diff options
| -rw-r--r-- | wqflask/base/webqtlFormData.py | 257 | ||||
| -rw-r--r-- | wqflask/utility/Plot.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/svg.py | 1068 | ||||
| -rw-r--r-- | wqflask/utility/webqtlUtil.py | 88 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 52 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 80 |
7 files changed, 22 insertions, 1540 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py deleted file mode 100644 index 1b41b2fc..00000000 --- a/wqflask/base/webqtlFormData.py +++ /dev/null @@ -1,257 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -from __future__ import print_function -from pprint import pformat as pf - -import string -import os - -import reaper - -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from utility import webqtlUtil - -class webqtlFormData(object): - 'Represents data from a WebQTL form page, needed to generate the next page' - - attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance' - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, - start_vars = None, - req = None): - # Todo: rework this whole thing - for item in webqtlFormData.attrs: - self.__dict__[item] = None - - for item in start_vars: - self.__dict__[item] = start_vars[item] - - #Todo: This can't be good below...rework - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - self.ppolar = None - self.mpolar = None - - if self.group: - _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group] - - def set_number(stringy): - return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000 - - self.nperm = set_number(self.nperm) - self.nboot = set_number(self.nboot) - - if self.allsamplelist: - self.allsamplelist = self.allsamplelist.split() - - if self.group == 'BXD300': - self.group = 'BXD' - - def __getitem__(self, key): - return self.__dict__[key] - - def get(self, key, default=None): - if key in self.__dict__: - return self.__dict__[key] - else: - return default - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - '''read genotype from .geno file''' - if self.group == 'BXD300': - self.group = 'BXD' - - assert self.group, "self.group needs to be set" - - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - - self.genotype_1 = reaper.Dataset() - - full_filename = locate(self.group + '.geno','genotype') - - # reaper barfs on unicode filenames, so here we ensure it's a string - full_filename = str(full_filename) - self.genotype_1.read(full_filename) - - print("Got to after read") - - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group] - except KeyError: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 = self.genotype_1 - if self.genotype_1.type == "group" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - - self.samplelist = list(self.genotype.prgy) - self.f1list = [] - self.parlist = [] - - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - - def readData(self, samplelist, incf1=None): - '''read user input data or from trait data and analysis form''' - - if incf1 == None: - incf1 = [] - - if not self.genotype: - self.readGenotype() - if not samplelist: - if incf1: - samplelist = self.f1list + self.samplelist - else: - samplelist = self.samplelist - - traitfiledata = getattr(self, "traitfile", None) - traitpastedata = getattr(self, "traitpaste", None) - variancefiledata = getattr(self, "variancefile", None) - variancepastedata = getattr(self, "variancepaste", None) - Nfiledata = getattr(self, "Nfile", None) - - #### Todo: Rewrite below when we get to someone submitting their own trait ##### - - def to_float(item): - try: - return float(item) - except ValueError: - return None - - print("bottle samplelist is:", samplelist) - if traitfiledata: - tt = traitfiledata.split() - values = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = traitpastedata.split() - values = map(webqtlUtil.StringAsFloat, tt) - else: - print("mapping formdataasfloat") - #values = map(self.FormDataAsFloat, samplelist) - values = [to_float(getattr(self, key)) for key in samplelist] - - - if len(values) < len(samplelist): - values += [None] * (len(samplelist) - len(values)) - elif len(values) > len(samplelist): - values = values[:len(samplelist)] - - if variancefiledata: - tt = variancefiledata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = variancepastedata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - else: - variances = map(self.FormVarianceAsFloat, samplelist) - - if len(variances) < len(samplelist): - variances += [None]*(len(samplelist) - len(variances)) - elif len(variances) > len(samplelist): - variances = variances[:len(samplelist)] - - if Nfiledata: - tt = string.split(Nfiledata) - nsamples = map(webqtlUtil.IntAsFloat, tt) - if len(nsamples) < len(samplelist): - nsamples += [None]*(len(samplelist) - len(nsamples)) - else: - nsamples = map(self.FormNAsFloat, samplelist) - - ##values, variances, nsamples is obsolete - self.allTraitData = {} - for i, _sample in enumerate(samplelist): - if values[i] != None: - self.allTraitData[_sample] = webqtlCaseData( - _sample, values[i], variances[i], nsamples[i]) - - def informativeStrains(self, samplelist=None, include_variances = None): - '''if readData was called, use this to output informative samples (sample with values)''' - - if not samplelist: - samplelist = self.samplelist - - samples = [] - values = [] - variances = [] - - for sample in samplelist: - if sample in self.allTraitData: - _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance - if _val != None: - if include_variances: - if _var != None: - samples.append(sample) - values.append(_val) - variances.append(_var) - else: - samples.append(sample) - values.append(_val) - variances.append(None) - - return samples, values, variances, len(samples) - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None
