| manage.py |
main |
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6 |
2 |
0 |
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67% |
| manage.py |
(no function) |
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5 |
0 |
0 |
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100% |
| rest_api/__init__.py |
(no function) |
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0 |
0 |
0 |
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| rest_api/admin.py |
(no function) |
|
18 |
0 |
0 |
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| rest_api/apps.py |
(no function) |
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4 |
0 |
0 |
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100% |
| rest_api/data_entry/annotation_import.py |
AnnotationImport.__init__ |
|
4 |
4 |
0 |
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0% |
| rest_api/data_entry/annotation_import.py |
AnnotationImport._import_vcf |
|
8 |
8 |
0 |
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| rest_api/data_entry/annotation_import.py |
AnnotationImport.convert_lines |
|
19 |
19 |
0 |
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| rest_api/data_entry/annotation_import.py |
AnnotationImport._parse_line_info |
|
12 |
12 |
0 |
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| rest_api/data_entry/annotation_import.py |
AnnotationImport.get_annotation_objs |
|
32 |
32 |
0 |
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| rest_api/data_entry/annotation_import.py |
AnnotationImport.get_annotation2mutation_objs |
|
7 |
7 |
0 |
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0% |
| rest_api/data_entry/annotation_import.py |
(no function) |
|
20 |
0 |
0 |
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100% |
| rest_api/data_entry/gbk_import.py |
import_gbk_file |
|
67 |
67 |
0 |
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0% |
| rest_api/data_entry/gbk_import.py |
determine_gene_type |
|
4 |
4 |
0 |
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| rest_api/data_entry/gbk_import.py |
_process_segments |
|
7 |
7 |
0 |
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0% |
| rest_api/data_entry/gbk_import.py |
_validate_segment_lengths |
|
3 |
3 |
0 |
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| rest_api/data_entry/gbk_import.py |
_determine_gene_accession |
|
7 |
7 |
0 |
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| rest_api/data_entry/gbk_import.py |
_determine_cds_accession |
|
9 |
9 |
0 |
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| rest_api/data_entry/gbk_import.py |
_determine_symbol |
|
5 |
5 |
0 |
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| rest_api/data_entry/gbk_import.py |
_put_gene_from_feature |
|
10 |
10 |
0 |
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| rest_api/data_entry/gbk_import.py |
_put_cds_from_feature |
|
11 |
11 |
0 |
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| rest_api/data_entry/gbk_import.py |
_put_peptide_from_feature |
|
8 |
8 |
0 |
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| rest_api/data_entry/gbk_import.py |
parse_date |
|
13 |
13 |
0 |
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| rest_api/data_entry/gbk_import.py |
_put_reference_from_record |
|
24 |
24 |
0 |
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| rest_api/data_entry/gbk_import.py |
_create_gene_segments |
|
3 |
3 |
0 |
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| rest_api/data_entry/gbk_import.py |
_create_cds_segments |
|
3 |
3 |
0 |
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| rest_api/data_entry/gbk_import.py |
calculate_cds_start_end |
|
19 |
19 |
0 |
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| rest_api/data_entry/gbk_import.py |
_create_peptide_segments |
|
4 |
4 |
0 |
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| rest_api/data_entry/gbk_import.py |
_temp_save_file |
|
6 |
6 |
0 |
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| rest_api/data_entry/gbk_import.py |
(no function) |
|
44 |
0 |
0 |
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100% |
| rest_api/data_entry/property_job.py |
find_or_create_property |
|
15 |
15 |
0 |
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0% |
| rest_api/data_entry/property_job.py |
delete_property |
|
6 |
6 |
0 |
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0% |
| rest_api/data_entry/property_job.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/data_entry/reference_job.py |
