f}"
+
+ locus_chr = line[15]
+ locus_mb = line[16]
+
+ max_lrs_text = "N/A"
+ if locus_chr and locus_mb:
+ max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
+ trait_dict['max_lrs_text'] = max_lrs_text
+
+ trait_dict['authors'] = line[7]
+
+ trait_dict['authors'] = line[7]
+ trait_dict['authors_display'] = trait_dict['authors']
+ author_list = trait_dict['authors'].split(",")
+ if len(author_list) >= 2:
+ trait_dict['authors_display'] = (",").join(author_list[:2]) + ", et al."
+
+ trait_dict['year'] = line[8]
+ trait_dict['pubmed_text'] = "N/A"
+ trait_dict['pubmed_link'] = "N/A"
+ if trait_dict['year'].isdigit():
+ trait_dict['pubmed_text'] = trait_dict['year']
+ if line[9] != "" and line[9] != None:
+ trait_dict['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
+ if line[12]:
+ trait_dict['display_name'] = line[12] + \
+ "_" + str(trait_dict['name'])
+
+ dataset_ob = SimpleNamespace(id=trait_dict["dataset_id"], type="Publish", species=trait_dict["species"])
+ permissions = check_resource_availability(dataset_ob, trait_dict['name'])
+ if type(permissions['data']) is list:
+ if "view" not in permissions['data']:
+ continue
+ else:
+ if permissions['data'] == 'no-access':
+ continue
+
+ trait_list.append(trait_dict)
self.trait_count = len(trait_list)
self.trait_list = trait_list
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 001bab3b..1c8a4ff6 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -8,12 +8,9 @@ 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.logger import getLogger
Redis = Redis()
-logger = getLogger(__name__)
-
class Heatmap:
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 8dffd21d..ef0c357e 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -42,17 +42,15 @@ from base import webqtlConfig
from base.GeneralObject import GeneralObject
from utility import webqtlUtil
from utility import Plot
-from utility.benchmark import Bench
from wqflask.interval_analyst import GeneUtil
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility.pillow_utils import draw_rotated_text, draw_open_polygon
-import utility.logger
+
try: # Only import this for Python3
from functools import reduce
except:
pass
-logger = utility.logger.getLogger(__name__)
RED = ImageColor.getrgb("red")
BLUE = ImageColor.getrgb("blue")
@@ -247,8 +245,6 @@ class DisplayMappingResults:
HELP_PAGE_REF = '/glossary.html'
def __init__(self, start_vars):
- logger.info("Running qtlreaper")
-
self.temp_uuid = start_vars['temp_uuid']
self.dataset = start_vars['dataset']
@@ -590,9 +586,8 @@ class DisplayMappingResults:
################################################################
showLocusForm = ""
intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
- with Bench("Drawing Plot"):
- gifmap = self.plotIntMapping(
- intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
+ gifmap = self.plotIntMapping(
+ intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
self.gifmap = gifmap.__str__()
@@ -3012,7 +3007,7 @@ class DisplayMappingResults:
else:
snpString = 0
- mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + \
+ mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm10&position=chr" + \
theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(
int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit"
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index ec12f9b7..646728ba 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -13,8 +13,6 @@ from utility.tools import TEMPDIR
from utility.tools import WEBSERVER_MODE
from gn3.computations.gemma import generate_hash_of_string
-import utility.logger
-logger = utility.logger.getLogger(__name__)
GEMMAOPTS = "-debug"
if WEBSERVER_MODE == 'PROD':
@@ -220,7 +218,7 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
marker['p_value'] = float(line.split("\t")[10])
- marker['additive'] = -(float(line.split("\t")[7]))
+ marker['additive'] = -(float(line.split("\t")[7])/2)
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
else:
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 2fa80841..75ee189e 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -5,9 +5,6 @@ from base.webqtlConfig import TMPDIR
from utility import webqtlUtil
from utility.tools import flat_files, PLINK_COMMAND
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
def run_plink(this_trait, dataset, species, vals, maf):
plink_output_filename = webqtlUtil.genRandStr(
@@ -15,13 +12,11 @@ def run_plink(this_trait, dataset, species, vals, maf):
gen_pheno_txt_file(dataset, vals)
plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
- logger.debug("plink_command:", plink_command)
os.system(plink_command)
count, p_values = parse_plink_output(plink_output_filename, species)
- logger.debug("p_values:", p_values)
dataset.group.markers.add_pvalues(p_values)
return dataset.group.markers.markers
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index c4b495d7..4d5db2ee 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -10,9 +10,6 @@ from base.trait import GeneralTrait
from base.data_set import create_dataset
from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
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):
"""Generates p-values for each marker using qtlreaper"""
@@ -67,8 +64,6 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list),
webqtlConfig.GENERATED_IMAGE_DIR,
output_filename))
-
- logger.debug("reaper_command:" + reaper_command)
os.system(reaper_command)
else:
output_filename, permu_filename, bootstrap_filename = output_files
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 3bf06ea6..7d112c68 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -17,9 +17,6 @@ from base.webqtlConfig import TMPDIR
from base.trait import create_trait
from utility.tools import locate, GN3_LOCAL_URL
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
def run_rqtl(trait_name, vals, samples, dataset, pair_scan, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors):
"""Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)"""
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index af229f5c..d9f33f8f 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -30,7 +30,6 @@ from base import data_set
from base import species
from base import webqtlConfig
from utility import webqtlUtil, helper_functions, hmac, Plot, Bunch, temp_data
-from utility.benchmark import Bench
from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
from wqflask.show_trait.SampleList import SampleList
@@ -38,9 +37,6 @@ from utility.tools import locate, locate_ignore_error, GEMMA_COMMAND, PLINK_COMM
from utility.external import shell
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
class RunMapping:
@@ -204,13 +200,12 @@ class RunMapping:
self.first_run = False
self.score_type = "-logP"
self.manhattan_plot = True
- with Bench("Running GEMMA"):
- if self.use_loco == "True":
- marker_obs, self.output_files = gemma_mapping.run_gemma(
- self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
- else:
- marker_obs, self.output_files = gemma_mapping.run_gemma(
- self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+ if self.use_loco == "True":
+ marker_obs, self.output_files = gemma_mapping.run_gemma(
+ self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+ else:
+ marker_obs, self.output_files = gemma_mapping.run_gemma(
+ self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
results = marker_obs
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
@@ -270,7 +265,6 @@ class RunMapping:
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
- logger.info("Running qtlreaper")
self.first_run = True
self.output_files = None
@@ -300,8 +294,6 @@ class RunMapping:
results = plink_mapping.run_plink(
self.this_trait, self.dataset, self.species, self.vals, self.maf)
#results = self.run_plink()
- else:
- logger.debug("RUNNING NOTHING")
self.no_results = False
if len(results) == 0:
@@ -376,33 +368,29 @@ class RunMapping:
self.qtl_results.append(marker)
total_markers = len(self.qtl_results)
+ export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+ self.mapping_method, self.mapping_scale, self.score_type,
+ self.transform, self.covariates, self.n_samples, self.vals_hash)
+
+ if len(self.qtl_results) > 30000:
+ self.qtl_results = trim_markers_for_figure(
+ self.qtl_results)
+ self.results_for_browser = trim_markers_for_figure(
+ self.results_for_browser)
+ filtered_annotations = []
+ for marker in self.results_for_browser:
+ for annot_marker in self.annotations_for_browser:
+ if annot_marker['rs'] == marker['rs']:
+ filtered_annotations.append(annot_marker)
+ break
+ self.annotations_for_browser = filtered_annotations
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
+ else:
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
- with Bench("Exporting Results"):
- export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
- self.mapping_method, self.mapping_scale, self.score_type,
- self.transform, self.covariates, self.n_samples, self.vals_hash)
-
- with Bench("Trimming Markers for Figure"):
- if len(self.qtl_results) > 30000:
- self.qtl_results = trim_markers_for_figure(
- self.qtl_results)
- self.results_for_browser = trim_markers_for_figure(
- self.results_for_browser)
- filtered_annotations = []
- for marker in self.results_for_browser:
- for annot_marker in self.annotations_for_browser:
- if annot_marker['rs'] == marker['rs']:
- filtered_annotations.append(annot_marker)
- break
- self.annotations_for_browser = filtered_annotations
- browser_files = write_input_for_browser(
- self.dataset, self.results_for_browser, self.annotations_for_browser)
- else:
- browser_files = write_input_for_browser(
- self.dataset, self.results_for_browser, self.annotations_for_browser)
-
- with Bench("Trimming Markers for Table"):
- self.trimmed_markers = trim_markers_for_table(results)
+ self.trimmed_markers = trim_markers_for_table(results)
chr_lengths = get_chr_lengths(
self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 5a5ee4ac..0840d4dd 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -62,13 +62,16 @@ def _get_diffs(
):
def __get_file_metadata(file_name: str) -> Dict:
author, resource_id, time_stamp, *_ = file_name.split(".")
