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-rw-r--r--wqflask/utility/tools.py132
1 files changed, 100 insertions, 32 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c28c617a..77db5d53 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -13,6 +13,11 @@ logger = logging.getLogger(__name__ )
OVERRIDES = {}
+def app_set(command_id, value):
+ """Set application wide value"""
+ app.config.setdefault(command_id,value)
+ return value
+
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with valid_path is a function checking whether the
@@ -40,15 +45,16 @@ def get_setting(command_id,guess=None):
def value(command):
if command:
# sys.stderr.write("Found "+command+"\n")
+ app_set(command_id,command)
return command
else:
return None
# ---- Check whether environment exists
- logger.debug("Looking for "+command_id+"\n")
+ # print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
- command = OVERRIDES.get(command_id)
+ command = OVERRIDES.get(command_id) # currently not in use
if command is None:
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
@@ -57,7 +63,7 @@ def get_setting(command_id,guess=None):
if command is None or command == "":
# print command
raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
- logger.debug("Set "+command_id+"="+str(command))
+ # print("Set "+command_id+"="+str(command))
return command
def get_setting_bool(id):
@@ -89,14 +95,29 @@ def valid_path(dir):
return dir
return None
-def pylmm_command(guess=None):
- return valid_bin(get_setting("PYLMM_COMMAND",guess))
+def js_path(module=None):
+ """
+ Find the JS module in the two paths
+ """
+ try_gn = get_setting("JS_GN_PATH")+"/"+module
+ if valid_path(try_gn):
+ return try_gn
+ try_guix = get_setting("JS_GUIX_PATH")+"/"+module
+ if valid_path(try_guix):
+ return try_guix
+ raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
+
+def reaper_command(guess=None):
+ return get_setting("REAPER_COMMAND",guess)
def gemma_command(guess=None):
- return valid_bin(get_setting("GEMMA_COMMAND",guess))
+ return assert_bin(get_setting("GEMMA_COMMAND",guess))
+
+def gemma_wrapper_command(guess=None):
+ return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
def plink_command(guess=None):
- return valid_bin(get_setting("PLINK_COMMAND",guess))
+ return assert_bin(get_setting("PLINK_COMMAND",guess))
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
@@ -108,6 +129,11 @@ def flat_files(subdir=None):
return assert_dir(base+"/"+subdir)
return assert_dir(base)
+def assert_bin(fn):
+ if not valid_bin(fn):
+ raise Exception("ERROR: can not find binary "+fn)
+ return fn
+
def assert_dir(dir):
if not valid_path(dir):
raise Exception("ERROR: can not find directory "+dir)
@@ -121,9 +147,14 @@ def assert_writable_dir(dir):
fh.close()
os.remove(fn)
except IOError:
- raise Exception('Unable to write test.txt to directory ' + dir )
+ raise Exception('Unable to write test.txt to directory ' + dir)
return dir
+def assert_file(fn):
+ if not valid_file(fn):
+ raise Exception('Unable to find file '+fn)
+ return fn
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
@@ -148,6 +179,9 @@ def locate(name, subdir=None):
if subdir: sys.stderr.write(subdir)
raise Exception("Can not locate "+name+" in "+base)
+def locate_phewas(name, subdir=None):
+ return locate(name,'/phewas/'+subdir)
+
def locate_ignore_error(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -186,7 +220,7 @@ def show_settings():
logger.info(OVERRIDES)
logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
- print "runserver.py: ****** Webserver configuration ******"
+ print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******"
keylist = app.config.keys()
keylist.sort()
for k in keylist:
@@ -199,40 +233,74 @@ def show_settings():
# Cached values
GN_VERSION = get_setting('GN_VERSION')
HOME = get_setting('HOME')
+SERVER_PORT = get_setting('SERVER_PORT')
WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
+GN2_BASE_URL = get_setting('GN2_BASE_URL')
+GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL')
GN_SERVER_URL = get_setting('GN_SERVER_URL')
+SERVER_PORT = get_setting_int('SERVER_PORT')
SQL_URI = get_setting('SQL_URI')
LOG_LEVEL = get_setting('LOG_LEVEL')
LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
LOG_SQL = get_setting_bool('LOG_SQL')
-LOG_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY')
+LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY')
LOG_BENCH = get_setting_bool('LOG_BENCH')
LOG_FORMAT = "%(message)s" # not yet in use
USE_REDIS = get_setting_bool('USE_REDIS')
USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
-TEMP_TRAITS = get_setting('TEMP_TRAITS')
-
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
-GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
-PLINK_COMMAND = plink_command()
+JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
+assert_dir(JS_GUIX_PATH)
+JS_GN_PATH = get_setting('JS_GN_PATH')
+# assert_dir(JS_GN_PATH)
+
+GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
+GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
+if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET:
+ GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \
+ GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
+ GITHUB_API_URL = get_setting('GITHUB_API_URL')
+
+ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
+ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
+ORCID_AUTH_URL = None
+if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
+ ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
+ ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
+ ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
+
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+# import utility.elasticsearch_tools as es
+# es.test_elasticsearch_connection()
+
+SMTP_CONNECT = get_setting('SMTP_CONNECT')
+SMTP_USERNAME = get_setting('SMTP_USERNAME')
+SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
+
+REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+assert(GEMMA_COMMAND is not None)
+PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
+GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+assert_dir(TEMPDIR)
+
+# ---- Handle specific JS modules
+JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
+assert_dir(JS_GUIX_PATH)
+assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
+
+CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
+# assert_dir(JS_PATH)
+
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
+assert_dir(JS_TWITTER_POST_FETCHER_PATH)
+assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
+
+JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
+assert_dir(JS_CYTOSCAPE_PATH)
+assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
-from six import string_types
-
-if os.environ.get('WQFLASK_OVERRIDES'):
- jsonfn = get_setting('WQFLASK_OVERRIDES')
- logger.error("WQFLASK_OVERRIDES: %s" % jsonfn)
- with open(jsonfn) as data_file:
- overrides = json.load(data_file)
- for k in overrides:
- cmd = overrides[k]
- if isinstance(cmd, string_types):
- OVERRIDES[k] = eval(cmd)
- else:
- OVERRIDES[k] = cmd
- logger.debug(OVERRIDES)
-
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))
+# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")