adding job submit ENVIRONMENT and minor improvement to runWorkflow #3040
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* inject study_type in EBI and improvements to current automatic processing pipeline (qiita-spots#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (qiita-spots#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix qiita-spots#2839 * fix qiita-spots#2868 (qiita-spots#3028) * fix qiita-spots#2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix qiita-spots#3022 (qiita-spots#3030) * fix qiita-spots#3022 * adding tests * fix qiita-spots#2320 (qiita-spots#3031) * fix qiita-spots#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 (qiita-spots#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 (qiita-spots#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]>
Codecov Report
@@ Coverage Diff @@
## master #3040 +/- ##
==========================================
+ Coverage 94.98% 95.02% +0.04%
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Files 74 74
Lines 14153 14315 +162
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+ Hits 13443 13603 +160
- Misses 710 712 +2
Continue to review full report at Codecov.
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ElDeveloper
approved these changes
Nov 9, 2020
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adding job submit ENVIRONMENT and minor improvement to runWorkflow