delete_reference |
|
5 |
5 |
0 |
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| rest_api/data_entry/reference_job.py |
(no function) |
|
3 |
0 |
0 |
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100% |
| rest_api/data_entry/sample_entry_job.py |
check_for_new_data |
|
35 |
35 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
import_archive |
|
104 |
104 |
0 |
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0% |
| rest_api/data_entry/sample_entry_job.py |
process_batch |
|
12 |
12 |
0 |
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0% |
| rest_api/data_entry/sample_entry_job.py |
process_batch_run |
|
31 |
31 |
0 |
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0% |
| rest_api/data_entry/sample_entry_job.py |
process_annotation |
|
13 |
13 |
0 |
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0% |
| rest_api/data_entry/sample_entry_job.py |
process_batch_single_thread |
|
33 |
33 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
import_property |
|
43 |
43 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
process_property_batch |
|
10 |
10 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
_process_property_file |
|
64 |
64 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
_create_property_updates |
|
13 |
13 |
0 |
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| rest_api/data_entry/sample_entry_job.py |
(no function) |
|
54 |
0 |
0 |
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100% |
| rest_api/data_entry/sample_import.py |
SonarImport.__init__ |
|
11 |
11 |
0 |
|
0% |
| rest_api/data_entry/sample_import.py |
SonarImport.get_sample_name |
|
1 |
1 |
0 |
|
0% |
| rest_api/data_entry/sample_import.py |
SonarImport.get_sequence_obj |
|
2 |
2 |
0 |
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| rest_api/data_entry/sample_import.py |
SonarImport.update_replicon_obj |
|
3 |
3 |
0 |
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0% |
| rest_api/data_entry/sample_import.py |
SonarImport.create_alignment |
|
4 |
4 |
0 |
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0% |
| rest_api/data_entry/sample_import.py |
SonarImport.get_mutation_objs_nt |
|
24 |
24 |
0 |
|
0% |
| rest_api/data_entry/sample_import.py |
SonarImport.is_same_mutation |
|
1 |
1 |
0 |
|
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| rest_api/data_entry/sample_import.py |
SonarImport.get_mutation_objs_cds_and_parent_relations |
|
28 |
28 |
0 |
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0% |
| rest_api/data_entry/sample_import.py |
SonarImport._import_pickle |
|
2 |
2 |
0 |
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0% |
| rest_api/data_entry/sample_import.py |
SonarImport._import_vars |
|
14 |
14 |
0 |
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| rest_api/data_entry/sample_import.py |
SonarImport._import_seq |
|
5 |
5 |
0 |
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| rest_api/data_entry/sample_import.py |
(no function) |
|
44 |
0 |
0 |
|
100% |
| rest_api/data_entry/sample_job.py |
delete_sequences |
|
10 |
10 |
0 |
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0% |
| rest_api/data_entry/sample_job.py |
delete_samples |
|
15 |
15 |
0 |
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0% |
| rest_api/data_entry/sample_job.py |
(no function) |
|
9 |
0 |
0 |
|
100% |
| rest_api/data_entry/sequence_job.py |
clean_unused_sequences |
|
4 |
4 |
0 |
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| rest_api/data_entry/sequence_job.py |
(no function) |
|
3 |
0 |
0 |
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100% |
| rest_api/management/commands/import_lineage.py |
LineageImport.__init__ |
|
2 |
2 |
0 |
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| rest_api/management/commands/import_lineage.py |
LineageImport.__enter__ |
|
1 |
1 |
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| rest_api/management/commands/import_lineage.py |
LineageImport.__exit__ |
|
1 |
1 |
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| rest_api/management/commands/import_lineage.py |
LineageImport.set_file |
|
4 |
4 |
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| rest_api/management/commands/import_lineage.py |
LineageImport.process_lineage_data |
|
31 |
31 |
0 |
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| rest_api/management/commands/import_lineage.py |
LineageImport.update_lineage_data |
|
5 |
5 |
0 |
