diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 72 |
1 files changed, 35 insertions, 37 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index a7dbed3d..b7e278ae 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -8,7 +8,8 @@ # ######################################### import os -from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR +from flask import Flask +from utility.tools import valid_path, mk_dir, assert_dir, get_setting, assert_writable_dir, flat_files # Debug Level # 1 for debug, mod python will reload import each time @@ -69,39 +70,36 @@ PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&gen 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' +def update_settings(app: Flask) -> Flask: + # 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 + TEMPDIR = assert_writable_dir(get_setting(app, "TEMPDIR")) + + TMPDIR = assert_writable_dir(mk_dir(TEMPDIR + '/gn2/')) + app.config["TMPDIR"] = TMPDIR + + app.config["CACHEDIR"] = assert_writable_dir(mk_dir(TMPDIR + '/cache/')) + # We can no longer write into the git tree: + app.config["GENERATED_IMAGE_DIR"] = assert_writable_dir(mk_dir(TMPDIR + 'generated/')) + app.config["GENERATED_TEXT_DIR"] = assert_writable_dir(mk_dir(TMPDIR + 'generated_text/')) + + # Flat file directories + app.config["GENODIR"] = assert_dir(flat_files(app, 'genotype') + '/') + # assert_dir(GENODIR+'bimbam') # for gemma + + # JSON genotypes are OBSOLETE + JSON_GENODIR = flat_files(app, 'genotype/json') + '/' + app.config["JSON_GENODIR"] = JSON_GENODIR + if not valid_path(JSON_GENODIR): + # fall back on old location (move the dir, FIXME) + app.config["JSON_GENODIR"] = flat_files(app, 'json') + + + app.config["TEXTDIR"] = os.path.join(os.environ.get( + "GNSHARE", "/gnshare/gn/"), "web/ProbeSetFreeze_DataMatrix") + # Are we using the following...? + app.config["PORTADDR"] = "http://50.16.251.170" + app.config["INFOPAGEHREF"] = '/dbdoc/%s.html' + app.config["CGIDIR"] = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' + return app |