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-rw-r--r--wqflask/runserver.py5
-rw-r--r--wqflask/utility/tools.py1
-rw-r--r--wqflask/wqflask/views.py139
3 files changed, 72 insertions, 73 deletions
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index f40d8a48..bfc27827 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -20,7 +20,10 @@ from wqflask import app
#_ch = logging.StreamHandler()
#_log.addHandler(_ch)
-print app.config
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+logger.info(app.config)
from utility.tools import WEBSERVER_MODE
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 08495c2f..824ce330 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -8,7 +8,6 @@ from wqflask import app
# Use the standard logger here to avoid a circular dependency
import logging
logger = logging.getLogger(__name__ )
-logging.basicConfig(level=logging.INFO)
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 06db7494..c07e03ff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1,4 +1,7 @@
# -*- coding: utf-8 -*-
+#
+# Main routing table for GN2
+
from __future__ import absolute_import, division, print_function
import sys
@@ -12,7 +15,6 @@ import cPickle as pickle
import uuid
import simplejson as json
-#import json
import yaml
#Switching from Redis to StrictRedis; might cause some issues
@@ -23,13 +25,10 @@ import flask
import base64
import array
import sqlalchemy
-#import config
-
from wqflask import app
-
from flask import (render_template, request, make_response, Response,
- Flask, g, config, jsonify, redirect, url_for, send_from_directory)
-
+ Flask, g, config, jsonify, redirect, url_for,
+ send_from_directory)
from wqflask import search_results
from wqflask import gsearch
from wqflask import update_search_results
@@ -45,7 +44,6 @@ from wqflask.marker_regression import marker_regression_gn1
from wqflask.correlation import show_corr_results
from wqflask.correlation_matrix import show_corr_matrix
from wqflask.correlation import corr_scatter_plot
-
from wqflask.wgcna import wgcna_analysis
from wqflask.ctl import ctl_analysis
@@ -61,9 +59,8 @@ from pprint import pformat as pf
from wqflask import user_manager
from wqflask import collect
-#import logging
-#logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
-#_log = logging.getLogger("correlation")
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
@app.before_request
def connect_db():
@@ -76,28 +73,28 @@ def connect_db():
@app.route("/")
def index_page():
- print("Sending index_page")
+ logger.info("Sending index_page")
#create_datasets_list()
#key = "all_datasets"
#result = Redis.get(key)
#if result:
- # print("Cache hit!!!")
+ # logger.info("Cache hit!!!")
# result = pickle.loads(result)
#else:
# with Bench("Creating DataSets object"):
# ds = DataSets()
# Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
# Redis.expire(key, 2*60)
- #print("[orange] ds:", ds.datasets)
+ #logger.info("[orange] ds:", ds.datasets)
return render_template("index_page.html")
@app.route("/tmp/<img_path>")
def tmp_page(img_path):
- print("In tmp_page")
- print("img_path:", img_path)
+ logger.info("In tmp_page")
+ logger.info("img_path:", img_path)
initial_start_vars = request.form
- print("initial_start_vars:", initial_start_vars)
+ logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = imgdata.encode("base64")
@@ -108,15 +105,15 @@ def tmp_page(img_path):
#@app.route("/data_sharing")
#def data_sharing_page():
-# print("In data_sharing")
+# logger.info("In data_sharing")
# fd = webqtlFormData.webqtlFormData(request.args)
-# print("1Have fd")
+# logger.info("1Have fd")
# sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
# info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
-# print("type(htmlfilelist):", type(htmlfilelist))
+# logger.info("type(htmlfilelist):", type(htmlfilelist))
# htmlfilelist = htmlfilelist.encode("utf-8")
# #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-# print("1 Made it to rendering")
+# logger.info("1 Made it to rendering")
# return render_template("data_sharing.html",
# info=info,
# htmlfilelist=htmlfilelist)
@@ -124,37 +121,37 @@ def tmp_page(img_path):
@app.route("/search", methods=('GET',))
def search_page():
- print("in search_page")
+ logger.info("in search_page")
if 'info_database' in request.args:
- print("Going to sharing_info_page")
+ logger.info("Going to sharing_info_page")
template_vars = sharing_info_page()
if template_vars.redirect_url:
- print("Going to redirect")
+ logger.info("Going to redirect")
return flask.redirect(template_vars.redirect_url)
else:
return render_template("data_sharing.html", **template_vars.__dict__)
else:
key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
- print("key is:", pf(key))
+ logger.info("key is:", pf(key))
if USE_REDIS:
with Bench("Trying Redis cache"):
result = Redis.get(key)
else:
- print("Skipping Redis cache (USE_REDIS=False)")
+ logger.info("Skipping Redis cache (USE_REDIS=False)")
result = None
if result:
- print("Cache hit on search results!!!")
