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authorZachary Sloan2013-01-11 23:59:41 +0000
committerZachary Sloan2013-01-11 23:59:41 +0000
commit2b2970d167c5b555e0e0ad0b34b72f817c1fac91 (patch)
tree36fa8c708138fff03593e0f50cc933bcb62b5592 /web/webqtl
parent1db9237a05fd27c80dc963db9916072594156198 (diff)
parentd39b691994a395c45fa242de6d64d12a5470af10 (diff)
downloadgenenetwork2-2b2970d167c5b555e0e0ad0b34b72f817c1fac91.tar.gz
Merge branch 'flask' of http://github.com/zsloan/genenetwork
Diffstat (limited to 'web/webqtl')
-rwxr-xr-xweb/webqtl/base/webqtlConfigLocal.py10
-rw-r--r--web/webqtl/base/webqtlTrait.py9
-rwxr-xr-xweb/webqtl/basicStatistics/updatedBasicStatisticsPage.py54
-rwxr-xr-xweb/webqtl/collection/ExportSelectionDetailInfoPage.py5
-rwxr-xr-xweb/webqtl/correlation/CorrelationPage.py171
-rwxr-xr-xweb/webqtl/maintainance/genSelectDatasetJS.py3
-rwxr-xr-xweb/webqtl/search/SearchResultPage.py6
-rwxr-xr-x[-rw-r--r--]web/webqtl/showTrait/DataEditingPage.py49
8 files changed, 169 insertions, 138 deletions
diff --git a/web/webqtl/base/webqtlConfigLocal.py b/web/webqtl/base/webqtlConfigLocal.py
index dc86bb10..1f986aa7 100755
--- a/web/webqtl/base/webqtlConfigLocal.py
+++ b/web/webqtl/base/webqtlConfigLocal.py
@@ -3,15 +3,15 @@
#########################################
MYSQL_SERVER = 'localhost'
-DB_NAME = 'db_webqtl'
-DB_USER = 'webqtl'
+DB_NAME = 'db_webqtl_zas1024'
+DB_USER = 'webqtlupd'
DB_PASSWD = 'webqtl'
MYSQL_UPDSERVER = 'localhost'
-DB_UPDNAME = 'db_webqtl'
-DB_UPDUSER = 'webqtl'
+DB_UPDNAME = 'db_webqtl_zas1024'
+DB_UPDUSER = 'webqtlupd'
DB_UPDPASSWD = 'webqtl'
-GNROOT = '/gnshare/gn/'
+GNROOT = '/home/zas1024/gn/'
PythonPath = '/usr/bin/python'
PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/'
diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
index f5051e45..2469504f 100644
--- a/web/webqtl/base/webqtlTrait.py
+++ b/web/webqtl/base/webqtlTrait.py
@@ -9,6 +9,10 @@ from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
+from __future__ import print_function, division
+
+from pprint import pformat as pf
+
class webqtlTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -215,6 +219,9 @@ class webqtlTrait:
def retrieveData(self, strainlist=[]):
assert self.db and self.cursor
+ debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w")
+ debug_file.write("strianlist is:" + strainlist + "\n")
+
if self.db.type == 'Temp':
query = '''
SELECT
@@ -341,6 +348,8 @@ class webqtlTrait:
#end if
else:
pass
+
+ debug_file.write("self.data is:", pf(self.data) + "\n")
def keys(self):
return self.__dict__.keys()
diff --git a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
index 156dafe7..ab7ed07d 100755
--- a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
+++ b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
@@ -63,9 +63,9 @@ class updatedBasicStatisticsPage(templatePage):
thisValFull = [strain_names[i], this_strain_val, this_strain_var]
vals.append(thisValFull)
- stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"),
+ stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"),
HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"),
- HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")]
+ HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")]
stats_tabs = HT.List(stats_tab_list)
stats_container = HT.Div(id="stats_tabs", Class="ui-tabs")
@@ -73,7 +73,7 @@ class updatedBasicStatisticsPage(templatePage):
stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs
- table_div = HT.Div(id="statstabs-1")
+ table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;")
table_container = HT.Paragraph()
statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
@@ -86,16 +86,21 @@ class updatedBasicStatisticsPage(templatePage):
table_div.append(table_container)
stats_container.append(table_div)
- boxplot_div = HT.Div(id="statstabs-2")
- boxplot_container = HT.Paragraph()
- boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
- boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
- boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))
- boxplot_container.append(boxplot)
- boxplot_div.append(boxplot_container)
- stats_container.append(boxplot_div)
+ normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;")
+ normalplot_container = HT.Paragraph()
+ normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
+ plotTitle = fd.formdata.getvalue("normalPlotTitle","")
+ normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
+ normalplot.append(HT.TR(HT.TD(normalplot_img)))
+ normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
+ normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
+ "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot",
+ target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))
+ normalplot_container.append(normalplot)
+ normalplot_div.append(normalplot_container)
+ stats_container.append(normalplot_div)
- barName_div = HT.Div(id="statstabs-3")
+ barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;")
barName_container = HT.Paragraph()
barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name")
@@ -104,7 +109,7 @@ class updatedBasicStatisticsPage(templatePage):
barName_div.append(barName_container)
stats_container.append(barName_div)
- barRank_div = HT.Div(id="statstabs-4")
+ barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;")
barRank_container = HT.Paragraph()
barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank")
@@ -112,20 +117,15 @@ class updatedBasicStatisticsPage(templatePage):
barRank_container.append(barRank)
barRank_div.append(barRank_container)
stats_container.append(barRank_div)
-
- normalplot_div = HT.Div(id="statstabs-5")
- normalplot_container = HT.Paragraph()
- normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
- plotTitle = fd.formdata.getvalue("normalPlotTitle","")
- normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
- normalplot.append(HT.TR(HT.TD(normalplot_img)))
- normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
- normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
- "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot",
- target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))
- normalplot_container.append(normalplot)
- normalplot_div.append(normalplot_container)
- stats_container.append(normalplot_div)
+
+ boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;")
+ boxplot_container = HT.Paragraph()
+ boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
+ boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
+ boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))
+ boxplot_container.append(boxplot)
+ boxplot_div.append(boxplot_container)
+ stats_container.append(boxplot_div)
stats_cell.append(stats_container)
stats_script.append(stats_script_text)
diff --git a/web/webqtl/collection/ExportSelectionDetailInfoPage.py b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
index 69f293b2..7238c797 100755
--- a/web/webqtl/collection/ExportSelectionDetailInfoPage.py
+++ b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
@@ -128,7 +128,10 @@ class ExportSelectionDetailInfoPage(templatePage):
count = count + 1
except:
pass
- mean = sum/count
+ if count == 0:
+ mean = 0
+ else:
+ mean = sum/count
text[-1].append(mean)
text[-1] += testval
if len(text[0]) < 255 or len(text) < 255:
diff --git a/web/webqtl/correlation/CorrelationPage.py b/web/webqtl/correlation/CorrelationPage.py
index ce8b8165..72e53f1d 100755
--- a/web/webqtl/correlation/CorrelationPage.py
+++ b/web/webqtl/correlation/CorrelationPage.py
@@ -91,7 +91,7 @@ class Trait(object):
#ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for
#There's probably a better way of dealing with this, but I'll have to ask Christian
- updated_raw_values = []
+ updated_raw_values = []
updated_values = []
for i in range(len(values)):
if values[i] != "None":
@@ -120,7 +120,7 @@ class Trait(object):
ZValue = ZValue*sqrt(self.overlap-3)
self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
+
#XZ, 01/14/2009: This method is for parallel computing only.
#XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
@@ -151,7 +151,7 @@ def get_correlation_method_key(form_data):
#XZ, 09/28/2008: if user select "2", then display 2, 3 and 5.
#XZ, 09/28/2008: if user select "3", then display 1, 3 and 4.
#XZ, 09/28/2008: if user select "4", then display 1, 3 and 4.
- #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
+ #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
method = form_data.formdata.getvalue("method")
if method not in ["1", "2", "3" ,"4", "5"]:
@@ -172,7 +172,7 @@ def get_custom_trait(form_data, cursor):
return None
-#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
+#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
def get_sample_data(form_data):
if form_data.allstrainlist:
mdpchoice = form_data.formdata.getvalue('MDPChoice')
@@ -194,8 +194,8 @@ def get_sample_data(form_data):
strainlist = form_data.allstrainlist
#XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
form_data.readData(form_data.allstrainlist)
- else:
- mdpchoice = None
+ else:
+ mdpchoice = None
strainlist = form_data.strainlist
#XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
form_data.readData()
@@ -267,7 +267,7 @@ class CorrelationPage(templatePage):
CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
"2" : "Genetic Correlation (Spearman's rho)",
"3" : "SGO Literature Correlation",
- "4" : "Tissue Correlation (Pearson's r)",
+ "4" : "Tissue Correlation (Pearson's r)",
"5" : "Tissue Correlation (Spearman's rho)"}
RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
@@ -338,7 +338,7 @@ class CorrelationPage(templatePage):
# 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.species, self.gene_id)
@@ -347,7 +347,7 @@ class CorrelationPage(templatePage):
self.tissue_probeset_freeze_id = 1
traitList = self.correlate(vals)
-
+
_log.info("Done doing correlation calculation")
############################################################################################################################################
@@ -356,12 +356,12 @@ class CorrelationPage(templatePage):
mainfmName = webqtlUtil.genRandStr("fm_")
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden'))
- hddn = {'FormID': 'showDatabase',
+ hddn = {'FormID': 'showDatabase',
'ProbeSetID': '_',
- 'database': self.target_db_name,
- 'databaseFull': self.db.fullname,
- 'CellID': '_',
- 'RISet': fd.RISet,
+ 'database': self.target_db_name,
+ 'databaseFull': self.db.fullname,
+ 'CellID': '_',
+ 'RISet': fd.RISet,
'identification': fd.identification}
if myTrait:
@@ -400,7 +400,7 @@ class CorrelationPage(templatePage):
##############
# Excel file #
- ##############
+ ##############
filename= webqtlUtil.genRandStr("Corr_")
xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button')
# Create a new Excel workbook
@@ -432,7 +432,7 @@ class CorrelationPage(templatePage):
heatmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'heatmap');" % mainfmName)
heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='mintmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
heatmap.append(heatmap_img)
- partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName)
+ partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName)
partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
partialCorr.append(partialCorr_img)
addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, mainfmName))
@@ -454,7 +454,7 @@ class CorrelationPage(templatePage):
selectandor.append(('AND','and'))
selectandor.append(('OR','or'))
selectandor.selected.append('AND')
-
+
#External analysis tools
GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GCAT');" % mainfmName)
@@ -473,8 +473,8 @@ setTimeout('openWebGestalt()', 2000);
function openWebGestalt(){
var thisForm = document['WebGestalt'];
makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
-}
- """ % (mainfmName, len(traitList)))
+}
+ """ % (mainfmName, len(traitList)))
'''
self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % self.db.name)
@@ -484,15 +484,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
GO_tree_value = result[0]
if GO_tree_value:
-
+
WebGestalt = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GOTree');" % mainfmName)
- WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
- WebGestalt.append(WebGestalt_img)
-
+ WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
+ WebGestalt.append(WebGestalt_img)
+
hddnWebGestalt = {
'id_list':'',
'correlation':'',
- 'id_value':'',
+ 'id_value':'',
'llid_list':'',
'id_type':GO_tree_value,
'idtype':'',
@@ -512,7 +512,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
hddnWebGestalt['org'] = 'Mus musculus'
else:
hddnWebGestalt['org'] = ''
-
+
for key in hddnWebGestalt.keys():
form.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
@@ -523,11 +523,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
containerTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="90%",border=0, align="Left")
-
+
if not GO_tree_value:
optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="480", height="80", border=0, align="Left")
optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), align="left"))
- optionsTable.append(HT.TR(HT.TD("&nbsp;"*1,"Select"), HT.TD("Deselect"), HT.TD("&nbsp;"*1,"Invert"), HT.TD("&nbsp;"*3,"Add"), HT.TD("Gene Set"), HT.TD("&nbsp;"*2,"GCAT")))
+ optionsTable.append(HT.TR(HT.TD("&nbsp;"*1,"Select"), HT.TD("Deselect"), HT.TD("&nbsp;"*1,"Invert"), HT.TD("&nbsp;"*3,"Add"), HT.TD("Gene Set"), HT.TD("&nbsp;"*2,"GCAT")))
else:
optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="560", height="80", border=0, align="Left")
optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), HT.TD(WebGestalt), align="left"))
@@ -548,11 +548,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
"""
- if (fd.formdata.getvalue('showHideOptions') == 'less'):
+ if (fd.formdata.getvalue('showHideOptions') == 'less'):
containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
containerTable.append(HT.TR(HT.TD("&nbsp;")))
- else:
- containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
+ else:
+ containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
containerTable.append(HT.TR(HT.TD("&nbsp;")))
"""
@@ -566,8 +566,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
tblobj = {}
if self.db.type=="Geno":
-
- containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
+ containerTable.append(HT.TR(HT.TD(xlsUrl, height=60)))
pageTable.append(HT.TR(HT.TD(containerTable)))
@@ -579,7 +578,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
- tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript)
+ tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript)
workbook.close()
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
@@ -604,15 +603,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
pageTable.append(HT.TR(HT.TD(containerTable)))
-
+
tblobj['header'], worksheet = self.getTableHeaderForPublish(method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
newrow += 1
sortby = self.getSortByValue( calculationMethod = self.method )
-
+
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
-
+
tblobj['body'], worksheet, corrScript = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=self.species)
workbook.close()
@@ -650,7 +649,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
workbook.close()
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
cPickle.dump(tblobj, objfile)
- objfile.close()
+ objfile.close()
#XZ: here is the table of traits
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1", hiddenColumns=["Gene ID","Homologene ID"]), corrScript, Id="sortable")
@@ -708,11 +707,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
if self.species == 'human':
heatmap = ""
-
+
form.append(HT.Input(name='ShowStrains',type='hidden', value =1),
HT.Input(name='ShowLine',type='hidden', value =1),
info, HT.BR(), pageTable, HT.BR())
-
+
TD_LR.append(corrHeading, form, HT.P())
@@ -745,7 +744,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
sortby = ("Tissue r", "down")
elif calculationMethod == "5":
sortby = ("Tissue rho", "down")
-
+
return sortby
@@ -808,7 +807,7 @@ Resorting this table <br>
def getStrainIds(self, species=None, strains=[]):
StrainIds = []
for item in strains:
- self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE
+ self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE
Strain.Name="%s" and Strain.SpeciesId=Species.Id and Species.name = "%s" ''' % (item, species))
Id = self.cursor.fetchone()[0]
StrainIds.append(Id)
@@ -855,16 +854,16 @@ Resorting this table <br>
#XZ, 12/16/2008: the input geneid is of mouse type
def checkSymbolForTissueCorr(self, tissueProbeSetFreezeId=0, symbol=""):
- q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol)
+ q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol)
self.cursor.execute(q)
try:
x = self.cursor.fetchone()
if x: return True
else: raise
except: return False
-
-
+
+
def fetchAllDatabaseData(self, species, GeneId, GeneSymbol, strains, db, method, returnNumber, tissueProbeSetFreezeId):
StrainIds = []
@@ -879,9 +878,9 @@ Resorting this table <br>
nnn += 1
oridata = []
- #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
+ #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
tempTable = None
- if GeneId and db.type == "ProbeSet":
+ if GeneId and db.type == "ProbeSet":
if method == "3":
tempTable = self.getTempLiteratureTable(species=species, input_species_geneid=GeneId, returnNumber=returnNumber)
@@ -892,7 +891,7 @@ Resorting this table <br>
temp = []
StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
for item in StrainIdstep: temp.append('T%s.value' % item)
-
+
if db.type == "Publish":
query = "SELECT PublishXRef.Id, "
