#########################################' # Environment Variables - public # # Note: much of this needs to handled by the settings/environment # scripts. But rather than migrating everything in one go, we'll # take it a step at a time. First the hard coded paths get replaced # with those in utility/tools.py # ######################################### from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR #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" # 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 # want to reach this base dir assert_writable_dir(TEMPDIR) TMPDIR = mk_dir(TEMPDIR+'/gn2/') 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/') # Make sure we have permissions to access these assert_writable_dir(CACHEDIR) assert_writable_dir(GENERATED_IMAGE_DIR) assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' if not valid_path(JSON_GENODIR): # fall back on old location (move the dir, FIXME) JSON_GENODIR = flat_files('json') # Are we using the following...? 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'