Merge branch 'master' of github.com:genenetwork/genenetwork2 into development

1 files changed, 0 insertions, 77 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
deleted file mode 100755
index 3eaeb56e..00000000
--- a/wqflask/base/webqtlConfig.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#########################################'
-#      Environment Variables - public
-#########################################
-
-#Debug Level
-#1 for debug, mod python will reload import each time
-DEBUG = 1
-
-#USER privilege
-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"
-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'
-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"
-
-
-GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later
-SECUREDIR = GNROOT + 'secure/'
-COMMON_LIB = GNROOT + 'support/admin'
-HTMLPATH = GNROOT + 'genotype_files/'
-PYLMM_PATH = '/home/zas1024/plink_gemma/'
-SNP_PATH = '/home/zas1024/snps/' 
-IMGDIR = GNROOT + '/wqflask/wqflask/static/output/'
-IMAGESPATH = HTMLPATH + 'images/'
-UPLOADPATH = IMAGESPATH + 'upload/'
-TMPDIR = '/home/zas1024/tmp/' # Will remove this and dependent items later
-GENODIR = HTMLPATH + 'genotypes/'
-NEWGENODIR = HTMLPATH + 'new_genotypes/'
-GENO_ARCHIVE_DIR = GENODIR + 'archive/'
-TEXTDIR = HTMLPATH + 'ProbeSetFreeze_DataMatrix/'
-CMDLINEDIR = HTMLPATH + 'webqtl/cmdLine/'
-ChangableHtmlPath = GNROOT + 'web/'
-
-SITENAME = 'GN'
-PORTADDR = "http://50.16.251.170"
-BASEHREF = '<base href="http://50.16.251.170/">'
-INFOPAGEHREF = '/dbdoc/%s.html'
-GLOSSARYFILE = "/glossary.html"
-CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
-SCRIPTFILE = 'main.py'
-REFRESHSTR = '<meta http-equiv="refresh" content="5;url=%s' + SCRIPTFILE +'?sid=%s">'
-REFRESHDIR = '%s' + SCRIPTFILE +'?sid=%s'