\ No newline at end of file diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index dbcee331..529cd117 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -37,7 +37,6 @@ from numarray import ones, array, dot, swapaxes import reaper -import svg import webqtlUtil import corestats from base import webqtlConfig diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py deleted file mode 100644 index 512bc9e6..00000000 --- a/wqflask/utility/svg.py +++ /dev/null @@ -1,1068 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -#!/usr/bin/env python -##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) -##All rights reserved. -## -##Redistribution and use in source and binary forms, with or without modification, -##are permitted provided that the following conditions are met: -## -##Redistributions of source code must retain the above copyright notice, this -##list of conditions and the following disclaimer. -## -##Redistributions in binary form must reproduce the above copyright notice, -##this list of conditions and the following disclaimer in the documentation and/or -##other materials provided with the distribution. -## -##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of -##its contributors may be used to endorse or promote products derived from this -##software without specific prior written permission. -## -##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -##Thanks to Gerald Rosennfellner for his help and useful comments. - -__doc__="""Use SVGdraw to generate your SVGdrawings. - -SVGdraw uses an object model drawing and a method toXML to create SVG graphics -by using easy to use classes and methods usualy you start by creating a drawing eg - - d=drawing() - #then you create a SVG root element - s=svg() - #then you add some elements eg a circle and add it to the svg root element - c=circle() - #you can supply attributes by using named arguments. - c=circle(fill='red',stroke='blue') - #or by updating the attributes attribute: - c.attributes['stroke-width']=1 - s.addElement(c) - #then you add the svg root element to the drawing - d.setSVG(s) - #and finaly you xmlify the drawing - d.toXml() - - -this results in the svg source of the drawing, which consists of a circle -on a white background. Its as easy as that;) -This module was created using the SVG specification of www.w3c.org and the -O'Reilly (www.oreilly.com) python books as information sources. A svg viewer -is available from www.adobe.com""" - -__version__="1.0" - -# there are two possibilities to generate svg: -# via a dom implementation and directly using <element>text</element> strings -# the latter is way faster (and shorter in coding) -# the former is only used in debugging svg programs -# maybe it will be removed alltogether after a while -# with the following variable you indicate whether to use the dom implementation -# Note that PyXML is required for using the dom implementation. -# It is also possible to use the standard minidom. But I didn't try that one. -# Anyway the text based approach is about 60 times faster than using the full dom implementation. -use_dom_implementation=0 - - -import exceptions -if use_dom_implementation<>0: - try: - from xml.dom import implementation - from xml.dom.ext import PrettyPrint - except: - raise exceptions.ImportError, "PyXML is required for using the dom implementation" -#The implementation is used for the creating the XML document. -#The prettyprint module is used for converting the xml document object to a xml file - -import sys -assert sys.version_info[0]>=2 -if sys.version_info[1]<2: - True=1 - False=0 - file=open - -sys.setrecursionlimit=50 -#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) -#won't eat up too much processor time. - -#the following code is pasted form xml.sax.saxutils -#it makes it possible to run the code without the xml sax package installed -#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts -def _escape(data, entities={}): - """Escape &, <, and > in a string of data. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - #data = data.replace("&", "&") - data = data.replace("<", "<") - data = data.replace(">", ">") - for chars, entity in entities.items(): - data = data.replace(chars, entity) - return data - -def _quoteattr(data, entities={}): - """Escape and quote an attribute value. - - Escape &, <, and > in a string of data, then quote it for use as - an attribute value. The \" character will be escaped as well, if - necessary. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - data = _escape(data, entities) - if '"' in data: - if "'" in data: - data = '"%s"' % data.replace('"', """) - else: - data = "'%s'" % data - else: - data = '"%s"' % data - return data - - - -def _xypointlist(a): - """formats a list of xy pairs""" - s='' - for e in a: #this could be done more elegant - s+=str(e)[1:-1] +' ' - return s - -def _viewboxlist(a): - """formats a tuple""" - s='' - for e in a: - s+=str(e)+' ' - return s - -def _pointlist(a): - """formats a list of numbers""" - return str(a)[1:-1] - -class pathdata: - """class used to create a pathdata object which can be used for a path. - although most methods are pretty straightforward it might be useful to look at the SVG specification.""" - #I didn't test the methods below. - def __init__(self,x=None,y=None): - self.path=[] - if x is not None and y is not None: - self.path.append('M '+str(x)+' '+str(y)) - def closepath(self): - """ends the path""" - self.path.append('z') - def move(self,x,y): - """move to absolute""" - self.path.append('M '+str(x)+' '+str(y)) - def relmove(self,x,y): - """move to relative""" - self.path.append('m '+str(x)+' '+str(y)) - def line(self,x,y): - """line to absolute""" - self.path.append('L '+str(x)+' '+str(y)) - def relline(self,x,y): - """line to relative""" - self.path.append('l '+str(x)+' '+str(y)) - def hline(self,x): - """horizontal line to absolute""" - self.path.append('H'+str(x)) - def relhline(self,x): - """horizontal line to relative""" - self.path.append('h'+str(x)) - def vline(self,y): - """verical line to absolute""" - self.path.append('V'+str(y)) - def relvline(self,y): - """vertical line to relative""" - self.path.append('v'+str(y)) - def bezier(self,x1,y1,x2,y2,x,y): - """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relbezier(self,x1,y1,x2,y2,x,y): - """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def smbezier(self,x2,y2,x,y): - """smooth bezier with xy2 to xy absolut""" - self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relsmbezier(self,x2,y2,x,y): - """smooth bezier with xy2 to xy relative""" - self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def qbezier(self,x1,y1,x,y): - """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def relqbezier(self,x1,y1,x,y): - """quadratic bezier with xy1 to xy relative""" - self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def smqbezier(self,x,y): - """smooth quadratic bezier to xy absolut""" - self.path.append('T'+str(x)+','+str(y)) - def relsmqbezier(self,x,y): - """smooth quadratic bezier to xy relative""" - self.path.append('t'+str(x)+','+str(y)) - def ellarc(self,rx,ry,xrot,laf,sf,x,y): - """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def relellarc(self,rx,ry,xrot,laf,sf,x,y): - """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def __repr__(self): - return ' '.join(self.path) - - - - -class SVGelement: - """SVGelement(type,attributes,elements,text,namespace,**args) - Creates a arbitrary svg element and is intended to be subclassed not used on its own. - This element is the base of every svg element it defines a class which resembles - a xml-element. The main advantage of this kind of implementation is that you don't - have to create a toXML method for every different graph object. Every element - consists of a type, attribute, optional subelements, optional text and an optional - namespace. Note the elements==None, if elements = None:self.elements=[] construction. - This is done because if you default to elements=[] every object has a reference - to the same empty list.""" - def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args): - self.type=type - if attributes==None: - self.attributes={} - else: - self.attributes=attributes - if elements==None: - self.elements=[] - else: - self.elements=elements - self.text=text - self.namespace=namespace - self.cdata=cdata - for arg in args.keys(): - arg2 = arg.replace("__", ":") - arg2 = arg2.replace("_", "-") - self.attributes[arg2]=args[arg] - def addElement(self,SVGelement): - """adds an element to a SVGelement - - SVGelement.addElement(SVGelement) - """ - self.elements.append(SVGelement) - - def toXml(self,level,f): - f.write('\t'*level) - f.write('<'+self.type) - for attkey in self.attributes.keys(): - f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey]))) - if self.namespace: - f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"') - if self.elements or self.text or self.cdata: - f.write('>') - if self.elements: - f.write('\n') - for element in self.elements: - element.toXml(level+1,f) - if self.cdata: - f.write('\n'+'\t'*(level+1)+'<![CDATA[') - for line in self.cdata.splitlines(): - f.write('\n'+'\t'*(level+2)+line) - f.write('\n'+'\t'*(level+1)+']]>\n') - if self.text: - if type(self.text)==type(''): #If the text is only text - f.write(_escape(str(self.text))) - else: #If the text is a spannedtext class - f.write(str(self.text)) - if self.elements: - f.write('\t'*level+'</'+self.type+'>\n') - elif self.text: - f.write('</'+self.type+'>\n') - elif self.cdata: - f.write('\t'*level+'</'+self.type+'>\n') - else: - f.write('/>\n') - -class tspan(SVGelement): - """ts=tspan(text='',**args) - - a tspan element can be used for applying formatting to a textsection - usage: - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - st=spannedtext() - st.addtspan(ts) - t=text(3,5,st) - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'tspan',**args) - if self.text<>None: - self.text=text - def __repr__(self): - s="<tspan" - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='>' - s+=self.text - s+='</tspan>' - return s - -class tref(SVGelement): - """tr=tref(link='',**args) - - a tref element can be used for referencing text by a link to its id. - usage: - tr=tref('#linktotext') - st=spannedtext() - st.addtref(tr) - t=text(3,5,st) - """ - def __init__(self,link,**args): - SVGelement.