\n",
+ " \n",
+ " | 2026-03-31 09:58:55.740269+00:00 | \n",
+ " INFO | \n",
+ " Memory limit set to 9.50 GB. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.740575+00:00 | \n",
+ " INFO | \n",
+ " Transformation image name: hdf5-cells. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.740725+00:00 | \n",
+ " INFO | \n",
+ " Transformation image version: 0.1.1. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.740850+00:00 | \n",
+ " INFO | \n",
+ " Configuration ID: 835356550. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741068+00:00 | \n",
+ " INFO | \n",
+ " Starting configuration validation... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741210+00:00 | \n",
+ " INFO | \n",
+ " Validating top-level configuration keys... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741337+00:00 | \n",
+ " INFO | \n",
+ " Validating biosample_metadata configuration... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741469+00:00 | \n",
+ " INFO | \n",
+ " Validating cell_metadata configuration... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741593+00:00 | \n",
+ " INFO | \n",
+ " Validating feature_metadata configuration... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741715+00:00 | \n",
+ " INFO | \n",
+ " Validating cell_expression configuration... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741834+00:00 | \n",
+ " INFO | \n",
+ " Configuration file validated successfully. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.741979+00:00 | \n",
+ " INFO | \n",
+ " Starting transformation for attachment GSF001458 (1/1)... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.765202+00:00 | \n",
+ " INFO | \n",
+ " Attachment metadata retrieved: {'genestack:accession': 'GSF001458', 'genestack:name': 'GSE210077_adata_healthy_diseased_nucseq_sparse.h5ad', 'Experimental Platform': 'Illumina NovaSeq 6000', 'Processing QC': 'Remove low-UMI nuclei; doublets removed', 'Source': 'Data was obtained from the Human Cell Atlas repository, project FibroticLiverWatsonMERFISH. Data available in https://explore.data.humancellatlas.org/projects/64809a52-f703-4aec-b3a5-eca808a971d0 ', 'Total Number of Cells or Nuclei': '27692', 'Library Preparation Protocol': '10x Genomics Chromium Single Cell 3′', 'Alignment & Quantification Method': 'Integration mapping with Cell Ranger v7.0.1 ', 'Comment': 'Original file adata_healthy_diseased_nucseq_.h5ad was obtained from the HCA repository (FibroticLiverWatsonMERFISH). It contained data from healthy and diseased patient samples, which were processed with snRNA-Seq. The file was converted to sparse format to reduce size and improve efficiency.', 'Preparation QC': 'DAPI-based nuclear QC and slide quality inspection', 'Genome Version': 'GRCh38', 'Nuclei Permeabilization': 'Nuclei isolated using lysis buffer (PBS+BSA+RNAse)', 'Normalization Method': 'Log-normalisation; spatial integration', 'Assay Type': 'Spatial-seq', 'Annotation': 'Annotation via liver cell markers; spatial integration', 'Data Class': 'Single-cell transcriptomics', 'Experimental Platform ID': 'GPL24676', 'Library Preparation Version': 'v3', 'Experiment Site': 'Massachusetts General Hospital, USA'}. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.779247+00:00 | \n",
+ " INFO | \n",
+ " Found study accession: GSF001440. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.779525+00:00 | \n",
+ " INFO | \n",
+ " Retrieving sample metadata for accession GSF001440... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.796022+00:00 | \n",
+ " INFO | \n",
+ " Sample metadata retrieved successfully. Total items: 6. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.816706+00:00 | \n",
+ " INFO | \n",
+ " The library group accession(s) found for the study: GSF001449. Will be used to link cell group to library group(s). If change is needed, please specify relevant sample, library or preparation group accession(s) in the config. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:58:55.816972+00:00 | \n",
+ " INFO | \n",
+ " Creating copy of the attachment file in temporary directory... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.316828+00:00 | \n",
+ " INFO | \n",
+ " Reading HDF5 file structure... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.317746+00:00 | \n",
