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1240 uploader look into processing h5ad in chunks #1291

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1240 uploader look into processing h5ad in chunks #1291

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b68baca
Removing outdated and unused lib packages.
adkinsrs Apr 10, 2026
68c296a
Progress commit of moving anndata processor code from CGI to lib
adkinsrs Apr 13, 2026
d890f42
Merge branch 'devel' into 1240-uploader---look-into-processing-h5ad-i…
adkinsrs May 4, 2026
73d19d6
Add type ignore comments for sanitize_obs_for_h5ad calls in AnndataPr…
adkinsrs May 4, 2026
c47b67b
progress commit to get anndata rabbitmq upload consumer working
adkinsrs May 5, 2026
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17 changes: 17 additions & 0 deletions docker/docker-compose.yml.template
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Expand Up @@ -86,6 +86,23 @@ services:
- ../lib:/gEAR/lib
- ../www/uploads/files:/gEAR/www/uploads/files

# AnnData object Upload RabbitMQ Consumer
# i.e. h5ad, mex, tar
anndata_upload_consumer:
build:
context: ..
dockerfile: listeners/Dockerfile.anndata_upload
depends_on:
- queue
image: adkinsrs/gear_anndata_upload_consumer:latest
networks:
- gear
restart: on-failure
volumes:
- ../listeners:/gEAR/listeners
- ../lib:/gEAR/lib
- ../www/uploads/files:/gEAR/www/uploads/files

volumes:
db:
driver: local
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10 changes: 10 additions & 0 deletions docs/developer/services/rabbitmq_consumers.md
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Expand Up @@ -25,6 +25,16 @@ Result Storage (Database, File System)

## Available Consumers

### Anndata Upload Consume

Facilitates uploading of various file formats into Anndata (H5AD) format.

- **Listener**: `listeners/anndata_upload_consumer.py`
- **Queue**: `anndata_upload_jobs`
- **Service Template**: `systemd/anndata-upload-consumer@.service`
- **Service Group**: `systemd/anndata-upload-consumer.target`


### Gosling Upload Consume

Facilitates uploading of track files for the epigenome uploader.
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