Updates to syntax for nmdc identifiers #1989

aclum · 2024-05-20T18:10:37Z

This PR includes:
-updates to ID syntax patterns to remove id_version and locus_tag from most Class

modifications to pattern for id_version to enforce a single period + digit
adding invalid tests to stress id patterns

…xamples to test id pattern constraints, update id_version pattern match to enforce it as a single dot followed by a digit

…ingActivity.yaml

…me_seequencing_activity_json.yaml

mbthornton-lbl

There is an empty file - if this is intentional add a comment to explain

src/data/invalid/DataObject-invalid_id.yaml

…executionactivity-subclasses' of https://github.com/microbiomedata/nmdc-schema into 1988-update-to-enforce-including-id_version-in-workflowexecutionactivity-subclasses

…working on

Removing id_version and locus_tag from most classes, adding invalid e…

a1d5686

…xamples to test id pattern constraints, update id_version pattern match to enforce it as a single dot followed by a digit

aclum linked an issue May 20, 2024 that may be closed by this pull request

update to enforce including id_version in WorkflowExecutionActivity subclasses #1988

Closed

7 tasks

aclum requested review from turbomam, mbthornton-lbl, sierra-moxon, scanon and dwinston May 20, 2024 18:10

aclum added 7 commits May 20, 2024 11:37

Fix example valid data

b36187f

Fix workflow identifier for Database-nom_analysis_activity_set.yaml

965c45a

update id value for MetabolomicsAnalysisActivity-1.yaml

2b7943f

fixing id and id mention patterns for Database-with-MetagenomeSequenc…

01eab47

…ingActivity.yaml

Fix id and id mentions for ReadQcAnalysisActivity-1.yaml

155b4f7

Updating ID and ID mentions for workflow activity example valid data

915b850

Fix id and id mentions for MetagenomeSequencingActivity-from-metageno…

f0cc038

…me_seequencing_activity_json.yaml

turbomam mentioned this pull request May 20, 2024

Report slots, as used by some class, that have another class in their range, when that range class has a strcutred pattern #1990

Merged

turbomam added 3 commits May 20, 2024 18:57

closing $ on many strucutured_pattern.syntaxes

01ed93c

smaller commit

e6fdbe6

slot is required, strucutred_pattern is not

3417913

mbthornton-lbl requested changes May 21, 2024

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src/data/invalid/DataObject-invalid_id.yaml Outdated Show resolved Hide resolved

aclum added 7 commits May 21, 2024 10:18

removing empty file DataObject-invalid_id.yaml

273dedd

Merge branch '1988-update-to-enforce-including-id_version-in-workflow…

267d735

…executionactivity-subclasses' of https://github.com/microbiomedata/nmdc-schema into 1988-update-to-enforce-including-id_version-in-workflowexecutionactivity-subclasses

remove empty DataObject invalid example

7eb247f

remove mixs.yaml changes, these were from another branch Mark M. was …

237225c

…working on

ending $ on ID syntaxes

8fffde8

adding more $ to end pattern syntaxes

ea437c7

fixing syntax pattern for Activity'

7db1399

aclum requested a review from mbthornton-lbl May 21, 2024 20:02

aclum marked this pull request as ready for review May 21, 2024 20:02

mbthornton-lbl approved these changes May 21, 2024

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turbomam approved these changes May 21, 2024

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aclum merged commit 3ad7068 into main May 21, 2024
2 checks passed

aclum deleted the 1988-update-to-enforce-including-id_version-in-workflowexecutionactivity-subclasses branch May 21, 2024 22:01

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Updates to syntax for nmdc identifiers #1989

Updates to syntax for nmdc identifiers #1989

aclum commented May 20, 2024

mbthornton-lbl left a comment

Updates to syntax for nmdc identifiers #1989

Updates to syntax for nmdc identifiers #1989

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aclum commented May 20, 2024

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