+ " INFO | \n",
+ " Keys (groups): 'X', 'layers', 'obs', 'obsm', 'obsp', 'raw', 'uns', 'var', 'varm', 'varp'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.318283+00:00 | \n",
+ " INFO | \n",
+ " Group: 'X'. Type: 'expression'. Shape: (27692, 24619). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.360563+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obs'. Type: 'metadata'. Shape: (27692, 27). Index: '(unnamed)', first values: 'Liver.32_AAACCCAAGACTACCT.1-0', 'Liver.32_AAACCCAAGGCTTAAA.1-0', 'Liver.32_AAACCCAGTCACTCTC.1-0', 'Liver.32_AAACCCAGTCTGTAGT.1-0', 'Liver.32_AAACCCATCTGAACGT.1-0'. Columns and data types: ('Condition', category), ('Sex', category), ('Age', category), ('log10GenesPerUMI_injured', float64), ('seurat_clusters_injured', category), ('CellType_injured', category), ('cell_type_final_injured', category), ('log10GenesPerUMI_healthy', float64), ('seurat_clusters_healthy', category), ('CellType_healthy', category), ('cell_type_final_healthy', category), ('batch', category), ('n_counts', float32), ('log_counts', float32), ('n_genes', int32), ('sample_id', category), ('organism_ontology_term_id', category), ('donor_id', category), ('development_stage_ontology_term_id', category), ('sex_ontology_term_id', category), ('self_reported_ethnicity_ontology_term_id', category), ('disease_ontology_term_id', category), ('tissue_type', category), ('tissue_ontology_term_id', category), ('cell_type_ontology_term_id', category), ('assay_ontology_term_id', category), ('suspension_type', category). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.361392+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obsm'. Type: 'embedding'. Item: 'X_pca'. Shape: (27692, 25). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.361680+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obsm'. Type: 'embedding'. Item: 'X_pca_harmony'. Shape: (27692, 25). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.361913+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obsm'. Type: 'embedding'. Item: 'X_umap'. Shape: (27692, 2). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.362302+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obsp'. Type: 'pairwise'. Item: 'connectivities'. Shape: (27692, 27692). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.362559+00:00 | \n",
+ " INFO | \n",
+ " Group: 'obsp'. Type: 'pairwise'. Item: 'distances'. Shape: (27692, 27692). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.362808+00:00 | \n",
+ " INFO | \n",
+ " Group: 'raw'. Type: 'raw'. Items: 'X', 'var', 'varm'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.363076+00:00 | \n",
+ " INFO | \n",
+ " Group: 'uns'. Type: 'unstructured'. Items: 'Age_colors', 'CellType_healthy_colors', 'CellType_injured_colors', 'Condition_colors', 'SampleID_colors', 'Sex_colors', 'batch_colors', 'cell_type_final_healthy_colors', 'cell_type_final_injured_colors', 'cell_type_ontology_term_id_colors', 'development_stage_ontology_term_id_colors', 'disease_ontology_term_id_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'sample_id_colors', 'seurat_clusters_healthy_colors', 'seurat_clusters_injured_colors', 'umap'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.375577+00:00 | \n",
+ " INFO | \n",
+ " Group: 'var'. Type: 'metadata'. Shape: (24619, 4). Index: '(unnamed)', first values: 'ENSG00000238009', 'ENSG00000268903', 'ENSG00000241860', 'ENSG00000228463', 'ENSG00000290385'. Columns and data types: ('highly_variable', bool), ('means', float64), ('dispersions', float64), ('dispersions_norm', float32). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.376146+00:00 | \n",
+ " INFO | \n",
+ " Group: 'varm'. Type: 'embedding'. Item: 'PCs'. Shape: (24619, 25). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.377246+00:00 | \n",
+ " INFO | \n",
+ " Extracting sample metadata from GSE210077_adata_healthy_diseased_nucseq_sparse.h5ad... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.377700+00:00 | \n",
+ " INFO | \n",
+ " Reading sample metadata from 'obs'... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.412825+00:00 | \n",
+ " INFO | \n",
+ " Configured sample column name: 'sample_id'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.413368+00:00 | \n",
+ " INFO | \n",
