feat: irods download refactoring and new generic sodar downloader with preset for dragen data (#226 ) #227
77.73% of diff hit (target 81.05%)
View this Pull Request on Codecov
77.73% of diff hit (target 81.05%)
Annotations
Check warning on line 41 in cubi_tk/irods/check.py
codecov / codecov/patch
cubi_tk/irods/check.py#L41
Added line #L41 was not covered by tests
Check warning on line 43 in cubi_tk/irods/check.py
codecov / codecov/patch
cubi_tk/irods/check.py#L43
Added line #L43 was not covered by tests
Check warning on line 118 in cubi_tk/irods/check.py
codecov / codecov/patch
cubi_tk/irods/check.py#L117-L118
Added lines #L117 - L118 were not covered by tests
Check warning on line 248 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L248
Added line #L248 was not covered by tests
Check warning on line 328 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L328
Added line #L328 was not covered by tests
Check warning on line 337 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L337
Added line #L337 was not covered by tests
Check warning on line 339 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L339
Added line #L339 was not covered by tests
Check warning on line 344 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L343-L344
Added lines #L343 - L344 were not covered by tests
Check warning on line 350 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L347-L350
Added lines #L347 - L350 were not covered by tests
Check warning on line 355 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L352-L355
Added lines #L352 - L355 were not covered by tests
Check warning on line 357 in cubi_tk/irods_common.py
codecov / codecov/patch
cubi_tk/irods_common.py#L357
Added line #L357 was not covered by tests
Check warning on line 686 in cubi_tk/snappy/check_remote.py
codecov / codecov/patch
cubi_tk/snappy/check_remote.py#L686
Added line #L686 was not covered by tests
Check warning on line 121 in cubi_tk/snappy/pull_data_common.py
codecov / codecov/patch
cubi_tk/snappy/pull_data_common.py#L121
Added line #L121 was not covered by tests
Check warning on line 125 in cubi_tk/snappy/pull_data_common.py
codecov / codecov/patch
cubi_tk/snappy/pull_data_common.py#L125
Added line #L125 was not covered by tests
Check warning on line 208 in cubi_tk/snappy/pull_processed_data.py
codecov / codecov/patch
cubi_tk/snappy/pull_processed_data.py#L208
Added line #L208 was not covered by tests
Check warning on line 191 in cubi_tk/snappy/pull_raw_data.py
codecov / codecov/patch
cubi_tk/snappy/pull_raw_data.py#L191
Added line #L191 was not covered by tests
Check warning on line 391 in cubi_tk/sodar/check_remote.py
codecov / codecov/patch
cubi_tk/sodar/check_remote.py#L391
Added line #L391 was not covered by tests
Check warning on line 162 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L162
Added line #L162 was not covered by tests
Check warning on line 166 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L166
Added line #L166 was not covered by tests
Check warning on line 171 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L169-L171
Added lines #L169 - L171 were not covered by tests
Check warning on line 179 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L176-L179
Added lines #L176 - L179 were not covered by tests
Check warning on line 185 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L184-L185
Added lines #L184 - L185 were not covered by tests
Check warning on line 189 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L189
Added line #L189 was not covered by tests
Check warning on line 191 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L191
Added line #L191 was not covered by tests
Check warning on line 195 in cubi_tk/sodar/pull_data_collection.py
codecov / codecov/patch
cubi_tk/sodar/pull_data_collection.py#L195
Added line #L195 was not covered by tests