- print("USE_REDIS=",USE_REDIS)
+ logger.info("Cache hit on search results!!!")
+ logger.info("USE_REDIS=",USE_REDIS)
with Bench("Loading results"):
result = pickle.loads(result)
else:
- print("calling search_results.SearchResultPage")
- print("request.args is", request.args)
+ logger.info("calling search_results.SearchResultPage")
+ logger.info("request.args is", request.args)
the_search = search_results.SearchResultPage(request.args)
result = the_search.__dict__
- print("result: ", pf(result))
+ logger.info("result: ", pf(result))
if USE_REDIS:
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)
@@ -175,7 +172,7 @@ def gsearchact():
@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
- print("REQUEST ARGS:", request.values)
+ logger.info("REQUEST ARGS:", request.values)
result = update_search_results.GSearch(request.args).__dict__
return result['results']
# type = request.args['type']
@@ -200,12 +197,12 @@ def help():
@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
- print("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis
+ logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis
return render_template("wgcna_setup.html", **request.form) # Display them using the template
@app.route("/wgcna_results", methods=('POST',))
def wcgna_results():
- print("In wgcna, request.form is:", request.form)
+ logger.info("In wgcna, request.form is:", request.form)
wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis
wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread
result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result
@@ -213,12 +210,12 @@ def wcgna_results():
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
- print("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis
+ logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis
return render_template("ctl_setup.html", **request.form) # Display them using the template
@app.route("/ctl_results", methods=('POST',))
def ctl_results():
- print("In ctl, request.form is:", request.form)
+ logger.info("In ctl, request.form is:", request.form)
ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis
ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread
result = ctl.process_results(ctlA) # After the analysis is finished store the result
@@ -257,11 +254,11 @@ def environments():
@app.route('/export_trait_excel', methods=('POST',))
def export_trait_excel():
"""Excel file consisting of the sample data from the trait data and analysis page"""
- print("In export_trait_excel")
- print("request.form:", request.form)
+ logger.info("In export_trait_excel")
+ logger.info("request.form:", request.form)
sample_data = export_trait_data.export_sample_table(request.form)
- print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
+ logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
buff = StringIO.StringIO()
workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
@@ -282,11 +279,11 @@ 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"""
- print("In export_trait_csv")
- print("request.form:", request.form)
+ logger.info("In export_trait_csv")
+ logger.info("request.form:", request.form)
sample_data = export_trait_data.export_sample_table(request.form)
- print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
+ logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
buff = StringIO.StringIO()
writer = csv.writer(buff)
@@ -326,22 +323,22 @@ def export_perm_data():
def show_trait_page():
# Here it's currently too complicated not to use an fd that is a webqtlFormData
#fd = webqtlFormData.webqtlFormData(request.args)
- #print("stp y1:", pf(vars(fd)))
+ #logger.info("stp y1:", pf(vars(fd)))
template_vars = show_trait.ShowTrait(request.args)
- #print("js_data before dump:", template_vars.js_data)
+ #logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")
# Sorting the keys messes up the ordered dictionary, so don't do that
#sort_keys=True)
- #print("js_data after dump:", template_vars.js_data)
- #print("show_trait template_vars:", pf(template_vars.__dict__))
+ #logger.info("js_data after dump:", template_vars.js_data)
+ #logger.info("show_trait template_vars:", pf(template_vars.__dict__))
return render_template("show_trait.html", **template_vars.__dict__)
@app.route("/heatmap", methods=('POST',))
def heatmap_page():
- print("In heatmap, request.form is:", pf(request.form))
+ logger.info("In heatmap, request.form is:", pf(request.form))
start_vars = request.form
temp_uuid = uuid.uuid4()
@@ -350,17 +347,17 @@ def heatmap_page():
if traits[0] != "":
version = "v5"
key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
- print("key is:", pf(key))
+ logger.info("key is:", pf(key))
with Bench("Loading cache"):
result = Redis.get(key)
if result:
- print("Cache hit!!!")
+ logger.info("Cache hit!!!")
with Bench("Loading results"):
result = pickle.loads(result)
else:
- print("Cache miss!!!")