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| rest_api/management/commands/import_lineage.py |
Command.add_arguments |
|
2 |
2 |
0 |
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| rest_api/management/commands/import_lineage.py |
Command.handle |
|
8 |
8 |
0 |
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| rest_api/management/commands/import_lineage.py |
(no function) |
|
22 |
0 |
0 |
|
100% |
| rest_api/migrations/0001_initial.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| rest_api/migrations/0002_alter_sample2property_value_varchar_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0003_sample_properties_alter_element_accession_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0004_sample_properties_alter_sample2property_value_text.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0005_alter_alignment_id_alter_element_id_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
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| rest_api/migrations/0006_alignment2mutation_mutation_mutation2annotation_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0007_entereddata.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0008_alter_entereddata_name.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0009_remove_mutation_aa_profile_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0010_alter_mutation_unique_together.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0011_alter_mutation_unique_together.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0012_alter_mutation_unique_together.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0013_alter_entereddata_unique_together_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0014_sample_collection_date_sample_country_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0015_gene_genepart_sourceelement_remove_element_molecule_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0016_alter_gene_table.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0017_remove_gene_symbol.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0018_alter_mutation_element.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0019_replicon_rename_genepart_genesegment_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0020_remove_reference_standard.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0021_remove_alignment_element_remove_mutation_element_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0022_mutation_type.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0023_mutation_mutation_gene_id_2f1f1c_idx_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0024_mutation_mutation_label_94967f_idx.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0025_alignment_alignment_gene_id_81f250_idx.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0026_alignment2mutation_alignment2m_alignme_d1c719_idx.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0027_mutation_mutation_type_bf4ac1_idx.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0028_remove_mutation_mutation_label_94967f_idx_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0029_remove_alignment_alignment_gene_id_81f250_idx_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0030_delete_mutation2property.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0031_remove_annotationtype_test.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0032_annotationtype_impact.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0033_alter_alignment_id_alter_annotationtype_id_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0034_mutation_unique_mutation.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0035_mutation_unique_mutation_null_gene.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0036_alter_alignment2mutation_unique_together_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0037_mutation_unique_mutation_null_alt_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0038_annotationtype_unique_annotation_null_region.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0039_alter_gene_cds_accession_alter_gene_cds_symbol_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0040_alter_mutation_alt_alter_mutation_ref.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0041_reference_translation_id.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0042_alter_mutation_ref.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0043_alter_alignment_replicon_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0044_alter_mutation_gene_alter_mutation_replicon.