bpaingest 6.4.2

Data management for Bioplatforms Australia projects

Bioplatforms Australia: CKAN ingest and sync

Usage

Primary usage information is contained in the comments at the top of the ingest/ingest.sh script, which is the gateway to synchronising the archive.

Generating CKAN schemas

bpa-ingest can generate ckanext-scheming schemas.

Usage:

$ bpa-ingest -p /tmp/ingest/ makeschema

Tracking metadata

Two types of tracking metadata are stored within this repository.

Google Drive metadata

The source of truth is "BPA Projects Data Transfer Summary", shared with BPA in Google Drive. This is maintained by the various project managers.

To update, use "File", "Download as", "CSV" within Google Sheets and replace the CSV sheets in track-metadata/google-drive

BPAM metadata

The source of truth is the BPA Metadata app.

To update, export each of the tracking datasets as CSV using the export button, then replace the files in track-metadata/bpam

• https://data.bioplatforms.com/bpa/adminsepsis/genomicsmiseqtrack/
• https://data.bioplatforms.com/bpa/adminsepsis/genomicspacbiotrack/
• https://data.bioplatforms.com/bpa/adminsepsis/metabolomicslcmstrack/
• https://data.bioplatforms.com/bpa/adminsepsis/proteomicsms1quantificationtrack/
• https://data.bioplatforms.com/bpa/adminsepsis/proteomicsswathmstrack/
• https://data.bioplatforms.com/bpa/adminsepsis/transcriptomicshiseqtrack/

AWS Lambda

We are gradually adding AWS Lambda functions to this project.

Each Lambda Function will have a handler() function which acts as an entrypoint. These are being collected in bpaingest/handlers/

Lambda functions should load their configuration from S3, from a bucket and key configured via environment variables. This configuration should be configured using AWS KMS. The Lambda function can be granted privileges to decrypt the configuration once it has been read from S3.

To store encrypted data at a key, this pattern works

$ aws kms encrypt --key-id <key> --plaintext fileb://config.json --output text --query CiphertextBlob | base64 --decode > config.enc
$ aws s3 cp config.enc s3://bucket/key

Local development:

For the development environment, you will need to have your local dev environment for bpa-ckan (consider dockercompose-bpa-ckan to do this).

Before you start, ensure you have installed Python 3.7

Bpa-ingest, atm, is just a python virtualenv (on command line),so to initialise a dev working environment:

cd bpa-ingest
git checkout next_release
git pull origin next_release
python3 -m venv ~/.virtual/bpa-ingest
. ~/.virtual/bpa-ingest/bin/activate
pip install -r requirements.txt
python setup.py install
python setup.py develop

Then (ensuring that you are still in python virtual env) source the environment variables (including API key), before running the ingest:

# if not already in virtual env:
. ~/.virtual/bpa-ingest/bin/activate

# source the environment variables
. /path/to/your/bpa.env

# dump the target state of the data portal to a JSON file for one data type
bpa-ingest -p /tmp/dump-metadata/ dumpstate test.json --dump-re 'omg-genomics-ddrad'

Look in /tmp/dump-metadata/ and you will see the working set of metadata sources used by the tool. Remember to delete the contents of /tmp (or subdirectory you are dumping too), when re-running command:

rm -Rf ./tmp/