Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17) #3441

jessebrennan · 2021-09-17T18:22:29Z

HumanCellAtlas/dcp2#17

PR title references issue
PR title matches issue title (preceded by Fix: for bugs) _{or there is a good reason why they're different}
Title of main commit references issue
PR is connected to Zenhub issue and description links to 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}
Added announcement to PR description _{or this PR does not require announcement}

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)

Operator (after pushing the merge commit)

Announce that devs will need to follow upgrading instructions
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}
Announce whether reindexing these snapshots succeeded or failed
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 · 2021-09-17T18:46:15Z

Codecov Report

Merging #3441 (d5c935f) into develop (019f103) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #3441   +/-   ##
========================================
  Coverage    82.02%   82.02%           
========================================
  Files          123      123           
  Lines        14417    14417           
========================================
  Hits         11825    11825           
  Misses        2592     2592

Continue to review full report at Codecov.

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Powered by Codecov. Last update 019f103...d5c935f. Read the comment docs.

coveralls · 2021-09-17T18:46:51Z

Coverage remained the same at 82.265% when pulling d5c935f on issues/jesse/dcp2-17-dev-snapshots into 019f103 on develop.

deployments/sandbox/environment.py

amarjandu · 2021-09-20T18:32:04Z

deployments/sandbox/environment.py

+            'tdr:datarepo-dev-87beea11:snapshot/hca_dev_ae71be1dddd84feb9bed24c3ddb6e1ad__20210916_20210916:4',
+            # Managed access snapshots:
+            'tdr:datarepo-dev-d4b988d6:snapshot/hca_dev_a004b1501c364af69bbd070c06dbc17d__20210830_20210903:4',
+            'tdr:datarepo-dev-02c59b72:snapshot/hca_dev_99101928d9b14aafb759e97958ac7403__20210830_20210903:4',


1190 links total, 84 under the common prefix 4

jessebrennan · 2021-09-20T23:46:00Z

Since we can't attach this to its ticket via Zenhub because of a permissions issue @hannes-ucsc mentioned, I'm assigning myself so that it stays on my board.

amarjandu

Need to update google project id.

amarjandu · 2021-09-20T23:49:49Z

deployments/sandbox/environment.py

+            'tdr:datarepo-dev-4c3e6011:snapshot/hca_dev_248fcf0316c64a41b6ccaad4d894ca42__20210907_20210907:4',
+            'tdr:datarepo-dev-76de829d:snapshot/hca_dev_2043c65a1cf84828a6569e247d4e64f1__20210831_20210907:4',
+            'tdr:datarepo-dev-24e9529e:snapshot/hca_dev_f83165c5e2ea4d15a5cf33f3550bffde__20210901_20210908:4',
+            'tdr:datarepo-dev-87beea11:snapshot/hca_dev_ae71be1dddd84feb9bed24c3ddb6e1ad__20210916_20210916:4',


The project name is wrong here. datarepo-dev-1dce87e5 should be used.
TDR team updated the spreadsheet.
https://docs.google.com/spreadsheets/d/1yYiB3TrX0wvLCHvtWY1GTZZcAf5MmMREgn52OKCHsqs/edit#gid=1005857707

amarjandu · 2021-09-20T23:50:01Z

deployments/dev/environment.py

+            'tdr:datarepo-dev-4c3e6011:snapshot/hca_dev_248fcf0316c64a41b6ccaad4d894ca42__20210907_20210907:',
+            'tdr:datarepo-dev-76de829d:snapshot/hca_dev_2043c65a1cf84828a6569e247d4e64f1__20210831_20210907:',
+            'tdr:datarepo-dev-24e9529e:snapshot/hca_dev_f83165c5e2ea4d15a5cf33f3550bffde__20210901_20210908:',
+            'tdr:datarepo-dev-87beea11:snapshot/hca_dev_ae71be1dddd84feb9bed24c3ddb6e1ad__20210916_20210916:',


hannes-ucsc · 2021-09-21T17:35:01Z

deployments/dev/environment.py

+            # Managed access snapshots:
+            'tdr:datarepo-dev-d4b988d6:snapshot/hca_dev_a004b1501c364af69bbd070c06dbc17d__20210830_20210903:',
+            'tdr:datarepo-dev-02c59b72:snapshot/hca_dev_99101928d9b14aafb759e97958ac7403__20210830_20210903:',


I changed my mind. We should list these in the same order as they occur in the spreadsheet.

