diff options
Diffstat (limited to 'wqflask')
47 files changed, 119 insertions, 13 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 900e050c..32032ba7 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -363,7 +363,7 @@ class GeneralTrait(object): FROM Homologene, Species, InbredSet WHERE - Homologene.GeneId =%s AND + Homologene.GeneId ='%s' AND InbredSet.Name = '%s' AND InbredSet.SpeciesId = Species.Id AND Species.TaxonomyId = Homologene.TaxonomyId diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/maintenance/__init__.py diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index ddc0ea82..b873e16f 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -31,6 +31,7 @@ import string from inspect import isfunction from pprint import pformat as pf from inspect import stack +import datetime from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT @@ -66,7 +67,10 @@ LOG_LEVEL_DEBUG (NYI). def error(self,*args): """Call logging.error for multiple args""" - self.collect(self.logger.error,*args) + now = datetime.datetime.utcnow() + time_str = now.strftime('%H:%M:%S UTC %Y%m%d') + l = [time_str]+list(args) + self.collect(self.logger.error,*l) def infof(self,*args): """Call logging.info for multiple args lazily""" diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index f2a2eb8c..f28407b3 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -41,6 +41,9 @@ from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMM from utility.external import shell from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR +import utility.logger +logger = utility.logger.getLogger(__name__ ) + class MarkerRegression(object): def __init__(self, start_vars, temp_uuid): @@ -197,6 +200,7 @@ class MarkerRegression(object): self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] + logger.info("Running qtlreaper") results = self.gen_reaper_results() elif self.mapping_method == "plink": results = self.run_plink() diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 9cef3cec..bc147f75 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -44,6 +44,9 @@ from utility import Plot from wqflask.interval_analyst import GeneUtil from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR +import utility.logger +logger = utility.logger.getLogger(__name__ ) + ######################################### # Inteval Mapping Plot Page ######################################### @@ -159,6 +162,7 @@ class MarkerRegression(object): #if not self.openMysql(): # return + logger.info("Running qtlreaper") #helper_functions.get_species_dataset_trait(self, start_vars) @@ -211,7 +215,7 @@ class MarkerRegression(object): self.plotScale = start_vars['mapping_scale'] else: self.plotScale = "physic" - + self.manhattan_plot = start_vars['manhattan_plot'] if 'permCheck' in start_vars.keys(): @@ -514,13 +518,13 @@ class MarkerRegression(object): if self.dataset.group.species == "mouse": if self.selectedChr == 20: - chrName = "X" + chrName = "X" else: chrName = self.selectedChr self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse") elif self.dataset.group.species == "rat": if self.selectedChr == 21: - chrName = "X" + chrName = "X" else: chrName = self.selectedChr self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat") @@ -860,7 +864,7 @@ class MarkerRegression(object): BootCoord = [] i = 0 startX = xLeftOffset - + if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for j, _chr in enumerate(self.genotype): BootCoord.append( []) @@ -883,8 +887,8 @@ class MarkerRegression(object): else: Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale BootCoord[-1].append([Xc, self.bootResult[i]]) - i += 1 - + i += 1 + #reduce bootResult if self.selectedChr > -1: maxBootBar = 80.0 @@ -1851,7 +1855,7 @@ class MarkerRegression(object): if j == 0: canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor) startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale - + centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2, strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black) @@ -2963,7 +2967,7 @@ class MarkerRegression(object): chr_as_int = 20 else: chr_as_int = int(theGO["Chromosome"]) - 1 - + geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) #geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1)) geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1)) diff --git a/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif Binary files differnew file mode 100644 index 00000000..2c68b5ee --- /dev/null +++ b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif b/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif Binary files differnew file mode 100644 index 00000000..e9d38277 --- /dev/null +++ b/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif 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b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif Binary files differnew file mode 100644 index 00000000..473212e4 --- /dev/null +++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html new file mode 100644 index 00000000..7ab2bf2f --- /dev/null +++ b/wqflask/wqflask/templates/error.html @@ -0,0 +1,61 @@ +{% extends "base.html" %} +{% block title %}Error: {{message}}{% endblock %} +{% block content %} +<!-- Start of body --> + +<div class="col-md-8"> +<div class="form-group has-error"> + <div class="control-label" for="inputError1"> + + <img src="/static/gif/error/{{ error_image }}"> + + <h1>ERROR</h1> + + <p> + This error is not what we wanted to see. Unfortunately errors + are part of all software systems and we need to resolve this + together. + </p> + <p> + <b>It is important to report this ERROR so we can fix it for everyone</b>. + </p> + + <p> + Report to the GeneNetwork team by recording the steps you take + to reproduce this ERROR. Next to those steps, copy-paste below + stack trace, either as + a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new + issue</a> or E-mail this full page to one of the developers + directly. + </p> + </div> + + <p> + (GeneNetwork error: {{message[:128]}}) + </p> + + <pre> + {{ stack[0] }} + {{ message }} (error) + {{ stack[-3] }} + {{ stack[-2] }} + </pre> + + <p> + To check if this already a known issue, search the + <a href="https://github.com/genenetwork/genenetwork2/issues">issue + tracker</a>. + </p> + + <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a> + <div id="Stack" class="collapse"> + <pre> + {% for line in stack %} {{ line }} + {% endfor %} + </pre> + </div> +</div> +</div> + + +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 41e2c7be..cf316bee 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -4,6 +4,11 @@ from __future__ import absolute_import, division, print_function +import traceback # for error page +import os # for error gifs +import random # for random error gif +import datetime # for errors +import time # for errors import sys import csv import xlsxwriter @@ -26,7 +31,7 @@ import base64 import array import sqlalchemy from wqflask import app -from flask import g, Response, request, render_template, send_from_directory, jsonify, redirect +from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect from wqflask import search_results from wqflask import gsearch from wqflask import update_search_results @@ -58,6 +63,8 @@ from wqflask import user_manager from wqflask import collect from wqflask.database import db_session +import werkzeug + import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -82,6 +89,31 @@ def shutdown_session(exception=None): # from wqflask import tracer # tracer.turn_on() +@app.errorhandler(Exception) +def handle_bad_request(e): + err_msg = str(e) + logger.error(err_msg) + logger.error(request.url) + # get the stack trace and send it to the logger + exc_type, exc_value, exc_traceback = sys.exc_info() + logger.error(traceback.format_exc()) + now = datetime.datetime.utcnow() + time_str = now.strftime('%l:%M%p UTC %b %d, %Y') + formatted_lines = [request.url + " ("+time_str+")"]+traceback.format_exc().splitlines() + + # Handle random animations + # Use a cookie to have one animation on refresh + animation = request.cookies.get(err_msg[:64]) + if not animation: + list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ] + animation = random.choice(list) + + resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation)) + + # logger.error("Set cookie %s with %s" % (err_msg, animation)) + resp.set_cookie(err_msg[:64],animation) + return resp + @app.route("/") def index_page(): logger.info("Sending index_page") @@ -395,6 +427,7 @@ def mapping_results_container_page(): @app.route("/marker_regression", methods=('POST',)) def marker_regression_page(): initial_start_vars = request.form + logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) temp_uuid = initial_start_vars['temp_uuid'] wanted = ( 'trait_id', @@ -432,11 +465,11 @@ def marker_regression_page(): 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno' ) - 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:')): start_vars[key] = value + logger.debug("Marker regression called with start_vars:", start_vars) version = "v3" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) @@ -546,7 +579,7 @@ def network_graph_page(): return render_template("network_graph.html", **template_vars.__dict__) else: return render_template("empty_collection.html", **{'tool':'Network Graph'}) - + @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) |