__init__(self,'tref',{'xlink:href':link},**args) - def __repr__(self): - s="<tref" - - for key,value in self.attributes.items(): - s+= ' %s="%s"' % (key,value) - s+='/>' - return s - -class spannedtext: - """st=spannedtext(textlist=[]) - - a spannedtext can be used for text which consists of text, tspan's and tref's - You can use it to add to a text element or path element. Don't add it directly - to a svg or a group element. - usage: - - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - tr=tref('#linktotext') - tr.attributes['fill']='red' - st=spannedtext() - st.addtspan(ts) - st.addtref(tr) - st.addtext('This text is not bold') - t=text(3,5,st) - """ - def __init__(self,textlist=None): - if textlist==None: - self.textlist=[] - else: - self.textlist=textlist - def addtext(self,text=''): - self.textlist.append(text) - def addtspan(self,tspan): - self.textlist.append(tspan) - def addtref(self,tref): - self.textlist.append(tref) - def __repr__(self): - s="" - for element in self.textlist: - s+=str(element) - return s - -class rect(SVGelement): - """r=rect(width,height,x,y,fill,stroke,stroke_width,**args) - - a rectangle is defined by a width and height and a xy pair - """ - def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args): - if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - -class ellipse(SVGelement): - """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) - - an ellipse is defined as a center and a x and y radius. - """ - def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): - if rx==None or ry== None: - if rx<>None: - raise ValueError, 'rx is required' - if ry<>None: - raise ValueError, 'ry is required' - else: - raise ValueError, 'both rx and ry are required' - SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - - -class circle(SVGelement): - """c=circle(x,y,radius,fill,stroke,stroke_width,**args) - - The circle creates an element using a x, y and radius values eg - """ - def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): - if r==None: - raise ValueError, 'r is required' - SVGelement.__init__(self,'circle',{'r':r},**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if fill<>None: - self.attributes['fill']=fill - if stroke<>None: - self.attributes['stroke']=stroke - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - -class point(circle): - """p=point(x,y,color) - - A point is defined as a circle with a size 1 radius. It may be more efficient to use a - very small rectangle if you use many points because a circle is difficult to render. - """ - def __init__(self,x,y,fill='black',**args): - circle.__init__(self,x,y,1,fill,**args) - -class line(SVGelement): - """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) - - A line is defined by a begin x,y pair and an end x,y pair - """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'line',**args) - if x1<>None: - self.attributes['x1']=x1 - if y1<>None: - self.attributes['y1']=y1 - if x2<>None: - self.attributes['x2']=x2 - if y2<>None: - self.attributes['y2']=y2 - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class polyline(SVGelement): - """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) - - a polyline is defined by a list of xy pairs - """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args) - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class polygon(SVGelement): - """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) - - a polygon is defined by a list of xy pairs - """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args) - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if stroke<>None: - self.attributes['stroke']=stroke - -class path(SVGelement): - """p=path(path,fill,stroke,stroke_width,**args) - - a path is defined by a path object and optional width, stroke and fillcolor - """ - def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): - SVGelement.__init__(self,'path',{'d':str(pathdata)},**args) - if stroke<>None: - self.attributes['stroke']=stroke - if fill<>None: - self.attributes['fill']=fill - if stroke_width<>None: - self.attributes['stroke-width']=stroke_width - if id<>None: - self.attributes['id']=id - - -class text(SVGelement): - """t=text(x,y,text,font_size,font_family,**args) - - a text element can bge used for displaying text on the screen - """ - def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): - SVGelement.__init__(self,'text',**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if font_size<>None: - self.attributes['font-size']=font_size - if font_family<>None: - self.attributes['font-family']=font_family - if text<>None: - self.text=text - if text_anchor<>None: - self.attributes['text-anchor']=text_anchor - - -class textpath(SVGelement): - """tp=textpath(text,link,**args) - - a textpath places a text on a path which is referenced by a link. - """ - def __init__(self,link,text=None,**args): - SVGelement.__init__(self,'textPath',{'xlink:href':link},**args) - if text<>None: - self.text=text - -class pattern(SVGelement): - """p=pattern(x,y,width,height,patternUnits,**args) - - A pattern is used to fill or stroke an object using a pre-defined - graphic object which can be replicated ("tiled") at fixed intervals - in x and y to cover the areas to be painted. - """ - def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): - SVGelement.