AUTO: update migrate.py schema_version 5.2.3->5.3.0 #1292
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ejmolinelli
changed the title
joyceyan
approved these changes
Mar 11, 2025
Adding Public and Private specific dataset updates, as well as CSR matrix checking according to single-cell-curation issue 1023.
Non_csr_list contains dataset_ids of datasets that have at least one non-csr matrix.
Adding Non_CSR_matrix check for checking sparsity of non csr matrices in migrate.py
jahilton
requested changes
Mar 12, 2025
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| # fmt: off | ||
| # ONTOLOGY TERMS TO UPDATE ACROSS ALL DATASETS IN CORPUS | ||
| # Initialization is AUTOMATED for newly deprecated terms that have 'Replaced By' terms in their ontology files |
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Let's keep these types of comments so this file can remain as a template for future migrations
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@jahilton I'll see if I can update the generator to keep the comments.
| import anndata as ad | ||
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| import pandas as pd |
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Can avoid pandas (below)
| }, | ||
| "development_stage": DEV_STAGE_AUTO_MIGRATE_MAP, |
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Keep as empty dict like the other fields for future use
| ] | ||
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| # Dictionary for CURATOR-DEFINED remapping of deprecated feature IDs, if any, to new feature IDs. | ||
| GENCODE_MAPPER = {} |
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| # Dictionary for CURATOR-DEFINED remapping of deprecated feature IDs, if any, to new feature IDs. | ||
| GENCODE_MAPPER = {} | ||
| df = pd.read_csv('migrate_files/non_csr_list.csv') |
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No need for a csv as it's a single columns. So remove the column header, and you can just read into a list without going through pandas
| # utils.replace_ontology_term(df, <ontology_name>, {"term_to_replace": "replacement_term", ...}) | ||
| # elif collection_id == "<collection_2_id>": | ||
| # <custom transformation logic beyond scope of replace_ontology_term> | ||
| # ... |
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| dataset.var.drop(columns="feature_type", inplace=True) | ||
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| if GENCODE_MAPPER: |
| dataset = utils.remap_deprecated_features(adata=dataset, remapped_features=GENCODE_MAPPER) | ||
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| # AUTOMATED, DO NOT CHANGE -- IF GENCODE UPDATED, DEPRECATED FEATURE FILTERING ALGORITHM WILL GO HERE. | ||
| if DEPRECATED_FEATURE_IDS: |
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This is an automated PR to update migrate.py from schema_version 5.2.3->5.3.0