[u] Define sources within catalog JSON (#3114) #3476

amarjandu · 2021-09-28T23:55:31Z

Split off from #3277

#3114

PR title references issue
PR title matches issue title (preceded by Fix: for bugs) _{or there is a good reason why they're different}
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PR is connected to Zenhub issue and description links to issue

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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}

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

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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

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Commented in issue about demo expectations _{or labelled issue as no demo}
Decided if PR can be labeled no sandbox
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Unassigned PR

coveralls · 2021-09-29T00:15:11Z

Coverage increased (+0.03%) to 82.138% when pulling b4075d4 on issues/amar/3114-json-catalogs into f5e686b on develop.

codecov · 2021-09-29T00:15:55Z

Codecov Report

Merging #3476 (f5e686b) into develop (f5e686b) will not change coverage.
The diff coverage is n/a.

❗ Current head f5e686b differs from pull request most recent head b4075d4. Consider uploading reports for the commit b4075d4 to get more accurate results

@@           Coverage Diff            @@
##           develop    #3476   +/-   ##
========================================
  Coverage    81.86%   81.86%           
========================================
  Files          123      123           
  Lines        14291    14291           
========================================
  Hits         11699    11699           
  Misses        2592     2592

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hannes-ucsc

I think you got the chain labels wrong.

hannes-ucsc · 2021-09-29T21:36:25Z

And remember to note the PR provenance in the description. See my edit to the description.

amarjandu · 2021-09-29T22:22:06Z

Added chain label to this PR, blocked #3277 on this PR.

hannes-ucsc · 2021-09-30T17:19:38Z

Because of it's disruptive effect on #3441 I'm pulling this from Approved.

amarjandu · 2021-10-04T22:09:16Z

self note: 13aeec0 IT passes

hannes-ucsc · 2021-10-05T00:23:03Z

deployments/dev/environment.py

+                                    plugins=dict(metadata=dict(name='hca'),
+                                                 repository=dict(name='tdr')),
+                                    sources=sources)
+            for name, atlas, sources in [


No point in looping over a singleton.

I was hoping to have this in a state where we can easily add the lungmap catalogs back in when we work on #3489 but i don't think we can have this and each snapshot on a line.

hannes-ucsc · 2021-10-05T00:24:19Z

deployments/dev/environment.py

+                    'dcp2',
+                    'hca',
+                    list(filter(None, [
+                        mksrc('datarepo-dev-a9252919',


Each snapshot must be a single line or we'll go nuts. With my diff, the lines are longer than 80 trimmed but don't exceed the 120 margin so they survive reformatting with PyCharm.

I just did the first three.