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0045_alter_alignment_sequence.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0046_alter_alignment2mutation_mutation_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0047_alter_sample2property_value_float.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0048_lineage_lineagealias_delete_lineages_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0049_alter_mutation_alt.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0050_alter_sample_sequence.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0051_importlog_delete_entereddata_alter_sample_sequence_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0052_alter_mutation2annotation_alignment_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0053_fileprocessing_processingjob_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0054_alter_processingjob_entry_time_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0055_alter_gene_gene_accession.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0056_alter_mutation_alt_alter_mutation_ref.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0057_remove_sample_processing_date_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0058_remove_lineagealias_lineage_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0059_lineage_unique_lineage_parent_null.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0060_alter_importlog_type.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0061_auto_20241031_1135.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0062_sample_sample_name_be7a19_idx_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0063_remove_mutation_parent_id_mutation_parent.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0064_remove_mutation_alignments_remove_mutation_gene_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0065_nucleotidemutation_unique_nt_mutation_null_alt_null_ref.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0066_remove_nucleotidemutation_unique_nt_mutation_null_alt_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0067_remove_aminoacidmutation_unique_aa_mutation_null_gene_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0068_cds_cdssegment_peptide_peptidesegment_and_more.py |
update_amino_acid_cds |
|
6 |
3 |
0 |
|
50% |
| rest_api/migrations/0068_cds_cdssegment_peptide_peptidesegment_and_more.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| rest_api/migrations/0069_remove_cdssegment_unique_cds_part_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0070_aminoacidmutation_is_frameshift_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/0071_alter_reference_name.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0072_remove_aminoacidmutation_is_frameshift_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0073_remove_sample_length_remove_sample_sequence_and_more.py |
_unique_sequence_name |
|
15 |
15 |
0 |
|
0% |
| rest_api/migrations/0073_remove_sample_length_remove_sample_sequence_and_more.py |
backfill_sequence_metadata |
|
20 |
11 |
0 |
|
45% |
| rest_api/migrations/0073_remove_sample_length_remove_sample_sequence_and_more.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| rest_api/migrations/0074_alter_sequence_seqhash.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0075_alter_cds_accession_alter_gene_accession_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0076_remove_gene_locus_tag_alter_gene_accession_and_more.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| rest_api/migrations/0077_remove_lineage_unique_lineage_and_more.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| rest_api/migrations/__init__.py |
(no function) |
|
0 |
0 |
0 |
|
100% |
| rest_api/models.py |
AnnotationType.__str__ |
|
1 |
0 |
0 |
|
100% |
| rest_api/models.py |
Lineage.get_sublineages |
|
3 |
3 |
0 |
|
0% |
| rest_api/models.py |
Lineage.get_sublineages_from_list |
|
10 |
10 |
0 |
|
0% |
| rest_api/models.py |
Lineage.__str__ |
|
1 |
1 |
0 |
|
0% |
| rest_api/models.py |
Sample.save |
|
3 |
3 |
0 |
|
0% |
| rest_api/models.py |
NucleotideMutation.__str__ |
|
1 |
1 |
0 |
|
0% |
| rest_api/models.py |
AminoAcidMutation.__str__ |
|
1 |
1 |
0 |
|
0% |
| rest_api/models.py |
(no function) |
|
229 |
0 |
0 |
|
100% |
| rest_api/serializers.py |
find_or_create |
|
6 |
6 |
0 |
|
0% |
| rest_api/serializers.py |
Sample2PropertySerializer.get_value |
|
1 |
1 |
0 |
|
0% |
| rest_api/serializers.py |
Sample2PropertySerializer.get_name |
|
