Gregor metadata airtable update #3556
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…roadinstitute/seqr into gregor-metadata-airtable-update
| content_rows = [[row.get(key) or blank_value for key in header] for row in rows] | ||
| content += '\n'.join([ | ||
| DELIMITERS[file_format].join(row) for row in content_rows | ||
| content = '\n'.join([ |
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fixes a bug when the table is empty
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Add a test for an empty table?
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out of scope, I just happened to notice it here but this endpoint can't return empty tables
seqr/views/apis/report_api.py
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| READ_RNA_TABLE_COLUMNS.insert(10, 'gene_annotation_details') | ||
| READ_RNA_TABLE_COLUMNS.insert(13, 'alignment_postprocessing') |
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The number is hard to maintain. Can we use indexOf() to get relative positions?
| RNA_ONLY = EXPERIMENT_RNA_TABLE_AIRTABLE_FIELDS + READ_RNA_TABLE_AIRTABLE_FIELDS + ['reference_assembly_uri'] | ||
| DATA_TYPE_OMIT = { | ||
| 'wgs': ['targeted_regions_method'] + RNA_ONLY, 'wes': RNA_ONLY, 'rna': [ | ||
| 'targeted_regions_method', 'target_insert_size', 'mean_coverage', 'aligned_dna_short_read_file', | ||
| 'aligned_dna_short_read_index_file', | ||
| ], | ||
| } | ||
| NO_DATA_TYPE_FIELDS = { | ||
| 'targeted_region_bed_file', 'reference_assembly', 'analysis_details', 'percent_rRNA', 'percent_mRNA', | ||
| 'alignment_software_dna', |
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It is worth defining constants for these field names.
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Why? We don't for the other 7 tables already in this report, why would we do it for this new one
| individual_data_types = defaultdict(set) | ||
| for individual_db_id, sample_type in sample_types: | ||
| individual_data_types[individual_db_id].add(sample_type) | ||
| individuals = Individual.objects.filter(id__in=individual_data_types).prefetch_related( |
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Interestingly, we don't have to use individual_data_types.keys() for Individual.objects.filter(id__in=individual_data_types).
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thats just how iterating a dictionary in python3 works
| content_rows = [[row.get(key) or blank_value for key in header] for row in rows] | ||
| content += '\n'.join([ | ||
| DELIMITERS[file_format].join(row) for row in content_rows | ||
| content = '\n'.join([ |
There was a problem hiding this comment.
Add a test for an empty table?
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