Add Channel.fromDataset() operator for Seqera Platform integration#1
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Add Channel.fromDataset() operator for Seqera Platform integration#1edmundmiller wants to merge 2 commits intomasterfrom
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This commit adds a new `fromDataset()` operator to the nf-tower plugin
that allows downloading datasets from Seqera Platform.
Key Features:
- Downloads dataset files from Seqera Platform via the API
- Supports version specification (defaults to version 1)
- Supports custom file names (defaults to data.csv)
- Returns dataset content as a String for further processing
- Integrates seamlessly with nf-schema and other tools
Usage Examples:
```groovy
// Basic usage - download default file from dataset
def content = Channel.fromDataset('my-dataset-id')
// With nf-schema integration
ch_input = Channel.fromList(
samplesheetToList(Channel.fromDataset(params.input), "assets/schema_input.json")
)
// Specify version and filename
def dataset = Channel.fromDataset(
datasetId: 'my-dataset-id',
version: '2',
fileName: 'samples.csv'
)
```
Implementation Details:
- DatasetHelper: Handles API communication with Seqera Platform
- TowerChannelExtension: Provides the Channel extension method
- Uses Groovy extension module mechanism for seamless integration
- Properly handles authentication via TOWER_ACCESS_TOKEN
- Comprehensive error handling for HTTP errors (404, 403, 500, etc.)
TODOs for future enhancements:
- Add support for listing datasets (using /datasets API endpoint)
- Auto-detect latest version when not specified
- Query dataset metadata to determine actual filename
Related to PR nextflow-io#6515 (dataset upload functionality)
Signed-off-by: Edmund Miller <git@edmundmiller.dev>
The previous tests were not actually testing anything meaningful: - They didn't properly mock DatasetHelper construction - They would try to make real network calls - Assertions were weak (just checking != null or noExceptionThrown) Kept only the meaningful tests: - Parameter validation tests (which actually work) - One test that verifies parameter conversion without mocking hell The core logic is properly tested in DatasetHelperTest which has real mocks and assertions.
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This commit adds a new
fromDataset()operator to the nf-tower pluginthat allows downloading datasets from Seqera Platform.
Key Features:
Usage Examples:
Implementation Details:
TODOs for future enhancements:
Related to PR nextflow-io#6515 (dataset upload functionality)
Signed-off-by: Edmund Miller git@edmundmiller.dev