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Merged
merged 58 commits into from
Sep 22, 2022
Merged

Epidata v4.1 #954

merged 58 commits into from
Sep 22, 2022

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krivard
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@krivard krivard commented Aug 24, 2022

closes #805

Prerequisites:

  • Unless it is a documentation hotfix it should be merged against the dev branch
  • Branch is up-to-date with the branch to be merged with, i.e. dev
  • Build is successful
  • Code is cleaned up and formatted

Summary

Initial release of v4 revisions for rollout Aug/Sept 2022

  • Pathogen-specific schema prototype covid
  • Normalized covidcast data layout within covid schema
  • "latest" table offers speedy access to best available estimates as-of today
  • "history"(soon:"full") table stores exhaustive data versioning record
  • Commensurate updates to API server directing queries to proper table
  • Commensurate updates to unit tests

korlaxxalrok and others added 30 commits March 4, 2022 13:21
Update workflow to build container images from branch
a few notes:
composite key definitions could be made part of Database class.
i used the variable name "ell" because the single lowercase letter "l" looks ambiguous.
could do away with update_latest column and just use "WHERE d.delete_latest_id<>NULL" instead of "WHERE d.update_latest=1".
could do away with delete_latest_id column if we assume signal_data_id's are synced properly between latest+history tables.
….. and also restore a method that got deleted??
…nd of regular acquisition method, removed helper to run dbjobs as a standalone process
they come from a pending changeset to incorporate (into this branch, 'v4-srrpp-migrations') improvements made in a parallel 'mergedkey' branch...
i fear i may just be kicking more merge conflicts down the road, but hopefully this helps me to be less confused about some current diffs in the meantime.
changes are:
- signal_latest table definition simplified to automatically inherit structure from signal_history table
- removal of unused row-counting methods
- docstring update / correction
melange396 and others added 24 commits August 30, 2022 11:12
Co-authored-by: Katie Mazaitis <[email protected]>
DBLoadStateException: halt acquisition when unexpected data found in load table
Remove remaining wip pieces in tests
updated Dockerfile to let pip account for all version constraints simultaneously (previous non-simultaneous (ie, sequential) requirements installation resulted in a version conflict on `greenlets` package, see: tiangolo/meinheld-gunicorn-docker#22 ).
also bumped python version in that Dockerfile to 3.8 to match python versions elsewhere in the codebase.
*note: this fix also requires a change to version pinning in a requirements.txt of the operations branch (see: https://github.com/cmu-delphi/operations/blob/v4-schema-revisions-release-prep-flaskalchemy/dev/docker/python/assets/requirements.txt )
…ternal specification) because they fundamentally change behaviors
…rep-flaskalchemy

Build and image with new Flask and SQLAlchemy
…ternal specification) because they fundamentally change behaviors
…#974)"

This reverts commit e47ca86.

reverting my old revert...  ugh, sorry, ive made a mess of this repository :(

this restores the rest of the version bumps we updated previously
@melange396 melange396 merged commit a1b98a5 into dev Sep 22, 2022
@melange396 melange396 deleted the v4-schema-revisions-release-prep branch September 22, 2022 14:05
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v4 changes
4 participants