__init__(self,'pattern',**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - if patternUnits<>None: - self.attributes['patternUnits']=patternUnits - -class title(SVGelement): - """t=title(text,**args) - - a title is a text element. The text is displayed in the title bar - add at least one to the root svg element - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'title',**args) - if text<>None: - self.text=text - -class description(SVGelement): - """d=description(text,**args) - - a description can be added to any element and is used for a tooltip - Add this element before adding other elements. - """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'desc',**args) - if text<>None: - self.text=text - -class lineargradient(SVGelement): - """lg=lineargradient(x1,y1,x2,y2,id,**args) - - defines a lineargradient using two xy pairs. - stop elements van be added to define the gradient colors. - """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): - SVGelement.__init__(self,'linearGradient',**args) - if x1<>None: - self.attributes['x1']=x1 - if y1<>None: - self.attributes['y1']=y1 - if x2<>None: - self.attributes['x2']=x2 - if y2<>None: - self.attributes['y2']=y2 - if id<>None: - self.attributes['id']=id - -class radialgradient(SVGelement): - """rg=radialgradient(cx,cy,r,fx,fy,id,**args) - - defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint. - stop elements van be added to define the gradient colors. - """ - def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): - SVGelement.__init__(self,'radialGradient',**args) - if cx<>None: - self.attributes['cx']=cx - if cy<>None: - self.attributes['cy']=cy - if r<>None: - self.attributes['r']=r - if fx<>None: - self.attributes['fx']=fx - if fy<>None: - self.attributes['fy']=fy - if id<>None: - self.attributes['id']=id - -class stop(SVGelement): - """st=stop(offset,stop_color,**args) - - Puts a stop color at the specified radius - """ - def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self,'stop',{'offset':offset},**args) - if stop_color<>None: - self.attributes['stop-color']=stop_color - -class style(SVGelement): - """st=style(type,cdata=None,**args) - - Add a CDATA element to this element for defing in line stylesheets etc.. - """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args) - - -class image(SVGelement): - """im=image(url,width,height,x,y,**args) - - adds an image to the drawing. Supported formats are .png, .jpg and .svg. - """ - def __init__(self,url,x=None,y=None,width=None,height=None,**args): - if width==None or height==None: - if width<>None: - raise ValueError, 'height is required' - if height<>None: - raise ValueError, 'width is required' - else: - raise ValueError, 'both height and width are required' - SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - -class cursor(SVGelement): - """c=cursor(url,**args) - - defines a custom cursor for a element or a drawing - """ - def __init__(self,url,**args): - SVGelement.__init__(self,'cursor',{'xlink:href':url},**args) - - -class marker(SVGelement): - """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args) - - defines a marker which can be used as an endpoint for a line or other pathtypes - add an element to it which should be used as a marker. - """ - def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): - SVGelement.__init__(self,'marker',**args) - if id<>None: - self.attributes['id']=id - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if refx<>None: - self.attributes['refX']=refx - if refy<>None: - self.attributes['refY']=refy - if markerWidth<>None: - self.attributes['markerWidth']=markerWidth - if markerHeight<>None: - self.attributes['markerHeight']=markerHeight - -class group(SVGelement): - """g=group(id,**args) - - a group is defined by an id and is used to contain elements - g.addElement(SVGelement) - """ - def __init__(self,id=None,**args): - SVGelement.__init__(self,'g',**args) - if id<>None: - self.attributes['id']=id - -class symbol(SVGelement): - """sy=symbol(id,viewbox,**args) - - defines a symbol which can be used on different places in your graph using - the use element. A symbol is not rendered but you can use 'use' elements to - display it by referencing its id. - sy.addElement(SVGelement) - """ - - def __init__(self,id=None,viewBox=None,**args): - SVGelement.__init__(self,'symbol',**args) - if id<>None: - self.attributes['id']=id - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - -class defs(SVGelement): - """d=defs(**args) - - container for defining elements - """ - def __init__(self,**args): - SVGelement.__init__(self,'defs',**args) - -class switch(SVGelement): - """sw=switch(**args) - - Elements added to a switch element which are "switched" by the attributes - requiredFeatures, requiredExtensions and systemLanguage. - Refer to the SVG specification for details. - """ - def __init__(self,**args): - SVGelement.__init__(self,'switch',**args) - - -class use(SVGelement): - """u=use(link,x,y,width,height,**args) - - references a symbol by linking to its id and its position, height and width - """ - def __init__(self,link,x=None,y=None,width=None,height=None,**args): - SVGelement.__init__(self,'use',{'xlink:href':link},**args) - if x<>None: - self.attributes['x']=x - if y<>None: - self.attributes['y']=y - - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - - -class link(SVGelement): - """a=link(url,**args) - - a link is defined by a hyperlink. add elements which have to be linked - a.addElement(SVGelement) - """ - def __init__(self,link='',**args): - SVGelement.__init__(self,'a',{'xlink:href':link},**args) - -class view(SVGelement): - """v=view(id,**args) - - a view can be used to create a view with different attributes""" - def __init__(self,id=None,**args): - SVGelement.