+ " First sample names: 'AM031', 'AM062', 'AM072', 'AM042', 'AM048'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.413550+00:00 | \n",
+ " INFO | \n",
+ " Renaming 'sample_id' column name to 'Sample Source ID'... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.417639+00:00 | \n",
+ " INFO | \n",
+ " Columns renamed: ('Condition' --> 'Condition Group'), ('self_reported_ethnicity_ontology_term_id' --> 'Donor Ethnicity Term ID'), ('tissue_type' --> 'Cell Source'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.418766+00:00 | \n",
+ " INFO | \n",
+ " Curated values — ('Sample Source ID': 'AM031' --> 'Liver-32', 'AM042' --> 'Liver-13', 'AM048' --> 'Liver-14', 'AM061' --> 'Liver-18', 'AM062' --> 'Liver-33', 'AM072' --> 'Liver-34'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.418971+00:00 | \n",
+ " INFO | \n",
+ " Shape of the transformed sample metadata table: (6, 4) (sample objects x attributes). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.419151+00:00 | \n",
+ " INFO | \n",
+ " Columns of the transformed sample metadata table: 'Sample Source ID', 'Condition Group', 'Donor Ethnicity Term ID', 'Cell Source'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.419330+00:00 | \n",
+ " INFO | \n",
+ " Saving sample metadata to GSF001458_sample_metadata.tsv file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.422860+00:00 | \n",
+ " INFO | \n",
+ " Sample metadata processing successfully completed. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.423472+00:00 | \n",
+ " INFO | \n",
+ " Validating existing sample metadata update... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.423690+00:00 | \n",
+ " INFO | \n",
+ " Retrieving sample metadata for accession GSF001440... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.442606+00:00 | \n",
+ " INFO | \n",
+ " Sample metadata retrieved successfully. Total items: 6. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.446735+00:00 | \n",
+ " INFO | \n",
+ " All 6 sample objects were found in existing study-associated metadata and will be updated with new attributes. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.447232+00:00 | \n",
+ " INFO | \n",
+ " Extracting cell metadata from GSE210077_adata_healthy_diseased_nucseq_sparse.h5ad... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.447871+00:00 | \n",
+ " INFO | \n",
+ " Reading cell metadata from 'obs'... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.482639+00:00 | \n",
+ " INFO | \n",
+ " Adding X_pca column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:06.813478+00:00 | \n",
+ " INFO | \n",
+ " Adding X_pca_harmony column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.147438+00:00 | \n",
+ " INFO | \n",
+ " Adding X_umap column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.196973+00:00 | \n",
+ " INFO | \n",
+ " Adding connectivities column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.209286+00:00 | \n",
+ " INFO | \n",
+ " Adding distances column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.218569+00:00 | \n",
+ " INFO | \n",
+ " Extracting index column of cell metadata... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.218839+00:00 | \n",
+ " INFO | \n",
+ " Unnamed index found, index column name set to: _index. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.219514+00:00 | \n",
+ " INFO | \n",
+ " Shape of the initial cell metadata table: (27692, 33) (cells x attributes). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.219720+00:00 | \n",
+ " INFO | \n",
+ " Columns of the initial cell metadata table: '_index', 'Condition', 'Sex', 'Age', 'log10GenesPerUMI_injured', 'seurat_clusters_injured', 'CellType_injured', 'cell_type_final_injured', 'log10GenesPerUMI_healthy', 'seurat_clusters_healthy', 'CellType_healthy', 'cell_type_final_healthy', 'batch', 'n_counts', 'log_counts', 'n_genes', 'sample_id', 'organism_ontology_term_id', 'donor_id', 'development_stage_ontology_term_id', 'sex_ontology_term_id', 'self_reported_ethnicity_ontology_term_id', 'disease_ontology_term_id', 'tissue_type', 'tissue_ontology_term_id', 'cell_type_ontology_term_id', 'assay_ontology_term_id', 'suspension_type', 'X_pca', 'X_pca_harmony', 'X_umap', 'mean_connectivities', 'mean_distances'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.219910+00:00 | \n",