Index: UPGRADING.rst IDEA additional info: Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP <+>UTF-8 =================================================================== diff --git a/UPGRADING.rst b/UPGRADING.rst --- a/UPGRADING.rst (revision 13aeec00ab57f58d5b1dea76b5fbafdf018e458e) +++ b/UPGRADING.rst (date 1633393162333) @@ -15,9 +15,9 @@ ======================================== The ``AZUL_TDR_SOURCES`` and ``AZUL_…_SOURCES`` environment variables have been -removed. Sources must be defined within the catalog configuration as a -list of sources. As always, use the sandbox deployment's ``environment.py`` as -a model when upgrading personal deployments. +removed. Sources must be defined within the catalog configuration as a list of +sources. As always, use the sandbox deployment's ``environment.py`` as a model +when upgrading personal deployments. HumanCellAtlas/dcp2#17 TDR dev dataset is stale Index: deployments/dev/environment.py IDEA additional info: Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP <+>UTF-8 =================================================================== diff --git a/deployments/dev/environment.py b/deployments/dev/environment.py --- a/deployments/dev/environment.py (revision 13aeec00ab57f58d5b1dea76b5fbafdf018e458e) +++ b/deployments/dev/environment.py (date 1633393139401) @@ -55,338 +55,326 @@ 'AZUL_DEPLOYMENT_STAGE': 'dev', 'AZUL_CATALOGS': json.dumps({ - f'{prefix}{name}': dict(atlas=atlas, - internal=internal, - plugins=dict(metadata=dict(name='hca'), - repository=dict(name='tdr')), - sources=sources) - for name, atlas, sources in [ - ( - 'dcp2', - 'hca', - list(filter(None, [ - mksrc('datarepo-dev-a9252919', - 'hca_dev_005d611a14d54fbf846e571a1f874f70__20210827_20210903', - 7), - mksrc('datarepo-dev-c148d39c', - 'hca_dev_027c51c60719469fa7f5640fe57cbece__20210827_20210902', - 8), - mksrc('datarepo-dev-e2ab8487', - 'hca_dev_03c6fce7789e4e78a27a664d562bb738__20210902_20210907', - 1530), - mksrc('datarepo-dev-37639c56', - 'hca_dev_05657a599f9d4bb9b77b24be13aa5cea__20210827_20210928', - 185), - mksrc('datarepo-dev-9f4012c9', - 'hca_dev_05be4f374506429bb112506444507d62__20210827_20210902', - 1544), - mksrc('datarepo-dev-baa2812f', - 'hca_dev_0792db3480474e62802c9177c9cd8e28__20210827_20210903', - 1450), - mksrc('datarepo-dev-38e08b5c', - 'hca_dev_08b794a0519c4516b184c583746254c5__20210901_20210903', - 2), - mksrc('datarepo-dev-2749da57', - 'hca_dev_091cf39b01bc42e59437f419a66c8a45__20210830_20210903', - 20), - mksrc('datarepo-dev-eab7fa76', - 'hca_dev_0c3b7785f74d40918616a68757e4c2a8__20210827_20210903', - 177), - mksrc('datarepo-dev-fef02a92', - 'hca_dev_0d4b87ea6e9e456982e41343e0e3259f__20210827_20210903', - 8), - mksrc('datarepo-dev-78bae095', - 'hca_dev_0fd8f91862d64b8bac354c53dd601f71__20210830_20210903', - 10), - mksrc('datarepo-dev-ff0a2fe7', - 'hca_dev_116965f3f09447699d28ae675c1b569c__20210827_20210903', - 8), - mksrc('datarepo-dev-4de1b9fd', - 'hca_dev_16ed4ad8731946b288596fe1c1d73a82__20210830_20210903', - 28), - mksrc('datarepo-dev-135f340c', - 'hca_dev_1c6a960d52ac44eab728a59c7ab9dc8e__20210827_20210928', - 10), - mksrc('datarepo-dev-86c60513', - 'hca_dev_1cd1f41ff81a486ba05b66ec60f81dcf__20210901_20210903', - 18), - mksrc('datarepo-dev-f5321179', - 'hca_dev_1ce3b3dc02f244a896dad6d107b27a76__20210827_20210903', - 421), - mksrc('datarepo-dev-76de829d', - 'hca_dev_2043c65a1cf84828a6569e247d4e64f1__20210831_20210907', - 1734), - mksrc('datarepo-dev-c808badb', - 'hca_dev_2086eb0510b9432bb7f0169ccc49d270__20210827_20210903', - 10), - mksrc('datarepo-dev-23782220', - 'hca_dev_23587fb31a4a4f58ad74cc9a4cb4c254__20210827_20210909', - 1476), - mksrc('datarepo-dev-4c3e6011', - 'hca_dev_248fcf0316c64a41b6ccaad4d894ca42__20210907_20210907', - 2958), - mksrc('datarepo-dev-1c2c69d9', - 'hca_dev_24c654a5caa5440a8f02582921f2db4a__20210830_20210903', - 3), - mksrc('datarepo-dev-38f08cd8', - 'hca_dev_2a64db431b554639aabb8dba0145689d__20210830_20210903', - 10), - mksrc('datarepo-dev-4cf05ce2', - 'hca_dev_2a72a4e566b2405abb7c1e463e8febb0__20210901_20210903', - 2290), - mksrc('datarepo-dev-3041c2cf', - 'hca_dev_2af52a1365cb4973b51339be38f2df3f__20210830_20210903', - 10), - mksrc('datarepo-dev-311340f6', - 'hca_dev_2d8460958a334f3c97d4585bafac13b4__20210902_20210907', - 3589), - mksrc('datarepo-dev-766bfb76', - 'hca_dev_2ef3655a973d4d699b4121fa4041eed7__20210827_20210903', - 8), - mksrc('datarepo-dev-1720b3c5', - 'hca_dev_379ed69ebe0548bcaf5ea7fc589709bf__20210827_20210902', - 4), - mksrc('datarepo-dev-ac6efd3f', - 'hca_dev_38449aea70b540db84b31e08f32efe34__20210830_20210903', - 42), - mksrc('datarepo-dev-40283c27', - 'hca_dev_3a69470330844ece9abed935fd5f6748__20210901_20210903', - 125), - mksrc('datarepo-dev-b08233fa', - 'hca_dev_3cfcdff5dee14a7ba591c09c6e850b11__20210827_20210903', - 8), - mksrc('datarepo-dev-bdc9f342', - 