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#########################################'
# 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"
ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%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'
SCRIPTFILE = 'main.py'
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