Merge branch 'master' of github.com:genenetwork/genenetwork2

1 files changed, 31 insertions, 9 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c28c617a..393ff2df 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)
+    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
@@ -40,6 +45,7 @@ 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
@@ -89,6 +95,18 @@ def valid_path(dir):
         return dir
     return None
 
+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+" (check JS_GN_PATH)"
+
 def pylmm_command(guess=None):
     return valid_bin(get_setting("PYLMM_COMMAND",guess))
 
@@ -205,21 +223,27 @@ 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) - don't enforce right now
+JS_GN_PATH         = get_setting('JS_GN_PATH')
+# assert_dir(JS_GN_PATH)
+
+PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
+GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
+PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 
+# ---- Handle specific JS modules
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
+assert_dir(JS_TWITTER_POST_FETCHER_PATH)
+
 from six import string_types
 
 if os.environ.get('WQFLASK_OVERRIDES'):
@@ -234,5 +258,3 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             else:
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
-
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))