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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/externalResource/GoTreePage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/externalResource/GoTreePage.py')
-rwxr-xr-xweb/webqtl/externalResource/GoTreePage.py154
1 files changed, 0 insertions, 154 deletions
diff --git a/web/webqtl/externalResource/GoTreePage.py b/web/webqtl/externalResource/GoTreePage.py
deleted file mode 100755
index 07144a23..00000000
--- a/web/webqtl/externalResource/GoTreePage.py
+++ /dev/null
@@ -1,154 +0,0 @@
-#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
-