+ " INFO | \n",
+ " Dropping columns... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.222661+00:00 | \n",
+ " INFO | \n",
+ " The following columns were dropped from metadata: 'Age', 'organism_ontology_term_id', 'donor_id', 'Condition', 'Sex', 'tissue_type', 'self_reported_ethnicity_ontology_term_id', 'tissue_ontology_term_id', 'batch', 'disease_ontology_term_id', 'development_stage_ontology_term_id', 'sex_ontology_term_id'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.223294+00:00 | \n",
+ " INFO | \n",
+ " Applying column name changes... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.227289+00:00 | \n",
+ " INFO | \n",
+ " Columns renamed: ('_index' --> 'barcode'), ('cell_type_ontology_term_id' --> 'cell_type'), ('sample_id' --> 'batch'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.227733+00:00 | \n",
+ " INFO | \n",
+ " Curating values... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.228807+00:00 | \n",
+ " INFO | \n",
+ " Curated values — ('batch': 'AM031' --> 'Liver-32', 'AM042' --> 'Liver-13', 'AM048' --> 'Liver-14', 'AM061' --> 'Liver-18', 'AM062' --> 'Liver-33', 'AM072' --> 'Liver-34'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.229909+00:00 | \n",
+ " INFO | \n",
+ " Mapping columns to standardized names... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.231510+00:00 | \n",
+ " INFO | \n",
+ " Checking for duplicate column names and applying suffix if needed... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.231708+00:00 | \n",
+ " INFO | \n",
+ " Final column renaming mapping to fit API requirements (Original --> Final ODM API Display Name): ('barcode' --> 'barcode'), ('log10GenesPerUMI_injured' --> 'log10genesperumiInjured'), ('seurat_clusters_injured' --> 'seuratClustersInjured'), ('CellType_injured' --> 'celltypeInjured'), ('cell_type_final_injured' --> 'cellTypeFinalInjured'), ('log10GenesPerUMI_healthy' --> 'log10genesperumiHealthy'), ('seurat_clusters_healthy' --> 'seuratClustersHealthy'), ('CellType_healthy' --> 'celltypeHealthy'), ('cell_type_final_healthy' --> 'cellTypeFinalHealthy'), ('n_counts' --> 'nCounts'), ('log_counts' --> 'logCounts'), ('n_genes' --> 'nGenes'), ('batch' --> 'batch'), ('cell_type' --> 'cellType'), ('assay_ontology_term_id' --> 'assayOntologyTermId'), ('suspension_type' --> 'suspensionType'), ('X_pca' --> 'pca'), ('X_pca_harmony' --> 'pcaHarmony'), ('X_umap' --> 'umap'), ('mean_connectivities' --> 'meanConnectivities'), ('mean_distances' --> 'meanDistances'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.233152+00:00 | \n",
+ " INFO | \n",
+ " Validating standard column data types... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.237855+00:00 | \n",
+ " WARNING | \n",
+ " Columns with missing values: 'cellType'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:07.238050+00:00 | \n",
+ " INFO | \n",
+ " Columns converted to expected dtypes: ('barcode': object --> string), ('batch': category --> string), ('cellType': category --> string), ('nCounts': float32 --> int64). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.315027+00:00 | \n",
+ " INFO | \n",
+ " Column data types validated successfully. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.315351+00:00 | \n",
+ " INFO | \n",
+ " Checking required columns for cell metadata... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.323871+00:00 | \n",
+ " INFO | \n",
+ " Performing columns reordering... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.329086+00:00 | \n",
+ " INFO | \n",
+ " The columns were placed in the following order: 'barcode', 'batch', 'log10genesperumiInjured', 'seuratClustersInjured', 'celltypeInjured', 'cellTypeFinalInjured', 'log10genesperumiHealthy', 'seuratClustersHealthy', 'celltypeHealthy', 'cellTypeFinalHealthy', 'nCounts', 'logCounts', 'nGenes', 'cellType', 'assayOntologyTermId', 'suspensionType', 'pca', 'pcaHarmony', 'umap', 'meanConnectivities', 'meanDistances'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.329317+00:00 | \n",
+ " INFO | \n",
+ " Verifying if default QC columns are present... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.329547+00:00 | \n",
+ " INFO | \n",
+ " Missing default QC metrics columns: 'mitoCounts', 'percentMito', 'riboCounts', 'percentRibo'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.329693+00:00 | \n",
