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[SCHEMATIC-192] V24.12.1 into Main#1562

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Merged

andrewelamb merged 105 commits intomainSage-Bionetworks/schematic:mainfrom v24.12.1-rc-devSage-Bionetworks/schematic:v24.12.1-rc-devCopy head branch name to clipboardDec 16, 2024

+1,255-460

Commits

Commits on Sep 10, 2024

• add new tests

  andrewelamb

  committed
  9286503

Commits on Oct 1, 2024

• handle merge conflict

  andrewelamb

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  3d6d3b3

Commits on Oct 3, 2024

• add unit tests

  andrewelamb

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Commits on Oct 4, 2024

• ran black

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Commits on Oct 10, 2024

• Update schematic/models/validate_attribute.py

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  andrewelamb

  and

  BryanFauble

  authored
  95d7686

Commits on Oct 11, 2024

• added tests

  andrewelamb

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  95a59c4

Commits on Oct 17, 2024

• Merge branch 'develop' into FDS-2333-ValidateAttribute-unit-tests

  andrewelamb

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  8e555f1

Commits on Oct 21, 2024

• Update README.md

  jaymedina

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• Update README.md

  jaymedina

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  9a40ce8

• add unit tests

  andrewelamb

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• run black

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Commits on Oct 22, 2024

• Update README.md

  jaymedina

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• temp commit

  andrewelamb

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• remove old tests

  andrewelamb

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  c987329

Commits on Oct 24, 2024

• [FDS-2386] Synapse entity tracking and code concurrency updates (#1505)

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  BryanFauble

  authored
  0bd946c

• Merge branch 'develop' into FDS-2333-ValidateAttribute-unit-tests

  andrewelamb

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• Merge branch 'develop' into FDS-2347

  andrewelamb

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• ran black

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Commits on Oct 25, 2024

• Update CODEOWNERS

  andrewelamb

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  ed85e4b

• Merge pull request #1525 from Sage-Bionetworks/andrewelamb-patch-1

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  andrewelamb

  authored
  2063508

• Merge pull request #1517 from Sage-Bionetworks/FDS-2333-ValidateAttribute-unit-tests

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  andrewelamb

  authored
  1fae4c5

• updated data model type rules to include error param

  andrewelamb

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  1765552

• fix validate type attribute to use msg level param

  andrewelamb

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  beb8663

• Merge branch 'develop' into FDS-2506-type-val

  andrewelamb

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  23106a4

• added error handling

  andrewelamb

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• run black

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• create Node class

  andrewelamb

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• sat up Node class so that nodes with no displayName fields cause an error on creation

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• ran black

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• ran mypy

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Commits on Oct 26, 2024

• Merge pull request #1523 from Sage-Bionetworks/FDS-2347

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  andrewelamb

  authored
  a87df1f

Commits on Oct 30, 2024

• Merge pull request #1522 from Sage-Bionetworks/develop-fds-2466-update-config.yml

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  andrewelamb

  authored
  c69ec88

• Merge pull request #1526 from Sage-Bionetworks/FDS-2506-type-val

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  andrewelamb

  authored
  59889b6

• added new configs for CLI tests

  andrewelamb

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  e8fb516

• added new manifests for testing CLI commands

  andrewelamb

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• automate manual CLI tests

  andrewelamb

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• ran black

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Commits on Nov 1, 2024

• Update CODEOWNERS

  thomasyu888

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• Update scan_repo.yml

  thomasyu888

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• Update .github/CODEOWNERS

  thomasyu888

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• Update .github/workflows/scan_repo.yml

  thomasyu888

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  469da57

• Merge pull request #1531 from Sage-Bionetworks/thomasyu888-patch-1

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  thomasyu888

  authored
  d1ef225

• Attach additional telemetry data to OTEL traces (#1519)

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  BryanFauble

  authored
  ad7c8f8

• feat: added tracing for cross manifest validation and file name validation (#1509)

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  linglp

  authored
  1c2d7be

Commits on Nov 4, 2024

• temp commit

  andrewelamb

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  d1cbc04

• Merge branch 'develop' into FDS-2238-automate-cli-tests

  andrewelamb

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  d6e99f3

Commits on Nov 5, 2024

• Updating contribution doc to expect squash and merge (#1534)

  BryanFauble

  authored
  c75c71c

• [FDS-2491] Integration tests for Schematic API Test plan (#1512)

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  BryanFauble

  authored
  4bbbb68

Commits on Nov 6, 2024

• [FDS-2500] Add Integration Tests for: Manifest Validation (#1516)

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  jaymedina

  authored
  39852a1

Commits on Nov 7, 2024

• [FDS-2449] Lock sphinx version and update poetry.lock (#1530)

