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This is the minimum information needed to bootstrap our system with the information needed to load a configuration via a .properties file. Here, the actual .properties file should be loaded in .S3
where <<encryption key>> is found on our unix system in
work/platform/PasswordsAndCredentials/platformPropertyEncryptionKey.txtS3 as described below
Setting up a Properties file in S3
For each stack, we have created a unique IAM User, encryption key, and configuration file. These values are passed into the container of the environments as described above. AWS access key ids, secret keys, encryption keys, and the url for an environment can be found on sodo at /work/platform/PasswordsAndCredentials/StackCredentials/IAMUsers in the appropriate .csv file. All stack environments run under this IAM User, and have permission to access their configuration file from S3. Configuration files can be loaded / updated in S3 under the elasticbeanstalk-us-east-1-325565585839 bucket (this is the same place the .war files are deployed). This will give URLs of the form https://s3.amazonaws.com/elasticbeanstalk-us-east-1-325565585839/beanstalk-<stack-name>-stack.properties If you are creating a new stack, you will have to create the IAM user and grant that user access to access the configuration file using the IAM tab of the AWS console. In most cases you should be able to keep the configuration the file the same, or replace it with a new file of the same name.
How to run the Data Loader
On Once environments are running, you can populate the system with a set of starting data. On one of the local servers, goto /work/platform/DatasetMetadataLoader and execute the following:
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# Make sure you have the latest version svn up # Execute the loader # Replace <repo_instance> and <auth_instance> by the repository and authentication instances. # Either make sure that <platform_admin_email> is a Synapse administrator on crowd, or replace it by a Synapse administrator account python datasetCsvLoader.py -d ./AllDatasets.csv -l ./AllDatasetLayerLocations.csv -e http://<repo_instance>/repo/v1 -a http://<auth_instance>/auth/v1 -m /work/platform/DatasetMetadataLoader/platform.md5sums.csv -u <platform_admin_email> -p <platform_admin_pw> |
This will create a publicly-accessible project called Sage BioCuration, and populate it with curated data from Sage's repository data team.
Verify Deployment
To verify deployment, run top-level queries against the repository instances from an authenticated account.
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