Merge branch 'pjotr-gn2' into chfi

5 files changed, 25 insertions, 25 deletions

diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 0342b7ad..adacc712 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -19,11 +19,18 @@ ENDC  = '\033[0m'
 import os
 app.config['SECRET_KEY'] = os.urandom(24)
 
-from utility.tools import WEBSERVER_MODE,get_setting_int
+from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting
 
 port = get_setting_int("SERVER_PORT")
 
-logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC))
+print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+
+import requests
+page = requests.get(get_setting("GN_SERVER_URL"))
+if page.status_code != 200:
+    raise Exception("API server not found!")
+
+print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
 
 werkzeug_logger = logging.getLogger('werkzeug')
 
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index bacb0aa4..128706df 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI).
     def warning(self,*args):
         """Call logging.warning for multiple args"""
         self.collect(self.logger.warning,*args)
-        self.logger.warning(self.collect(*args))
+        # self.logger.warning(self.collect(*args))
 
     def error(self,*args):
         """Call logging.error for multiple args"""
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 77cb6ac5..9860f63e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -121,9 +121,14 @@ 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)
@@ -234,4 +239,7 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             logger.debug(OVERRIDES)
 
 assert_dir(get_setting("JS_BIODALLIANCE"))
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
 assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index e198f8fe..843c7ed9 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -414,9 +414,9 @@
                    provides_entrypoints: true
      });
      BD.putSource({name: 'Genotype',
-                   controlURI: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/BXD.json",
-                   URIBase: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/",
-                   tier_type: 'rqtl-genotype',
+                   controlURI: "{{gn_server_url}}/api_pre1/genotype/mouse/BXD.json",
+                   URIBase:    "{{gn_server_url}}/api_pre1/genotype/mouse/",
+                   tier_type:  'rqtl-genotype',
                    vOffset: 8,
                    pinned: true,
                    transposed: true,
@@ -466,7 +466,7 @@
      });
      BD.putSource({name: 'QTL',
                    tier_type: 'qtl',
-                   uri: 'http://localhost:5003/generated_text/{{csv_filename}}',
+                   uri: '/generated_text/{{csv_filename}}',
                    style: [{
                        type: 'default',
                        style: {
@@ -481,7 +481,7 @@
                    }],
      });
      BD.putSource({name: 'SNP density',
-                   jbURI: "http://test-gn2.genenetwork.org/api_pre1/snp",
+                   jbURI: "{{gn_server_url}}/api_pre1/snp",
                    jbQuery: "",
                    refetchOnZoom: true,
                    style: [{
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 289d2dc6..9fdaabf3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -549,6 +549,7 @@ def marker_regression_page():
             gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
             gn1_template_vars['json_filename'] = json_filename;
             gn1_template_vars['csv_filename'] = csv_filename;
+            gn1_template_vars['gn_server_url'] = GN_SERVER_URL;
 
             pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
             logger.info("pickled result length:", len(pickled_result))
@@ -558,22 +559,6 @@ def marker_regression_page():
             with Bench("Rendering template"):
                 rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
 
-    # with Bench("Rendering template"):
-        # if result['pair_scan'] == True:
-            # img_path = result['pair_scan_filename']
-            # logger.info("img_path:", img_path)
-            # initial_start_vars = request.form
-            # logger.info("initial_start_vars:", initial_start_vars)
-            # imgfile = open(TEMPDIR + '/' + img_path, 'rb')
-            # imgdata = imgfile.read()
-            # imgB64 = imgdata.encode("base64")
-            # bytesarray = array.array('B', imgB64)
-            # result['pair_scan_array'] = bytesarray
-            # rendered_template = render_template("pair_scan_results.html", **result)
-        # else:
-            # rendered_template = render_template("marker_regression.html", **result)
-            # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
-
     return rendered_template