'hca_dev_3e329187a9c448ec90e3cc45f7c2311c__20210901_20210903', - 1001), - mksrc('datarepo-dev-ec07c8d8', - 'hca_dev_4037007b0eff4e6db7bd8dd8eec80143__20210831_20210903', - 39), - mksrc('datarepo-dev-c0ec174a', - 'hca_dev_403c3e7668144a2da5805dd5de38c7ff__20210827_20210903', - 63), - mksrc('datarepo-dev-31b3553a', - 'hca_dev_414accedeba0440fb721befbc5642bef__20210827_20210903', - 4), - mksrc('datarepo-dev-b4789901', - 'hca_dev_41fb1734a121461695c73b732c9433c7__20210830_20210903', - 12), - mksrc('datarepo-dev-4e5ffd52', - 'hca_dev_42d4f8d454224b78adaee7c3c2ef511c__20210830_20210903', - 9), - mksrc('datarepo-dev-5ef7f2e2', - 'hca_dev_455b46e6d8ea4611861ede720a562ada__20210901_20210903', - 74), - mksrc('datarepo-dev-a6c6b953', - 'hca_dev_4bec484dca7a47b48d488830e06ad6db__20210830_20210903', - 14), - mksrc('datarepo-dev-f31edbc2', - 'hca_dev_4d6f6c962a8343d88fe10f53bffd4674__20210901_20210903', - 12), - mksrc('datarepo-dev-bb8fbae4', - 'hca_dev_51f02950ee254f4b8d0759aa99bb3498__20210827_20210928', - 6), - mksrc('datarepo-dev-71de019e', - 'hca_dev_520afa10f9d24e93ab7a26c4c863ce18__20210827_20210928', - 649), - mksrc('datarepo-dev-ffcf8b00', - 'hca_dev_52b29aa4c8d642b4807ab35be94469ca__20210830_20210903', - 467), - mksrc('datarepo-dev-f76414c8', - 'hca_dev_52d10a60c8d14d068a5eaf0d5c0d5034__20210827_20210902', - 176), - mksrc('datarepo-dev-319b80f7', - 'hca_dev_577c946d6de54b55a854cd3fde40bff2__20210827_20210903', - 7), - mksrc('datarepo-dev-279f1986', - 'hca_dev_5ee710d7e2d54fe2818d15f5e31dae32__20210901_20210903', - 41), - mksrc('datarepo-dev-0abea017', - 'hca_dev_6072616c87944b208f52fb15992ea5a4__20210827_20210902', - 603), - mksrc('datarepo-dev-da221b1a', - 'hca_dev_60ea42e1af4942f58164d641fdb696bc__20210827_20210903', - 1145), - mksrc('datarepo-dev-c3d623dc', - 'hca_dev_63b5b6c1bbcd487d8c2e0095150c1ecd__20210830_20210903', - 11), - mksrc('datarepo-dev-ecb9c129', - 'hca_dev_67a3de0945b949c3a068ff4665daa50e__20210827_20210903', - 732), - mksrc('datarepo-dev-3545971c', - 'hca_dev_71436067ac414acebe1b2fbcc2cb02fa__20210827_20210928', - 4), - mksrc('datarepo-dev-12b7a9e1', - 'hca_dev_7880637a35a14047b422b5eac2a2a358__20210901_20210903', - 366), - mksrc('datarepo-dev-7913b094', - 'hca_dev_78b2406dbff246fc8b6120690e602227__20210827_20210902', - 216), - mksrc('datarepo-dev-4747d8fe', - 'hca_dev_7adede6a0ab745e69b67ffe7466bec1f__20210830_20210903', - 1601), - mksrc('datarepo-dev-aba01389', - 'hca_dev_7b947aa243a74082afff222a3e3a4635__20210831_20210907', - 7), - mksrc('datarepo-dev-bf3a4c8a', - 'hca_dev_8185730f411340d39cc3929271784c2b__20210830_20210903', - 12), - # FIXME: https://github.com/HumanCellAtlas/dcp2/issues/48 - None and mksrc('datarepo-dev-a86993e6', - 'hca_dev_83f5188e3bf749569544cea4f8997756__20210929_20210929', - 1612), - mksrc('datarepo-dev-bd995e95', - 'hca_dev_842605c7375a47c59e2ca71c2c00fcad__20210830_20210903', - 8), - mksrc('datarepo-dev-d0772077', - 'hca_dev_8787c23889ef4636a57d3167e8b54a80__20210827_20210903', - 3), - mksrc('datarepo-dev-8eb2ffd1', - 'hca_dev_87d52a86bdc7440cb84d170f7dc346d9__20210830_20210903', - 16), - mksrc('datarepo-dev-0c5c20b5', - 'hca_dev_8c3c290ddfff4553886854ce45f4ba7f__20210902_20210907', - 6640), - mksrc('datarepo-dev-a198b032', - 'hca_dev_90bd693340c048d48d76778c103bf545__20210827_20210903', - 2245), - mksrc('datarepo-dev-59d37b9a', - 'hca_dev_946c5add47d1402a97bba5af97e8bce7__20210831_20210903', - 149), - mksrc('datarepo-dev-788c3b52', - 'hca_dev_955dfc2ca8c64d04aa4d907610545d11__20210831_20210903', - 13), - mksrc('datarepo-dev-4b88b45b', - 'hca_dev_962bd805eb894c54bad2008e497d1307__20210830_20210903', - 28), - mksrc('datarepo-dev-02c59b72', - 'hca_dev_99101928d9b14aafb759e97958ac7403__20210830_20210903', - 1190, - ma=1), - mksrc('datarepo-dev-a6312a94', - 'hca_dev_992aad5e7fab46d9a47ddf715e8cfd24__20210830_20210903', - 41), - mksrc('datarepo-dev-75589244', - 'hca_dev_996120f9e84f409fa01e732ab58ca8b9__20210827_20210903', - 26), - mksrc('datarepo-dev-d4b988d6', - 'hca_dev_a004b1501c364af69bbd070c06dbc17d__20210830_20210903', - 16, - ma=1), - mksrc('datarepo-dev-9ec7beb6', - 'hca_dev_a29952d9925e40f48a1c274f118f1f51__20210827_20210902', - 26), - mksrc('datarepo-dev-d3d5bbfa', - 'hca_dev_a39728aa70a04201b0a281b7badf3e71__20210830_20210903', - 33), - mksrc('datarepo-dev-7b7daff7', - 'hca_dev_a96b71c078a742d188ce83c78925cfeb__20210827_20210902', - 6), - mksrc('datarepo-dev-58610528', - 'hca_dev_a9c022b4c7714468b769cabcf9738de3__20210827_20210903', - 23), - mksrc('datarepo-dev-1dce87e5', - 'hca_dev_ae71be1dddd84feb9bed24c3ddb6e1ad__20210916_20210916', - 3515), - mksrc('datarepo-dev-b2004d1c', - 'hca_dev_b4a7d12f6c2f40a39e359756997857e3__20210831_20210903', - 24), - mksrc('datarepo-dev-0b465564', - 'hca_dev_b51f49b40d2e4cbdbbd504cd171fc2fa__20210830_20210903', - 193), - mksrc('datarepo-dev-cd97e83a', - 'hca_dev_b963bd4b4bc14404842569d74bc636b8__20210827_20210928', - 