Merge pull request #1 from genenetwork/testing

Updating my testing branch

1 files changed, 29 insertions, 30 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..018d5d54 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -20,45 +20,44 @@ 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'
-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
+UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
+NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%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/homologene/?term=%s"
+GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s"
+GTEX_URL = "https://www.gtexportal.org/home/gene/%s"
+GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s"
+GENEMANIA_URL = "https://genemania.org/search/%s/%s"
+UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
+BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s"
+STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s"
+PANTHER_URL = "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=%s"
+GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s"
+ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s"
+EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
+WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
+ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
+DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
+PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
+OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
+UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
+RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
@@ -70,8 +69,8 @@ assert_writable_dir(TMPDIR)
 
 CACHEDIR             = mk_dir(TMPDIR+'/cache/')
 # We can no longer write into the git tree:
-GENERATED_IMAGE_DIR  = mk_dir(TMPDIR+'/generated/')
-GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'/generated_text/')
+GENERATED_IMAGE_DIR  = mk_dir(TMPDIR+'generated/')
+GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'generated_text/')
 
 # Make sure we have permissions to access these
 assert_writable_dir(CACHEDIR)
@@ -81,6 +80,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
 assert_dir(GENODIR)
+assert_dir(GENODIR+'bimbam') # for gemma
 
 # JSON genotypes are OBSOLETE
 JSON_GENODIR         = flat_files('genotype/json')+'/'
@@ -92,4 +92,3 @@ if not valid_path(JSON_GENODIR):
 PORTADDR = "http://50.16.251.170"
 INFOPAGEHREF = '/dbdoc/%s.html'
 CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
-SCRIPTFILE = 'main.py'