-
+ try:
+ author = json.loads(redis_conn.hget("users", author)).get(
+ "full_name"
+ )
+ except (AttributeError, TypeError):
+ author = author
return {
"resource_id": resource_id,
"file_name": file_name,
- "author": json.loads(redis_conn.hget("users", author)).get(
- "full_name"
- ),
+ "author": author,
"time_stamp": time_stamp,
"roles": get_highest_user_access_role(
resource_id=resource_id,
@@ -124,40 +127,7 @@ def edit_probeset(conn, name):
columns=list(probeset_mapping.values()),
where=Probeset(name=name),
)
- json_data = fetchall(
- conn, "metadata_audit", where=MetadataAudit(dataset_id=probeset_.id_)
- )
- Edit = namedtuple("Edit", ["field", "old", "new", "diff"])
- Diff = namedtuple("Diff", ["author", "diff", "timestamp"])
- diff_data = []
- for data in json_data:
- json_ = json.loads(data.json_data)
- timestamp = json_.get("timestamp")
- author = json_.get("author")
- for key, value in json_.items():
- if isinstance(value, dict):
- for field, data_ in value.items():
- diff_data.append(
- Diff(
- author=author,
- diff=Edit(
- field,
- data_.get("old"),
- data_.get("new"),
- "\n".join(
- difflib.ndiff(
- [data_.get("old")], [data_.get("new")]
- )
- ),
- ),
- timestamp=timestamp,
- )
- )
- diff_data_ = None
- if len(diff_data) > 0:
- diff_data_ = groupby(diff_data, lambda x: x.timestamp)
return {
- "diff": diff_data_,
"probeset": probeset_,
}
@@ -227,8 +197,7 @@ def update_phenotype(dataset_id: str, name: str):
diff_data = {}
with database_connection() as conn:
headers = ["Strain Name", "Value", "SE", "Count"] + list(
- get_case_attributes(conn).keys()
- )
+ map(lambda x: x[1], get_case_attributes(conn)))
diff_data = remove_insignificant_edits(
diff_data=csv_diff(
base_csv=(
@@ -552,21 +521,31 @@ def show_diff(name):
@metadata_edit.route("/<dataset_id>/traits/<name>/history")
-def show_history(dataset_id: str, name: str):
+@metadata_edit.route("/probeset/<name>")
+def show_history(dataset_id: str = "", name: str = ""):
diff_data_ = None
with database_connection() as conn:
- publish_xref = fetchone(
- conn=conn,
- table="PublishXRef",
- where=PublishXRef(id_=name, inbred_set_id=dataset_id),
- )
-
- json_data = fetchall(
- conn,
- "metadata_audit",
- where=MetadataAudit(dataset_id=publish_xref.id_),
- )
-
+ json_data = None
+ if dataset_id: # This is a published phenotype
+ json_data = fetchall(
+ conn,
+ "metadata_audit",
+ where=MetadataAudit(dataset_id=fetchone(
+ conn=conn,
+ table="PublishXRef",
+ where=PublishXRef(id_=name, inbred_set_id=dataset_id),
+ ).id_),
+ )
+ else: # This is a probeset
+ json_data = fetchall(
+ conn, "metadata_audit",
+ where=MetadataAudit(dataset_id=fetchone(
+ conn=conn,
+ table="ProbeSet",
+ columns=list(probeset_mapping.values()),
+ where=Probeset(name=name),
+ ).id_)
+ )
Edit = namedtuple("Edit", ["field", "old", "new", "diff"])
Diff = namedtuple("Diff", ["author", "diff", "timestamp"])
diff_data = []
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 7a808ac9..ddf48d90 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -21,9 +21,6 @@ import re
from pprint import pformat as pf
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
def parse(pstring):
"""
@@ -45,7 +42,6 @@ def parse(pstring):
for item in pstring:
splat = re.split(separators, item)
- logger.debug("splat is:", splat)
# splat is an array of 1 if no match, otherwise more than 1
if len(splat) > 1:
@@ -73,7 +69,6 @@ def parse(pstring):
search_term=[item])
items.append(term)
- logger.debug("* items are:", pf(items) + "\n")
return(items)
diff --git a/wqflask/wqflask/partial_correlations_views.py b/wqflask/wqflask/partial_correlations_views.py
index ce5e46e0..358a9d3b 100644
--- a/wqflask/wqflask/partial_correlations_views.py
+++ b/wqflask/wqflask/partial_correlations_views.py
@@ -139,6 +139,7 @@ def target_db_error(args, with_target_db: bool):
def method_error(args):
methods = (
+ "pearson's r", "spearman's rho",
"genetic correlation, pearson's r",
"genetic correlation, spearman's rho",
"sgo literature correlation",
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index eb8879dd..a835f631 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -25,8 +25,6 @@ from utility.authentication_tools import check_resource_availability
from utility.tools import GN2_BASE_URL
from utility.type_checking import is_str
-from utility.logger import getLogger
-logger = getLogger(__name__)
class SearchResultPage:
#maxReturn = 3000
@@ -56,7 +54,6 @@ class SearchResultPage:
rx = re.compile(
r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
if rx.match(search):
- logger.debug("Regex failed search")
self.search_term_exists = False
return
else:
@@ -192,6 +189,8 @@ class SearchResultPage:
trait_dict['additive'] = "N/A" if not result[8] else f"{result[8]:.3f}"
+ trait_dict['trait_info_str'] = trait_info_str(trait_dict, self.dataset.type)
+
# Convert any bytes in dict to a normal utf-8 string
for key in trait_dict.keys():
if isinstance(trait_dict[key], bytes):
@@ -336,6 +335,49 @@ class SearchResultPage:
else:
return None
+def trait_info_str(trait, dataset_type):
+ """Provide a string representation for given trait"""
+ def __trait_desc(trt):
+ if dataset_type == "Geno":
+ return f"Marker: {trait['display_name']}"
+ return trait['description'] or "N/A"
+
+ def __symbol(trt):
+ if dataset_type == "ProbeSet":
+ return (trait['symbol'] or "N/A")[:20]
+
+ def __lrs(trt):
+ if dataset_type == "Geno":
+ return 0
+ else:
+ if trait['lod_score'] != "N/A":
+ return (
+ f"{float(trait['lod_score']):0.3f}" if float(trait['lod_score']) > 0
+ else f"{trait['lod_score']}")
+ else:
+ return "N/A"
+
+ def __lrs_location(trt):
+ if 'lrs_location' in trait:
+ return trait['lrs_location']
+ else:
+ return "N/A"
+
+ def __location(trt):
+ if 'location' in trait:
+ return trait['location']
+ else:
+ return None
+
+ def __mean(trt):
+ if 'mean' in trait:
+ return trait['mean']
+ else:
+ return 0
+
+ return "{}|||{}|||{}|||{}|||{}|||{}|||{}|||{}".format(
+ trait['display_name'], trait['dataset'], __trait_desc(trait), __symbol(trait),
+ __location(trait), __mean(trait), __lrs(trait), __lrs_location(trait))
def get_GO_symbols(a_search):
query = """SELECT genes
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 7fabc3f6..019d4d73 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,3 +1,4 @@
+import datetime
import simplejson as json
from pprint import pformat as pf
@@ -5,32 +6,43 @@ from functools import cmp_to_key
from base.trait import create_trait
from base import data_set
-
def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
trait_name = targs['trait_display_name']
- meta_data = get_export_metadata(targs['trait_id'], targs['dataset'])
+ meta_data = get_export_metadata(targs)
final_sample_data = meta_data
- column_headers = ["Name", "Value"]
+ column_headers = ["Index", "Name", "Value"]
+ attr_pos = 2
if any(sample["se"] for sample in sample_data['primary_samples']):
column_headers.append("SE")
+ attr_pos = 3
if any(sample["num_cases"] for sample in sample_data['primary_samples']):
column_headers.append("N")
+ attr_pos = 4
+
+ for key in sample_data["primary_samples"][0].keys():
+ if key not in ["name", "value", "se", "num_cases"]:
+ column_headers.append(key)
final_sample_data.append(column_headers)
for sample_group in ['primary_samples', 'other_samples']:
- for row in sample_data[sample_group]:
- sorted_row = dict_to_sorted_list(row)
+ for i, row in enumerate(sample_data[sample_group]):
+ sorted_row = [i + 1] + dict_to_sorted_list(row)[:attr_pos]
+ for attr in sample_data['attributes']:
+ sorted_row.append(row[attr])
final_sample_data.append(sorted_row)
return trait_name, final_sample_data
-def get_export_metadata(trait_id, dataset_name):
+def get_export_metadata(trait_metadata):
+
+ trait_id, display_name, dataset_name = trait_metadata['trait_id'], trait_metadata['trait_display_name'], trait_metadata['dataset']
+
dataset = data_set.create_dataset(dataset_name)
this_trait = create_trait(dataset=dataset,
name=trait_id,
@@ -39,30 +51,34 @@ def get_export_metadata(trait_id, dataset_name):
metadata = []
if dataset.type == "Publish":
- metadata.append(["Phenotype ID: " + trait_id])
- metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
+ metadata.append(["Phenotype ID:", display_name])
+ metadata.append(["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=" + \
trait_id + "&dataset=" + dataset_name])
- metadata.append(["Group: " + dataset.group.name])
+ metadata.append(["Group: ", dataset.group.name])
metadata.append(
- ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
+ ["Phenotype: ", this_trait.description_display.replace(",", "\",\"")])
metadata.append(
- ["Authors: " + (this_trait.authors if this_trait.authors else "N/A")])
+ ["Authors: ", (this_trait.authors if this_trait.authors else "N/A")])
metadata.append(
- ["Title: " + (this_trait.title if this_trait.title else "N/A")])
+ ["Title: ", (this_trait.title if this_trait.title else "N/A")])
metadata.append(
- ["Journal: " + (this_trait.journal if this_trait.journal else "N/A")])
+ ["Journal: ", (this_trait.journal if this_trait.journal else "N/A")])
+
metadata.append(
- ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
+ ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
else:
- metadata.append(["Record ID: " + trait_id])
- metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
+ metadata.append(["Record ID: ", trait_id])
+ metadata.append(["Trait URL: ", "http://genenetwork.org/show_trait?trait_id=" + \
trait_id + "&dataset=" + dataset_name])
if this_trait.symbol:
- metadata.append(["Symbol: " + this_trait.symbol])
- metadata.append(["Dataset: " + dataset.name])
- metadata.append(["Group: " + dataset.group.name])
+ metadata.append(["Symbol: ", this_trait.symbol])
+ metadata.append(["Dataset: ", dataset.name])
+ metadata.append(["Group: ", dataset.group.name])
+ metadata.append(
+ ["Export Date: ", datetime.datetime.now().strftime("%B %d, %Y")])
+ metadata.append(
+ ["Export Time: ", datetime.datetime.now().strftime("%H:%M GMT")])
- metadata.append([])
return metadata
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d9821d9c..c1d9ad84 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -550,21 +550,21 @@ def get_max_digits(trait_vals):
return max_digits
-def quantile_normalize_vals(sample_groups, trait_vals):
- def normf(trait_vals):
- ranked_vals = ss.rankdata(trait_vals)
- p_list = []
- for i, val in enumerate(trait_vals):
- p_list.append(((i + 1) - 0.5) / len(trait_vals))
+def normf(trait_vals):
+ ranked_vals = ss.rankdata(trait_vals)
+ p_list = []
+ for i, val in enumerate(trait_vals):
+ p_list.append(((i + 1) - 0.5) / len(trait_vals))
- z = ss.norm.ppf(p_list)
+ z = ss.norm.ppf(p_list)
- normed_vals = []
- for rank in ranked_vals:
- normed_vals.append("%0.3f" % z[int(rank) - 1])
+ normed_vals = []
+ for rank in ranked_vals:
+ normed_vals.append("%0.3f" % z[int(rank) - 1])
- return normed_vals
+ return normed_vals
+def quantile_normalize_vals(sample_groups, trait_vals):
qnorm_by_group = []
for i, sample_type in enumerate(sample_groups):
qnorm_vals = normf(trait_vals[i])
diff --git a/wqflask/wqflask/static/new/javascript/scatterplot.js b/wqflask/wqflask/static/new/javascript/scatterplot.js
index d7f2a4a5..3fea0503 100644
--- a/wqflask/wqflask/static/new/javascript/scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/scatterplot.js
@@ -67,15 +67,14 @@ scatterplot = function() {
x = data.data[xvar];
y = data.data[yvar];
}
- console.log("x:", x);
- console.log("y:", y);
+
indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null;
indID = indID != null ? indID : (function() {
_results = [];
for (var _i = 1, _ref1 = x.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); }
return _results;
}).apply(this);
- console.log("indID:", indID);
+
group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() {
var _j, _len, _results1;
_results1 = [];
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 1b79e261..e9ea5afb 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1113,7 +1113,7 @@ switchQNormData = function() {
};
$('#qnorm').click(switchQNormData);
-getSampleTableData = function(table_name) {
+getSampleTableData = function(table_name, attributes_as_list) {
var samples;
samples = [];
@@ -1123,20 +1123,29 @@ getSampleTableData = function(table_name) {
if ($('#' + table_name).length){
tableApi = $('#' + table_name).DataTable();
sample_vals = [];
+ attr_col = 4
name_nodes = tableApi.column(2).nodes().to$();
val_nodes = tableApi.column(3).nodes().to$();
if (js_data.se_exists){
var_nodes = tableApi.column(5).nodes().to$();
+ attr_col = 6
if (js_data.has_num_cases) {
n_nodes = tableApi.column(6).nodes().to$();
+ attr_col = 7
}
} else {
if (js_data.has_num_cases){
n_nodes = tableApi.column(4).nodes().to$();
+ attr_col = 5
}
}
+ attribute_nodes = []
+ for (_i = 0; _i < attributes_as_list.length; _i++){
+ attribute_nodes.push(table_api.column(attr_col + _i).nodes().to$())
+ }
+
for (_j = 0; _j < val_nodes.length; _j++){
sample_val = val_nodes[_j].childNodes[0].value
sample_name = $.trim(name_nodes[_j].childNodes[0].textContent)
@@ -1164,12 +1173,18 @@ getSampleTableData = function(table_name) {
sample_n = null;
}
}
+
row_dict = {
name: sample_name,
value: sample_val,
se: sample_var,
num_cases: sample_n
}
+
+ for (_k = 0; _k < attribute_nodes.length; _k++){
+ row_dict[attributes_as_list[_k]] = attribute_nodes[_k][_j].textContent;
+ }
+
samples.push(row_dict)
}
}
@@ -1179,9 +1194,15 @@ getSampleTableData = function(table_name) {
};
exportSampleTableData = function() {
var format, json_sample_data, sample_data;
+
+ var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
+ return js_data.attributes[key].name;
+ });
+
sample_data = {};
- sample_data.primary_samples = getSampleTableData('samples_primary');
- sample_data.other_samples = getSampleTableData('samples_other');
+ sample_data.primary_samples = getSampleTableData('samples_primary', attributes_as_list);
+ sample_data.other_samples = getSampleTableData('samples_other', attributes_as_list);
+ sample_data.attributes = attributes_as_list;
json_sample_data = JSON.stringify(sample_data);
$('input[name=export_data]').val(json_sample_data);
format = $('input[name=export_format]').val();
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
deleted file mode 100644
index b21a88cc..00000000
--- a/wqflask/wqflask/submit_bnw.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from base.trait import GeneralTrait
-from base import data_set
-from utility import helper_functions
-
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
-
-def get_bnw_input(start_vars):
- logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/templates/bnw_page.html b/wqflask/wqflask/templates/bnw_page.html
index 317b4bd7..a3e090a5 100644
--- a/wqflask/wqflask/templates/bnw_page.html
+++ b/wqflask/wqflask/templates/bnw_page.html
@@ -1,5 +1,5 @@
<title>Opening BNW</title>
-<form method="post" action="https://bnw.genenetwork.org/sourcecodes/bn_genenet.php" name="bnwform" id="bnwform">
+<form method="post" action="http://bnw.genenetwork.org/sourcecodes/bn_genenet.php" name="bnwform" id="bnwform">
<input type="hidden" name="My_Genenet" value="{{ form_value }}">
</form>
<script type="text/javascript">
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index a9c84cb0..4b63453e 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -20,7 +20,7 @@
<h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
<div class="tool-button-container">
- <form id="collection_form" action="/delete" method="post" target="_blank">
+ <form id="collection_form" action="/delete" method="post">
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
<input type="hidden" name="collection_name" id="collection_name" value="{{ uc.name }}" />
<input type="hidden" name="tool_used" value="" />
@@ -309,13 +309,14 @@
submit_special = function(url) {
$("#collection_form").attr("action", url);
- e.stopImmediatePropagation();
- return $("#collection_form").submit();
+ $("#collection_form").attr('target', '_blank').submit();
+ return false;
};
$("#delete").on("click", function() {
url = $(this).data("url")
- return submit_special(url)
+ $("#collection_form").attr("action", url);
+ return $("#collection_form").removeAttr('target').submit();
});
$("#remove").on("click", function() {
@@ -324,8 +325,8 @@
return $(this).val();
}).get();
$("#trait_list").val(traits)
-
- return submit_special(url)
+ $("#collection_form").attr("action", url);
+ return $("#collection_form").removeAttr('target').submit();
});
$("#change_collection_name").on("click", function() {
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index e90accf2..d392be34 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -11,7 +11,7 @@
<div class="container" width="100%">
<h1>Correlation Matrix</h1>
-<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from -0.4 to -1.0 range from dark blue to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div>
+<div style="width: 100%; max-width: 850px;">Select any cell in the matrix to generate a <b>scatter plot.</b><br><b>Lower left</b> cells list Pearson product-moment correlations; <b>upper right</b> cells list Spearman rank order correlations. Each cell also contains the <b><i>n</i> of cases</b> in parenthesis. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from –0.4 to –1.0 range from dark blue to white.</div>
<hr style="height: 1px; background-color: #A9A9A9;">
{% if lowest_overlap < 8 %}
<div style="margin-bottom: 10px;"><i><font style="color: red;">Caution</font>: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</i></div>
@@ -37,7 +37,7 @@
<tr>
<td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td>
<td align="right" style="padding-right: 4px;" >
- <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 14px; font-style: Bold;"><b>Trait {{ loop.index }}: {{ trait.dataset.name }}&nbsp;&nbsp;{{ trait.name }}</b></font></a>
+ <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 14px; font-style: Bold;"><b>{{ loop.index }}: {{ trait.dataset.name }}&nbsp;&nbsp;{{ trait.name }}</b></font></a>
<div class="shortName">{% if trait.dataset.type == "ProbeSet" %}Gene Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Trait Symbol: {{ trait.post_publication_abbreviation }}{% elif trait.dataset.type == "Geno" %}Genotype{% endif %} </div>
<div class="verboseName" style="display: none;">
{% if trait.dataset.type == "ProbeSet" %}
@@ -56,7 +56,7 @@
{% if result[1] == 0 %}
<td nowrap="ON" align="middle" bgcolor="#eeeeee" style="padding: 3px; line-height: 1.1;">N/A</td>
{% else %}
- <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?method={% if loop.index > outer_loop %}spearman{% else %}pearson{% endif %}&dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+ <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?method={% if loop.index > outer_loop %}spearman{% else %}pearson{% endif %}&dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><span class="corr_value" style="font-size: 14px; color: #3071a9; font-weight: bold;">{{ '%0.2f' % result[1] }}</span><br><span class="corr_value" style="font-size: 12px; color: #3071a9; font-weight: bold;">({{ result[2] }})</span></a></td>
{% endif %}
{% endif %}
{% endfor %}
@@ -72,12 +72,11 @@
</form>
<br>
-<div style="margin:20x;">
+{% if pca_works == "True" %}
+<div>
{% include 'pca_scree_plot.html' %}
-
</div>
-{% if pca_works == "True" %}
<h2>PCA Traits</h2>
<div style="margin-bottom: 20px; overflow:hidden; width: 450px;">
<table id="pca_table" class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
diff --git a/wqflask/wqflask/templates/edit_history.html b/wqflask/wqflask/templates/edit_history.html
index f181fd87..7538324b 100644
--- a/wqflask/wqflask/templates/edit_history.html
+++ b/wqflask/wqflask/templates/edit_history.html
@@ -9,7 +9,7 @@
<!-- Start of body -->
<div class="container">
- <h1>Edit history: {{}}</h1>
+ <h1>History</h1>
{% if diff %}
<div class="row">
<table id="history" class="table-responsive table-hover table-striped cell-border">
diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index a0b7a6eb..feeadadb 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -17,53 +17,6 @@
<small><a href="{{url_for('metadata_edit.show_history', dataset_id=dataset_id, name=name)}}" target="_blank">[View History]</a></small>
</div>
- {% if diff %}
-
- <div class="container text-left">
- <details class="col-md-12 col-lg-20 col-lg-22">
- <summary>
- <h2>Update History</h2>
- </summary>
- <table class="table">
- <tbody>
- <tr>
- <th>Timestamp</th>
- <th>Editor</th>
- <th>Field</th>
- <th>Diff</th>
- </tr>
- {% set ns = namespace(display_cell=True) %}
-
- {% for timestamp, group in diff %}
- {% set ns.display_cell = True %}
- {% for i in group %}
- <tr>
- {% if ns.display_cell and i.timestamp == timestamp %}
-
- {% set author = i.author %}
- {% set timestamp_ = i.timestamp %}
-
- {% else %}
-
- {% set author = "" %}
- {% set timestamp_ = "" %}
-
- {% endif %}
- <td>{{ timestamp_ }}</td>
- <td>{{ author }}</td>
- <td>{{ i.diff.field }}</td>
- <td><pre>{{ i.diff.diff }}</pre></td>
- {% set ns.display_cell = False %}
- </tr>
- {% endfor %}
- {% endfor %}
- </tbody>
- </table>
- </details>
-
- </div>
-
- {% endif %}
<form id="edit-form" class="container form-horizontal" method="post" action="/datasets/{{dataset_id}}/traits/{{ publish_xref.id_ }}?resource-id={{ resource_id }}" enctype='multipart/form-data'>
<div class="form-group">
<div class="controls left-block col-sm-8 col-lg-8" style="width: max-content;">
diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html
index ab91b701..6c068e63 100644
--- a/wqflask/wqflask/templates/edit_probeset.html
+++ b/wqflask/wqflask/templates/edit_probeset.html
@@ -2,226 +2,187 @@
{% block title %}Trait Submission{% endblock %}
{% block content %}
<!-- Start of body -->
-Edit Trait for Probeset
-Submit Trait | Reset
-
-{% if diff %}
-
<div class="container">
- <details class="col-sm-12 col-md-10 col-lg-12">
- <summary>
- <h2>Update History</h2>
- </summary>
- <table class="table">
- <tbody>
- <tr>
- <th>Timestamp</th>
- <th>Editor</th>
- <th>Field</th>
- <th>Diff</th>
- </tr>
- {% set ns = namespace(display_cell=True) %}
-
- {% for timestamp, group in diff %}
- {% set ns.display_cell = True %}
- {% for i in group %}
- <tr>
- {% if ns.display_cell and i.timestamp == timestamp %}
-
- {% set author = i.author %}
- {% set timestamp_ = i.timestamp %}
-
- {% else %}
-
- {% set author = "" %}
- {% set timestamp_ = "" %}
-
- {% endif %}
- <td>{{ timestamp_ }}</td>
- <td>{{ author }}</td>
- <td>{{ i.diff.field }}</td>
- <td><pre>{{ i.diff.diff }}</pre></td>
- {% set ns.display_cell = False %}
- </tr>
- {% endfor %}
- {% endfor %}
- </tbody>
- </table>
- </details>
-
+ <div class="page-header text-left">
+ <h1>Probeset Editing Form: {{ probeset.name }}</h1>
+ <small><a href="{{url_for('metadata_edit.show_history', name=name)}}" target="_blank">[View History]</a></small>
+ </div>
+ <form id="edit-form" class="container form-horizontal" method="post" action="/datasets/traits/{{ name }}?resource-id={{ resource_id }}" enctype='multipart/form-data'>
+ <div class="form-group">
+ <div class="controls left-block col-sm-8 col-lg-8" style="width: max-content;">
+ <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
+ <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-success form-control col-xs-2 changed" value="Submit Change">
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="symbol" class="col-sm-3 col-lg-2 control-label text-left">Symbol</label>
+ <div class="col-sm-4">
+ <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea>
+ <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="description" class="col-sm-3 col-lg-2 control-label text-left">Description</label>
+ <div class="col-sm-4">
+ <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea>
+ <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_target_description" class="col-sm-3 col-lg-2 control-label text-left">Probe Target Description</label>
+ <div class="col-sm-4">
+ <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea>
+ <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="chr" class="col-sm-3 col-lg-2 control-label text-left">Chr</label>
+ <div class="col-sm-4">
+ <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea>
+ <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="mb" class="col-sm-3 col-lg-2 control-label text-left">Mb</label>
+ <div class="col-sm-4">
+ <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea>
+ <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="alias" class="col-sm-3 col-lg-2 control-label text-left">
+ Alias:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea>
+ <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="geneid" class="col-sm-3 col-lg-2 control-label text-left">
+ Gene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea>
+ <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="homologeneid" class="col-sm-3 col-lg-2 control-label text-left">
+ Homolegene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
+ <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="unigeneid" class="col-sm-3 col-lg-2 control-label text-left">
+ Unigene Id:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea>
+ <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="omim" class="col-sm-3 col-lg-2 control-label text-left">OMIM</label>
+ <div class="col-sm-4">
+ <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea>
+ <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="refseq_transcriptid" class="col-sm-3 col-lg-2 control-label text-left">
+ Refseq TranscriptId:
+ </label>
+ <div class="col-sm-4">
+ <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea>
+ <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="blatseq" class="col-sm-3 col-lg-2 control-label text-left">BlatSeq</label>
+ <div class="col-sm-8">
+ <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea>
+ <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="targetseq" class="col-sm-3 col-lg-2 control-label text-left">TargetSeq</label>
+ <div class="col-sm-8">
+ <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea>
+ <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="strand_probe" class="col-sm-3 col-lg-2 control-label text-left">Strand Probe</label>
+ <div class="col-sm-2">
+ <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea>
+ <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_target_region" class="col-sm-3 col-lg-2 control-label text-left">Probe Set Target Region</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea>
+ <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_specificity" class="col-sm-3 col-lg-2 control-label text-left">Probeset Specificity</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea>
+ <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_score" class="col-sm-3 col-lg-2 control-label text-left">Probeset Blat Score</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_mb_start" class="col-sm-3 col-lg-2 control-label text-left">
+ Probeset Blat Mb Start</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_blat_mb_end" class="col-sm-3 col-lg-2 control-label text-left">Probeset Blat Mb End</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea>
+ <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_strand" class="col-sm-3 col-lg-2 control-label text-left">Probeset Strand</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea>
+ <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="probe_set_note_by_rw" class="col-sm-3 col-lg-2 control-label text-left">Probeset Strand</label>
+ <div class="col-sm-8">
+ <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea>
+ <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/>
+ </div>
+ </div>
+ <div class="controls left-block col-sm-8 col-lg-8" style="width: max-content;">
