API: GN_SERVER_URL and test

5 files changed, 19 insertions, 11 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index ac5dc266..08eae024 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -26,7 +26,7 @@ GN_VERSION = open("../VERSION","r").read()
 SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
 SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
 SQLALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/"
+GN_SERVER_URL = "http://test-gn2.genenetwork.org/"
 
 # ---- Flask configuration (see website)
 TRAP_BAD_REQUEST_ERRORS = True
@@ -37,7 +37,7 @@ SECURITY_RECOVERABLE = True
 SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
 SECURITY_POST_LOGIN_VIEW = "/thank_you"
 
-SERVER_PORT = 5003
+SERVER_PORT = 5003          # running on localhost
 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
 
 # ---- Behavioural settings (defaults) note that logger and log levels can
@@ -45,6 +45,7 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
 WEBSERVER_MODE  = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
 WEBSERVER_BRANDING = None   # Set the branding (nyi)
 WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
+WEBSERVER_URL    = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
 
 LOG_LEVEL       = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
 LOG_LEVEL_DEBUG = '0'       # logger.debugf log level (0-5, 5 = show all)
@@ -72,4 +73,3 @@ LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files
 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())
-
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/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index a39da73a..7aceabee 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,
@@ -465,7 +465,7 @@
      });
      BD.putSource({name: 'QTL',
                    tier_type: 'qtl',
-                   uri: 'http://localhost:5003/generated_text/{{csv_filename}}',
+                   uri: '/generated_text/{{csv_filename}}',
                    style: [{
                        type: 'default',
                        style: {
@@ -480,7 +480,7 @@
                    }],
      });
      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..8d5eadb6 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))