+ logger.info("Cache miss!!!")
template_vars = heatmap.Heatmap(request.form, temp_uuid)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -370,10 +367,10 @@ def heatmap_page():
result = template_vars.__dict__
for item in template_vars.__dict__.keys():
- print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+ logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- print("pickled result length:", len(pickled_result))
+ logger.info("pickled result length:", len(pickled_result))
Redis.set(key, pickled_result)
Redis.expire(key, 60*60)
@@ -429,7 +426,7 @@ def marker_regression_page():
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno'
)
- print("Marker regression called with initial_start_vars:", initial_start_vars)
+ logger.info("Marker regression called with initial_start_vars:", initial_start_vars)
start_vars = {}
for key, value in initial_start_vars.iteritems():
if key in wanted or key.startswith(('value:')):
@@ -437,21 +434,21 @@ def marker_regression_page():
version = "v3"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
- print("key is:", pf(key))
+ logger.info("key is:", pf(key))
with Bench("Loading cache"):
result = None # Just for testing
#result = Redis.get(key)
- #print("************************ Starting result *****************")
- #print("result is [{}]: {}".format(type(result), result))
- #print("************************ Ending result ********************")
+ #logger.info("************************ Starting result *****************")
+ #logger.info("result is [{}]: {}".format(type(result), result))
+ #logger.info("************************ Ending result ********************")
if result:
- print("Cache hit!!!")
+ logger.info("Cache hit!!!")
with Bench("Loading results"):
result = pickle.loads(result)
else:
- print("Cache miss!!!")
+ logger.info("Cache miss!!!")
with Bench("Total time in MarkerRegression"):
template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
@@ -464,9 +461,9 @@ def marker_regression_page():
if result['pair_scan']:
with Bench("Rendering template"):
img_path = result['pair_scan_filename']
- print("img_path:", img_path)
+ logger.info("img_path:", img_path)
initial_start_vars = request.form
- print("initial_start_vars:", initial_start_vars)
+ logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(TEMPDIR + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = imgdata.encode("base64")
@@ -475,12 +472,12 @@ def marker_regression_page():
rendered_template = render_template("pair_scan_results.html", **result)
else:
#for item in template_vars.__dict__.keys():
- # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+ # logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- print("pickled result length:", len(pickled_result))
+ logger.info("pickled result length:", len(pickled_result))
Redis.set(key, pickled_result)
Redis.expire(key, 1*60)
@@ -490,9 +487,9 @@ def marker_regression_page():
# with Bench("Rendering template"):
# if result['pair_scan'] == True:
# img_path = result['pair_scan_filename']
- # print("img_path:", img_path)
+ # logger.info("img_path:", img_path)
# initial_start_vars = request.form
- # print("initial_start_vars:", initial_start_vars)
+ # logger.info("initial_start_vars:", initial_start_vars)
# imgfile = open(TEMPDIR + '/' + img_path, 'rb')
# imgdata = imgfile.read()
# imgB64 = imgdata.encode("base64")
@@ -508,7 +505,7 @@ def marker_regression_page():
@app.route("/export", methods = ('POST',))
def export():
- print("request.form:", request.form)
+ logger.info("request.form:", request.form)
svg_xml = request.form.get("data", "Invalid data")
filename = request.form.get("filename", "manhattan_plot_snp")
response = Response(svg_xml, mimetype="image/svg+xml")
@@ -518,9 +515,9 @@ def export():
@app.route("/export_pdf", methods = ('POST',))
def export_pdf():
import cairosvg
- print("request.form:", request.form)
+ logger.info("request.form:", request.form)
svg_xml = request.form.get("data", "Invalid data")
- print("svg_xml:", svg_xml)
+ logger.info("svg_xml:", svg_xml)
filename = request.form.get("filename", "interval_map_pdf")
filepath = GENERATED_IMAGE_DIR+filename
pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
@@ -530,14 +527,14 @@ def export_pdf():
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
- print("In corr_compute, request.form is:", pf(request.form))
+ logger.info("In corr_compute, request.form is:", pf(request.form))
#fd = webqtlFormData.webqtlFormData(request.form)
template_vars = show_corr_results.CorrelationResults(request.form)
return render_template("correlation_page.html", **template_vars.__dict__)
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
- print("In corr_matrix, request.form is:", pf(request.form))
+ logger.info("In corr_matrix, request.form is:", pf(request.form))
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -563,7 +560,7 @@ def corr_scatter_plot_page():
# Todo: Can we simplify this? -Sam
def sharing_info_page():
"""Info page displayed when the user clicks the "Info" button next to the dataset selection"""
- print("In sharing_info_page")
+ logger.info("In sharing_info_page")
fd = webqtlFormData.webqtlFormData(request.args)
template_vars = SharingInfoPage.SharingInfoPage(fd)
return template_vars
@@ -594,7 +591,7 @@ def json_default_handler(obj):
if hasattr(obj, '__dict__'):
return obj.__dict__
#elif type(obj) == "Dataset":
- # print("Not going to serialize Dataset")
+ # logger.info("Not going to serialize Dataset")
# return None
else:
raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 16:39:50 +0000