+ <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+ <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
+ <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-success form-control col-xs-2 changed" value="Submit Change">
+ </div>
+ </form>
</div>
-{% endif %}
-
-<form id="edit-form" class="form-horizontal" method="post" action="/datasets/traits/{{ name }}?resource-id={{ resource_id }}">
- <h2 class="text-center">Probeset Information:</h2>
- <div class="form-group">
- <label for="symbol" class="col-sm-2 control-label">Symbol:</label>
- <div class="col-sm-4">
- <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea>
- <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="description" class="col-sm-2 control-label">Description:</label>
- <div class="col-sm-5">
- <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea>
- <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_target_description" class="col-sm-2 control-label">Probe Target Description:</label>
- <div class="col-sm-4">
- <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea>
- <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="chr" class="col-sm-2 control-label">Chr:</label>
- <div class="col-sm-4">
- <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea>
- <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="mb" class="col-sm-2 control-label">Mb:</label>
- <div class="col-sm-4">
- <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea>
- <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="alias" class="col-sm-2 control-label">
- Alias:
- </label>
- <div class="col-sm-4">
- <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea>
- <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="geneid" class="col-sm-2 control-label">
- Gene Id:
- </label>
- <div class="col-sm-4">
- <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea>
- <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="homologeneid" class="col-sm-2 control-label">
- Homolegene Id:
- </label>
- <div class="col-sm-4">
- <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
- <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="unigeneid" class="col-sm-2 control-label">
- Unigene Id:
- </label>
- <div class="col-sm-4">
- <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea>
- <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="omim" class="col-sm-2 control-label">OMIM:</label>
- <div class="col-sm-4">
- <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea>
- <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="refseq_transcriptid" class="col-sm-2 control-label">
- Refseq TranscriptId:
- </label>
- <div class="col-sm-4">
- <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea>
- <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="blatseq" class="col-sm-2 control-label">BlatSeq:</label>
- <div class="col-sm-8">
- <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea>
- <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="targetseq" class="col-sm-2 control-label">TargetSeq:</label>
- <div class="col-sm-8">
- <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea>
- <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="strand_probe" class="col-sm-2 control-label">Strand Probe:</label>
- <div class="col-sm-2">
- <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea>
- <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_target_region" class="col-sm-2 control-label">Probe Set Target Region:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea>
- <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_specificity" class="col-sm-2 control-label">Probeset Specificity:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea>
- <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_blat_score" class="col-sm-2 control-label">Probeset Blat Score:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea>
- <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_blat_mb_start" class="col-sm-2 control-label">
- Probeset Blat Mb Start:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea>
- <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_blat_mb_end" class="col-sm-2 control-label">Probeset Blat Mb End:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea>
- <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_strand" class="col-sm-2 control-label">Probeset Strand:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea>
- <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/>
- </div>
- </div>
- <div class="form-group">
- <label for="probe_set_note_by_rw" class="col-sm-2 control-label">Probeset Strand:</label>
- <div class="col-sm-8">
- <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea>
- <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/>
- </div>
- </div>
- <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
- <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
- <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
- <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
- <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
- <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
- </div>
-</form>
-
{%endblock%}
{% block js %}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index af0e2fa2..2b72d6b2 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -59,7 +59,7 @@
<div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
<section id="search">
<div class="page-header">
- <h2>Select and search</h2>
+ <h2>Select and Search</h2>
</div>
<form method="get" action="/search" target="_blank" name="SEARCHFORM",
data-gn_server_url="{{gn_server_url}}">
@@ -148,7 +148,7 @@
<input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
</div>
<div class="col-2 controls" style="padding-left: 20px;">
- <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
+ <button type="button" id="make_default" class="btn btn-primary form-control">Save Settings</button>
</div>
</div>
</div>
@@ -164,7 +164,7 @@
</section>
<section id="advanced">
<div class="page-header">
- <h2>Advanced commands</h2>
+ <h2>Advanced Commands</h2>
</div>
<p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p>
diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html b/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
index fc60aa3e..fe7f8cd4 100644
--- a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
+++ b/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
@@ -29,6 +29,8 @@
{%endwith%}
<input type="hidden" value="{{trait_list_str}}" name="trait_list">
+ <h1>Partial Correlation</h1>
+ <div>Please select one primary trait, one to three control traits, and at least one target trait.</div>
<br />
<table id="pcorrs_traits_table"
class="table-hover table-striped cell-border dataTable"
@@ -106,16 +108,8 @@
<label for="corr-method-input" class="form-label">Compute</label>
<select id="corr-method-input" required="required" name="method"
class="form-control">
- <option value="Genetic Correlation, Pearson's r">
- Genetic Correlation, Pearson's r</option>
- <option value="Genetic Correlation, Spearman's rho">
- Genetic Correlation, Spearman's rho</option>
- <option value="SGO Literature Correlation">
- SGO Literature Correlation</option>
- <option value="Tissue Correlation, Pearson's r">
- Tissue Correlation, Pearson's r</option>
- <option value="Tissue Correlation, Spearman's rho">
- Tissue Correlation, Spearman's rho</option>
+ <option value="Pearson's r">Pearson's r</option>
+ <option value="Spearman's rho">Spearman's rho</option>
</select>
</div>
diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/wqflask/wqflask/templates/pca_scree_plot.html
index a9a6e761..74eb2c15 100644
--- a/wqflask/wqflask/templates/pca_scree_plot.html
+++ b/wqflask/wqflask/templates/pca_scree_plot.html
@@ -9,7 +9,8 @@
<body>
<div>
-
+ <h2>Scree Plot</h2>
+ <div style="padding-bottom: 10px;">Review more on <a href="https://en.wikipedia.org/wiki/Scree_plot">scree plots</a>.</div>
<div id="scree_plot" style="width:700px;height:600px;"></div>
</div>
</body>
@@ -21,19 +22,9 @@ let { x_coord, y_coord } = js_data["scree_data"]
const layout = {
-
- title: {
- text: "<b>PCA Scree Plot</b>",
- font: {
- "size": 24,
- "family": "Arial",
- "color": "#000000"
- }
- },
-
yaxis: {
title: {
- text: "Percent of total variance %",
+ text: "% of Variance",
font: {
"size": 18,
"color": ""
@@ -44,7 +35,7 @@ const layout = {
xaxis: {
title: {
- text: "PCA components",
+ text: "Principal Components",
font: {
"size": 18,
"color": ""
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index bd832420..9cbff200 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -11,49 +11,54 @@
{% endblock %}
{% block content %}
<!-- Start of body -->
- <div style="padding-left: 10px;">
+ <div style="margin-left: 20px;">
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
<div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
<!-- Need to customize text more for other types of searches -->
- <p><b>Search Results:</b> We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
- to find all records
+ <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+ <br>
+ to find all records
{% if go_term is not none %}
- with <u>Gene Ontology ID</u> <strong>GO:{{ go_term }}</strong>.
+ with <span style="font-family: Courier New"><b>Gene Ontology ID</b></span> <strong>GO:{{ go_term }}</strong>.
