Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

11 files changed, 39 insertions, 27 deletions

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index d992942f..00000000
--- a/.DS_Store
+++ /dev/null
diff --git a/.gitignore b/.gitignore
index 70d0273d..701623e7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,3 @@
-# gitignore
 *.pyc
 *.orig
 *.bak
diff --git a/README.md b/README.md
index 523eeb76..47519118 100644
--- a/README.md
+++ b/README.md
@@ -25,16 +25,15 @@ Once installed GN2 can be run online through a browser interface
 genenetwork2
 ```
 
-(default is http://localhost:5003/). For full examples (you'll need to
-set a number of environment variables), including running scripts and
-a Python REPL, for example
+(default is http://localhost:5003/). A quick example is
 
 ```sh
-env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=~/data/gn2_data ./bin/genenetwork2
+env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 GENENETWORK_FILES=~/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
 ```
 
-see the startup script
-[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
+For full examples (you may need to set a number of environment
+variables), including running scripts and a Python REPL, also see the
+startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
 
 Also Mysql and Elasticsearch need to be running, see
 [INSTALL](./doc/README.org).
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 1c538e86..759c71dc 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -209,7 +209,7 @@ if [ "$1" = '-gunicorn-prod' ] ; then
     echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     PID=$TMPDIR/gunicorn.$USER.pid
-    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
+    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 6000 --max-requests 1000 --timeout 1200 wsgi"
     echo RUNNING gunicorn $cmd
     gunicorn $cmd
     exit $?
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 4a35f42d..64a78686 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -25,6 +25,10 @@ import os
 import sys
 
 GN_VERSION = open("../etc/VERSION","r").read()
+GN_SERVER_URL = "http://localhost:8880/" # REST API server
+
+# ---- MySQL
+
 SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
 SQL_ALCHEMY_POOL_RECYCLE = 3600
 GN_SERVER_URL = "http://localhost:8880/" # REST API server
@@ -45,13 +49,13 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
 
 GITHUB_CLIENT_ID = "UNKNOWN"
 GITHUB_CLIENT_SECRET = "UNKNOWN"
-GITHUB_AUTH_URL = "UNKNOWN"
-GITHUB_API_URL = "UNKNOWN"
+GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize"
+GITHUB_API_URL = "https://api.github.com/user"
 
 ORCID_CLIENT_ID = "UNKNOWN"
 ORCID_CLIENT_SECRET = "UNKNOWN"
-ORCID_AUTH_URL = "UNKNOWN"
-ORCID_TOKEN_URL = "UNKNOWN"
+ORCID_AUTH_URL = "https://orcid.org/oauth/authorize"
+ORCID_TOKEN_URL = "https://orcid.org/oauth/token"
 
 ELASTICSEARCH_HOST = "localhost"
 ELASTICSEARCH_PORT = '9200'
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8652e6b7..1f99df49 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -64,7 +64,7 @@ logger = getLogger(__name__ )
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
 
@@ -77,7 +77,7 @@ def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_sampleli
 
 class Dataset_Types(object):
 
-    def __init__(self, rebuild=False):
+    def __init__(self):
         """Create a dictionary of samples where the value is set to Geno,
 Publish or ProbeSet. E.g.
 
@@ -93,13 +93,9 @@ Publish or ProbeSet. E.g.
 
         """
         self.datasets = {}
-        if rebuild: #ZS: May make this the only option
-            data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content)
-            #data = gen_menu.gen_dropdown_json()
-        else:
-            file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
-            with open(file_name, 'r') as fh:
-                data = json.load(fh)
+        data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content)
+        #data = gen_menu.gen_dropdown_json()
+
 
         for species in data['datasets']:
             for group in data['datasets'][species]:
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 7c06356b..15572d97 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -9,6 +9,7 @@
 
 from wqflask import app
 
+
 import logging
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9354ece6..2914d354 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -233,6 +233,7 @@ 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')
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 64a413c2..adf66fb5 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -36,11 +36,6 @@ def gen_dropdown_json():
                 types=types,
                 datasets=datasets)
 
-    output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json"""
-
-    with open(output_file, 'w') as fh:
-        json.dump(data, fh, indent=3, sort_keys=True)
-
     return data
 
 def get_species():
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index daf818b1..679e38b0 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -5172,6 +5172,23 @@
                   "HSNIH-Rat-PL-RSeq-0818", 
                   "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog"
                ]
+            ],
+            "Prefrontal Cortex mRNA": [
+               [
+                  "864",
+                  "HSNIH-Rat-VoLo-RSeq-0818",
+                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "863",
+                  "HSNIH-Rat-PL-RSeq-0818",
+                  "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "861",
+                  "HSNIH-Rat-IL-RSeq-0818",
+                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
+               ]
             ]
          }, 
          "HSNIH-RGSMC": {
@@ -7564,4 +7581,4 @@
          ]
       }
    }
-}
\ No newline at end of file
+}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 777d4a2d..777d4a2d 100644..100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html