2), - mksrc('datarepo-dev-376d3f4a', - 'hca_dev_bd40033154b94fccbff66bb8b079ee1f__20210901_20210903', - 18), - mksrc('datarepo-dev-aa783adb', - 'hca_dev_c5f4661568de4cf4bbc2a0ae10f08243__20210827_20210928', - 1), - mksrc('datarepo-dev-990234a8', - 'hca_dev_c6ad8f9bd26a4811b2ba93d487978446__20210827_20210903', - 639), - mksrc('datarepo-dev-61b8d081', - 'hca_dev_c715cd2fdc7c44a69cd5b6a6d9f075ae__20210827_20210902', - 9), - mksrc('datarepo-dev-71926fdc', - 'hca_dev_c893cb575c9f4f26931221b85be84313__20210901_20210903', - 20), - mksrc('datarepo-dev-2f4bfe5d', - 'hca_dev_ccd1f1ba74ce469b9fc9f6faea623358__20210827_20210902', - 222), - mksrc('datarepo-dev-aa8357fb', - 'hca_dev_ccef38d7aa9240109621c4c7b1182647__20210831_20210903', - 1314), - mksrc('datarepo-dev-24e672db', - 'hca_dev_cddab57b68684be4806f395ed9dd635a__20210831_20210907', - 2545), - mksrc('datarepo-dev-f4cb2365', - 'hca_dev_ce33dde2382d448cb6acbfb424644f23__20210827_20210928', - 189), - mksrc('datarepo-dev-0d6f73ac', - 'hca_dev_d012d4768f8c4ff389d6ebbe22c1b5c1__20210827_20210903', - 8), - mksrc('datarepo-dev-5674b4eb', - 'hca_dev_d2111fac3fc44f429b6d32cd6a828267__20210830_20210903', - 735), - mksrc('datarepo-dev-b3632667', - 'hca_dev_d3446f0c30f34a12b7c36af877c7bb2d__20210901_20210903', - 40), - mksrc('datarepo-dev-92c3a1de', - 'hca_dev_d3a4ceac4d66498497042570c0647a56__20210831_20210903', - 14), - mksrc('datarepo-dev-4e88d60b', - 'hca_dev_d3ac7c1b53024804b611dad9f89c049d__20210827_20210928', - 11), - mksrc('datarepo-dev-dbc582d9', - 'hca_dev_dbcd4b1d31bd4eb594e150e8706fa192__20210827_20210902', - 84), - mksrc('datarepo-dev-848e2d4f', - 'hca_dev_dbd836cfbfc241f0983441cc6c0b235a__20210827_20210902', - 1), - mksrc('datarepo-dev-d7517bce', - 'hca_dev_dc1a41f69e0942a6959e3be23db6da56__20210827_20210902', - 5), - mksrc('datarepo-dev-27ad01e5', - 'hca_dev_df88f39f01a84b5b92f43177d6c0f242__20210827_20210928', - 1), - mksrc('datarepo-dev-b839d6c7', - 'hca_dev_e526d91dcf3a44cb80c5fd7676b55a1d__20210902_20210907', - 606), - mksrc('datarepo-dev-3faef568', - 'hca_dev_e5d455791f5b48c3b568320d93e7ca72__20210827_20210903', - 8), - mksrc('datarepo-dev-e304a8fe', - 'hca_dev_e77fed30959d4fadbc15a0a5a85c21d2__20210830_20210903', - 333), - mksrc('datarepo-dev-6fdac3db', - 'hca_dev_e8808cc84ca0409680f2bba73600cba6__20210902_20210907', - 898), - mksrc('datarepo-dev-dbc3e131', - 'hca_dev_eaefa1b6dae14414953b17b0427d061e__20210827_20210903', - 385), - # FIXME: https://github.com/HumanCellAtlas/dcp2/issues/45 - None and mksrc('datarepo-dev-6883f2a5', - 'hca_dev_f48e7c39cc6740559d79bc437892840c__20210830_20210929', - 14), - mksrc('datarepo-dev-10f0610a', - 'hca_dev_f81efc039f564354aabb6ce819c3d414__20210827_20210903', - 4), - mksrc('datarepo-dev-24e9529e', - 'hca_dev_f83165c5e2ea4d15a5cf33f3550bffde__20210901_20210908', - 7663), - mksrc('datarepo-dev-67240cf2', - 'hca_dev_f86f1ab41fbb4510ae353ffd752d4dfc__20210901_20210903', - 20), - mksrc('datarepo-dev-e8e0a59a', - 'hca_dev_f8aa201c4ff145a4890e840d63459ca2__20210901_20210903', - 384), - mksrc('datarepo-dev-96d8e08c', - 'hca_dev_faeedcb0e0464be7b1ad80a3eeabb066__20210831_20210903', - 62), - ])), - ), - ] for prefix, internal in [ + f'{prefix}dcp2': { + 'atlas': 'hca', + 'internal': internal, + 'plugins': {'metadata': {'name': 'hca'}, 'repository': {'name': 'tdr'}}, + 'sources': list(filter(None, [ + mksrc('datarepo-dev-a9252919', 'hca_dev_005d611a14d54fbf846e571a1f874f70__20210827_20210903', 7), + mksrc('datarepo-dev-c148d39c', 'hca_dev_027c51c60719469fa7f5640fe57cbece__20210827_20210902', 8), + mksrc('datarepo-dev-e2ab8487', 'hca_dev_03c6fce7789e4e78a27a664d562bb738__20210902_20210907', 1530), + mksrc('datarepo-dev-37639c56', + 'hca_dev_05657a599f9d4bb9b77b24be13aa5cea__20210827_20210928', + 185), + mksrc('datarepo-dev-9f4012c9', + 'hca_dev_05be4f374506429bb112506444507d62__20210827_20210902', + 1544), + mksrc('datarepo-dev-baa2812f', + 'hca_dev_0792db3480474e62802c9177c9cd8e28__20210827_20210903', + 1450), + mksrc('datarepo-dev-38e08b5c', + 'hca_dev_08b794a0519c4516b184c583746254c5__20210901_20210903', + 2), + mksrc('datarepo-dev-2749da57', + 'hca_dev_091cf39b01bc42e59437f419a66c8a45__20210830_20210903', + 20), + mksrc('datarepo-dev-eab7fa76', + 'hca_dev_0c3b7785f74d40918616a68757e4c2a8__20210827_20210903', + 177), + mksrc('datarepo-dev-fef02a92', + 'hca_dev_0d4b87ea6e9e456982e41343e0e3259f__20210827_20210903', + 8), + mksrc('datarepo-dev-78bae095', + 'hca_dev_0fd8f91862d64b8bac354c53dd601f71__20210830_20210903', + 10), + mksrc('datarepo-dev-ff0a2fe7', + 'hca_dev_116965f3f09447699d28ae675c1b569c__20210827_20210903', + 8), + mksrc('datarepo-dev-4de1b9fd', + 'hca_dev_16ed4ad8731946b288596fe1c1d73a82__20210830_20210903', + 28), + mksrc('datarepo-dev-135f340c', + 'hca_dev_1c6a960d52ac44eab728a59c7ab9dc8e__20210827_20210928', + 10), + mksrc('datarepo-dev-86c60513', + 'hca_dev_1cd1f41ff81a486ba05b66ec60f81dcf__20210901_20210903', + 