{% else %}
{% for word in search_terms %}
{% if word.key|lower == "rif" %}
- with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>GeneRIF</b></span> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.key|lower == "go" %}
- with <u>Gene Ontology ID</u> <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>Gene Ontology ID</b></span> <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.key|lower == "wiki" %}
- with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>GeneWiki</b></span> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.key|lower == "mean" %}
- with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>mean</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.key|lower == "range" %}
- with <u>RANGE</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>RANGE</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.key|lower == "lrs" or word.key|lower == "lod" or word.key|lower == "translrs" or word.key|lower == "cislrs" or word.key|lower == "translod" or word.key|lower == "cislod" %}
{% if word.search_term|length == 1 %}
- with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.search_term|length == 2 %}
- with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>{{ word.key|upper }}</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.search_term|length == 3 %}
- with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>{{ word.key|upper }}</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if loop.last %}{% else %} and {% endif %}
{% elif word.search_term|length == 4 %}
- with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[3] }}</strong> with an exclusion zone of <strong>{{ word.search_term[2] }}</strong> Mb
+ with <span style="font-family: Courier New"><b>{{ word.key|upper }}</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[3] }}</strong> with an exclusion zone of <strong>{{ word.search_term[2] }}</strong> Mb
{% elif word.search_term|length == 5 %}
- with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
+ with <span style="font-family: Courier New"><b>{{ word.key|upper }}</b></span> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}{% else %} and {% endif %}
{% endif %}
{% elif word.key|lower == "position" or word.key|lower == "mb" %}
- with <u>target genes</u> on chromosome <strong>{% if (word.search_term[0]|lower).split('chr')|length > 1 %}{{ (word.search_term[0]|lower).split('chr')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
+ with <u>target genes</u> on chromosome <strong>{% if (word.search_term[0]|lower).split('chr')|length > 1 %}{{ (word.search_term[0]|lower).split('chr')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}{% else %} and {% endif %}
{% else %}
- {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>{{ word.search_term[0] }}</b>{% if loop.last %}{% else %} and {% endif %}{% endif %}
+ {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match: {% endif %}<b>{{ word.search_term[0] }}</b>{% if loop.last %}{% else %} and {% endif %}{% endif %}
{% endif %}
{% endfor %}
{% endif %}
<br>
- A total of {{ results|count }} records were found.
+ {% if results|count > 0 %}
+ <b>{{ results|count }}</b> record{% if results|count > 1 %}s{% else %}{% endif %} found
+ {% else %}
+ No (<b>0</b>) records found for this search. Modify your search, check target dataset, or use <b>Search All</b> above.
+ {% endif %}
</p>
{% if results|count > 0 %}
@@ -69,7 +74,7 @@
{% if too_many_results %}
<p>Your search generated over 50000 results. Please modify your search to generate 50000 or fewer matches.</p>
{% else %}
- <div style="min-width: 950px;">
+ <div style="min-width: 1050px;">
<form id="trait_submission_form" target="_blank" action="/corr_matrix" method="post">
<input type="hidden" name="tool_used" value="" />
<input type="hidden" name="form_url" value="" />
@@ -142,7 +147,7 @@
{% endif %}
{% else %}
<br>
- <button type="button" onclick="window.location.href='/'">Return To Index Page</button>
+ <button type="button" onclick="window.location.href='/'">Return To Search</button>
{% endif %}
</div>
<div id="myModal"></div>
@@ -164,6 +169,7 @@
<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>
<script language="javascript" type="text/javascript" src="/static/new/javascript/create_datatable.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/partial_correlations.js"></script>
<script type='text/javascript'>
var traitsJson = {{ trait_list|safe }};
@@ -188,13 +194,52 @@
var widthChange = 0; //ZS: For storing the change in width so overall table width can be adjusted by that amount
columnDefs = [
- {
- 'data': null,
- 'width': "5px",
- 'orderDataType': "dom-checkbox",
- 'targets': 0,
- 'render': function(data) {
- return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
+ {
+ 'data': null,
+ 'width': "5px",
+ 'orderDataType': "dom-checkbox",
+ 'targets': 0,
+ 'render': function(data) {
+ return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '" data-trait-info="' + data.trait_info_str + '">'
+ }
+ },
+ {
+ 'title': "Index",
+ 'type': "natural",
+ 'width': "35px",
+ "searchable": false,
+ "orderable": false,
+ 'targets': 1,
+ 'data': "index"
+ }
+ {% if dataset.type == 'ProbeSet' %},
+ {
+ 'title': "Record",
+ 'type': "natural-minus-na",
+ 'data': null,
+ 'width': "{{ max_widths.display_name * 8 }}px",
+ 'targets': 2,
+ 'render': function(data) {
+ return '<a target="_blank" href="/show_trait?trait_id=' + data.display_name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
+ }
+ },
+ {
+ 'title': "Symbol",
+ 'type': "natural",
+ 'width': "{{ max_widths.symbol * 8 }}px",
+ 'targets': 3,
+ 'data': "symbol"
+ },
+ {
+ 'title': "Description",
+ 'type': "natural",
+ 'data': null,
+ 'targets': 4,
+ 'render': function(data) {
+ try {
+ return decodeURIComponent(escape(data.description))
+ } catch(err){
+ return escape(data.description)
}
},
{
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 2f98f14e..69fb5d3b 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -119,6 +119,10 @@
<div class="col-xs-3 controls">
<input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
</div>
+
+ <div class="col-xs-3 controls">
+ <input type="button" class="btn test_corr_compute submit_special btn-success" data-url="/test_corr_compute" title="Compute Correlation" value="Test Compute">
+ </div>
</div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html
index c3927495..c6d1476c 100644
--- a/wqflask/wqflask/templates/tool_buttons.html
+++ b/wqflask/wqflask/templates/tool_buttons.html
@@ -30,10 +30,6 @@
MultiMap
</button>
-<button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
- Comparison Bar Chart
-</button>
-
<button id="partial-correlations"
class="btn btn-primary submit_special"
data-url="{{url_for('partial_correlations')}}"
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 2e467dc8..f132e2c6 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -5,11 +5,6 @@ from base.data_set import create_dataset
from base.trait import GeneralTrait
from db import webqtlDatabaseFunction
-from utility.benchmark import Bench
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
class GSearch:
@@ -46,19 +41,15 @@ class GSearch:
ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
LIMIT 6000
""" % (self.terms)
- with Bench("Running query"):
- logger.sql(sql)
- re = g.db.execute(sql).fetchall()
+ re = g.db.execute(sql).fetchall()
self.trait_list = []
- with Bench("Creating trait objects"):
- for line in re:
- dataset = create_dataset(
- line[3], "ProbeSet", get_samplelist=False)
- trait_id = line[4]
- # with Bench("Building trait object"):
- this_trait = GeneralTrait(
- dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
- self.trait_list.append(this_trait)
+ for line in re:
+ dataset = create_dataset(
+ line[3], "ProbeSet", get_samplelist=False)
+ trait_id = line[4]
+ this_trait = GeneralTrait(
+ dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ self.trait_list.append(this_trait)
elif self.type == "phenotype":
sql = """
@@ -92,16 +83,14 @@ class GSearch:
ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
LIMIT 6000
""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
- logger.sql(sql)
re = g.db.execute(sql).fetchall()
self.trait_list = []
- with Bench("Creating trait objects"):
- for line in re:
- dataset = create_dataset(line[2], "Publish")
- trait_id = line[3]
- this_trait = GeneralTrait(
- dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
- self.trait_list.append(this_trait)
+ for line in re:
+ dataset = create_dataset(line[2], "Publish")
+ trait_id = line[3]
+ this_trait = GeneralTrait(
+ dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ self.trait_list.append(this_trait)
self.results = self.convert_to_json()
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 45a12f77..ae61edb0 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -2,7 +2,6 @@ import os
import hashlib
import datetime
import time
-import logging
import uuid
import hmac
import base64
@@ -21,9 +20,6 @@ from utility import hmac
from utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
Redis = get_redis_conn()
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
from smtplib import SMTP
from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
@@ -129,7 +125,6 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.login(SMTP_USERNAME, SMTP_PASSWORD)
server.sendmail(fromaddr, toaddr, msg)
server.quit()
- logger.info("Successfully sent email to " + toaddr)
def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject="GeneNetwork e-mail verification"):
@@ -346,7 +341,6 @@ def get_github_user_details(access_token):
@app.route("/n/logout")
def logout():
- logger.debug("Logging out...")
UserSession().delete_session()
flash("You are now logged out. We hope you come back soon!")
response = make_response(redirect(url_for('index_page')))
@@ -404,7 +398,6 @@ def forgot_password_submit():
email_address = params['email_address']
next_page = None
if email_address != "":
- logger.debug("Wants to send password E-mail to ", email_address)
user_details = get_user_by_unique_column(
"email_address", email_address)
if user_details:
@@ -425,8 +418,6 @@ def forgot_password_submit():
@app.route("/n/password_reset", methods=['GET'])
def password_reset():
"""Entry point after user clicks link in E-mail"""
- logger.debug("in password_reset request.url is:", request.url)
-
verification_code = request.args.get('code')
hmac = request.args.get('hm')
@@ -446,8 +437,6 @@ def password_reset():
@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
- logger.debug("in password_reset request.url is:", request.url)
-
errors = []
user_email = request.form['user_encode']
user_id = get_user_id("email_address", user_email)
@@ -515,7 +504,6 @@ def register():
params = params.to_dict(flat=True)
if params:
- logger.debug("Attempting to register the user...")
