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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py111
1 files changed, 75 insertions, 36 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 993fc2d9..6a3eeccc 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -34,7 +34,8 @@ import httplib
from flask import Flask, g
-from htmlgen import HTMLgen2 as HT
+from htmlgen import (Element,Paragraph,LineBreak,Image,Link,Form,
+ Input)
from base import webqtlConfig
from base.GeneralObject import GeneralObject
@@ -48,6 +49,41 @@ 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
#########################################
@@ -79,7 +115,7 @@ class DisplayMappingResults(object):
DRAW_DETAIL_MB = 4
DRAW_UTR_LABELS_MB = 4
- qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
+ qmarkImg = make_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.
@@ -445,7 +481,7 @@ class DisplayMappingResults(object):
self.filename= webqtlUtil.genRandStr("Itvl_")
intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png')
- intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
+ intImg=make_image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
#Scales plot differently for high resolution
if self.draw2X:
@@ -458,11 +494,13 @@ class DisplayMappingResults(object):
################################################################
#this form is used for opening Locus page or trait page, only available for genetic mapping
if showLocusForm:
- showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
- name=showLocusForm, submit=HT.Input(type='hidden'))
+ 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"))
hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
- showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+ showLocusForm.append(make_input(name=key, value=hddn[key], type='hidden'))
showLocusForm.append(intImg)
else:
showLocusForm = intImg
@@ -473,10 +511,11 @@ class DisplayMappingResults(object):
################################################################
# footnote goes here
################################################################
- btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
+ btminfo = Paragraph()
+ btminfo.set_attribute("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(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.')
+ 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.')
def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
#calculating margins
@@ -529,7 +568,7 @@ class DisplayMappingResults(object):
drawAreaHeight -= 60
#Image map
- gifmap = HT.Map(name = "WebQTLImageMap")
+ gifmap = make_map(name = "WebQTLImageMap")
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
@@ -835,7 +874,7 @@ 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 = HT.Area(shape='rect',coords=COORDS,href=HREF)
+ Areas = make_map_area(shape='rect',coords=COORDS,href=HREF)
gifmap.areas.append(Areas)
def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
@@ -1152,7 +1191,7 @@ 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(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+ gifmap.areas.append(make_map_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):
@@ -1308,7 +1347,7 @@ 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(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+ gifmap.areas.append(make_map_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.
@@ -1405,7 +1444,7 @@ 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(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+ gifmap.areas.append(make_map_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)
@@ -1416,7 +1455,7 @@ class DisplayMappingResults(object):
else:
PHENOGEN_HREF = "https://phenogen.ucdenver.edu/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(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+ gifmap.areas.append(make_map_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)
@@ -1426,7 +1465,7 @@ 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(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+ gifmap.areas.append(make_map_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)
@@ -1436,7 +1475,7 @@ 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(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+ gifmap.areas.append(make_map_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
@@ -1618,7 +1657,7 @@ 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=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
+ Areas=make_map_area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
gifmap.areas.append(Areas)
##piddle bug
if j == 0:
@@ -1745,8 +1784,8 @@ 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 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
- Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
+ Areas1 = make_map_area(shape='rect',coords=sugg_coords,title=sugg_title)
+ Areas2 = make_map_area(shape='rect',coords=sig_coords,title=sig_title)
gifmap.areas.append(Areas1)
gifmap.areas.append(Areas2)
@@ -2033,7 +2072,7 @@ 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 = HT.Area(shape='rect',coords=COORDS,href=HREF)
+ Areas = make_map_area(shape='rect',coords=COORDS,href=HREF)
gifmap.areas.append(Areas)
startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
@@ -2118,7 +2157,7 @@ class DisplayMappingResults(object):
tableIterationsCnt = tableIterationsCnt + 1
this_row = [] #container for the cells of each row
- selectCheck = HT.Input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row
+ selectCheck = make_input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], class_="checkbox trait_checkbox") #checkbox for each row
geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
tenPercentLength = geneLength*0.0001
@@ -2129,9 +2168,9 @@ 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 = 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"],
+ 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"],
theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]),
- text=theGO["snpCount"], target="_blank", Class="normalsize")
+ content=(theGO["snpCount"],), target="_blank", class_="normalsize")
else:
snpString = 0
@@ -2176,27 +2215,27 @@ class DisplayMappingResults(object):
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
- 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__(),
+ 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__(),
snpString,
snpDensityStr,
avgExpr,
humanChr,
- HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
+ make_link(humanStartString, content=(humanStartDisplay,), target="_blank").__str__(),
literatureCorrelationString,
geneDescription]
else:
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
- 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__(),
+ 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__(),
snpString,
snpDensityStr,
avgExpr,
humanChr,
- HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
+ make_link(humanStartString, content=(humanStartDisplay,), target="_blank").__str__(),
geneDescription]
gene_table_body.append(this_row)
@@ -2204,12 +2243,12 @@ 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 = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
+ selectCheck = make_input(type_="checkbox", name="searchResult", class_="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
- webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
+ webqtlSearch = make_link(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], content=(">>",), target="_blank").__str__()
if theGO["GeneID"] != "":
- 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__()
+ 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__()
else:
geneSymbolNCBI = theGO["GeneSymbol"]
@@ -2249,7 +2288,7 @@ class DisplayMappingResults(object):
str(gIndex+1),
webqtlSearch.__str__() + geneSymbolNCBI,
theGO["TxStart"],
- HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(),
+ make_link(geneLengthURL, content=("%0.3f" % (geneLength*1000.0),)).__str__(),
avgExprVal,
mouseChr,
mouseTxStart,
@@ -2278,4 +2317,4 @@ class DisplayMappingResults(object):
lCorr = lCorr[0]
break
except: raise #lCorr = None
- return lCorr \ No newline at end of file
+ return lCorr
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 14:40:25 +0000