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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py110
1 files changed, 36 insertions, 74 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 00f9acb3..2834f1c3 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -35,8 +35,7 @@ import json
from flask import Flask, g
-from htmlgen import (Element,Paragraph,LineBreak,Image,Link,Form,
- Input)
+from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from base.GeneralObject import GeneralObject
@@ -50,41 +49,6 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
-def set_attributes(element, attributes):
- for attr_name, attr_value in attributes.items():
- if attr_value is not None:
- if attr_value.endswith("_"):
- element.set_attribute(attr_name[:-1], attr_value)
- else:
- element.set_attribute(attr_name, attr_value)
-
- return element
-
-def make_map(**kwargs):
- return set_attributes(Element("map"), kwargs)
-
-def make_map_area(**kwargs):
- return set_attributes(Element("area"), kwargs)
-
-def make_image(url, alt=None, width=None, height=None, border=None):
- img = Image(url=url, alternate_text=alt)
- if width:
- img.width = width
-
- if height:
- img.height = height
-
- if border:
- img.border = border
-
- return img
-
-def make_input(type_, name, value, class_=None, onClick=None):
- return set_attributes(Input(type_=type_), kwargs)
-
-def make_link(url, content=(), **kwargs):
- return set_attributes(Link(url, *content), kwargs)
-
#########################################
# Inteval Mapping Plot Page
#########################################
@@ -116,7 +80,7 @@ class DisplayMappingResults(object):
DRAW_DETAIL_MB = 4
DRAW_UTR_LABELS_MB = 4
- qmarkImg = make_image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
+ qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
# Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
# like the ones on the image, though, which is why we don't use it here.
@@ -489,7 +453,7 @@ class DisplayMappingResults(object):
self.filename= webqtlUtil.genRandStr("Itvl_")
intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png')
- intImg=make_image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
+ intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
#Scales plot differently for high resolution
if self.draw2X:
@@ -502,13 +466,11 @@ class DisplayMappingResults(object):
################################################################
#this form is used for opening Locus page or trait page, only available for genetic mapping
if showLocusForm:
- showLocusForm = Form(url= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE))
- showLocusForm.multipart = True # enctype='multipart/form-data'
- showLocusForm.set_attribute("name", showLocusForm)
- showLocusForm.append(make_input(type='hidden', name="submit"))
+ showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
+ name=showLocusForm, submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
- showLocusForm.append(make_input(name=key, value=hddn[key], type='hidden'))
+ showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
showLocusForm.append(intImg)
else:
showLocusForm = intImg
@@ -519,11 +481,10 @@ class DisplayMappingResults(object):
################################################################
# footnote goes here
################################################################
- btminfo = Paragraph()
- btminfo.set_attribute("id", "smallsize") #Small('More information about this graph is available here.')
+ btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
- btminfo.append(LineBreak(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
+ btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
#calculating margins
@@ -576,7 +537,7 @@ class DisplayMappingResults(object):
drawAreaHeight -= 60
#Image map
- gifmap = make_map(name = "WebQTLImageMap")
+ gifmap = HT.Map(name = "WebQTLImageMap")
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
@@ -882,7 +843,7 @@ class DisplayMappingResults(object):
if thisTrait.db:
COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
- Areas = make_map_area(shape='rect',coords=COORDS,href=HREF)
+ Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
gifmap.areas.append(Areas)
def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
@@ -1199,7 +1160,7 @@ class DisplayMappingResults(object):
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
# NL: 06-02-2011 Rob required to display NCBI info in a new window
- gifmap.areas.append(make_map_area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+ gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
## BEGIN HaplotypeAnalyst
def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1355,7 +1316,7 @@ class DisplayMappingResults(object):
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
HREF = ''
- gifmap.areas.append(make_map_area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+ gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
# if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
# resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
@@ -1452,7 +1413,7 @@ class DisplayMappingResults(object):
WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
- gifmap.areas.append(make_map_area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
@@ -1463,7 +1424,7 @@ class DisplayMappingResults(object):
else:
PHENOGEN_HREF = "https://phenogen.org/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