18), + mksrc('datarepo-dev-f5321179', + 'hca_dev_1ce3b3dc02f244a896dad6d107b27a76__20210827_20210903', + 421), + mksrc('datarepo-dev-76de829d', + 'hca_dev_2043c65a1cf84828a6569e247d4e64f1__20210831_20210907', + 1734), + mksrc('datarepo-dev-c808badb', + 'hca_dev_2086eb0510b9432bb7f0169ccc49d270__20210827_20210903', + 10), + mksrc('datarepo-dev-23782220', + 'hca_dev_23587fb31a4a4f58ad74cc9a4cb4c254__20210827_20210909', + 1476), + mksrc('datarepo-dev-4c3e6011', + 'hca_dev_248fcf0316c64a41b6ccaad4d894ca42__20210907_20210907', + 2958), + mksrc('datarepo-dev-1c2c69d9', + 'hca_dev_24c654a5caa5440a8f02582921f2db4a__20210830_20210903', + 3), + mksrc('datarepo-dev-38f08cd8', + 'hca_dev_2a64db431b554639aabb8dba0145689d__20210830_20210903', + 10), + mksrc('datarepo-dev-4cf05ce2', + 'hca_dev_2a72a4e566b2405abb7c1e463e8febb0__20210901_20210903', + 2290), + mksrc('datarepo-dev-3041c2cf', + 'hca_dev_2af52a1365cb4973b51339be38f2df3f__20210830_20210903', + 10), + mksrc('datarepo-dev-311340f6', + 'hca_dev_2d8460958a334f3c97d4585bafac13b4__20210902_20210907', + 3589), + mksrc('datarepo-dev-766bfb76', + 'hca_dev_2ef3655a973d4d699b4121fa4041eed7__20210827_20210903', + 8), + mksrc('datarepo-dev-1720b3c5', + 'hca_dev_379ed69ebe0548bcaf5ea7fc589709bf__20210827_20210902', + 4), + mksrc('datarepo-dev-ac6efd3f', + 'hca_dev_38449aea70b540db84b31e08f32efe34__20210830_20210903', + 42), + mksrc('datarepo-dev-40283c27', + 'hca_dev_3a69470330844ece9abed935fd5f6748__20210901_20210903', + 125), + mksrc('datarepo-dev-b08233fa', + 'hca_dev_3cfcdff5dee14a7ba591c09c6e850b11__20210827_20210903', + 8), + mksrc('datarepo-dev-bdc9f342', + 'hca_dev_3e329187a9c448ec90e3cc45f7c2311c__20210901_20210903', + 1001), + mksrc('datarepo-dev-ec07c8d8', + 'hca_dev_4037007b0eff4e6db7bd8dd8eec80143__20210831_20210903', + 39), + mksrc('datarepo-dev-c0ec174a', + 'hca_dev_403c3e7668144a2da5805dd5de38c7ff__20210827_20210903', + 63), + mksrc('datarepo-dev-31b3553a', + 'hca_dev_414accedeba0440fb721befbc5642bef__20210827_20210903', + 4), + mksrc('datarepo-dev-b4789901', + 'hca_dev_41fb1734a121461695c73b732c9433c7__20210830_20210903', + 12), + mksrc('datarepo-dev-4e5ffd52', + 'hca_dev_42d4f8d454224b78adaee7c3c2ef511c__20210830_20210903', + 9), + mksrc('datarepo-dev-5ef7f2e2', + 'hca_dev_455b46e6d8ea4611861ede720a562ada__20210901_20210903', + 74), + mksrc('datarepo-dev-a6c6b953', + 'hca_dev_4bec484dca7a47b48d488830e06ad6db__20210830_20210903', + 14), + mksrc('datarepo-dev-f31edbc2', + 'hca_dev_4d6f6c962a8343d88fe10f53bffd4674__20210901_20210903', + 12), + mksrc('datarepo-dev-bb8fbae4', + 'hca_dev_51f02950ee254f4b8d0759aa99bb3498__20210827_20210928', + 6), + mksrc('datarepo-dev-71de019e', + 'hca_dev_520afa10f9d24e93ab7a26c4c863ce18__20210827_20210928', + 649), + mksrc('datarepo-dev-ffcf8b00', + 'hca_dev_52b29aa4c8d642b4807ab35be94469ca__20210830_20210903', + 467), + mksrc('datarepo-dev-f76414c8', + 'hca_dev_52d10a60c8d14d068a5eaf0d5c0d5034__20210827_20210902', + 176), + mksrc('datarepo-dev-319b80f7', + 'hca_dev_577c946d6de54b55a854cd3fde40bff2__20210827_20210903', + 7), + mksrc('datarepo-dev-279f1986', + 'hca_dev_5ee710d7e2d54fe2818d15f5e31dae32__20210901_20210903', + 41), + mksrc('datarepo-dev-0abea017', + 'hca_dev_6072616c87944b208f52fb15992ea5a4__20210827_20210902', + 603), + mksrc('datarepo-dev-da221b1a', + 'hca_dev_60ea42e1af4942f58164d641fdb696bc__20210827_20210903', + 1145), + mksrc('datarepo-dev-c3d623dc', + 'hca_dev_63b5b6c1bbcd487d8c2e0095150c1ecd__20210830_20210903', + 11), + mksrc('datarepo-dev-ecb9c129', + 'hca_dev_67a3de0945b949c3a068ff4665daa50e__20210827_20210903', + 732), + mksrc('datarepo-dev-3545971c', + 'hca_dev_71436067ac414acebe1b2fbcc2cb02fa__20210827_20210928', + 4), + mksrc('datarepo-dev-12b7a9e1', + 'hca_dev_7880637a35a14047b422b5eac2a2a358__20210901_20210903', + 366), + mksrc('datarepo-dev-7913b094', + 'hca_dev_78b2406dbff246fc8b6120690e602227__20210827_20210902', + 216), + mksrc('datarepo-dev-4747d8fe', + 'hca_dev_7adede6a0ab745e69b67ffe7466bec1f__20210830_20210903', + 1601), + mksrc('datarepo-dev-aba01389', + 'hca_dev_7b947aa243a74082afff222a3e3a4635__20210831_20210907', + 7), + mksrc('datarepo-dev-bf3a4c8a', + 'hca_dev_8185730f411340d39cc3929271784c2b__20210830_20210903', + 12), + # FIXME: https://github.com/HumanCellAtlas/dcp2/issues/48 + None and mksrc('datarepo-dev-a86993e6', + 'hca_dev_83f5188e3bf749569544cea4f8997756__20210929_20210929', + 1612), + mksrc('datarepo-dev-bd995e95', + 'hca_dev_842605c7375a47c59e2ca71c2c00fcad__20210830_20210903', + 8), + mksrc('datarepo-dev-d0772077', + 'hca_dev_8787c23889ef4636a57d3167e8b54a80__20210827_20210903', + 3), + mksrc('datarepo-dev-8eb2ffd1', + 'hca_dev_87d52a86bdc7440cb84d170f7dc346d9__20210830_20210903', + 16), + mksrc('datarepo-dev-0c5c20b5', + 'hca_dev_8c3c290ddfff4553886854ce45f4ba7f__20210902_20210907', + 6640), + mksrc('datarepo-dev-a198b032', + 