dataStartPos = 1
@@ -910,12 +909,12 @@ Resorting this table <br>
# as we would not have litCorr data.
if method == "3":
- query = "SELECT %s.Name, %s.value," % (db.type,tempTable)
- dataStartPos = 2
+ query = "SELECT %s.Name, %s.value," % (db.type,tempTable)
+ dataStartPos = 2
if method == "4" or method == "5":
- query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable)
- dataStartPos = 3
-
+ query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable)
+ dataStartPos = 3
+
query += string.join(temp,', ')
query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type)
if method == "3":
@@ -925,8 +924,8 @@ Resorting this table <br>
#XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
for item in StrainIdstep:
query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
-
- if method == "3":
+
+ if method == "3":
query += "WHERE ProbeSet.GeneId IS NOT NULL AND %s.value IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
if method == "4" or method == "5":
query += "WHERE ProbeSet.Symbol IS NOT NULL AND %s.Correlation IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
@@ -939,7 +938,7 @@ Resorting this table <br>
for item in StrainIdstep:
query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-
+
self.cursor.execute(query)
results = self.cursor.fetchall()
oridata.append(results)
@@ -971,17 +970,17 @@ Resorting this table <br>
- # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name.
+ # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name.
# XZ, 09/20/2008: It stores top literature correlation values associated with the input geneId.
# XZ, 09/20/2008: Attention: In each row, the input geneId is always in column GeneId1.
#XZ, 12/16/2008: the input geneid can be of mouse, rat or human type
def getTempLiteratureTable(self, species, input_species_geneid, returnNumber):
# according to mysql the TEMPORARY TABLE name should not have to be unique because
- # it is only available to the current connection. This program will be invoked via command line, but if it
+ # it is only available to the current connection. This program will be invoked via command line, but if it
# were to be invoked over mod_python this could cuase problems. mod_python will keep the connection alive
# in its executing threads ( i think) so there is a potential for the table not being dropped between users.
#XZ, 01/29/2009: To prevent the potential risk, I generate random table names and drop the tables after use them.
-
+
# the 'input_species_geneid' could be rat or human geneid, need to translate it to mouse geneid
translated_mouse_geneid = self.translateToMouseGeneID (species, input_species_geneid)
@@ -1022,7 +1021,7 @@ Resorting this table <br>
translated_species_geneid = record[0]
if translated_species_geneid:
- self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) )
+ self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) )
counter = counter + 1
#pay attention to the number
@@ -1054,9 +1053,9 @@ Resorting this table <br>
symbolCorrList.sort(cmpTissCorrAbsoluteValue)
symbolCorrList = symbolCorrList[0 : 2*returnNumber]
-
+
tmpTableName = webqtlUtil.genRandStr(prefix="TOPTISSUE")
-
+
q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmpTableName
self.cursor.execute(q1)
@@ -1166,7 +1165,7 @@ Resorting this table <br>
return traitList
def get_trait(self, cached, vals):
-
+
if cached:
_log.info("Using the fast method because the file exists")
lit_corrs = {}
@@ -1194,7 +1193,7 @@ Resorting this table <br>
#XZ: The new method uses all strains stored in variable dataset_strains to create a new variable
#XZ: _newvals. _newvals has the same length as dataset_strains. The items in _newvals is in
#XZ: the same order of items in dataset_strains. The value of each item in _newvals is either
- #XZ: the value of correspinding strain in _vals or 'None'.
