fix #2868 #3028
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fix #2868 #3028
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Codecov Report
@@ Coverage Diff @@
## dev #3028 +/- ##
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+ Coverage 94.95% 94.97% +0.01%
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Files 74 74
Lines 14291 14177 -114
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- Hits 13570 13464 -106
+ Misses 721 713 -8
Continue to review full report at Codecov.
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This is ready for review. There are lots of changes but there is only one main change here, which is then propagated to all the rest of the changes to make the tests more DRY. |
ElDeveloper
approved these changes
Sep 3, 2020
qiita_db/sql_connection.py
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| @@ -493,6 +493,24 @@ def add_post_rollback_func(self, func, *args, **kwargs): | |||
| TRNADMIN = Transaction(admin=True) | |||
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| def encapsulated_query(sql, parameters=None): | |||
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Name is fine but I think it would be nice to make it clear that queries are executed as transactions? Up to your discretion. What about execute_as_transaction.
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Yeah, selected single_query first, then changed it to encapsulted_query but still not happy. execute_as_transaction is a decorator we hace; thus, gonna change to perform_as_transaction.
antgonza
commented
Sep 4, 2020
qiita_db/sql_connection.py
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| @@ -493,6 +493,24 @@ def add_post_rollback_func(self, func, *args, **kwargs): | |||
| TRNADMIN = Transaction(admin=True) | |||
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| def encapsulated_query(sql, parameters=None): | |||
There was a problem hiding this comment.
Yeah, selected single_query first, then changed it to encapsulted_query but still not happy. execute_as_transaction is a decorator we hace; thus, gonna change to perform_as_transaction.
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Thanks @antgonza would you mind fixing the conflicts? |
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Done, didn't see them before ... thank you! |
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Thanks! |
antgonza
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Sep 16, 2020
* inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
ElDeveloper
added a commit
that referenced
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Nov 9, 2020
* Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * fix #3036 Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
ElDeveloper
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Nov 9, 2020
…3040) * Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * adding job submit ENVIRONMENT and minor improvement to runWorkflow * fix test Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
ElDeveloper
added a commit
that referenced
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Nov 9, 2020
* Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * fix #2920 * fix test Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
ElDeveloper
added a commit
that referenced
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Nov 10, 2020
* Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * rm create_qiime_mapping_file * fixing some tests * fixing more tests * fix even more tests * rm npt.assert_warns * qiime-map -> sample-file * update not_merged_samples.txt * adding @ElDeveloper changes Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
ElDeveloper
added a commit
that referenced
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Nov 17, 2020
* Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Antonio Gonzalez <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * adding qiita.study autoloaded column * cleaning tests * fix redbiom test * avoiding clog submissions * Apply suggestions from code review Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> Co-authored-by: Daniel McDonald <[email protected]> Co-authored-by: Mirte Kuijpers <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
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