1 |
1 |
0 |
|
0% |
| rest_api/serializers.py |
Sample2PropertyBulkCreateOrUpdateSerializer.validate |
|
6 |
6 |
0 |
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0% |
| rest_api/serializers.py |
Sample2PropertyBulkCreateOrUpdateSerializer.get_unique_together_validators |
|
1 |
1 |
0 |
|
0% |
| rest_api/serializers.py |
RepliconSerializer.create |
|
2 |
2 |
0 |
|
0% |
| rest_api/serializers.py |
GeneSerializer.create |
|
3 |
3 |
0 |
|
0% |
| rest_api/serializers.py |
SampleGenomesSerializer.get_properties |
|
24 |
0 |
0 |
|
100% |
| rest_api/serializers.py |
SampleGenomesSerializer.get_genomic_profiles |
|
16 |
1 |
0 |
|
94% |
| rest_api/serializers.py |
SampleGenomesSerializer.get_proteomic_profiles |
|
28 |
1 |
0 |
|
96% |
| rest_api/serializers.py |
SampleGenomesSerializer.define_proteomic_label |
|
6 |
0 |
0 |
|
100% |
| rest_api/serializers.py |
SampleGenomesSerializer.create_NT_format |
|
11 |
3 |
0 |
|
73% |
| rest_api/serializers.py |
SampleGenomesSerializerVCF.get_genomic_profiles |
|
18 |
18 |
0 |
|
0% |
| rest_api/serializers.py |
SampleGenomesExportStreamSerializer.get_row |
|
35 |
35 |
0 |
|
0% |
| rest_api/serializers.py |
(no function) |
|
140 |
0 |
0 |
|
100% |
| rest_api/test/__init__.py |
(no function) |
|
0 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
FixtureModelTestCase.get_object |
|
3 |
3 |
0 |
|
0% |
| rest_api/test/mixins.py |
FixtureApiMixin.get_request_user |
|
3 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
FixtureApiMixin.get_user |
|
12 |
12 |
0 |
|
0% |
| rest_api/test/mixins.py |
CustomTestMixin.test_reverse_url_lookup |
|
2 |
1 |
0 |
|
50% |
| rest_api/test/mixins.py |
CustomTestMixin.get_instance_or_none |
|
4 |
4 |
0 |
|
0% |
| rest_api/test/mixins.py |
ListViewSetTestMixin.get_list_response |
|
4 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
ListViewSetTestMixin.test_list |
|
3 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
ListViewSetTestMixin._test_list_filtering |
|
5 |
5 |
0 |
|
0% |
| rest_api/test/mixins.py |
RetrieveViewSetTestMixin.get_instance_and_lookup_field |
|
5 |
1 |
0 |
|
80% |
| rest_api/test/mixins.py |
RetrieveViewSetTestMixin.test_retrieve |
|
1 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
RetrieveViewSetTestMixin._test_retrieve |
|
8 |
0 |
0 |
|
100% |
| rest_api/test/mixins.py |
UpdateViewSetTestMixin._test_update |
|
27 |
27 |
0 |
|
0% |
| rest_api/test/mixins.py |
UpdateViewSetTestMixin._test_update_error_examples |
|
26 |
26 |
0 |
|
0% |
| rest_api/test/mixins.py |
DestroyViewSetTestMixin.test_destroy |
|
1 |
1 |
0 |
|
0% |
| rest_api/test/mixins.py |
DestroyViewSetTestMixin._test_destroy |
|
10 |
10 |
0 |
|
0% |
| rest_api/test/mixins.py |
CreateViewSetTestMixin._test_create |
|
9 |
9 |
0 |
|
0% |
| rest_api/test/mixins.py |
CreateViewSetTestMixin._test_error_examples |
|
14 |
14 |
0 |
|
0% |
| rest_api/test/mixins.py |
ListSchemaTestMixin._test_list_schema |
|
12 |
12 |
0 |
|
0% |
| rest_api/test/mixins.py |
OrderingTestMixin._test_list_ordering |
|
17 |
17 |
0 |
|
0% |
| rest_api/test/mixins.py |
(no function) |
|
59 |
0 |
0 |
|
100% |
| rest_api/test/test_views/__init__.py |
(no function) |
|
0 |
0 |
0 |
|
100% |
| rest_api/test/test_views/test_viewsets.py |
AlignmentViewSetTest.test_get_alignment_data |
|
1 |
0 |
0 |
|
100% |
| rest_api/test/test_views/test_viewsets.py |
SampleViewSetTest.test_genome_filters |
|
7 |
0 |
0 |
|
100% |
| rest_api/test/test_views/test_viewsets.py |
(no function) |
|
19 |
0 |
0 |
|
100% |
| rest_api/tests.py |
StatusViewTests.test_status_returns_backend_version |
|
4 |
0 |
0 |
|
100% |
| rest_api/tests.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| rest_api/urls.py |
(no function) |
|
23 |
0 |
0 |
|
100% |
| rest_api/utils.py |
write_to_file |
|
4 |
4 |
0 |
|
0% |
| rest_api/utils.py |
strtobool |
|
6 |
2 |
0 |
|
67% |
| rest_api/utils.py |
resolve_ambiguous_NT_AA |
|
5 |
5 |
0 |
|
0% |
| rest_api/utils.py |
define_profile |
|
70 |
70 |
0 |
|
0% |
| rest_api/utils.py |
generate_job_ID |
|
5 |
5 |
0 |
|
0% |
| rest_api/utils.py |
parse_date |
|
9 |
9 |
0 |
|
0% |
| rest_api/utils.py |
get_distinct_gene_symbols |
|
4 |
1 |
0 |
|
75% |
| rest_api/utils.py |
get_distinct_replicon_accessions |
|
5 |
5 |
0 |
|
0% |
| rest_api/utils.py |
get_distinct_cds_accessions |
|
7 |
7 |
0 |
|
0% |
| rest_api/utils.py |
get_distinct_peptide_descriptions |
|
4 |
4 |
0 |
|
0% |
| rest_api/utils.py |
parse_default_data |
|
3 |
3 |
0 |
|
0% |
| rest_api/utils.py |
