From 23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 23:07:33 +0000
Subject: Removed svg.py, which I know isn't used, and webqtlFormData, which
I'm pretty sure also isn't used any more.
Also removed some other unused code from the files listed
---
wqflask/base/webqtlFormData.py | 257 -----
wqflask/utility/Plot.py | 1 -
wqflask/utility/svg.py | 1068 --------------------
wqflask/utility/webqtlUtil.py | 88 --
wqflask/wqflask/correlation/show_corr_results.py | 52 -
.../marker_regression/marker_regression_gn1.py | 16 -
wqflask/wqflask/views.py | 80 +-
7 files changed, 22 insertions(+), 1540 deletions(-)
delete mode 100644 wqflask/base/webqtlFormData.py
delete mode 100644 wqflask/utility/svg.py
(limited to 'wqflask')
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 text 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 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)+'\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+'\n')
- elif self.text:
- f.write('\n')
- elif self.cdata:
- f.write('\t'*level+'\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="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("\n")
- xml.write("\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():
--
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