From d734346335f056955fb2e3b657c45eb2f6ae1f81 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 9 Dec 2015 16:57:05 +0000
Subject: Fixed search result page text to make sense for all working search
terms
Added a bunch of print statements to GN1 mapping code to locate where code stalls
---
wqflask/wqflask/do_search.py | 5 +++-
.../marker_regression/marker_regression_gn1.py | 16 +++++++++++--
wqflask/wqflask/templates/search_result_page.html | 27 ++++++++++++++++++++--
3 files changed, 43 insertions(+), 5 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 617d7942..a6f9c949 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -861,7 +861,10 @@ class PositionSearch(DoSearch):
try:
self.chr = int(self.chr)
except:
- self.chr = int(self.chr.replace('chr', ''))
+ if 'chr' in self.chr:
+ self.chr = int(self.chr.replace('chr', ''))
+ else:
+ self.chr = int(self.chr.replace('CHR', ''))
def run(self):
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index c838b3ec..f2fc12a4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -344,8 +344,6 @@ class MarkerRegression(object):
self.GraphInterval = self.MbGraphInterval #Mb
else:
self.GraphInterval = self.cMGraphInterval #cM
-
-
################################################################
# Get Trait Values and Infomation
@@ -509,12 +507,16 @@ class MarkerRegression(object):
################################################################
# Plots goes here
################################################################
+ print("BEFORE GN1 PLOT")
if self.plotScale != 'physic' or self.multipleInterval:
showLocusForm = webqtlUtil.genRandStr("fm_")
else:
showLocusForm = ""
+ print("BEFORE PIL CANVAS")
intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
+ print("BEFORE PLOTINTMAPPING")
gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
+ print("AFTER PLOTINTMAPPING")
filename= webqtlUtil.genRandStr("Itvl_")
intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
@@ -527,6 +529,8 @@ class MarkerRegression(object):
intCanvasX2.save(os.path.join(webqtlConfig.IMGDIR, filename+"X2"), format='png')
#DLintImgX2=HT.Href(text='Download',url = '/image/'+filename+'X2.png', Class='smallsize', target='_blank')
+ print("AFTER GN1 PLOT")
+
textUrl = self.writeQTL2Text(fd, filename)
################################################################
@@ -739,6 +743,7 @@ class MarkerRegression(object):
endPixelX = (xLeftOffset + plotWidth)
#Drawing Area Height
+ print("DRAWING AREA HEIGHT")
drawAreaHeight = plotHeight
if self.plotScale == 'physic' and self.selectedChr > -1:
drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
@@ -764,6 +769,7 @@ class MarkerRegression(object):
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
+ print("DRAW BACKGROUND")
plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
#draw bootstap
@@ -772,6 +778,7 @@ class MarkerRegression(object):
# Draw clickable region and gene band if selected
if self.plotScale == 'physic' and self.selectedChr > -1:
+ print("DRAW CLICKABLE REGION")
self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
if self.geneChecked and self.geneCol:
self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
@@ -779,14 +786,18 @@ class MarkerRegression(object):
self.drawSNPTrackNew(canvas, offset=newoffset, zoom = 2*zoom, startMb=startMb, endMb = endMb)
## BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked:
+ print("DRAW HAPLOTYPE")
self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
## END HaplotypeAnalyst
# Draw X axis
+ print("DRAW X AXIS")
self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
# Draw QTL curve
+ print("DRAW QTL CURVE")
self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
#draw legend
+ print("DRAW LEGEND")
if self.multipleInterval:
self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
elif self.legendChecked:
@@ -795,6 +806,7 @@ class MarkerRegression(object):
pass
#draw position, no need to use a separate function
+ print("DRAW PROBESET POSITION")
if self.genotype.Mbmap:
self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 7b3df00f..7b7f0037 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -17,9 +17,32 @@
<!-- Need to customize text more for other types of searches -->
<p>We searched <a href="/static/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
- to find all records that match
+ to find all records
{% for word in search_terms %}
- <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
+ {% if word.key|lower == "rif" %}
+ with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "go" %}
+ with <u>Gene Ontology ID</u> <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "wiki" %}
+ with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "mean" %}
+ with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.key|lower == "lrs" or word.key|lower == "translrs" or word.key|lower == "cislrs" %}
+ {% if word.search_term|length == 1 %}
+ with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 2 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 3 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if not loop.last %} and {% endif %}
+ {% elif word.search_term|length == 5 %}
+ with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if not loop.last %} and {% endif %}
+ {% endif %}
+ {% elif word.key|lower == "position" %}
+ with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if not loop.last %} and {% endif %}
+ {% else %}
+ with {{ word.key|lower }} matching {{ word.search_term[0] }}
+ {% endif %}
+ <!--<strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}-->
{% endfor %}.
</p>
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