+ " INFO | \n",
+ " Calculating missing QC metrics and adding to metadata... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.330368+00:00 | \n",
+ " INFO | \n",
+ " Using raw counts for QC metrics calculation. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.341290+00:00 | \n",
+ " INFO | \n",
+ " Using var_df index for gene names. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.897842+00:00 | \n",
+ " INFO | \n",
+ " Columns added to cell metadata: 'mitoCounts', 'riboCounts', 'percentMito', 'percentRibo'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.898526+00:00 | \n",
+ " INFO | \n",
+ " Shape of the transformed cell metadata table: (27692, 25) (cells x attributes). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.898767+00:00 | \n",
+ " INFO | \n",
+ " Columns of the transformed cell metadata table: 'barcode', 'batch', 'log10genesperumiInjured', 'seuratClustersInjured', 'celltypeInjured', 'cellTypeFinalInjured', 'log10genesperumiHealthy', 'seuratClustersHealthy', 'celltypeHealthy', 'cellTypeFinalHealthy', 'nCounts', 'logCounts', 'nGenes', 'cellType', 'assayOntologyTermId', 'suspensionType', 'pca', 'pcaHarmony', 'umap', 'meanConnectivities', 'meanDistances', 'mitoCounts', 'riboCounts', 'percentMito', 'percentRibo'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:09.898946+00:00 | \n",
+ " INFO | \n",
+ " Saving cell metadata to GSF001458_cell_metadata.tsv file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.339660+00:00 | \n",
+ " INFO | \n",
+ " Cell metadata processing successfully completed. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.340443+00:00 | \n",
+ " INFO | \n",
+ " Extracting feature metadata from GSE210077_adata_healthy_diseased_nucseq_sparse.h5ad... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.341045+00:00 | \n",
+ " INFO | \n",
+ " Reading feature metadata from 'var'... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.353733+00:00 | \n",
+ " INFO | \n",
+ " Adding PCs column from group... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.475829+00:00 | \n",
+ " INFO | \n",
+ " Extracting index column of feature metadata... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.476084+00:00 | \n",
+ " INFO | \n",
+ " Unnamed index found, index column name set to: _index. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.476773+00:00 | \n",
+ " INFO | \n",
+ " Shape of the initial feature metadata table: (24619, 6) (features x attributes). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.476947+00:00 | \n",
+ " INFO | \n",
+ " Columns of the initial feature metadata table: '_index', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'PCs'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.477102+00:00 | \n",
+ " INFO | \n",
+ " Applying column name changes... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.478687+00:00 | \n",
+ " INFO | \n",
+ " Columns renamed: ('_index' --> 'gene'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.479586+00:00 | \n",
+ " INFO | \n",
+ " Mapping columns to standardized names... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.479916+00:00 | \n",
+ " INFO | \n",
+ " Checking for duplicate column names and applying suffix if needed... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.480079+00:00 | \n",
+ " INFO | \n",
+ " Final column renaming mapping to fit API requirements (Original --> Final ODM API Display Name): ('gene' --> 'gene'), ('highly_variable' --> 'highlyVariable'), ('means' --> 'meanCounts'), ('dispersions' --> 'dispersions'), ('dispersions_norm' --> 'dispersionsNorm'), ('PCs' --> 'PCs'). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.480892+00:00 | \n",
+ " INFO | \n",
+ " Validating standard column data types... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.482897+00:00 | \n",
+ " INFO | \n",
+ " Columns converted to expected dtypes: ('gene': object --> string). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.483251+00:00 | \n",
+ " INFO | \n",
+ " Column data types validated successfully. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.483413+00:00 | \n",
+ " INFO | \n",
+ " Starting mapping of gene IDs to gene symbols... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.483571+00:00 | \n",