errors = register_user(params)
if len(errors) == 0:
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 00b268a7..1ed5b802 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -13,8 +13,6 @@ 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
Redis = get_redis_conn()
-from utility.logger import getLogger
-logger = getLogger(__name__)
THREE_DAYS = 60 * 60 * 24 * 3
THIRTY_DAYS = 60 * 60 * 24 * 30
@@ -54,7 +52,6 @@ def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = hmac.hmac_creation(the_uuid)
uuid_signed = the_uuid + ":" + signature
- logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a371d983..acd65587 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -64,6 +64,7 @@ from wqflask.marker_regression import display_mapping_results
from wqflask.network_graph import network_graph
from wqflask.correlation.show_corr_results import set_template_vars
from wqflask.correlation.correlation_gn3_api import compute_correlation
+from wqflask.correlation.rust_correlation import compute_correlation_rust
from wqflask.correlation_matrix import show_corr_matrix
from wqflask.correlation import corr_scatter_plot
# from wqflask.wgcna import wgcna_analysis
@@ -94,37 +95,34 @@ from utility.redis_tools import get_redis_conn
from base.webqtlConfig import GENERATED_IMAGE_DIR, DEFAULT_PRIVILEGES
-from utility.benchmark import Bench
from pprint import pformat as pf
-import utility.logger
-
Redis = get_redis_conn()
-logger = utility.logger.getLogger(__name__)
-
@app.before_request
def connect_db():
db = getattr(g, '_database', None)
if request.endpoint not in ("static", "js") and db is None:
- logger.debug(
- f"Creating a database connection\n"
- f"\t\tfor request: {request.endpoint}")
- g.db = g._database = sqlalchemy.create_engine(
- SQL_URI, encoding="latin1")
+ try:
+ g.db = sqlalchemy.create_engine(
+ SQL_URI, encoding="latin1")
+ except Exception: # Capture everything
+ app.logger.error(f"DATABASE: Error creating connection for: {request.endpoint}")
@app.teardown_appcontext
def shutdown_session(exception=None):
db = getattr(g, '_database', None)
if db is not None:
- logger.debug(f"Removing the session")
- g.db.dispose()
- g.db = None
- logger.debug(f"g.db: {g.db}\n\tg._database: {g._database}")
+ try:
+ g.db.dispose()
+ except Exception: # Capture Everything
+ app.logger.error(f"DATABASE: Error disposing: {g.db=}")
+ finally: # Reset regardless of what happens
+ g.db = None
@app.errorhandler(Exception)
@@ -158,8 +156,6 @@ def handle_generic_exceptions(e):
stack={formatted_lines},
error_image=animation,
version=GN_VERSION))
-
- # logger.error("Set cookie %s with %s" % (err_msg, animation))
resp.set_cookie(err_msg[:32], animation)
return resp
@@ -171,8 +167,6 @@ def no_access_page():
@app.route("/")
def index_page():
- logger.info("Sending index_page")
- logger.info(request.url)
params = request.args
if 'import_collections' in params:
import_collections = params['import_collections']
@@ -184,11 +178,7 @@ def index_page():
@app.route("/tmp/<img_path>")
def tmp_page(img_path):
- logger.info("In tmp_page")
- logger.info("img_path:", img_path)
- logger.info(request.url)
initial_start_vars = request.form
- logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = base64.b64encode(imgdata)
@@ -224,22 +214,13 @@ def twitter(filename):
@app.route("/search", methods=('GET',))
def search_page():
- logger.info("in search_page")
- logger.info(request.url)
result = None
if USE_REDIS:
- with Bench("Trying Redis cache"):
- key = "search_results:v1:" + \
- json.dumps(request.args, sort_keys=True)
- logger.debug("key is:", pf(key))
- result = Redis.get(key)
- if result:
- logger.info("Redis cache hit on search results!")
- result = pickle.loads(result)
- else:
- logger.info("Skipping Redis cache (USE_REDIS=False)")
-
- logger.info("request.args is", request.args)
+ key = "search_results:v1:" + \
+ json.dumps(request.args, sort_keys=True)
+ result = Redis.get(key)
+ if result:
+ result = pickle.loads(result)
the_search = SearchResultPage(request.args)
result = the_search.__dict__
valid_search = result['search_term_exists']
@@ -256,15 +237,7 @@ def search_page():
@app.route("/search_table", methods=('GET',))
def search_page_table():
- logger.info("in search_page table")
- logger.info(request.url)
-
- logger.info("request.args is", request.args)
the_search = search_results.SearchResultPage(request.args)
-
- logger.info(type(the_search.trait_list))
- logger.info(the_search.trait_list)
-
current_page = server_side.ServerSideTable(
len(the_search.trait_list),
the_search.trait_list,
@@ -277,7 +250,6 @@ def search_page_table():
@app.route("/gsearch", methods=('GET',))
def gsearchact():
- logger.info(request.url)
result = GSearch(request.args).__dict__
type = request.args['type']
if type == "gene":
@@ -288,8 +260,6 @@ def gsearchact():
@app.route("/gsearch_table", methods=('GET',))
def gsearchtable():
- logger.info(request.url)
-
gsearch_table_data = GSearch(request.args)
current_page = server_side.ServerSideTable(
gsearch_table_data.trait_count,
@@ -303,15 +273,12 @@ def gsearchtable():
@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
- logger.info("REQUEST ARGS:", request.values)
- logger.info(request.url)
result = UpdateGSearch(request.args).__dict__
return result['results']
@app.route("/docedit")
def docedit():
- logger.info(request.url)
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":
doc = Docs(request.args['entry'], request.args)
@@ -324,13 +291,11 @@ def docedit():
@app.route('/generated/<filename>')
def generated_file(filename):
- logger.info(request.url)
return send_from_directory(GENERATED_IMAGE_DIR, filename)
@app.route("/help")
def help():
- logger.info(request.url)
doc = Docs("help", request.args)
return render_template("docs.html", **doc.__dict__)
@@ -338,8 +303,6 @@ def help():
@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
# We are going to get additional user input for the analysis
- logger.info("In wgcna, request.form is:", request.form)
- logger.info(request.url)
# Display them using the template
return render_template("wgcna_setup.html", **request.form)
@@ -350,19 +313,16 @@ def wcgna_results():
results = run_wgcna(dict(request.form))
return render_template("gn3_wgcna_results.html", **results)
+
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
# We are going to get additional user input for the analysis
- logger.info("In ctl, request.form is:", request.form)
- logger.info(request.url)
# Display them using the template
return render_template("ctl_setup.html", **request.form)
-
@app.route("/ctl_results", methods=["POST"])
def ctl_results():
-
ctl_results = run_ctl(request.form)
return render_template("gn3_ctl_results.html", **ctl_results)
@@ -371,10 +331,11 @@ def ctl_results():
def fetch_network_files(file_name, file_type):
file_path = f"{file_name}.{file_type}"
- file_path = os.path.join("/tmp/",file_path)
+ file_path = os.path.join("/tmp/", file_path)
return send_file(file_path)
+
@app.route("/intro")
def intro():
doc = Docs("intro", request.args)
@@ -400,7 +361,6 @@ def update_page():
@app.route("/submit_trait")
def submit_trait_form():
- logger.info(request.url)
species_and_groups = get_species_groups()
return render_template(
"submit_trait.html",
@@ -411,7 +371,6 @@ def submit_trait_form():
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
- logger.info(request.url)
doc = Docs("links")
return render_template("links.html", **doc.__dict__)
@@ -422,9 +381,6 @@ def export_trait_excel():
trait_name, sample_data = export_trait_data.export_sample_table(
request.form)
app.logger.info(request.url)
- logger.info("sample_data - type: %s -- size: %s" %
- (type(sample_data), len(sample_data)))
-
buff = io.BytesIO()
workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
worksheet = workbook.add_worksheet()
@@ -443,15 +399,9 @@ def export_trait_excel():
@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"""
- logger.info("In export_trait_csv")
- logger.info("request.form:", request.form)
- logger.info(request.url)
trait_name, sample_data = export_trait_data.export_sample_table(
request.form)
- logger.info("sample_data - type: %s -- size: %s" %
- (type(sample_data), len(sample_data)))
-
buff = io.StringIO()
writer = csv.writer(buff)
for row in sample_data:
@@ -467,9 +417,6 @@ def export_trait_csv():
@app.route('/export_traits_csv', methods=('POST',))
def export_traits_csv():
"""CSV file consisting of the traits from the search result page"""
- logger.info("In export_traits_csv")
- logger.info("request.form:", request.form)
- logger.info(request.url)
file_list = export_traits(request.form, "metadata")
if len(file_list) > 1:
@@ -498,10 +445,10 @@ def export_collection_csv():
mimetype='text/csv',
headers={"Content-Disposition": "attachment;filename=" + out_file[0] + ".csv"})
+
@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():
"""CSV file consisting of the permutation data for the mapping results"""
- logger.info(request.url)
perm_info = json.loads(request.form['perm_info'])
now = datetime.datetime.now()
@@ -572,9 +519,6 @@ def show_trait_page():
@app.route("/heatmap", methods=('POST',))
def heatmap_page():
- logger.info("In heatmap, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
temp_uuid = uuid.uuid4()
@@ -583,18 +527,12 @@ def heatmap_page():
version = "v5"
key = "heatmap:{}:".format(
version) + json.dumps(start_vars, sort_keys=True)
- logger.info("key is:", pf(key))
- with Bench("Loading cache"):
- result = Redis.get(key)
+ result = Redis.get(key)
if result:
- logger.info("Cache hit!!!")
