Study autoloaded #3046
Merged
Study autoloaded #3046
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* 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 <yoshiki@ucsd.edu> Co-authored-by: Antonio Gonzalez <antgonza@gmail.com> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * 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 <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Daniel McDonald <danielmcdonald@ucsd.edu> Co-authored-by: Mirte Kuijpers <67341505+mcmk3@users.noreply.github.com> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu>
adswafford
approved these changes
Nov 12, 2020
Codecov Report
@@ Coverage Diff @@
## dev #3046 +/- ##
==========================================
- Coverage 95.03% 95.02% -0.01%
==========================================
Files 74 74
Lines 14284 14279 -5
==========================================
- Hits 13575 13569 -6
- Misses 709 710 +1
Continue to review full report at Codecov.
|
ElDeveloper
suggested changes
Nov 17, 2020
Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu>
|
Thank you for review; that's a good question! I don't think we should display it but it will be good to limit functionality for those studies we didn't submit ... |
|
Yes, I think I was thinking mostly in terms of a meta-analysis to easily check for systematic effects. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes to support a study flag to mark as automatically loaded. In general, it should always be false, once we support autoloading we will use this flag.