+ " INFO | \n",
+ " Gene names already present in gene metadata. Skipping ID mapping. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.483722+00:00 | \n",
+ " INFO | \n",
+ " Shape of the transformed feature metadata table: (24619, 6) (features x attributes). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.483885+00:00 | \n",
+ " INFO | \n",
+ " Columns of the transformed feature metadata table: 'gene', 'highlyVariable', 'meanCounts', 'dispersions', 'dispersionsNorm', 'PCs'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.484036+00:00 | \n",
+ " INFO | \n",
+ " Saving feature metadata to GSF001458_feature_metadata.tsv file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.615490+00:00 | \n",
+ " INFO | \n",
+ " Feature metadata processing successfully completed. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.660628+00:00 | \n",
+ " INFO | \n",
+ " Processing expression matrix... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.660923+00:00 | \n",
+ " INFO | \n",
+ " Reading cell metadata file GSF001458_cell_metadata.tsv... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.892376+00:00 | \n",
+ " INFO | \n",
+ " First 5 cell names: 'Liver.32_AAACCCAAGACTACCT.1-0', 'Liver.32_AAACCCAAGGCTTAAA.1-0', 'Liver.32_AAACCCAGTCACTCTC.1-0', 'Liver.32_AAACCCAGTCTGTAGT.1-0', 'Liver.32_AAACCCATCTGAACGT.1-0'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.892702+00:00 | \n",
+ " INFO | \n",
+ " Reading feature metadata file GSF001458_feature_metadata.tsv... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.934817+00:00 | \n",
+ " INFO | \n",
+ " Feature ID column: 'gene'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.935297+00:00 | \n",
+ " INFO | \n",
+ " Feature metadata columns to include: 'highlyVariable', 'meanCounts', 'dispersions', 'dispersionsNorm', 'PCs'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.969658+00:00 | \n",
+ " INFO | \n",
+ " Reading feature and cell expression data from the input HDF5 file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.983696+00:00 | \n",
+ " INFO | \n",
+ " First 5 feature names: 'ENSG00000238009', 'ENSG00000268903', 'ENSG00000241860', 'ENSG00000228463', 'ENSG00000290385'. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.985888+00:00 | \n",
+ " INFO | \n",
+ " Number of cells in expression matrix: 27692. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.986054+00:00 | \n",
+ " INFO | \n",
+ " Number of features in expression matrix: 24619. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.986471+00:00 | \n",
+ " INFO | \n",
+ " Number of non-zero values: 52698313. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.986642+00:00 | \n",
+ " INFO | \n",
+ " First 5 non-zero values: 0.4216345, 0.4216345, 0.4216345, 0.4216345, 0.4216345. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.986899+00:00 | \n",
+ " INFO | \n",
+ " Auto-detected number format '%.7g' and matrix dtype 'float32' from native dtype. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.987047+00:00 | \n",
+ " INFO | \n",
+ " User-provided chunk size: 2000 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:10.987201+00:00 | \n",
+ " INFO | \n",
+ " Writing cell expression data to GSF001458_cell_expression.br file using brotli compression... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:19.135008+00:00 | \n",
+ " INFO | \n",
+ " Processed 2000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:27.250167+00:00 | \n",
+ " INFO | \n",
+ " Processed 4000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:35.405850+00:00 | \n",
+ " INFO | \n",
+ " Processed 6000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:43.211718+00:00 | \n",
+ " INFO | \n",
+ " Processed 8000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:51.226030+00:00 | \n",
+ " INFO | \n",
+ " Processed 10000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 09:59:59.259393+00:00 | \n",
+ " INFO | \n",
+ " Processed 12000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:07.129478+00:00 | \n",
+ " INFO | \n",
+ " Processed 14000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:14.838689+00:00 | \n",
+ " INFO | \n",
+ " Processed 16000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:22.398363+00:00 | \n",
+ " INFO | \n",
