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-rw-r--r--.DS_Storebin6148 -> 0 bytes
-rw-r--r--.gitignore1
-rw-r--r--README.md11
-rwxr-xr-xbin/genenetwork22
-rw-r--r--etc/default_settings.py12
-rw-r--r--wqflask/base/data_set.py14
-rw-r--r--wqflask/runserver.py1
-rw-r--r--wqflask/utility/tools.py1
-rw-r--r--wqflask/wqflask/api/gen_menu.py5
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json19
-rwxr-xr-x[-rw-r--r--]wqflask/wqflask/templates/show_trait_mapping_tools.html0
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
Binary files differ
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 04:19:07 +0000