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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/externalResource/GoTreePage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/externalResource/GoTreePage.py')
-rwxr-xr-xweb/webqtl/externalResource/GoTreePage.py154
1 files changed, 154 insertions, 0 deletions
diff --git a/web/webqtl/externalResource/GoTreePage.py b/web/webqtl/externalResource/GoTreePage.py
new file mode 100755
index 00000000..07144a23
--- /dev/null
+++ b/web/webqtl/externalResource/GoTreePage.py
@@ -0,0 +1,154 @@
+#GoTreePage.py
+
+import string
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+from dbFunction import webqtlDatabaseFunction
+
+
+#########################################
+# GoTree Page
+#########################################
+class GoTreePage(templatePage):
+
+ def __init__(self,fd):
+
+ self.theseTraits = []
+ TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
+
+ templatePage.__init__(self, fd)
+
+ if not self.openMysql():
+ return
+
+ self.searchResult = fd.formdata.getvalue('searchResult', [])
+ if type("1") == type(self.searchResult):
+ self.searchResult = [self.searchResult]
+
+ #XZ, self.theseTraits holds the "ProbeSet" traits.
+
+ for item in self.searchResult:
+ try:
+ thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+ thisTrait.retrieveInfo(QTL=1)
+ if thisTrait.db.type == "ProbeSet":
+ self.theseTraits.append(thisTrait)
+ except:
+ pass
+
+ if self.theseTraits:
+ pass
+ else:
+ templatePage.__init__(self, fd)
+ heading = 'WebGestalt'
+ detail = ['You need to select at least one microarray trait to submit.']
+ self.error(heading=heading,detail=detail)
+ return
+
+ chipName = self.testChip(fd)
+
+ #XZ, 8/24/2009: the name of arraylist is misleading. It holds the name of traits.
+ arraylist, geneIdList = self.genGeneIdList(fd)
+
+ target_url = "http://bioinfo.vanderbilt.edu/webgestalt/webgestalt.php"
+
+ formWebGestalt = HT.Form(cgi=target_url, enctype='multipart/form-data', name='WebGestalt', submit = HT.Input(type='hidden'))
+
+ id_type = chipName
+
+ hddnWebGestalt = {'id_list':string.join(arraylist, ","),
+ 'id_type':id_type}
+
+ hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
+ hddnWebGestalt['analysis_type'] = 'GO'
+ hddnWebGestalt['significancelevel'] = 'Top10'
+ hddnWebGestalt['stat'] = 'Hypergeometric'
+ hddnWebGestalt['mtc'] = 'BH'
+ hddnWebGestalt['min'] = '2'
+ hddnWebGestalt['id_value'] = fd.formdata.getvalue('correlation')
+
+ species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+
+ if species == 'rat':
+ hddnWebGestalt['org'] = 'Rattus norvegicus'
+ elif species == 'human':
+ hddnWebGestalt['org'] = 'Homo sapiens'
+ elif species == 'mouse':
+ hddnWebGestalt['org'] = 'Mus musculus'
+ else:
+ hddnWebGestalt['org'] = ''
+
+ hddnWebGestalt['org'] = hddnWebGestalt['org'].replace(' ','_')
+
+ for key in hddnWebGestalt.keys():
+ formWebGestalt.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
+
+ TD_LR.append(formWebGestalt)
+
+ TD_LR.append(HT.Paragraph("Your selection of %d traits is being submitted to GO Tree" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
+
+ # updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
+ # moved unknownChipError() to webqtl.js and change it to unknownChipError(chipName)
+ if chipName == 'mixed':
+ methodName = "WebGestalt"
+ self.dict['js1'] = """
+ <SCRIPT LANGUAGE="JavaScript">
+ setTimeout("mixedChipError('%s')" ,1000);
+ </SCRIPT>
+ """ % methodName
+ elif chipName.find('_NA') > 0:
+ chipName = chipName[0:-3]
+ self.dict['js1'] = """
+ <SCRIPT LANGUAGE="JavaScript">
+ setTimeout("unknownChipError('%s')",1000);
+ </SCRIPT>
+ """ % chipName
+ else:
+ self.dict['js1'] = """
+ <SCRIPT LANGUAGE="JavaScript">
+ setTimeout('document.WebGestalt.submit()',1000);
+ </SCRIPT>
+ """
+
+ self.dict['body'] = TD_LR
+
+ def testChip(self, fd):
+ chipName0 = ""
+
+ for item in self.theseTraits:
+ 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"' % item.db.name)
+ result = self.cursor.fetchone()
+ if result:
+ chipName = result[0]
+ if chipName:
+ if chipName != chipName0:
+ if chipName0:
+ return 'mixed'
+ else:
+ chipName0 = chipName
+ else:
+ pass
+ else:
+ self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+ result = self.cursor.fetchone()
+ chipName = '%s_NA' % result[0]
+ return chipName
+ else:
+ self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+ result = self.cursor.fetchone()
+ chipName = '%s_NA' % result[0]
+ return chipName
+ return chipName
+
+ def genGeneIdList(self, fd):
+ arrayList = []
+ geneList = []
+ for item in self.theseTraits:
+ arrayList.append(item.name)
+ item.retrieveInfo()
+ geneList.append(str(item.geneid))
+ return arrayList, geneList
+