+ #XZ: the value of correspinding strain in _vals or 'None'.
new_vals = []
for name in cached_sample_names:
if name in self.sample_names:
@@ -1211,13 +1210,13 @@ Resorting this table <br>
data_start = 1
for line in datasetFile:
raw_trait = webqtlUtil.readLineCSV(line)
- trait = Trait.from_csv(raw_trait, data_start)
+ trait = Trait.from_csv(raw_trait, data_start)
trait.lit_corr = lit_corrs.get(trait.name)
trait.tissue_corr, trait.p_tissue = tissue_corrs.get(trait.name, (None, None))
traits.append(trait)
return traits, new_vals
-
+
else:
_log.info("Using the slow method for correlation")
@@ -1318,7 +1317,7 @@ Resorting this table <br>
#the top ones always have p value 0. So comparing p values actually does nothing.
#In addition, for the tissue data in our database, the N is always the same.
#So it's safe to compare with tissue corr statistic value.
- #That's the same as literature corr.
+ #That's the same as literature corr.
#if self.method in [METHOD_LIT, METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] and self.gene_id:
# traits.sort(webqtlUtil.cmpLitCorr)
#else:
@@ -1348,13 +1347,13 @@ Resorting this table <br>
# NL, 07/19/2010
# js function changed, add a new parameter rankOrder for js function 'showTissueCorrPlot'
db_trait.RANK_ORDER = self.RANK_ORDERS[self.method]
-
+
#XZ, 26/09/2008: Method is 4 or 5. Have fetched tissue corr, but no literature correlation yet.
if self.method in TISSUE_METHODS:
db_trait.tissueCorr = trait.tissue_corr
db_trait.tissuePValue = trait.p_tissue
addTissueCorr = True
-
+
#XZ, 26/09/2008: Method is 3, Have fetched literature corr, but no tissue corr yet.
elif self.method == METHOD_LIT:
@@ -1374,13 +1373,13 @@ Resorting this table <br>
trait_list.append(db_trait)
if addLiteratureCorr:
- trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id,
+ trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id,
self.species, trait_list)
if addTissueCorr:
trait_list = self.getTissueCorrelationByList(
- primaryTraitSymbol = self.trait_symbol,
+ primaryTraitSymbol = self.trait_symbol,
traitList = trait_list,
- TissueProbeSetFreezeId = TISSUE_MOUSE_DB,
+ TissueProbeSetFreezeId = TISSUE_MOUSE_DB,
method=self.method)
return trait_list
@@ -1446,7 +1445,7 @@ Resorting this table <br>
if myTrait:
if method in ["1","2"]: #genetic correlation
- info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"),
+ info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"),
" database were compared to all %d records in the " % self.record_count, HT.Href(text=db.fullname,url=webqtlConfig.INFOPAGEHREF % target_db_name,target="_blank", Class="fwn"),
' database. The top %d correlations ranked by the %s are displayed.' % (returnNumber,methodDict[method]),
' You can resort this list using the small arrowheads in the top row.')
