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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py74
1 files changed, 49 insertions, 25 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 255e3b74..ccdafa14 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -35,7 +35,7 @@ import json
from flask import Flask, g
-from htmlgen import HTMLgen2 as HT
+import htmlgen as HT
from base import webqtlConfig
from base.GeneralObject import GeneralObject
@@ -88,35 +88,60 @@ class HtmlGenWrapper:
"""Wrapper Methods for HTML gen"""
@staticmethod
def create_image_tag(**kwargs):
- return HT.Image(**kwargs)
+ image = HT.Image("", "")
+ for key, value in list(kwargs.items()):
+ image.set_attribute(key, value)
+ return image
@staticmethod
def create_form_tag(**kwargs):
- return HT.Form(**kwargs)
+ form = HT.Form("POST", "") # Default method is POST
+
+ for key, value in list(kwargs.items()):
+ if key == "submit":
+ form.append(value)
+ continue
+ form.set_attribute(key.replace("cgi", "action"), str(value))
+ return form
@staticmethod
def create_p_tag(**kwargs):
- return HT.Paragraph(**kwargs)
+ paragraph = HT.Paragraph()
+ for key, value in list(kwargs.items()):
+ paragraph.set_attribute(key, value)
+ return paragraph
@staticmethod
def create_br_tag():
- return HT.BR()
+ return HT.VoidElement("br")
@staticmethod
def create_input_tag(**kwargs):
- return HT.Input(**kwargs)
+ input_ = HT.Input()
+ for key, value in list(kwargs.items()):
+ input_.set_attribute(key.lower().replace("_", ""), value)
+ return input_
@staticmethod
def create_area_tag(**kwargs):
- return HT.Area(**kwargs)
+ area = HT.VoidElement("area")
+ for key, value in list(kwargs.items()):
+ area.set_attribute(key, value)
+ return area
@staticmethod
def create_link_tag(href, content, **kwargs):
- return HT.Href(href, content, **kwargs)
+ link = HT.Link(href, content)
+ for key, value in list(kwargs.items()):
+ link.set_attribute(key, value)
+ return link
@staticmethod
def create_map_tag(**kwargs):
- return HT.Map(**kwargs)
+ map_ = HT.Element("map")
+ for key, value in list(kwargs.items()):
+ map_.set_attribute(key, value)
+ return map_
class DisplayMappingResults(object):
@@ -554,7 +579,6 @@ class DisplayMappingResults(object):
src="/image/{}.png".format(self.filename),
border="0", usemap='#WebQTLImageMap'
)
- self.intImg = intImg
#Scales plot differently for high resolution
if self.draw2X:
@@ -575,12 +599,12 @@ class DisplayMappingResults(object):
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
enctype='multipart/form-data',
name=showLocusForm,
- submit=HtmlGenWrapper.create_input_tag(type='hidden'))
+ submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
showLocusForm.append(HtmlGenWrapper.create_input_tag(
- name=key, value=hddn[key], type='hidden'))
+ name=key, value=hddn[key], type_='hidden'))
showLocusForm.append(intImg)
else:
showLocusForm = intImg
@@ -1002,7 +1026,7 @@ class DisplayMappingResults(object):
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 = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF)
- gifmap.areas.append(Areas) ### TODO
+ gifmap.append(Areas) ### TODO
def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
im_drawer = ImageDraw.Draw(canvas)
@@ -1404,7 +1428,7 @@ 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(
+ gifmap.append(
HtmlGenWrapper.create_area_tag(
shape='rect',
coords=COORDS,
@@ -1578,7 +1602,7 @@ 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(
+ gifmap.append(
HtmlGenWrapper.create_area_tag(
shape='rect',
coords=COORDS,
@@ -1702,7 +1726,7 @@ 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(
+ gifmap.append(
HtmlGenWrapper.create_area_tag(
shape='rect',
coords=WEBQTL_COORDS,
@@ -1724,7 +1748,7 @@ class DisplayMappingResults(object):
else:
PHENOGEN_HREF = "https://phenogen.org/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(
+ gifmap.append(
HtmlGenWrapper.create_area_tag(
shape='rect',
coords=PHENOGEN_COORDS,
@@ -1745,7 +1769,7 @@ 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(
+ gifmap.append(
HtmlGenWrapper.create_area_tag(
shape='rect',
coords=UCSC_COORDS,
@@ -1767,7 +1791,7 @@ 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(HtmlGenWrapper.create_area_tag(
+ gifmap.append(HtmlGenWrapper.create_area_tag(
shape='rect',
coords=ENSEMBL_COORDS,
href=ENSEMBL_HREF,
@@ -2011,7 +2035,7 @@ class DisplayMappingResults(object):
href=HREF,
target="_blank",
title="Locus : {}".format(Lname))
- gifmap.areas.append(Areas)
+ gifmap.append(Areas)
##piddle bug
if j == 0:
im_drawer.line(
@@ -2227,8 +2251,8 @@ class DisplayMappingResults(object):
shape='rect',
coords=sig_coords,
title=sig_title)
- gifmap.areas.append(Areas1)
- gifmap.areas.append(Areas2)
+ gifmap.append(Areas1)
+ gifmap.append(Areas2)
start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale
return start_pos_x
@@ -2682,7 +2706,7 @@ class DisplayMappingResults(object):
shape='rect',
coords=COORDS,
href=HREF)
- gifmap.areas.append(Areas)
+ gifmap.append(Areas)
startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
return plotXScale
@@ -2768,7 +2792,7 @@ class DisplayMappingResults(object):
this_row = [] #container for the cells of each row
selectCheck = HtmlGenWrapper.create_input_tag(
- type="checkbox",
+ type_="checkbox",
name="selectCheck",
value=theGO["GeneSymbol"],
Class="checkbox trait_checkbox") # checkbox for each row
@@ -2887,7 +2911,7 @@ class DisplayMappingResults(object):
for gIndex, theGO in enumerate(geneCol):
this_row = [] # container for the cells of each row
selectCheck = str(HtmlGenWrapper.create_input_tag(
- type="checkbox",
+ type_="checkbox",
name="selectCheck",
Class="checkbox trait_checkbox")) # checkbox for each row
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 00:32:32 +0000