Index hca_dev_20201203___20210524_lattice into dcp2 on dev (#3075)

[nadove-ucsc]

…#3075)

Author

• PR title references issue
• Title of main commit references issue
• PR is linked to Zenhub issue

Author (reindex)

• Added r tag to commit title _{or this PR does not require reindexing}
• Added reindex label to PR _{or this PR does not require reindexing}

Author (freebies & chains)

• Freebies are blocked on this PR _{or there are no freebies in this PR}
• Freebies are referenced in commit titles _{or there are no freebies in this PR}
• This PR is blocked by previous PR in the chain _{or this PR is not chained to another PR}
• Added chain label to the blocking PR _{or this PR is not chained to another PR}

Author (upgrading)

• Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading}
• Added u tag to commit title _{or this PR does not require upgrading}
• Added upgrade label to PR _{or this PR does not require upgrading}

Author (requirements, before every review)

• Ran make requirements_update _{or this PR leaves requirements*.txt, common.mk and Makefile untouched}
• Added R tag to commit title _{or this PR leaves requirements*.txt untouched}
• Added reqs label to PR _{or this PR leaves requirements*.txt untouched}

Author (before every review)

• make integration_test passes in personal deployment _{or this PR does not touch functionality that could break the IT}
• Rebased branch on develop, squashed old fixups

Primary reviewer (after approval)

• Commented in issue about demo expectations _{or labelled issue as no demo}
• Decided if PR can be labeled no sandbox
• PR title is appropriate as title of merge commit
• Moved ticket to Approved column
• Assigned PR to an operator

Operator (before pushing merge the commit)

• Checked reindex label and r commit title tag
• Checked that demo expectations are clear _{or issue is labeled as no demo}
• Rebased and squashed branch
• Sanity-checked history
• Pushed PR branch to Github
• Branch pushed to Gitlab _{or PR is labeled no sandbox}
• Build passes in sandbox and added sandbox label _{or PR is labeled no sandbox}
• Started reindex in sandbox _{or this PR does not require reindexing sandbox}
• Checked for failures in sandbox _{or this PR does not require reindexing sandbox}
• Added PR reference to merge commit title
• Collected commit title tags in merge commit title
• Moved linked issue to Merged column
• Pushed merge commit to Github

Operator (after pushing the merge commit)

• Moved freebies to Merged column _{or there are no freebies in this PR}
• Shortened the PR chain _{or this PR is not the base of another PR}
• Verified that N reviews labelling is accurate
• Pushed merge commit to Gitlab _{or this changes can be pushed later, together with another PR}
• Deleted PR branch from Github and Gitlab

Operator (reindex)

• Started reindex in dev _{or this PR does not require reindexing or does not target dev}
• Checked for failures in dev _{or this PR does not require reindexing or does not target dev}
• Started reindex in prod _{or this PR does not require reindexing or does not target prod}
• Checked for failures in prod _{or this PR does not require reindexing or does not target prod}

Operator

• Unassigned PR

[codecov]

Codecov Report

Merging #3081 (7d3edbe) into develop (7d3edbe) will not change coverage.
The diff coverage is n/a.

❗ Current head 7d3edbe differs from pull request most recent head d4d4c58. Consider uploading reports for the commit d4d4c58 to get more accurate results

@@           Coverage Diff            @@
##           develop    #3081   +/-   ##
========================================
  Coverage    82.50%   82.50%           
========================================
  Files          115      115           
  Lines        12269    12269           
========================================
  Hits         10123    10123           
  Misses        2146     2146           

---

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[coveralls]

Coverage remained the same at 83.081% when pulling d4d4c58 on issues/noah-aviel-dove/3075-index-hca_dev_20201203___20210524_lattice-dcp2-dev into 7d3edbe on develop.

[nadove-ucsc]

IT failed, cancelling review request

[nadove-ucsc]

No failures from reindexing sandbox.

[nadove-ucsc]

Reindex completed with five failures as expected:

40733888-3b9f-500e-84fd-1a18a64aadbe
94565940-7b2f-5fd7-beb1-dc309687fe09
9d0f5cd1-0ef6-5eed-8dd7-f15d36a34185
ae338c4e-650f-545b-8631-3c8d755aa2f9
c12a6ca2-3234-5182-ad0b-f8c2fb881ab5  

4 of these correspond to #2873 , the other is presumably from #2870 but that ticket doesn't seem to mention the bundle UUID.

[nadove-ucsc]

Confirmed that the last UUID (94565940...) corresponds to #2870