__init__(self,'view',**args) - if id<>None: - self.attributes['id']=id - -class script(SVGelement): - """sc=script(type,type,cdata,**args) - - adds a script element which contains CDATA to the SVG drawing - - """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args) - -class animate(SVGelement): - """an=animate(attribute,from,to,during,**args) - - animates an attribute. - """ - def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur - -class animateMotion(SVGelement): - """an=animateMotion(pathdata,dur,**args) - - animates a SVGelement over the given path in dur seconds - """ - def __init__(self,pathdata,dur,**args): - SVGelement.__init__(self,'animateMotion',**args) - if pathdata<>None: - self.attributes['path']=str(pathdata) - if dur<>None: - self.attributes['dur']=dur - -class animateTransform(SVGelement): - """antr=animateTransform(type,from,to,dur,**args) - - transform an element from and to a value. - """ - def __init__(self,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args) - #As far as I know the attributeName is always transform - if type<>None: - self.attributes['type']=type - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur -class animateColor(SVGelement): - """ac=animateColor(attribute,type,from,to,dur,**args) - - Animates the color of a element - """ - def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args) - if type<>None: - self.attributes['type']=type - if fr<>None: - self.attributes['from']=fr - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur -class set(SVGelement): - """st=set(attribute,to,during,**args) - - sets an attribute to a value for a - """ - def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self,'set',{'attributeName':attribute},**args) - if to<>None: - self.attributes['to']=to - if dur<>None: - self.attributes['dur']=dur - - - -class svg(SVGelement): - """s=svg(viewbox,width,height,**args) - - a svg or element is the root of a drawing add all elements to a svg element. - You can have different svg elements in one svg file - s.addElement(SVGelement) - - eg - d=drawing() - s=svg((0,0,100,100),'100%','100%') - c=circle(50,50,20) - s.addElement(c) - d.setSVG(s) - d.toXml() - """ - def __init__(self,viewBox=None, width=None, height=None,**args): - SVGelement.__init__(self,'svg',**args) - if viewBox<>None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if width<>None: - self.attributes['width']=width - if height<>None: - self.attributes['height']=height - self.namespace="http://www.w3.org/2000/svg" - -class drawing: - """d=drawing() - - this is the actual SVG document. It needs a svg element as a root. - Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG - source to the screen or to a file - d=drawing() - d.addSVG(svg) - d.toXml(optionalfilename) - """ - - def __init__(self, entity={}): - self.svg=None - self.entity = entity - def setSVG(self,svg): - self.svg=svg - #Voeg een element toe aan de grafiek toe. - if use_dom_implementation==0: - def toXml(self, filename='',compress=False): - import cStringIO - xml=cStringIO.StringIO() - xml.write("<?xml version='1.0' encoding='UTF-8'?>\n") - xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") - if self.entity: - xml.write(" [\n") - for item in self.entity.keys(): - xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item])) - xml.write("]") - xml.write(">\n") - self.svg.toXml(0,xml) - if not filename: - if compress: - import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - if filename[-4:]=='svgz': - import gzip - f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f=file(filename,'w') - f.write(xml.getvalue()) - f.close() - - else: - def toXml(self,filename='',compress=False): - """drawing.toXml() ---->to the screen - drawing.toXml(filename)---->to the file - writes a svg drawing to the screen or to a file - compresses if filename ends with svgz or if compress is true - """ - doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') - - global root - #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but - #that is a bit messy. - root=implementation.createDocument(None,None,doctype) - #Create the xml document. - global appender - def appender(element,elementroot): - """This recursive function appends elements to an element and sets the attributes - and type. It stops when alle elements have been appended""" - if element.namespace: - e=root.createElementNS(element.namespace,element.type) - else: - e=root.createElement(element.type) - if element.text: - textnode=root.createTextNode(element.text) - e.appendChild(textnode) - for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2 - e.setAttribute(attribute,str(element.attributes[attribute])) - if element.elements: - for el in element.elements: - e=appender(el,e) - elementroot.appendChild(e) - return elementroot - root=appender(self.svg,root) - if not filename: - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) - if compress: - import gzip - f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - try: - if filename[-4:]=='svgz': - import gzip - import cStringIO - xml=cStringIO.StringIO() - PrettyPrint(root,xml) - f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f=open(filename,'w') - PrettyPrint(root,f) - f.close() - except: - print "Cannot write SVG file: " + filename - def validate(self): - try: - import xml.parsers.xmlproc.xmlval - except: - raise exceptions.ImportError,'PyXml is required for