A set of scripts for exporting the Targeted Assertions database as KGX-compatible TSV files.
usage: exporter.py [-h] -t TARGET -uni UNIPROT_BUCKET [-i INSTANCE] [-d DATABASE] [-u USER] [-p PASSWORD] [-c CHUNK_SIZE] [-l LIMIT] [-ao ASSERTION_OFFSET] [-al ASSERTION_LIMIT] [-v]
optional arguments:
-h, --help show this help message and exit
-t TARGET, --target TARGET
the export target: edges, nodes, or metadata
-uni UNIPROT_BUCKET, --uniprot_bucket UNIPROT_BUCKET
storage bucket for UniProt data
-i INSTANCE, --instance INSTANCE
GCP DB instance name
-d DATABASE, --database DATABASE
database name
-u USER, --user USER database username
-p PASSWORD, --password PASSWORD
database password
-c CHUNK_SIZE, --chunk_size CHUNK_SIZE
number of assertions to process at a time
-l LIMIT, --limit LIMIT
maximum number of publications to export per edge
-ao ASSERTION_OFFSET, --assertion_offset ASSERTION_OFFSET
number of assertions to skip past
-al ASSERTION_LIMIT, --assertion_limit ASSERTION_LIMIT
number of assertions to output
-v, --verbose
Note that, despite being listed under "optional arguments", the target and uniprot_bucket parameters are always required.
If the target is edges or nodes then the database parameters (instance, database, user, password) are also required.
Additionally, the script will look for a file named prod-creds.json in the working directory, which should be a valid credentials file with permissions to access the Google Cloud Storage bucket where the exported files will be stored.