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G3-342: refactor Geneweaver client get values as ensembl mouse function #42

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bergsalex
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This will make it easier to use the mapping code as a module, outside of CLI usage.

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github-actions bot commented Aug 7, 2024

Test Coverage Report

---------- coverage: platform linux, python 3.11.9-final-0 -----------
Name                                                                     Stmts   Miss  Cover
--------------------------------------------------------------------------------------------
src/geneweaver/client/__init__.py                                            2      0   100%
src/geneweaver/client/api/__init__.py                                        0      0   100%
src/geneweaver/client/api/aon.py                                            32     12    62%
src/geneweaver/client/api/exc.py                                             3      0   100%
src/geneweaver/client/api/genes.py                                           8      0   100%
src/geneweaver/client/api/genesets.py                                       22      2    91%
src/geneweaver/client/api/graph.py                                          50     30    40%
src/geneweaver/client/api/mapping.py                                        22      1    95%
src/geneweaver/client/api/utils.py                                          21      0   100%
src/geneweaver/client/auth.py                                               76     13    83%
src/geneweaver/client/batch/__init__.py                                      0      0   100%
src/geneweaver/client/cli/__init__.py                                        0      0   100%
src/geneweaver/client/cli/beta/__init__.py                                   5      0   100%
src/geneweaver/client/cli/beta/auth.py                                      22      0   100%
src/geneweaver/client/cli/main.py                                           14      0   100%
src/geneweaver/client/core/__init__.py                                       1      0   100%
src/geneweaver/client/core/app_dir.py                                       22     13    41%
src/geneweaver/client/core/config.py                                         2      0   100%
src/geneweaver/client/core/config_class.py                                  26      0   100%
src/geneweaver/client/datasets/__init__.py                                   1      0   100%
src/geneweaver/client/datasets/base.py                                      30      0   100%
src/geneweaver/client/datasets/nci60/__init__.py                             1      0   100%
src/geneweaver/client/datasets/nci60/dna_combined_acgh_gene_summary.py      26     10    62%
src/geneweaver/client/exceptions.py                                          1      0   100%
src/geneweaver/client/gedb.py                                              174     51    71%
src/geneweaver/client/parser/__init__.py                                     1      0   100%
src/geneweaver/client/parser/batch.py                                       61     51    16%
src/geneweaver/client/parser/general.py                                     42     12    71%
src/geneweaver/client/render/__init__.py                                     0      0   100%
src/geneweaver/client/user_config.py                                        20     20     0%
src/geneweaver/client/utils/__init__.py                                      0      0   100%
src/geneweaver/client/utils/aon.py                                          15      0   100%
src/geneweaver/client/utils/cli/__init__.py                                  0      0   100%
src/geneweaver/client/utils/cli/decorators/__init__.py                       0      0   100%
src/geneweaver/client/utils/cli/decorators/errors.py                        12      2    83%
src/geneweaver/client/utils/cli/decorators/options.py                       21     21     0%
src/geneweaver/client/utils/cli/print/__init__.py                            0      0   100%
src/geneweaver/client/utils/cli/print/csv.py                                12      8    33%
src/geneweaver/client/utils/cli/print/file_info.py                          10      0   100%
src/geneweaver/client/utils/cli/print/tables.py                             10      0   100%
src/geneweaver/client/utils/cli/prompt/__init__.py                           0      0   100%
src/geneweaver/client/utils/cli/prompt/bool.py                              10      0   100%
src/geneweaver/client/utils/cli/prompt/enum.py                              49     25    49%
src/geneweaver/client/utils/cli/prompt/generic.py                           33     13    61%
src/geneweaver/client/utils/cli/prompt/list.py                              26      4    85%
src/geneweaver/client/utils/cli/prompt/none.py                              15      3    80%
src/geneweaver/client/utils/cli/prompt/pydantic.py                          41      0   100%
--------------------------------------------------------------------------------------------
TOTAL                                                                      939    291    69%
Coverage HTML written to dir htmlcov

FAIL Required test coverage of 70% not reached. Total coverage: 69.01%
================= 6377 passed, 8 skipped, 4 warnings in 22.85s =================

@bergsalex bergsalex marked this pull request as ready for review August 7, 2024 12:43
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@gerring gerring left a comment

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No test change which exercises these new code blocks and checks that they had the desired effect?

@bergsalex bergsalex requested a review from gerring August 7, 2024 13:33
@bergsalex bergsalex merged commit 5e2cd9d into main Aug 7, 2024
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3 participants