validating SVG' - svg=self.toXml() - xv=xml.parsers.xmlproc.xmlval.XMLValidator() - try: - xv.feed(svg) - except: - raise "SVG is not well formed, see messages above" - else: - print "SVG well formed" -if __name__=='__main__': - - - d=drawing() - s=svg((0,0,100,100)) - r=rect(-100,-100,300,300,'cyan') - s.addElement(r) - - t=title('SVGdraw Demo') - s.addElement(t) - g=group('animations') - e=ellipse(0,0,5,2) - g.addElement(e) - c=circle(0,0,1,'red') - g.addElement(c) - pd=pathdata(0,-10) - for i in range(6): - pd.relsmbezier(10,5,0,10) - pd.relsmbezier(-10,5,0,10) - an=animateMotion(pd,10) - an.attributes['rotate']='auto-reverse' - an.attributes['repeatCount']="indefinite" - g.addElement(an) - s.addElement(g) - for i in range(20,120,20): - u=use('#animations',i,0) - s.addElement(u) - for i in range(0,120,20): - for j in range(5,105,10): - c=circle(i,j,1,'red','black',.5) - s.addElement(c) - d.setSVG(s) - - print d.toXml() diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 2336e722..94dd7cbf 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -34,9 +34,6 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig - - - # NL, 07/27/2010. moved from webqtlForm.py #Dict of Parents and F1 information, In the order of [F1, Mat, Pat] ParInfo ={ @@ -64,43 +61,10 @@ ParInfo ={ 'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'] } - -# NL, 07/27/2010. moved from template.py -IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py -IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py -IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py -IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py - -IMGASC = HT.Image("/images/sortup.gif", border=0) -IMGASCON = HT.Image("/images/sortupon.gif", border=0) -IMGDESC = HT.Image("/images/sortdown.gif", border=0) -IMGDESCON = HT.Image("/images/sortdownon.gif", border=0) - -""" -IMGASC = HT.Image("/images/sortup_icon.gif", border=0) -IMGASCON = HT.Image("/images/sortupon.gif", border=0) -IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0) -IMGDESCON = HT.Image("/images/sortdownon.gif", border=0) -IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0) -""" - -PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0) - ######################################### # Accessory Functions ######################################### -def decodeEscape(str): - a = str - pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])') - match = pattern.findall(a) - matched = [] - for item in match: - if item not in matched: - a = a.replace(item, '%c' % eval("0x"+item[-2:])) - matched.append(item) - return a - def exportData(hddn, tdata, NP = None): for key in tdata.keys(): _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N @@ -136,37 +100,6 @@ def genShortStrainName(RISet='', input_strainName=''): pass return strainName -def toInt(in_str): - "Converts an arbitrary string to an unsigned integer" - start = -1 - end = -1 - for i, char in enumerate(in_str): - if char >= '0' and char <= '9': - if start < 0: - start = i - end = i+1 - else: - if start >= 0: - break - if start < end: - return int(in_str[start:end]) - else: - return -1 - -def transpose(m): - 'transpose a matrix' - n = len(m) - return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))] - -def asymTranspose(m): - 'transpose a matrix' - t = max(map(len, m)) - n = len(m) - m2 = [["-"]]*n - for i in range(n): - m2[i] = m[i] + [""]*(t- len(m[i])) - return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))] - def genRandStr(prefix = "", length=8, chars=string.letters+string.digits): from random import choice _str = prefix[:] @@ -174,27 +107,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits): _str += choice(chars) return _str -def generate_session(): - import sha - return sha.new(str(time.time())).hexdigest() - -def cvt2Dict(x): - tmp = {} - for key in x.keys(): - tmp[key] = x[key] - return tmp - -def dump_session(session_obj, filename): - "It seems mod python can only cPickle most basic data type" - import cPickle - session_file = open(filename, 'wb') - #try: - # pass - #except: - # pass - cPickle.dump(session_obj, session_file) - session_file.close() - def StringAsFloat(str): 'Converts string to float but catches any exception and returns None' try: diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 73072423..abf9fc89 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -296,60 +296,8 @@ class CorrelationResults(object): if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": self.do_tissue_correlation_for_trait_list() - #print("self.correlation_results: ", pf(self.correlation_results)) - self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) - #XZ, 09/18/2008: get all information about the user selected database. - #target_db_name = fd.corr_dataset - #self.target_db_name = start_vars['corr_dataset'] - - # Zach said this is ok - # Auth if needed - #try: - # auth_user_for_db(self.db, self.cursor, self.target_db_name, self.privilege, self.userName) - #except AuthException as e: - # detail = [e.message] - # return self.error(detail) - - #XZ, 09/18/2008: filter out the strains that have no value. - #self.sample_names, vals, vars, N = fd.informativeStrains(sample_list) - - #print("samplenames is:", pf(self.sample_names)) - #CF - If less than a minimum number of strains/cases in common, don't calculate anything - #if len(self.sample_names) < self.corr_min_informative: - # detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)] - # self.error(heading=None, detail=detail) - - #correlation_method = self.CORRELATION_METHODS[self.method] - #rankOrder = self.RANK_ORDERS[self.method] - - # CF - Number of results returned - # Todo: Get rid of self.returnNumber - - #self.record_count = 0 - - #myTrait = get_custom_trait(fd, self.cursor) - - - # We will not get Literature Correlations if there is no GeneId because there is nothing - # to look against - #self.geneid = self.this_trait.geneid - - # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against - #self.trait_symbol = myTrait.symbol - - - #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid - #self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.dataset.group.species, self.geneid) - - #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)' - #self.tissue_probeset_freeze_id = 1 - - #traitList = self.correlate() - - #print("Done doing correlation calculation") - ############################################################################################################################################ def get_formatted_corr_type(self): diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 632c2f8f..81da8976 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -190,21 +190,6 @@ class MarkerRegression(object): self.js_data = start_vars['js_data'] self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table - #ZS: Think I can just get all this from dataset object now - #RISet and Species - #if not fd.genotype: - # fd.readGenotype() - # - #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression') - # - #if ((fd.parentsf14regression == 'on') and fd.genotype_2): - # fd.genotype = fd.genotype_2 - #else: - # fd.genotype = fd.genotype_1 - #fd.strainlist = list(fd.genotype.prgy) - # - #self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - if self.dataset.group.species == "rat": self._ucscDb = "rn3" elif self.dataset.group.species == "mouse": @@ -212,7 +197,6 @@ class MarkerRegression(object): else: self._ucscDb = "" - ##################################### # Options ##################################### diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3c2cca94..8ff359a7 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -57,7 +57,6 @@ from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH from utility.helper_functions import get_species_groups -from base import webqtlFormData from base.webqtlConfig import GENERATED_IMAGE_DIR from utility.benchmark import Bench @@ -163,62 +162,37 @@ def css(filename): def twitter(filename): return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) -#@app.route("/data_sharing") -#def data_sharing_page(): -# logger.info("In data_sharing") -# fd = webqtlFormData.webqtlFormData(request.args) -# logger.info("1Have fd") -# sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) -# info, htmlfilelist = sharingInfoObject.getBody(infoupdate="") -# logger.info("type(htmlfilelist):", type(htmlfilelist)) -# htmlfilelist = htmlfilelist.encode("utf-8") -# #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) -# logger.info("1 Made it to rendering") -# return render_template("data_sharing.html", -# info=info, -# htmlfilelist=htmlfilelist) - - @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") logger.info(request.url) - if 'info_database' in request.args: - logger.info("Going to sharing_info_page") - template_vars = sharing_info_page() - if template_vars.redirect_url: - logger.info("Going to redirect") - return flask.redirect(template_vars.redirect_url) - else: - return render_template("data_sharing.html", **template_vars.__dict__) + 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: - 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("Skipping Redis cache (USE_REDIS=False)") - logger.info("request.args is", request.args) - the_search = search_results.SearchResultPage(request.args) - result = the_search.__dict__ - valid_search = result['search_term_exists'] + logger.info("request.args is", request.args) + the_search = search_results.SearchResultPage(request.args) + result = the_search.__dict__ + valid_search = result['search_term_exists'] - logger.debugf("result", result) + logger.debugf("result", result) - if USE_REDIS and valid_search: - Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*60) + if USE_REDIS and valid_search: + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) - if valid_search: - return render_template("search_result_page.html", **result) - else: - return render_template("search_error.html") + if valid_search: + return render_template("search_result_page.html", **result) + else: + return render_template("search_error.html") @app.route("/gsearch", methods=('GET',)) def gsearchact(): @@ -741,7 +715,6 @@ def network_graph_page(): def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) logger.info(request.url) - #fd = webqtlFormData.webqtlFormData(request.form) template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) @@ -777,15 +750,6 @@ def submit_bnw(): template_vars = get_bnw_input(request.form) return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) -# 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""" - logger.info("In sharing_info_page") - logger.info(request.url) - fd = webqtlFormData.webqtlFormData(request.args) - template_vars = SharingInfoPage.SharingInfoPage(fd) - return template_vars - # Take this out or secure it before putting into production @app.route("/get_temp_data") def get_temp_data(): |