'hca_dev_90bd693340c048d48d76778c103bf545__20210827_20210903', + 2245), + mksrc('datarepo-dev-59d37b9a', + 'hca_dev_946c5add47d1402a97bba5af97e8bce7__20210831_20210903', + 149), + mksrc('datarepo-dev-788c3b52', + 'hca_dev_955dfc2ca8c64d04aa4d907610545d11__20210831_20210903', + 13), + mksrc('datarepo-dev-4b88b45b', + 'hca_dev_962bd805eb894c54bad2008e497d1307__20210830_20210903', + 28), + mksrc('datarepo-dev-02c59b72', + 'hca_dev_99101928d9b14aafb759e97958ac7403__20210830_20210903', + 1190, + ma=1), + mksrc('datarepo-dev-a6312a94', + 'hca_dev_992aad5e7fab46d9a47ddf715e8cfd24__20210830_20210903', + 41), + mksrc('datarepo-dev-75589244', + 'hca_dev_996120f9e84f409fa01e732ab58ca8b9__20210827_20210903', + 26), + mksrc('datarepo-dev-d4b988d6', + 'hca_dev_a004b1501c364af69bbd070c06dbc17d__20210830_20210903', + 16, + ma=1), + mksrc('datarepo-dev-9ec7beb6', + 'hca_dev_a29952d9925e40f48a1c274f118f1f51__20210827_20210902', + 26), + mksrc('datarepo-dev-d3d5bbfa', + 'hca_dev_a39728aa70a04201b0a281b7badf3e71__20210830_20210903', + 33), + mksrc('datarepo-dev-7b7daff7', + 'hca_dev_a96b71c078a742d188ce83c78925cfeb__20210827_20210902', + 6), + mksrc('datarepo-dev-58610528', + 'hca_dev_a9c022b4c7714468b769cabcf9738de3__20210827_20210903', + 23), + mksrc('datarepo-dev-1dce87e5', + 'hca_dev_ae71be1dddd84feb9bed24c3ddb6e1ad__20210916_20210916', + 3515), + mksrc('datarepo-dev-b2004d1c', + 'hca_dev_b4a7d12f6c2f40a39e359756997857e3__20210831_20210903', + 24), + mksrc('datarepo-dev-0b465564', + 'hca_dev_b51f49b40d2e4cbdbbd504cd171fc2fa__20210830_20210903', + 193), + mksrc('datarepo-dev-cd97e83a', + 'hca_dev_b963bd4b4bc14404842569d74bc636b8__20210827_20210928', + 2), + mksrc('datarepo-dev-376d3f4a', + 'hca_dev_bd40033154b94fccbff66bb8b079ee1f__20210901_20210903', + 18), + mksrc('datarepo-dev-aa783adb', + 'hca_dev_c5f4661568de4cf4bbc2a0ae10f08243__20210827_20210928', + 1), + mksrc('datarepo-dev-990234a8', + 'hca_dev_c6ad8f9bd26a4811b2ba93d487978446__20210827_20210903', + 639), + mksrc('datarepo-dev-61b8d081', + 'hca_dev_c715cd2fdc7c44a69cd5b6a6d9f075ae__20210827_20210902', + 9), + mksrc('datarepo-dev-71926fdc', + 'hca_dev_c893cb575c9f4f26931221b85be84313__20210901_20210903', + 20), + mksrc('datarepo-dev-2f4bfe5d', + 'hca_dev_ccd1f1ba74ce469b9fc9f6faea623358__20210827_20210902', + 222), + mksrc('datarepo-dev-aa8357fb', + 'hca_dev_ccef38d7aa9240109621c4c7b1182647__20210831_20210903', + 1314), + mksrc('datarepo-dev-24e672db', + 'hca_dev_cddab57b68684be4806f395ed9dd635a__20210831_20210907', + 2545), + mksrc('datarepo-dev-f4cb2365', + 'hca_dev_ce33dde2382d448cb6acbfb424644f23__20210827_20210928', + 189), + mksrc('datarepo-dev-0d6f73ac', + 'hca_dev_d012d4768f8c4ff389d6ebbe22c1b5c1__20210827_20210903', + 8), + mksrc('datarepo-dev-5674b4eb', + 'hca_dev_d2111fac3fc44f429b6d32cd6a828267__20210830_20210903', + 735), + mksrc('datarepo-dev-b3632667', + 'hca_dev_d3446f0c30f34a12b7c36af877c7bb2d__20210901_20210903', + 40), + mksrc('datarepo-dev-92c3a1de', + 'hca_dev_d3a4ceac4d66498497042570c0647a56__20210831_20210903', + 14), + mksrc('datarepo-dev-4e88d60b', + 'hca_dev_d3ac7c1b53024804b611dad9f89c049d__20210827_20210928', + 11), + mksrc('datarepo-dev-dbc582d9', + 'hca_dev_dbcd4b1d31bd4eb594e150e8706fa192__20210827_20210902', + 84), + mksrc('datarepo-dev-848e2d4f', + 'hca_dev_dbd836cfbfc241f0983441cc6c0b235a__20210827_20210902', + 1), + mksrc('datarepo-dev-d7517bce', + 'hca_dev_dc1a41f69e0942a6959e3be23db6da56__20210827_20210902', + 5), + mksrc('datarepo-dev-27ad01e5', + 'hca_dev_df88f39f01a84b5b92f43177d6c0f242__20210827_20210928', + 1), + mksrc('datarepo-dev-b839d6c7', + 'hca_dev_e526d91dcf3a44cb80c5fd7676b55a1d__20210902_20210907', + 606), + mksrc('datarepo-dev-3faef568', + 'hca_dev_e5d455791f5b48c3b568320d93e7ca72__20210827_20210903', + 8), + mksrc('datarepo-dev-e304a8fe', + 'hca_dev_e77fed30959d4fadbc15a0a5a85c21d2__20210830_20210903', + 333), + mksrc('datarepo-dev-6fdac3db', + 'hca_dev_e8808cc84ca0409680f2bba73600cba6__20210902_20210907', + 898), + mksrc('datarepo-dev-dbc3e131', + 'hca_dev_eaefa1b6dae14414953b17b0427d061e__20210827_20210903', + 385), + # FIXME: https://github.com/HumanCellAtlas/dcp2/issues/45 + None and mksrc('datarepo-dev-6883f2a5', + 'hca_dev_f48e7c39cc6740559d79bc437892840c__20210830_20210929', + 14), + mksrc('datarepo-dev-10f0610a', + 'hca_dev_f81efc039f564354aabb6ce819c3d414__20210827_20210903', + 4), + mksrc('datarepo-dev-24e9529e', + 'hca_dev_f83165c5e2ea4d15a5cf33f3550bffde__20210901_20210908', + 7663), + mksrc('datarepo-dev-67240cf2', + 'hca_dev_f86f1ab41fbb4510ae353ffd752d4dfc__20210901_20210903', + 20), + mksrc('datarepo-dev-e8e0a59a', + 'hca_dev_f8aa201c4ff145a4890e840d63459ca2__20210901_20210903', + 384), + mksrc('datarepo-dev-96d8e08c', + 'hca_dev_faeedcb0e0464be7b1ad80a3eeabb066__20210831_20210903', + 62), + ]))} + for prefix, internal in [ ('', False), ('it0', True) ]

