[r] Index hca_dev_20201203__20210507 into dcp2 on dev (#3049)

[dsotirho-ucsc]

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 on demo expectations _{or labelled PR 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 PR 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 #3050 (be23a3c) into develop (eb2ee02) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #3050   +/-   ##
========================================
  Coverage    82.64%   82.64%           
========================================
  Files          117      117           
  Lines        12246    12246           
========================================
  Hits         10121    10121           
  Misses        2125     2125           

---

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[coveralls]

Coverage remained the same at 83.165% when pulling be23a3c on issues/danielsotirhos/3049-index-snapshot-hca_dev_20201203__20210507 into eb2ee02 on develop.

[dsotirho-ucsc]

5 messages found in dev fail queue:

(azul1) daniel@Crispin ~/repo/azul1 $ python scripts/manage_queues.py list
2021-05-12 12:00:39,574 INFO    MainThread: Listing queues

Queue Name                          Messages Available  Messages In Flight  Messages Delayed

2021-05-12 12:00:39,621 INFO    MainThread: Found credentials in environment variables.
azul-notifications-dev                      0                   0                  0
azul-notifications_retry-dev                0                   0                  0
azul-tallies-dev.fifo                       0                   0                  0
azul-tallies_retry-dev.fifo                 0                   0                  0
azul-tallies_fail-dev.fifo                  0                   0                  0
azul-notifications_fail-dev                 5                   0                  0

All failures relate to bundles with known issues:

The following 4 bundles mentioned in #2873

"MessageId": "b5d3fba6-a613-4b05-9665-fc7cfcb4b225",
"bundle_uuid": "ae338c4e-650f-545b-8631-3c8d755aa2f9",
"bundle_version": "2020-12-03T00:00:01.000000Z"
"SentTimestamp": "2021-05-11T21:23:53.995000-07:00",

"MessageId": "6805b20c-d641-438c-9c01-92ea55e5169f",
"bundle_uuid": "9d0f5cd1-0ef6-5eed-8dd7-f15d36a34185",
"bundle_version": "2020-12-03T00:00:01.000000Z"
"SentTimestamp": "2021-05-11T21:23:53.424000-07:00",

"MessageId": "9fefa2f0-c99f-45dc-ba73-20e7b83cd739",
"bundle_uuid": "c12a6ca2-3234-5182-ad0b-f8c2fb881ab5",
"bundle_version": "2020-12-03T00:00:01.000000Z"
"SentTimestamp": "2021-05-11T21:23:57.474000-07:00",

"MessageId": "4f8ecea4-5991-45a2-9d2e-5f6992c84b46",
"bundle_uuid": "40733888-3b9f-500e-84fd-1a18a64aadbe",
"bundle_version": "2020-12-03T00:00:01.000000Z"
"SentTimestamp": "2021-05-11T21:23:57.474000-07:00",

And the following 1 bundle mentioned in #2870

"MessageId": "8796aa64-ea89-4119-85eb-7e1c8e97f0bd",
"bundle_uuid": "94565940-7b2f-5fd7-beb1-dc309687fe09",
"bundle_version": "2021-02-10T17:01:03.177554Z"
"SentTimestamp": "2021-05-11T21:23:50.607000-07:00",