@@ -1498,7 +1497,7 @@ Resorting this table <br>
titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
##Write title Info
- # Modified by Hongqiang Li
+ # Modified by Hongqiang Li
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([2, 0], "Trait : %s" % identification, titleStyle)
@@ -1568,7 +1567,7 @@ Resorting this table <br>
tr = []
trId = str(thisTrait)
-
+
corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr))
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))
@@ -1616,7 +1615,7 @@ Resorting this table <br>
tblobj_header = []
if method in ["1","3","4"]:
- tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
+ tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1),
THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2),
THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3),
@@ -1626,7 +1625,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_r"),
+ url = "/correlationAnnotation.html#genetic_r"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=7),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8),
THCell(HT.TD(HT.Href(
@@ -1639,7 +1638,7 @@ Resorting this table <br>
worksheet.write([newrow, ncol], item, headingStyle)
worksheet.set_column([ncol, ncol], 2*len(item))
else:
- tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
+ tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1),
THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2),
THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3),
@@ -1649,7 +1648,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_rho"),
+ url = "/correlationAnnotation.html#genetic_rho"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=7),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8),
THCell(HT.TD(HT.Href(
@@ -1674,7 +1673,7 @@ Resorting this table <br>
tr = []
trId = str(thisTrait)
-
+
corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr))
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))
@@ -1757,7 +1756,7 @@ Resorting this table <br>
tr.append(TDCell(HT.TD(repr,nowrap='ON', Class="fs12 fwn ffl b1 c222", align='right'),repr,thisTrait.corrPValue))
tblobj_body.append(tr)
-
+
for ncol, item in enumerate([thisTrait.name, PhenotypeString, thisTrait.authors, thisTrait.year, thisTrait.pubmed_id, LRS_score_repr, LRS_location_repr, thisTrait.corr, thisTrait.nOverlap, thisTrait.corrPValue]):
worksheet.write([newrow, ncol], item)
newrow += 1
@@ -1783,7 +1782,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_r"),
+ url = "/correlationAnnotation.html#genetic_r"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=10),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11),
THCell(HT.TD(HT.Href(
@@ -1825,7 +1824,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_rho"),
+ url = "/correlationAnnotation.html#genetic_rho"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=10),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11),
THCell(HT.TD(HT.Href(
@@ -1885,17 +1884,17 @@ Resorting this table <br>
#XZ, 12/08/2008: probeset name
tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name,url="javascript:showTrait('%s', '%s')" % (formName,thisTrait.name), Class="fs12 fwn"), Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name.upper()))
- #XZ, 12/08/2008: gene id
+ #XZ, 12/08/2008: gene id
if thisTrait.geneid:
tr.append(TDCell(None, thisTrait.geneid, val=999))
else:
- tr.append(TDCell(None, thisTrait.geneid, val=999))
-
+ tr.append(TDCell(None, thisTrait.geneid, val=999))
+
#XZ, 12/08/2008: homologene id
if thisTrait.homologeneid:
tr.append(TDCell("", thisTrait.homologeneid, val=999))
else:
- tr.append(TDCell("", thisTrait.homologeneid, val=999))
+ tr.append(TDCell("", thisTrait.homologeneid, val=999))
#XZ, 12/08/2008: gene symbol
tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),thisTrait.symbol, thisTrait.symbol.upper()))
diff --git a/web/webqtl/maintainance/genSelectDatasetJS.py b/web/webqtl/maintainance/genSelectDatasetJS.py
index bc88beec..d03cc7af 100755
--- a/web/webqtl/maintainance/genSelectDatasetJS.py
+++ b/web/webqtl/maintainance/genSelectDatasetJS.py
@@ -27,6 +27,9 @@
# created by Ning Liu 07/01/2010
# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/.