(no function) |
|
23 |
0 |
0 |
|
100% |
| rest_api/views_status.py |
status |
|
1 |
0 |
0 |
|
100% |
| rest_api/views_status.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| rest_api/viewsets.py |
Echo.write |
|
1 |
1 |
0 |
|
0% |
| rest_api/viewsets.py |
AlignmentViewSet.get_alignment_data |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets.py |
AlignmentViewSet.get_bulk_alignment_data |
|
8 |
8 |
0 |
|
0% |
| rest_api/viewsets.py |
RepliconViewSet.distinct_accessions |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets.py |
RepliconViewSet.get_molecule_data |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets.py |
GeneViewSet.distinct_gene_symbols |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets.py |
GeneViewSet.get_gene_data |
|
56 |
56 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.import_gbk |
|
9 |
9 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.dataset_options |
|
19 |
19 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.delete_reference |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.distinct_accessions |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.get_all_references |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets.py |
ReferenceViewSet.get_reference_file |
|
22 |
22 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.distinct_properties |
|
15 |
15 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.distinct_property_names |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.add_property |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.delete_property |
|
7 |
7 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.get_all_properties |
|
35 |
35 |
1 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.get_distinct_property_names |
|
7 |
7 |
0 |
|
0% |
| rest_api/viewsets.py |
PropertyViewSet.get_custom_property_names |
|
4 |
4 |
0 |
|
0% |
| rest_api/viewsets.py |
ResourceViewSet.get_translation_table |
|
7 |
7 |
0 |
|
0% |
| rest_api/viewsets.py |
FileUploadViewSet._convert_property_column_mapping |
|
1 |
1 |
0 |
|
0% |
| rest_api/viewsets.py |
FileUploadViewSet.import_upload |
|
44 |
44 |
0 |
|
0% |
| rest_api/viewsets.py |
FileUploadViewSet.start_file_import |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets.py |
LineageViewSet.distinct_lineages |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets.py |
LineageViewSet.full_lineages |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets.py |
LineageViewSet.get_sublineages |
|
6 |
6 |
0 |
|
0% |
| rest_api/viewsets.py |
LineageViewSet.update_lineages |
|
14 |
14 |
0 |
|
0% |
| rest_api/viewsets.py |
LineageViewSet._temp_save_file |
|
4 |
4 |
0 |
|
0% |
| rest_api/viewsets.py |
TasksView.generate_job_id |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets.py |
TasksView.get_all_jobs |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets.py |
TasksView.get_files_by_job_id |
|
13 |
13 |
0 |
|
0% |
| rest_api/viewsets.py |
(no function) |
|
138 |
0 |
0 |
|
100% |
| rest_api/viewsets_database.py |
DatabaseInfoView.get_database_tables_status |
|
8 |
8 |
0 |
|
0% |
| rest_api/viewsets_database.py |
DatabaseInfoView.get_database_info |
|
32 |
32 |
0 |
|
0% |
| rest_api/viewsets_database.py |
DatabaseInfoView.get_database_size |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets_database.py |
DatabaseInfoView.get_database_version |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets_database.py |
(no function) |
|
17 |
0 |
0 |
|
100% |
| rest_api/viewsets_sample.py |
LineageInfo.__hash__ |
|
1 |
1 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
Echo.write |
|
1 |
1 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_label_to_methods |
|
1 |
0 |
0 |
|
100% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.get_gene_symbols |
|
5 |
0 |
0 |
|
100% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.get_replicons |
|
6 |
6 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.get_cds_accessions |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin._get_reference_replicon_count |
|
1 |
1 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin._resolve_replicon_for_query |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.resolve_recursive_genome_filter |
|
14 |
3 |
0 |
|
79% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.eval_basic_filter |
|
6 |
1 |
0 |
|
83% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.get_filtered_queryset |
|
13 |
3 |
0 |
|
77% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_label |