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  jaymedina

  authored
  1cd5efa

• Merge branch 'develop' into FDS-2238-automate-cli-tests

  andrewelamb

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  dd00932

• manual test files now being saved in manifests folder

  andrewelamb

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  318171e

• manual test files now being saved in manifests folder

  andrewelamb

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  4e1d5b1

• remove lines to delete json files that were under git control

  andrewelamb

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• ran black

  andrewelamb

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• add try finally blocks to remove created files

  andrewelamb

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• ran black

  andrewelamb

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• add lines to remove created json files

  andrewelamb

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• Update file annotation store process to require filename be present in order to annotate file

  BryanFauble

  committed
  f57c718

• add lines to remove created json files

  andrewelamb

  committed
  35d440b

• Revert "Update file annotation store process to require filename be present in order to annotate file"

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  BryanFauble

  committed
  e832d02

• Don't attempt to annotate the table

  BryanFauble

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  11be01a

Commits on Nov 8, 2024

• add code in finally blocks to reset config to default values, when tests change them

  andrewelamb

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• complete submit manifest command test

  andrewelamb

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• ran black

  andrewelamb

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Commits on Nov 11, 2024

• add test for bug case

  GiaJordan

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  f3d878d

• update test for table tidyness

  GiaJordan

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  7dcc88f

• remove unused import

  GiaJordan

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  6d0cdd0

• remove etag column if already present when building temp file view

  GiaJordan

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  37cd4cd

Commits on Nov 12, 2024

• catch all exceptions to switch to sequential mode

  GiaJordan

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  68b0b24

• update test for updated data

  GiaJordan

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  255e3c0

• Revert "update test for updated data"

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  GiaJordan

  committed
  6c122ee

• Revert "catch all exceptions to switch to sequential mode"

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  GiaJordan

  committed
  ad71660

• catch ValueErrors as well

  GiaJordan

  committed
  cc1fb27

• Updates for integration test failures (#1537)

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  BryanFauble

  authored
  e30e32c

• Merge branch 'develop' into schematic-126-file-annotation-storage-update

  BryanFauble

  committed
  3064d00

• Merge branch 'develop' into FDS-2238-automate-cli-tests

  andrewelamb

  committed
  3099be3

Commits on Nov 13, 2024

• Merge pull request #1535 from Sage-Bionetworks/schematic-126-file-annotation-storage-update

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  thomasyu888

  authored
  4f82822

• Merge pull request #1538 from Sage-Bionetworks/schematic-1-existing-eTag

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  thomasyu888

  authored
  f6d015b

• add todos for removing config resets

  andrewelamb

  committed
  ec896e6

• [FDS-2525] Authenticated export of telemetry data (#1527)

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  BryanFauble

  authored
  778bf54

• temp reduce tests

  andrewelamb

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  8655b8d

• restore tests

  andrewelamb

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  4050e71

• uncomment tests

  andrewelamb

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  a610955

• redid how files are deleted, manual tests values are set

  andrewelamb

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• ran black

  andrewelamb

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Commits on Nov 14, 2024

• Merge pull request #1528 from Sage-Bionetworks/FDS-2238-automate-cli-tests

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  thomasyu888

  authored
  1e5da3c

• [SCHEMATIC-157] Make some dependencies required to avoid schematic CLI commands from potentially erroring when doing a pip install (#1540)

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  thomasyu888

  authored
  39459e7

• Merge branch 'main' into develop

  thomasyu888

  committed
  c7eace9

Commits on Nov 15, 2024

• Include schematic_api for now (#1547)

  thomasyu888

  authored
  2ed7837

• update toml version to 24.11.1 (#1548)

  andrewelamb

  authored
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Commits on Nov 19, 2024

• Merge branch 'main' into develop

  thomasyu888

  committed
  1ef9818

• [SCHEMATIC-193] Support exporting telemetry data from GH integration test runs (#1550)

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  BryanFauble

  authored
  14aa510

Commits on Nov 23, 2024

• [SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size (#1542)

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  thomasyu888

  and

  BryanFauble

  authored
  998e295

Commits on Nov 25, 2024

• [SCHEMATIC-212] Prevent traces from being combined (#1552)

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  BryanFauble

  authored
  c3e0732

Commits on Dec 2, 2024

• [SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't have entityId (#1551)

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  BWMac

  authored
  c681346

Commits on Dec 10, 2024

• [SCHEMATIC-183] Use paths from file view for manifest generation (#1529)

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  GiaJordan

  authored
  ef87c39

Commits on Dec 13, 2024

• [SCHEMATIC-214] Wrap pandas functions to support not including None with the NA values argument (#1553)

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  4 peopleauthored
  70813f1

• incremented packge version number

  andrewelamb

  committed
  9ed3474

• Update publish.yml

  andrewelamb

  authored
  3d4b591

• Update test.yml

  andrewelamb

  authored
  b35eef1

• Update api_test.yml

  andrewelamb

  authored
  1204e0a

• Update pdoc.yml

  andrewelamb

  authored
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• Update version.py

  andrewelamb

  authored
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Commits on Dec 16, 2024

• updates publish.yml (#1558) (#1561)

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  andrewelamb

  and

  BWMac

  authored
  c657388