Scripts to download and update metadata analysis in batch for Virusseq portal

Download song analysis in batch from song server

./get-song-dump.py -s study_id -m song_url -d file_dump

Inputs

• study_id: Provide study_id you want to retrieve all the analysis from the server. If not provide, will download for all studies.
• song_url: Provide song_url of the song server. Default: https://song.dev.cancogen.cancercollaboratory.org.
• file_dump: Provide the path prefix to the file_dump. Default: data/virusseq-song.

Outputs

You will find song-dump file under folder data/. E.g,

data
└── virusseq-song.UHTC-ON.2022-06-23.jsonl

Prepare the metadata update dump

./prep-migration.py -d dump_path -s source_metadata_files -e env

Inputs

• dump_path: Path to song dump jsonl file.
• source_metadata_files: Source metadata files to get information for requested fields.
• env: Specify environment to prepare the migration payloads. Default: dev

Outputs

• You will find payloads for updating being generated under folder virusseq_song_update/dev/date. E.g,

virusseq_song_update/dev
└── 2022-06-27
    ├── migrate_consensus_sequence.UHTC-ON.jsonl

• You can print the running logs into a log file for verification.

Execute the song payload updating

./song-migrate.py -d dump_path -s song_url -t token -x exclude

Inputs

• dump_path: Path to migrated dump jsonl file. Required
• song_url: Song server URL. Default: https://song.dev.cancogen.cancercollaboratory.org
• token: Access token. Required
• exclude: The list of analysis to exclude from updating. Optional

Outputs

• The song analysis will be updated, and portal will pick up the updated changes and reflect them on the portal.
• You can print the running logs into a log file for verification.