|
26 |
26 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_annotation |
|
7 |
7 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_property |
|
23 |
11 |
0 |
|
52% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_nt_mutations |
|
6 |
1 |
0 |
|
83% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_aa_mutations |
|
6 |
2 |
0 |
|
67% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_snp_profile_nt |
|
7 |
3 |
0 |
|
57% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_snp_profile_aa |
|
9 |
9 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_del_profile_nt |
|
4 |
1 |
0 |
|
75% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_del_profile_aa |
|
6 |
2 |
0 |
|
67% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_ins_profile_nt |
|
2 |
0 |
0 |
|
100% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_ins_profile_aa |
|
4 |
1 |
0 |
|
75% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_sample |
|
6 |
6 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_replicon |
|
3 |
1 |
0 |
|
67% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_reference |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleFilterMixin.filter_sublineages |
|
16 |
16 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._get_genomic_and_proteomic_profiles_queryset |
|
10 |
0 |
0 |
|
100% |
| rest_api/viewsets_sample.py |
SampleViewSet.genomes |
|
37 |
10 |
0 |
|
73% |
| rest_api/viewsets_sample.py |
SampleViewSet._apply_ordering |
|
10 |
10 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._get_genomic_and_proteomic_profile_columns |
|
13 |
13 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._return_csv_stream |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._return_vcf_format |
|
3 |
3 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._stream_serialized_data |
|
7 |
7 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet._temp_save_file |
|
4 |
4 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet.get_sequence_data |
|
9 |
9 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet.get_bulk_sequence_data |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet.delete_sample_data |
|
8 |
8 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleViewSet.delete_sequence_data |
|
8 |
8 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
SampleGenomeViewSet.match |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets_sample.py |
(no function) |
|
113 |
0 |
0 |
|
100% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetStatistics.get_statistics |
|
11 |
11 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetStatistics.get_populated_metadata_fields |
|
21 |
21 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetStatistics.statistics |
|
2 |
2 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetStatistics.filtered_statistics |
|
4 |
4 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.get_metadata_coverage |
|
44 |
44 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots._get_samples_per_week |
|
6 |
6 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots._get_grouped_lineages_per_week |
|
22 |
22 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots._get_custom_property_plot |
|
12 |
12 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.plot_samples_per_week |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.plot_grouped_lineages_per_week |
|
6 |
6 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.plot_metadata_coverage |
|
4 |
4 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.plot_custom |
|
5 |
5 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
SampleViewSetPlots.plot_custom_xy |
|
48 |
48 |
0 |
|
0% |
| rest_api/viewsets_statistics_and_plots.py |
(no function) |
|
48 |
0 |
0 |
|
100% |
| sonar_backend/__init__.py |
(no function) |
|
2 |
0 |
0 |
|
100% |
| sonar_backend/celery.py |
(no function) |
|
9 |
0 |
0 |
|
100% |
| sonar_backend/settings.py |
(no function) |
|
67 |
6 |
0 |
|
91% |
| sonar_backend/urls.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| sonar_backend/utils.py |
CustomisedJSONFormatter.json_record |
|
6 |
1 |
0 |
|
83% |
| sonar_backend/utils.py |
(no function) |
|
5 |
0 |
0 |
|
100% |
| sonar_backend/version.py |
_read_version_file |
|
7 |
7 |
0 |
|
0% |
| sonar_backend/version.py |
_read_pyproject_version |
|
7 |
7 |
0 |
|
0% |
| sonar_backend/version.py |
get_version |
|
4 |
1 |
0 |
|
75% |
| sonar_backend/version.py |
(no function) |
|
7 |
0 |
0 |
|
100% |