Dataset sc lung #27
Dataset sc lung #27
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This PR removed or changed files that were very important for the project, including the |
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Hi @Kraftfahrzeughaftpflichtversicherung ! Thanks for your contributions!
I proposed some changes to make this align better with existing components :)
| FILE_PATHS = {"file": TMP_DIR / "cropped_sc.h5ad"} | ||
| os.system(f'wget http://192.168.2.46:8000/file/cropped_sc.h5ad -P ./tmp/') | ||
| adata = ad.read_h5ad( './tmp/cropped_sc.h5ad') |
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This code is pointing to local endpoints, which unfortunately won't work.
| name: process_nsclc_sc_zuani | ||
| namespace: datasets/workflows | ||
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| argument_groups: |
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Can we add a section for the input file?
| argument_groups: | |
| argument_groups: | |
| - name: Inputs | |
| arguments: | |
| - type: file | |
| name: --input | |
| description: Path to the dataset | |
| required: true | |
| example: "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad" |
| uns_info = { "dataset_id": "E-MTAB-13526" , | ||
| "dataset_name":"E-MTAB-13526" , | ||
| "dataset_url":"https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13526" , | ||
| "dataset_reference": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13526", | ||
| "dataset_summary": 'none', | ||
| "dataset_description":'none', | ||
| "dataset_organism": 'Homo sapiens' | ||
| } | ||
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| for key in ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"]: | ||
| adata.uns[key] = uns_info[key] |
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values like 'dataset_id' and 'dataset_name' are arguments, but are also being hardcoded here. These values should be retrieved from the par and should be passed as part of the dataset script.
| uns_info = { "dataset_id": "E-MTAB-13526" , | |
| "dataset_name":"E-MTAB-13526" , | |
| "dataset_url":"https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13526" , | |
| "dataset_reference": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13526", | |
| "dataset_summary": 'none', | |
| "dataset_description":'none', | |
| "dataset_organism": 'Homo sapiens' | |
| } | |
| for key in ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"]: | |
| adata.uns[key] = uns_info[key] | |
| for key in ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"]: | |
| adata.uns[key] = par[key] |
make sure to add a script similar to this one: https://github.com/openproblems-bio/task_ist_preprocessing/blob/ea67087326ae00912e0006d1f643d990576ed414/scripts/create_resources/process_10x_xenium.sh
I tried my best to integrate this dataset, and it even passed tests, failing only in the latest one
Unfortunatelly my computational recources said "bye" for me now, and I need to fix it, so it probably will take some time
Now I will add all that I have for now.
and I didn't change anything in common folder, why is it highlited here ??