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, 107 insertions, 0 deletions

diff --git a/gn2/base/webqtlConfig.py b/gn2/base/webqtlConfig.py
new file mode 100644
index 00000000..998c0efc
--- /dev/null
+++ b/gn2/base/webqtlConfig.py
@@ -0,0 +1,107 @@
+# '
+#      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 gn2.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'