diff options
| -rw-r--r-- | etc/default_settings.py | 24 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
3 files changed, 27 insertions, 10 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py index f3ca2e58..aa4e8d83 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,17 +2,19 @@ # webserver running in developer mode with limited console # output. Copy this file and run it from ./bin/genenetwork2 configfile # -# Note that these settings are fetched in ./wqflask/utilities/tools.py +# Note: these settings are fetched in ./wqflask/utilities/tools.py # which has support for overriding them through environment variables, # e.g. # # env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2 # -# Note also that in the near future we will additionally fetch +# Note: in the near future we will additionally fetch # settings from a JSON file # -# Note that values for False and 0 have to be strings here - otherwise +# Note: values for False and 0 have to be strings here - otherwise # Flask won't pick them up +# +# Final note: see below information to pick up the GNU Guix paths import os import sys @@ -49,13 +51,23 @@ LOG_BENCH = True # Log bench marks USE_REDIS = True # REDIS caching (note that redis will be phased out) USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls -# Path overrides for Genenetwork +# For GNU Guix deployment also check the paths in +# +# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py + +# General paths for Genenetwork + HOME=os.environ['HOME'] LOGFILE = HOME+"/genenetwork2.log" GENENETWORK_FILES = HOME+"/gn2_data" + +# Paths to JS libraries + +BIODALLIANCE_JS = os.environ['HOME']+"/genenetwork/biodalliance" + +# Paths to invoked binaries + PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) - -BIODALLIANCE_PATH = os.environ['HOME']+"/dalliance" diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index a6c942dc..774c7a09 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -265,9 +265,14 @@ /* This section checks for paths to JS libraries by checking the headers */ list = [ + /* check for static path */ "/static/new/javascript/biodalliance.js", - "http://d3js.org/d3.v3.min.js", "/static/new/js_external/underscore-min.js", + /* check for dalliance JS (see ./etc/default_settings.py) */ + "/dalliance/build/dalliance-all.js", + /* D3 path (FIXME) */ + "http://d3js.org/d3.v3.min.js", + /* datatables path (FIXME) */ "https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js" ]; for (var i = 0; i < list.length; i++) { @@ -280,8 +285,8 @@ }, error: function() { // page does not exist - console.log("Failed to load "+url); - alert("Failed to load Javascript for "+url); + console.log("Failed to load "+this.url); + alert("Failed to load Javascript for "+this.url); } })}; </script> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 1f967dc9..14e019d2 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -110,7 +110,7 @@ def tmp_page(img_path): @app.route("/dalliance/<path:filename>") def bd_files(filename): - bd_path = app.config['BIODALLIANCE_PATH'] + bd_path = app.config['BIODALLIANCE_JS'] return send_from_directory(bd_path, filename) |