- with Bench("Loading results"):
- result = pickle.loads(result)
+ result = pickle.loads(result)
else:
- logger.info("Cache miss!!!")
-
template_vars = heatmap.Heatmap(request.form, temp_uuid)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
@@ -602,17 +540,10 @@ def heatmap_page():
result = template_vars.__dict__
- for item in list(template_vars.__dict__.keys()):
- logger.info(
- " ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
-
pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- logger.info("pickled result length:", len(pickled_result))
Redis.set(key, pickled_result)
Redis.expire(key, 60 * 60)
-
- with Bench("Rendering template"):
- rendered_template = render_template("heatmap.html", **result)
+ rendered_template = render_template("heatmap.html", **result)
else:
rendered_template = render_template(
@@ -623,9 +554,6 @@ def heatmap_page():
@app.route("/bnw_page", methods=('POST',))
def bnw_page():
- logger.info("In run BNW, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -643,9 +571,6 @@ def bnw_page():
@app.route("/webgestalt_page", methods=('POST',))
def webgestalt_page():
- logger.info("In run WebGestalt, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -663,9 +588,6 @@ def webgestalt_page():
@app.route("/geneweaver_page", methods=('POST',))
def geneweaver_page():
- logger.info("In run WebGestalt, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -683,9 +605,6 @@ def geneweaver_page():
@app.route("/comparison_bar_chart", methods=('POST',))
def comp_bar_chart_page():
- logger.info("In comp bar chart, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -712,7 +631,6 @@ def mapping_results_container_page():
@app.route("/loading", methods=('POST',))
def loading_page():
- # logger.info(request.url)
initial_start_vars = request.form
start_vars_container = {}
n_samples = 0 # ZS: So it can be displayed on loading page
@@ -734,7 +652,8 @@ def loading_page():
dataset = create_dataset(start_vars['dataset'])
start_vars['trait_name'] = start_vars['trait_id']
if dataset.type == "Publish":
- start_vars['trait_name'] = dataset.group.code + "_" + start_vars['trait_name']
+ start_vars['trait_name'] = dataset.group.code + \
+ "_" + start_vars['trait_name']
samples = dataset.group.samplelist
if 'genofile' in start_vars:
if start_vars['genofile'] != "":
@@ -751,9 +670,11 @@ def loading_page():
n_samples += 1
start_vars['n_samples'] = n_samples
- start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict))
- if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits
- start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
+ start_vars['vals_hash'] = generate_hash_of_string(
+ str(sample_vals_dict))
+ if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits
+ start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(
+ start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
@@ -769,7 +690,6 @@ def loading_page():
@app.route("/run_mapping", methods=('POST',))
def mapping_results_page():
initial_start_vars = request.form
- logger.info(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
'trait_id',
@@ -836,55 +756,42 @@ def mapping_results_page():
version = "v3"
key = "mapping_results:{}:".format(
version) + json.dumps(start_vars, sort_keys=True)
- with Bench("Loading cache"):
- result = None # Just for testing
- #result = Redis.get(key)
-
- #logger.info("************************ Starting result *****************")
- #logger.info("result is [{}]: {}".format(type(result), result))
- #logger.info("************************ Ending result ********************")
+ result = None # Just for testing
if result:
- logger.info("Cache hit!!!")
- with Bench("Loading results"):
- result = pickle.loads(result)
+ result = pickle.loads(result)
else:
- logger.info("Cache miss!!!")
- with Bench("Total time in RunMapping"):
- try:
- template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
- if template_vars.no_results:
- rendered_template = render_template("mapping_error.html")
- return rendered_template
- except:
+ try:
+ template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
+ if template_vars.no_results:
rendered_template = render_template("mapping_error.html")
return rendered_template
+ except:
+ rendered_template = render_template("mapping_error.html")
+ return rendered_template
- if not template_vars.pair_scan:
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
+ if not template_vars.pair_scan:
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
- result = template_vars.__dict__
+ result = template_vars.__dict__
- if result['pair_scan']:
- with Bench("Rendering template"):
- rendered_template = render_template(
- "pair_scan_results.html", **result)
- else:
- gn1_template_vars = display_mapping_results.DisplayMappingResults(
- result).__dict__
+ if result['pair_scan']:
+ rendered_template = render_template(
+ "pair_scan_results.html", **result)
+ else:
+ gn1_template_vars = display_mapping_results.DisplayMappingResults(
+ result).__dict__
- rendered_template = render_template(
- "mapping_results.html", **gn1_template_vars)
+ rendered_template = render_template(
+ "mapping_results.html", **gn1_template_vars)
return rendered_template
@app.route("/export_mapping_results", methods=('POST',))
def export_mapping_results():
- logger.info("request.form:", request.form)
- logger.info(request.url)
file_path = request.form.get("results_path")
results_csv = open(file_path, "r").read()
response = Response(results_csv,
@@ -908,8 +815,6 @@ def export_corr_matrix():
@app.route("/export", methods=('POST',))
def export():
- logger.info("request.form:", request.form)
- logger.info(request.url)
svg_xml = request.form.get("data", "Invalid data")
filename = request.form.get("filename", "manhattan_plot_snp")
response = Response(svg_xml, mimetype="image/svg+xml")
@@ -920,10 +825,7 @@ def export():
@app.route("/export_pdf", methods=('POST',))
def export_pdf():
import cairosvg
- logger.info("request.form:", request.form)
- logger.info(request.url)
svg_xml = request.form.get("data", "Invalid data")
- logger.info("svg_xml:", svg_xml)
filename = request.form.get("filename", "interval_map_pdf")
pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
response = Response(pdf_file, mimetype="application/pdf")
@@ -933,8 +835,6 @@ def export_pdf():
@app.route("/network_graph", methods=('POST',))
def network_graph_page():
- logger.info("In network_graph, request.form is:", pf(request.form))
- logger.info(request.url)
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
if traits[0] != "":
@@ -951,21 +851,29 @@ def network_graph_page():
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
correlation_results = compute_correlation(request.form, compute_all=True)
+
correlation_results = set_template_vars(request.form, correlation_results)
return render_template("correlation_page.html", **correlation_results)
@app.route("/test_corr_compute", methods=["POST"])
def test_corr_compute_page():
- correlation_data = compute_correlation(request.form, compute_all=True)
- return render_template("test_correlation_page.html", **correlation_data)
+
+ start_vars = request.form
+
+ correlation_results = compute_correlation_rust(start_vars,
+ start_vars["corr_type"],
+ start_vars['corr_sample_method'],
+ int(start_vars.get("corr_return_results", 500)),True)
+
+ correlation_results = set_template_vars(request.form, correlation_results)
+
+ return render_template("correlation_page.html", **correlation_results)
+ # return render_template("test_correlation_page.html", **correlation_data)
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
- logger.info("In corr_matrix, request.form is:", pf(request.form))
- logger.info(request.url)
-
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
if len(traits) > 1:
@@ -981,7 +889,6 @@ def corr_matrix_page():
@app.route("/corr_scatter_plot")
def corr_scatter_plot_page():
- logger.info(request.url)
template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
@@ -991,7 +898,6 @@ def corr_scatter_plot_page():
@app.route("/snp_browser", methods=('GET',))
def snp_browser_page():
- logger.info(request.url)
template_vars = snp_browser.SnpBrowser(request.args)
return render_template("snp_browser.html", **template_vars.__dict__)
@@ -1006,7 +912,6 @@ def db_info_page():
@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
- logger.info(request.url)
snp_table_data = snp_browser.SnpBrowser(request.args)
current_page = server_side.ServerSideTable(
snp_table_data.rows_count,
@@ -1021,20 +926,17 @@ def snp_browser_table():
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
# ZS: Currently just links to GN1
- logger.info(request.url)
return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
@app.route("/tutorial/security", methods=('GET',))
def security_tutorial_page():
# ZS: Currently just links to GN1
- logger.info(request.url)
return render_template("admin/security_help.html")
@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
- logger.info(request.url)
return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})
# Take this out or secure it before putting into production
@@ -1042,7 +944,6 @@ def submit_bnw():
@app.route("/get_temp_data")
def get_temp_data():
- logger.info(request.url)
temp_uuid = request.args['key']
return flask.jsonify(temp_data.TempData(temp_uuid).get_all())
@@ -1097,9 +998,8 @@ def display_diffs_users():
author = g.user_session.record.get(b'user_name').decode("utf-8")
if os.path.exists(DIFF_DIR):
files = os.listdir(DIFF_DIR)
- files = filter(lambda x: not(x.endswith((".approved", ".rejected"))) \
+ files = filter(lambda x: not(x.endswith((".approved", ".rejected")))
and author in x,
files)
return render_template("display_files_user.html",
files=files)
-