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hosted cellxgene, add an environment variable to specify the config file (#1288)

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Fixes #1272
This commit is contained in:
bmccandless
2020-03-24 11:43:35 -07:00
committed by GitHub
parent 752b9e4ab3
commit bea1836386
2 changed files with 53 additions and 14 deletions
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server/eb/README.md
+32 -9
View File
@@ -38,34 +38,57 @@ There are many more options to these commands that may be important or necessary
eb init -p python-3.6 $EB_APP
```
3. Create the artifact.zip file for the application
3. Configuring cellxgene
All the cellxgene configuration options can be set from a configuration file.
This file can be generated like this:
```cellxgene launch --dump-default-config > myconfig.yaml```
The config file may then be customized before the app is deployed.
If your config file is named "config.yaml" and exists in this directory, then it will be bundled with the
application zip file and installed along side the app on the EB servers.
However, a potentially more flexible approach is to place your config file in a location accessible to the EB
servers, such as along side the matrix files in S3. For example: s3://my-bucket/my-datasets/config.yaml.
Set the CXG_CONFIG_FILE environment variable to specify this location.
Another option is to set the CXG_DATAROOT environment variable. The dataroot
is the location where the matrix files are located.
This environment variable will override the dataroot in the config file (if specified).
- Note: Certain features, such as diffexp and user annotations, are automatically disabled by the EB app,
and cannot be enabled using configuration. They may be enabled manually by modifying app.py, however
this is not supported or recommended at this time.
4. Create the artifact.zip file for the application
If you have additional configuration for the application,
place that application in server/eb/config.yaml. This will
be included in the eb deployment.
```
make build
```
4. Create an environment
5. Create an environment
```
# name of the environment
EB_ENV=cellxgene-env
# type of ec2 instance to run the cellxgene server.
EB_INSTANCE=m5.large
# One or both of the following environment variables needs to be set
CXG_DATAROOT=<location to your S3 bucket>
CXG_CONFIG_FILE=<location to your config file>
eb create $EB_ENV --instance-type $EB_INSTANCE --envvars CXG_DATAROOT=$CXG_DATAROOT
eb create $EB_ENV --instance-type $EB_INSTANCE \
--envvars CXG_DATAROOT=$CXG_DATAROOT,CXG_CONFIG_FILE=$CXG_CONFIG_FILE
```
5. Give the elastic beanstalk environment access to the S3 bucket.
6. Give the elastic beanstalk environment access to the S3 bucket.
This link may provide some useful information:
https://aws.amazon.com/premiumsupport/knowledge-center/elastic-beanstalk-s3-bucket-instance/
6. Deploy the application
7. Deploy the application
```
eb deploy $EB_ENV
server/eb/app.py
+21 -5
View File
@@ -24,6 +24,7 @@ try:
from server.common.app_config import AppConfig
from server.app.app import Server
from server.data_common.matrix_loader import MatrixDataCacheManager
from server.common.data_locator import DataLocator
except Exception:
logging.critical("Exception importing server modules", exc_info=True)
sys.exit(1)
@@ -39,13 +40,28 @@ class WSGIServer(Server):
try:
dataroot = os.getenv("CXG_DATAROOT")
app_config = AppConfig()
config_file = "config.yaml"
if os.path.exists(config_file):
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(config_file)
dataroot = os.getenv("CXG_DATAROOT")
config_file = os.getenv("CXG_CONFIG_FILE")
if config_file:
config_location = DataLocator(config_file)
if config_location.exists():
with config_location.local_handle() as lh:
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(lh)
else:
logging.critical(f"Configuration file not found {config_file}")
sys.exit(1)
else:
# no config file specified, try "config.yaml" in the current working directory
config_file = "config.yaml"
config_location = DataLocator(config_file)
if config_location.exists():
with config_location.local_handle() as lh:
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(lh)
if dataroot:
logging.info(f"Configuration from CXG_DATAROOT")