# This script will be run automatically every one hour or manually when database has been changed .
+
+from __future__ import print_function, division
+
import sys, os
current_file_name = __file__
diff --git a/web/webqtl/search/SearchResultPage.py b/web/webqtl/search/SearchResultPage.py
index 029a54c4..d62bb449 100755
--- a/web/webqtl/search/SearchResultPage.py
+++ b/web/webqtl/search/SearchResultPage.py
@@ -14,7 +14,7 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
-from base.webqtlDataset import webqtlDataset
+from base.data_set import DataSet
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from utility import webqtlUtil
@@ -65,12 +65,12 @@ class SearchResultPage(templatePage):
InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
PublishFreeze.InbredSetId""")
results = self.cursor.fetchall()
- self.database = map(lambda x: webqtlDataset(x[0], self.cursor), results)
+ self.database = map(lambda x: DataSet(x[0], self.cursor), results)
self.databaseCrosses = map(lambda x: x[1], results)
self.databaseCrossIds = map(lambda x: x[2], results)
self.singleCross = False
else:
- self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database)
+ self.database = map(lambda x: DataSet(x, self.cursor), self.database)
#currently, webqtl wouldn't allow multiple crosses
#for other than multiple publish db search
#so we can use the first database as example
diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py
index f38b9880..c240d8a0 100644..100755
--- a/web/webqtl/showTrait/DataEditingPage.py
+++ b/web/webqtl/showTrait/DataEditingPage.py
@@ -280,13 +280,13 @@ class DataEditingPage(templatePage):
if snpurl:
snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl)
- snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="addselect", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
+ snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
snpBrowserButton.append(snpBrowserButton_img)
snpBrowserText = "SNPs"
#XZ: Show GeneWiki for all species
geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol))
- geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="addselect", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
+ geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
geneWikiButton.append(geneWikiButton_img)
geneWikiText = 'GeneWiki'
@@ -295,7 +295,7 @@ class DataEditingPage(templatePage):
if _Species in ("mouse", "rat", "human"):
similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species)
similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl)
- similarButton_img = HT.Image("/images/find_icon.jpg", name="addselect", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
+ similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
similarButton.append(similarButton_img)
similarText = "Find"
else:
@@ -416,13 +416,15 @@ class DataEditingPage(templatePage):
UTHSC_BLAT_URL = ""
if UCSC_BLAT_URL:
- verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
- verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+ verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
+ verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ",
+ title=" Check probe locations at UCSC ", style="border:none;")
verifyButton.append(verifyButtonImg)
verifyText = 'Verify'
if UTHSC_BLAT_URL:
- rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
- rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+ rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL)
+ rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ",
+ title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
rnaseqButton.append(rnaseqButtonImg)
rnaseqText = 'RNA-seq'
tSpan.append(HT.BR())
@@ -442,8 +444,8 @@ class DataEditingPage(templatePage):
if probeResult[0] > 0:
probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \
% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet)
- probeButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % probeurl)
- probeButton_img = HT.Image("/images/probe_icon.jpg", name="addselect", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
+ probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl)
+ probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
probeButton.append(probeButton_img)
probeText = "Probes"
@@ -590,10 +592,24 @@ class DataEditingPage(templatePage):
url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \
% thisTrait.symbol,Class="fs14 fwn", \
title="Protein interactions: known and inferred"), style=linkStyle), "&nbsp;"*2)
- if thisTrait.geneid:
+ if thisTrait.symbol:
+ #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input
+ #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users
+ if _Species == "mouse":
+ species_scientific = "Mus%20musculus"
+ elif _Species == "rat":
+ species_scientific = "Rattus%20norvegicus"
+ elif _Species == "human":
+ species_scientific = "Homo%20sapiens"
+ elif _Species == "drosophila":
+ species_scientific = "Drosophila%20melanogaster"
+ else:
+ species_scientific = "all"
+
+ species_scientific
tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
- url="http://www.pantherdb.org/genes/gene.do?acc=%s" \
- % thisTrait.geneid,Class="fs14 fwn", \
+ url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \
+ % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \
title="Gene and protein data resources from Celera-ABI"), style=linkStyle), "&nbsp;"*2)
else:
pass
@@ -755,12 +771,13 @@ class DataEditingPage(templatePage):
UCSC_BLAT_URL = ""
UTHSC_BLAT_URL = ""
if UCSC_BLAT_URL:
- verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
- verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+ #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
+ verifyButton = HT.Href(url="#")
+ verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
verifyButton.append(verifyButtonImg)
verifyText = "Verify"
- rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
- rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+ rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
+ rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
rnaseqButton.append(rnaseqButtonImg)
rnaseqText = "RNA-seq"