@hannes-ucsc the source that pass in ma=1 arguments and 2 problematic None and mksrc() lines still wont fit under the 120 char limit with the suggested changes, should we just make an exception to the 4 lines that go over this 120 char length limit?

make format pep8 does not attempt to automatically format or throw a warning for these lines.

When using the Pycharm formatter it attempts to use aligned wraps, but not for all arguments (against contributing guidelines)...

# FIXME: https://github.com/HumanCellAtlas/dcp2/issues/48 None and mksrc('datarepo-dev-a86993e6', 'hca_dev_83f5188e3bf749569544cea4f8997756__20210929_20210929', 1612), mksrc('datarepo-dev-bd995e95', 'hca_dev_842605c7375a47c59e2ca71c2c00fcad__20210830_20210903', 8), mksrc('datarepo-dev-d0772077', 'hca_dev_8787c23889ef4636a57d3167e8b54a80__20210827_20210903', 3), mksrc('datarepo-dev-8eb2ffd1', 'hca_dev_87d52a86bdc7440cb84d170f7dc346d9__20210830_20210903', 16), mksrc('datarepo-dev-0c5c20b5', 'hca_dev_8c3c290ddfff4553886854ce45f4ba7f__20210902_20210907', 6640), mksrc('datarepo-dev-a198b032', 'hca_dev_90bd693340c048d48d76778c103bf545__20210827_20210903', 2245), mksrc('datarepo-dev-59d37b9a', 'hca_dev_946c5add47d1402a97bba5af97e8bce7__20210831_20210903', 149), mksrc('datarepo-dev-788c3b52', 'hca_dev_955dfc2ca8c64d04aa4d907610545d11__20210831_20210903', 13), mksrc('datarepo-dev-4b88b45b', 'hca_dev_962bd805eb894c54bad2008e497d1307__20210830_20210903', 28), mksrc('datarepo-dev-02c59b72', 'hca_dev_99101928d9b14aafb759e97958ac7403__20210830_20210903', 1190, ma=1),

