Create event when order with external samples is submitted - #5292
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Double check that the auth info for NATS is gathered from the environment rather than cg.yaml since the ordering service is running on the VM |
islean
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September 9, 2026 12:29
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mogmi
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Sep 10, 2026
…) (minor) ## Description Provide support to message publishing using nats-py. Currently used in the new `external_sample_transferred_handler` and in the order storing service. ### Added - New methods to the event publisher that establish a connection to the NATS server, publish a message and drain the connection asynchronously. - `external_sample_transferred_handler` that adds the transferred files to HK and publishes an event using the new event_publisher method to start an analysis - New HK API method that adds bundle and version to the DB transaction but does not commit. - New HK method that hard-links files to the bundle dirs and commits ### Changed - The OrderSubmitter now recieved a NatsConfig object and a store as parameters - NATS env variables can now be parsed by the app_config obj - ### Fixed - Unifies all event names and payload fields in constants in `cg/services/events/constants.py` - rename directory `tests/services/orders/validation_service` to `tests/services/orders/validation` --------- Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Moe Darrah <41540288+moedarrah@users.noreply.github.com> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se> Co-authored-by: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com> * Create event when order with external samples is submitted (#5292) * WIP * fix type hints * Add TODOs * WIP * TODO * add statusdb to order * add passing function * Work on submitter * WIP * implement tests for submit with new functionality * WIP * add tests * Fix typehint for Order external_samples (#5296) * wip red * add app_config settings for NATS * Work on adding NatsConfig in the app_config * wip red * rename nats env variables * update renaming * Change order of publishing of events * red wip * Fix failing tests * Change logging --------- Co-authored-by: Moe Darrah <41540288+moedarrah@users.noreply.github.com> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se> Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> * Standardise event and field names (#5303) * Start standardising names * Rework the field names * Start on event names * WIP * Green tests * return hint --------- Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Moe Darrah <41540288+moedarrah@users.noreply.github.com> Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se> * rename constants from subject to events * rename constants from subject to events * Clarify event publisher function names (#5306) * Rename publish_command to get_publish_command * Rename publish to publish_event * Address comments * Send in event_name to publish_command --------- Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Moe Darrah <41540288+moedarrah@users.noreply.github.com> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se> Co-authored-by: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com> Co-authored-by: islean <isak.ohlsson.angnell@gmail.com>
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