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Hardcode url in zuanei dataloader
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  • src/datasets/loaders/zuani_human_nsclc_sc

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src/datasets/loaders/zuani_human_nsclc_sc/script.py

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,8 +29,14 @@
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# Helper variables
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TMP_DIR = Path(meta["temp_dir"] or "./tmp")
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TMP_DIR.mkdir(parents=True, exist_ok=True)
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FILE_PATH = TMP_DIR / par["input"].split("/")[-1]
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DOWNLOAD_URL = par["input"]
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#FILE_PATH = TMP_DIR / par["input"].split("/")[-1]
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#DOWNLOAD_URL = par["input"]
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# Hard code the download url since it fails running on seqera: (TODO: either keep it like this and remove the input argument or remove this and resolve the issue)
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# (--2025-07-16 05:34:27-- http://_viash_par/input_1/10X_Lung_Tumour_Annotated_v2.h5ad
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# Resolving _viash_par (_viash_par)... failed: Name or service not known.
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# wget: unable to resolve host address ‘_viash_par’)
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FILE_PATH = TMP_DIR / "10X_Lung_Tumour_Annotated_v2.h5ad"
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DOWNLOAD_URL = "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
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# Download the data (55GB)
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os.system(f'wget "{DOWNLOAD_URL}" -P "{TMP_DIR}/"')

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