Each of the two MA sources should have the comment

# Managed access:

preceding it.

hannes-ucsc · 2021-10-02T00:30:03Z

I'll provide demo instructions later.

nadove-ucsc · 2021-10-02T01:29:47Z

Failed in GitLab due to inconsistent snapshot storage locations: https://gitlab.dev.singlecell.gi.ucsc.edu/ucsc/azul/-/jobs/30152

The offending snapshots (location != 'US') are

TDRClient.TDRSource(project='datarepo-dev-bdc9f342', id='d5222430-0f7a-4bd1-8706-c58b4397a9b8', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-12b7a9e1', id='58a0eacf-0caa-449b-9fc8-4fe629e99176', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-02c59b72', id='cddb722a-4229-47bb-ba86-736b7898406f', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-71926fdc', id='403ef1b1-7b7f-4e13-bf4a-d898f047310a', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-dbc582d9', id='79f24905-a9e2-4328-91da-fc18036b77eb', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-10f0610a', id='2c5901f6-67bf-40cc-aea1-621a60c19baa', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-71de019e', id='768c4624-c07b-4496-8b7b-76275a149774', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-78bae095', id='f142a2f7-4c50-458d-a047-27bdb8e0d367', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-a9252919', id='90c2d68f-a000-4c8d-a493-8be93a71b44d', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-1c2c69d9', id='c594fc9a-f1c5-4770-acaa-013c2852e660', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-a198b032', id='38c7e1c4-db48-4cd7-bdf2-36bebc169eac', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-d4b988d6', id='2c4ec571-f489-4277-b215-da8dedd86803', location='us-central1')
TDRClient.TDRSource(project='datarepo-dev-7b7daff7', id='385eb563-005e-43ed-adb7-d3c9e0a8ae93', location='us-central1')

hannes-ucsc · 2021-10-04T06:13:11Z

Reindex in dev resulted in 16 failed notifications, no failed tallies.

Due to the catalog duplication, there are 8 distinct failures.

7 tracked in HumanCellAtlas/dcp2#45
1 tracked in HumanCellAtlas/dcp2#48

hannes-ucsc · 2021-10-04T16:14:40Z

@jessebrennan, the checklist item "Announce whether reindexing these snapshots succeeded or failed" is lacking the information where to announce that.

hannes-ucsc · 2021-10-04T16:20:47Z

I made the announcement: https://humancellatlas.slack.com/archives/C01360XN04S/p1633364377176400?thread_ts=1631840213.076200&cid=C01360XN04S

hannes-ucsc · 2021-10-04T16:51:29Z

UPGRADING.rst

+
+Before upgrading to this commit, run::
+
+    python scripts/reindex.py --delete --catalog dcp2ebi


This doesn't delete the corresponding IT catalog it2ebi and the flag name is --catalogs not --catalog.

hannes-ucsc · 2021-10-04T17:18:31Z

Another announcement: https://humancellatlas.slack.com/archives/C01360XN04S/p1633367887177300?thread_ts=1631635383.071300&cid=C01360XN04S

github-actions bot added the orange [process] Done by the Azul team label Sep 17, 2021

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[u r] Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17)

dcd6e1b

nadove-ucsc force-pushed the issues/jesse/dcp2-17-dev-snapshots branch from ca832a8 to dcd6e1b Compare October 2, 2021 00:33

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nadove-ucsc added 2 commits October 1, 2021 19:13

Change TDR source location to us-central1 in dev and sandbox

cae18ec

Remove lungmap catalogs from dev and sandbox

d5c935f

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Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17) #3441

Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17) #3441

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hannes-ucsc commented Oct 4, 2021


		Before upgrading to this commit, run::

		python scripts/reindex.py --delete --catalog dcp2ebi

Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17) #3441

Fix: TDR dev dataset is stale (HumanCellAtlas/dcp2#17) #3441

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