This release is a pre-release and may not be stable for production use.
BIOMERO.importer - Automated Data Import System
🚀 This package is part of
BIOMERO 2.0 — For complete deployment and FAIR infrastructure setup, start with the NL-BIOMERO Documentation 📖
The BIOMERO.importer system enables automated uploading of image data from microscope workstations to an OMERO server. BIOMERO.importer is a database-driven system that polls a PostgreSQL database for new import orders and processes them automatically, including the option of running preprocessing containers for e.g. file conversion or pyramid creation.
Documentation
- Importer documentation: configuration, storage, import orders and development.
- Shallow Zarr: local normalization and importing remotely shallowed results.
- NL-BIOMERO deployment guide: deploying the complete platform.
- Release history.
Getting started
Deploy the importer with the shared storage, OMERO and PostgreSQL settings described in the administration guide. The NL-BIOMERO setup provides the container and its service configuration.
For Python clients:
pip install 'biomero-importer[identity]'
Configure the database and OMERO connection before submitting an order.
Use get_importer_capabilities() and submit_import_order() from
biomero_importer; see the import-order guide.
Shallow storage is opt-in. Enabling it permits explicit shallow import operations; it does not deduplicate every ordinary upload. See the shallow-storage guide.
Development
See development and migrations for environment setup, tests and database changes. Documentation uses MkDocs:
pip install -r docs/requirements.txt
mkdocs serve
License
GPL-2.0; see LICENSE.
1 maintainer
Metadata
1 maintainer
Release files for biomero-importer 1.5.0b6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| biomero_importer-1.5.0b6.tar.gz | 2.2 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biomero_importer-1.5.0b6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 4.4 MB
Release files / biomero_importer-1.5.0b6.tar.gz
| Download URL | biomero_importer-1.5.0b6.tar.gz |
|---|---|
| Size | 2.2 MB |
| Tags | Source |
|
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Release files / biomero_importer-1.5.0b6-py3-none-any.whl
| Download URL | biomero_importer-1.5.0b6-py3-none-any.whl |
|---|---|
| Size | 2.2 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.9.25
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