- gifmap.areas.append(make_map_area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR)
canvas.drawLine(xBrowse1, phenogenPaddingTop, xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
@@ -1473,7 +1434,7 @@ class DisplayMappingResults(object):
else:
UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
- gifmap.areas.append(make_map_area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
@@ -1483,7 +1444,7 @@ class DisplayMappingResults(object):
else:
ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
- gifmap.areas.append(make_map_area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
# end for
@@ -1665,7 +1626,7 @@ class DisplayMappingResults(object):
xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
- Areas=make_map_area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
+ Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
gifmap.areas.append(Areas)
##piddle bug
if j == 0:
@@ -1800,8 +1761,8 @@ class DisplayMappingResults(object):
else:
sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
- Areas1 = make_map_area(shape='rect',coords=sugg_coords,title=sugg_title)
- Areas2 = make_map_area(shape='rect',coords=sig_coords,title=sig_title)
+ Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
+ Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
gifmap.areas.append(Areas1)
gifmap.areas.append(Areas2)
@@ -2095,7 +2056,7 @@ class DisplayMappingResults(object):
#add by NL 09-03-2010
HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList)
#HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
- Areas = make_map_area(shape='rect',coords=COORDS,href=HREF)
+ Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
gifmap.areas.append(Areas)
startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
@@ -2180,7 +2141,7 @@ class DisplayMappingResults(object):
tableIterationsCnt = tableIterationsCnt + 1
this_row = [] #container for the cells of each row
- selectCheck = make_input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], class_="checkbox trait_checkbox") #checkbox for each row
+ selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row
geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
tenPercentLength = geneLength*0.0001
@@ -2191,9 +2152,9 @@ class DisplayMappingResults(object):
geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
if theGO["snpCount"]:
- snpString = make_link(url="http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (theGO["Chromosome"],
+ snpString = HT.Href(url="http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (theGO["Chromosome"],
theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]),
- content=(theGO["snpCount"],), target="_blank", class_="normalsize")
+ text=theGO["snpCount"], target="_blank", Class="normalsize")
else:
snpString = 0
@@ -2238,27 +2199,27 @@ class DisplayMappingResults(object):
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
- make_link(geneIdString, content=(theGO["GeneSymbol"],), target="_blank").__str__(),
- make_link(mouseStartString, content=("%0.6f" % txStart,), target="_blank").__str__(),
- make_link("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), content=("%0.3f" % geneLength,)).__str__(),
+ HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(),
+ HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(),
+ HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
snpString,
snpDensityStr,
avgExpr,
humanChr,
- make_link(humanStartString, content=(humanStartDisplay,), target="_blank").__str__(),
+ HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
literatureCorrelationString,
geneDescription]
else:
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
- make_link(geneIdString, content=(theGO["GeneSymbol"],), target="_blank").__str__(),
- make_link(mouseStartString, content=("%0.6f" % txStart,), target="_blank").__str__(),
- make_link("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), content=("%0.3f" % geneLength,)).__str__(),
+ HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(),
+ HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(),
+ HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
snpString,
snpDensityStr,
avgExpr,
humanChr,
- make_link(humanStartString, content=(humanStartDisplay,), target="_blank").__str__(),
+ HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
geneDescription]
gene_table_body.append(this_row)
@@ -2266,12 +2227,13 @@ class DisplayMappingResults(object):
elif self.dataset.group.species == 'rat':
for gIndex, theGO in enumerate(geneCol):
this_row = [] #container for the cells of each row
- selectCheck = make_input(type_="checkbox", name="searchResult", class_="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
+ selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row
- #webqtlSearch = make_link(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], content=(">>",), target="_blank").__str__()
+ #ZS: May want to get this working again later
+ #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
if theGO["GeneID"] != "":
- geneSymbolNCBI = make_link("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], content=(theGO["GeneSymbol"],), class_="normalsize", target="_blank").__str__()
+ geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blank").__str__()
else:
geneSymbolNCBI = theGO["GeneSymbol"]
@@ -2340,4 +2302,4 @@ class DisplayMappingResults(object):
lCorr = lCorr[0]
break
except: raise #lCorr = None
- return lCorr
+ return lCorr \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 10:46:12 +0000