Removed some unused code in webqtlConfig; some might need to be added back in later when other third party links are implemented on the trait/collection pages

2 files changed, 1 insertions, 67 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1e66e957..4708bf0a 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -20,46 +20,20 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 #minimum number of informative strains
 KMININFORMATIVE = 5
 
-#maximum number of traits for interval mapping
-MULTIPLEMAPPINGLIMIT = 11
-
-#maximum number of traits for correlation
-MAXCORR = 100
-
 #Daily download limit from one IP
 DAILYMAXIMUM = 1000
 
 #maximum LRS value
 MAXLRS = 460.0
 
-#temporary data life span
-MAXLIFE = 86400
-
 #MINIMUM Database public value
 PUBLICTHRESH = 0
 
-#NBCI address
-NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s"
-UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
-GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
-OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
-HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
+#EXTERNAL LINK ADDRESSES
 PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
 UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
-ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
-DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
-UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
-GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
-
-# The following paths are no longer in use!
-#   HTMLPATH is replaced by GENODIR
-#   IMGDIR is replaced by GENERATED_IMAGE_DIR
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index a55b6c10..c196b58b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -406,51 +406,11 @@ class MarkerRegression(object):
         else:
             self.GraphInterval = self.cMGraphInterval #cM
 
-        ################################################################
-        # Get Trait Values and Infomation
-        ################################################################
-        ##input from search page or selection page
-        #self.searchResult = fd.formdata.getvalue('searchResult')
-        ##convert single selection into a list
-        #if type("1") == type(self.searchResult):
-        #    self.searchResult = string.split(self.searchResult,'\t')
-        #
-        #self.traitList = []
-        #if self.searchResult and len(self.searchResult) > webqtlConfig.MULTIPLEMAPPINGLIMIT:
-        #    heading = 'Multiple Interval Mapping'
-        #    detail = ['In order to get clear result, do not select more than %d traits for \
-        #            Multiple Interval Mapping analysis.' % webqtlConfig.MULTIPLEMAPPINGLIMIT]
-        #    self.error(heading=heading,detail=detail)
-        #    return
-        #elif self.searchResult:
-        #    self.dataSource = 'selectionPage'
-        #    for item in self.searchResult:
-        #        thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-        #        thisTrait.retrieveInfo()
-        #        thisTrait.retrieveData(fd.strainlist)
-        #        self.traitList.append(thisTrait)
-        #else:
-
-        #input from data editing page
-        #fd.readData()
-        #if not fd.allTraitData:
-        #    heading = "Mapping"
-        #    detail = ['No trait data was selected for %s data set. No mapping attempted.' % fd.RISet]
-        #    self.error(heading=heading,detail=detail)
-        #    return
-
         self.dataSource = 'editingPage'
         self.traitList = []
         thisTrait = start_vars['this_trait']
-        #fullname = fd.formdata.getvalue('fullname', '')
-        #if fullname:
-        #    thisTrait = webqtlTrait(fullname=fullname, data=fd.allTraitData, cursor=self.cursor)
-        #    thisTrait.retrieveInfo()
-        #else:
-        #    thisTrait = webqtlTrait(data=fd.allTraitData)
         self.traitList.append(thisTrait)
 
-
 ## BEGIN HaplotypeAnalyst
 ## count the amount of individuals to be plotted, and increase self.graphHeight
         if self.haplotypeAnalystChecked and self.selectedChr > -1: