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add process dataset api file
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KaiWaldrant committed Jun 28, 2024
1 parent 41679cf commit 1fbb961
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32 changes: 32 additions & 0 deletions src/api/comp_process_dataset.yaml
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functionality:
namespace: "label_projection"
info:
type: process_dataset
type_info:
label: Data processor
summary: A label projection dataset processor.
description: |
A component for processing a Common Dataset into a task-specific dataset.
arguments:
- name: "--input"
__merge__: file_common_dataset.yaml
direction: input
required: true
- name: "--output_train"
__merge__: file_train.yaml
direction: output
required: true
- name: "--output_test"
__merge__: file_test.yaml
direction: output
required: true
- name: "--output_solution"
__merge__: file_solution.yaml
direction: output
required: true
test_resources:
- path: /resources_test/common/pancreas
dest: resources_test/common/pancreas
- type: python_script
path: /common/component_tests/run_and_check_output.py

41 changes: 41 additions & 0 deletions src/api/file_common_dataset.yaml
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#TODO: Change to the required and/or optional fields of the anndata
type: file
example: "resources_test/common/pancreas/dataset.h5ad"
info:
label: "Common Dataset"
summary: A subset of the common dataset.
slots:
layers:
- type: integer
name: counts
description: Raw counts
required: true
uns:
- type: string
name: dataset_id
description: "A unique identifier for the dataset"
required: true
- name: dataset_name
type: string
description: Nicely formatted name.
required: true
- type: string
name: dataset_url
description: Link to the original source of the dataset.
required: false
- name: dataset_reference
type: string
description: Bibtex reference of the paper in which the dataset was published.
required: false
- name: dataset_summary
type: string
description: Short description of the dataset.
required: true
- name: dataset_description
type: string
description: Long description of the dataset.
required: true
- name: dataset_organism
type: string
description: The organism of the sample in the dataset.
required: false

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