+ " Processed 18000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:29.856843+00:00 | \n",
+ " INFO | \n",
+ " Processed 20000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:36.707095+00:00 | \n",
+ " INFO | \n",
+ " Processed 22000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:42.847886+00:00 | \n",
+ " INFO | \n",
+ " Processed 24000 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.933951+00:00 | \n",
+ " INFO | \n",
+ " Processed 24619 / 24619 features. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.937313+00:00 | \n",
+ " INFO | \n",
+ " Cell expression data processing successfully completed. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.944302+00:00 | \n",
+ " INFO | \n",
+ " Extracting expression metadata from source file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.947006+00:00 | \n",
+ " INFO | \n",
+ " Saving expression metadata to GSF001458_expression_metadata.tsv file... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.947920+00:00 | \n",
+ " INFO | \n",
+ " Starting upload of transformed files to ODM... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:44.948096+00:00 | \n",
+ " INFO | \n",
+ " Updating existing sample objects... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:46.614785+00:00 | \n",
+ " INFO | \n",
+ " Updated sample group accession(s): GSF001441. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:46.620640+00:00 | \n",
+ " INFO | \n",
+ " Starting import of cells to ODM. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:47.646433+00:00 | \n",
+ " INFO | \n",
+ " Waiting for import job to complete. Job exec ID: 159. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:00:47.661020+00:00 | \n",
+ " INFO | \n",
+ " Job status: RUNNING | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:02.687732+00:00 | \n",
+ " INFO | \n",
+ " Cells upload completed. Group accession: GSF001465. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:02.688059+00:00 | \n",
+ " INFO | \n",
+ " Single library group accession(s) will be used for cells linking: GSF001449. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:02.688243+00:00 | \n",
+ " INFO | \n",
+ " Linking cell group to library group. Cell group accession: GSF001465, Library group accession: GSF001449. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:03.289374+00:00 | \n",
+ " INFO | \n",
+ " Cell group has been fully linked to library group. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:03.442087+00:00 | \n",
+ " INFO | \n",
+ " Starting import of expression to ODM. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:06.437843+00:00 | \n",
+ " INFO | \n",
+ " Waiting for import job to complete. Job exec ID: 160. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:06.451592+00:00 | \n",
+ " INFO | \n",
+ " Job status: RUNNING | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:21.489144+00:00 | \n",
+ " INFO | \n",
+ " Expression upload completed. Group accession: GSF001467. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:21.514075+00:00 | \n",
+ " INFO | \n",
+ " Linking expression group to cell group. Expression group accession: GSF001467, Cell group accession: GSF001465. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:21.760597+00:00 | \n",
+ " INFO | \n",
+ " Expression group has been fully linked to cell group. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:22.051941+00:00 | \n",
+ " INFO | \n",
+ " Transformation of attachment GSF001458 completed successfully with 1 warning(s). | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:22.053246+00:00 | \n",
+ " INFO | \n",
+ " Saving transformation metadata to GSF001458_transformation_metadata_20260331_100122.tsv... | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:22.054650+00:00 | \n",
+ " INFO | \n",
+ " Starting import of transformation logs to ODM. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:23.145380+00:00 | \n",
+ " INFO | \n",
+ " Waiting for import job to complete. Job exec ID: 161. | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:23.162113+00:00 | \n",
+ " INFO | \n",
+ " Job status: RUNNING | \n",
+ "
\n",
+ " \n",
+ " | 2026-03-31 10:01:38.193377+00:00 | \n",
+ " INFO | \n",
+ " Transformation logs upload completed. Accession: GSF001468. | \n",
+ "
\n",
+ " \n",
+ "