Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 0 insertions, 107 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
deleted file mode 100644
index a7dbed3d..00000000
--- a/wqflask/base/webqtlConfig.py
+++ /dev/null
@@ -1,107 +0,0 @@
-# '
-#      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
-#
-#########################################
-import os
-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}
-
-# Set privileges
-SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
-DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'}
-
-# 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
-
-# Groups to treat as unique when drawing correlation dropdowns (not sure if this logic even makes sense or is necessary)
-BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD']
-
-# 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"
-PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn7&section=geneEQTL"
-RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
-RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%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')
-
-
-TEXTDIR = os.path.join(os.environ.get(
-    "GNSHARE", "/gnshare/gn/"), "web/ProbeSetFreeze_DataMatrix")
-# 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'