#########################################' # 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 #Daily download limit from one IP DAILYMAXIMUM = 1000 #maximum LRS value MAXLRS = 460.0 #MINIMUM Database public value PUBLICTHRESH = 0 #EXTERNAL LINK ADDRESSES PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" 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' 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 # 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) assert_dir(GENODIR+'bimbam') # for gemma # 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'