amarjandu · 2021-10-12T01:19:27Z

self note : 648b58b passes IT, used sandbox config.

hannes-ucsc · 2021-10-12T05:53:48Z

deployments/prod/environment.py

                (
-                    'dcp9',
+                    (


Rule of thumb: lists for repeating elements of a homogeneous type, tuples for non-repeating structures of heterogeneous types.

This can be compressed a bit:

Index: deployments/prod/environment.py IDEA additional info: Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP <+>UTF-8 =================================================================== diff --git a/deployments/prod/environment.py b/deployments/prod/environment.py --- a/deployments/prod/environment.py (revision 0d00fb640605b9b84aa35920906615eaa52c71b4) +++ b/deployments/prod/environment.py (date 1634017810974) @@ -41,52 +41,40 @@ 'AZUL_CATALOGS': json.dumps({ f'{name}': dict(atlas=atlas, - internal=internal, + internal=bool(i), plugins=dict(metadata=dict(name='hca'), repository=dict(name='tdr')), sources=sources) - for catalog_type, atlas, sources in [ + for atlas, names, sources in [ ( - ( - ('dcp9', False), - ('it9', True) - ), 'hca', + ['dcp9', 'it9'], [ 'tdr:tdr-fp-546ade29:snapshot/hca_prod_20201120_dcp2___20210910_dcp9:', ] ), ( - ( - ('dcp10', False), - ('it10', True) - ), 'hca', + ['dcp10', 'it10'], [ 'tdr:tdr-fp-43194825:snapshot/hca_prod_20201120_dcp2___20211004_dcp10:' ] ), ( - ( - ('dcp1', False), - ('it1', True) - ), 'hca', + ['dcp1', 'it1'], [ 'tdr:broad-datarepo-terra-prod-hca2:snapshot/hca_prod_20201118_dcp1___20201209:', ] ), ( - ( - ('lungmap', False), - ('it0lungmap', True) - ), 'lungmap', + ['lungmap', 'it0lungmap'], [ 'tdr:tdr-fp-9f58860b:snapshot/hca_prod_00f056f273ff43ac97ff69ca10e38c89__20211004_lungmap_20211005:' ] ) - ] for name, internal in catalog_type + ] for i, name in enumerate(names) }), 'AZUL_PARTITION_PREFIX_LENGTH': '2',

achave11-ucsc · 2021-10-14T04:44:03Z

This PR is no demo according to this issue comment.

achave11-ucsc

pro-forma approval in order to merge into develop

github-actions bot added the orange [process] Done by the Azul team label Sep 28, 2021

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Fix: IT catalog names are inconsistent (#3113) #3277

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[u] Define sources within catalog JSON (#3114)

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This was referenced Oct 15, 2021

test_can_bundle_canned_repository IT fails in dev deployment #3544

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EBNF for sources was deleted #3562

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[u] Define sources within catalog JSON (#3114) #3476

[u] Define sources within catalog JSON (#3114) #3476

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[u] Define sources within catalog JSON (#3114) #3476

[u] Define sources within catalog JSON (#3114) #3476

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