Reimplement Workflow with its own schema #7203

labkey-susanh · 2025-11-12T17:50:33Z

Rationale

Having our workflow implementation based on the Exp schema leads to lots of inefficiencies and makes it difficult to expand the capabilities. The related PR moves the data into dedicated tables in the database, producing a new rendition of the workflow schema. The changes here make that transition better.

Related Pull Requests

Changes

A bit of renaming
Add some additional getter and setter methods in CreatedModified
Update AbstractQueryUpdateService to have overridable methods for checking permissions
Create PageUtils.AppUrls class as a base class for URL providers for apps (extracted from NotebookController)

…sk RowId instead of exp.ProtocolApplication

XingY

isSampleWorkflowProtocol and related utils in ExpProtocol are still being used. I believe those should be removed.

XingY · 2025-11-12T20:00:14Z

api/src/org/labkey/api/dataiterator/NameExpressionDataIteratorBuilder.java


    public NameExpressionDataIteratorBuilder(DataIteratorBuilder pre, TableInfo parentTable)
    {
        _pre = pre;


can just call this(pre, parentTable, "name", "nameExpression")

Ah yes. Done.

XingY · 2025-11-24T20:17:05Z

experiment/src/org/labkey/experiment/XarExporter.java

-            String workflowObjectId = Lsid.parse(workflowTask.getLSID()).getObjectId();
-            xRun.setWorkflowTaskLSID("${WorkflowTaskReference}:" + workflowObjectId);
-        }
+        // TODO need to update this for run workflowTaskId support in XAR on workflow job folder export/import is supported


Is this for a future story?

Yes. Follow on story.

Copilot

Pull request overview

This PR reimplements workflow functionality by moving it from the Exp (experiment) schema to a dedicated workflow schema in the samplemanagement module. The changes streamline the API by replacing complex object relationships with simpler ID-based references.

Key changes:

Refactored workflow task references from ExpProtocolApplication objects to Long IDs throughout the assay and experiment APIs
Enhanced CreatedModified class with additional convenience getters/setters for Date and User objects
Made AbstractQueryUpdateService permission checks overridable to support custom authorization logic
Extracted PageFlowUtil.AppUrls as a reusable base class for application URL providers
Moved NamePlusIdDataIterator from assay.plate.query to the api.dataiterator package and parameterized name generation components for broader reusability

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
experiment/src/org/labkey/experiment/api/ExpRunTableImpl.java	Updates WorkflowTask column FK to reference new workflow.Task schema with module check
experiment/src/org/labkey/experiment/api/ExpRunImpl.java	Simplifies workflow task methods to return/accept IDs instead of objects
experiment/src/org/labkey/experiment/XarReader.java	Comments out workflow task LSID handling pending XAR format update
experiment/src/org/labkey/experiment/XarExporter.java	Comments out workflow task export pending XAR format update
experiment/src/org/labkey/experiment/ExperimentModule.java	Bumps schema version to 25.014
experiment/src/org/labkey/experiment/ExperimentMigrationSchemaHandler.java	Removes FK constraint management for workflow task (moved to SQL scripts)
experiment/resources/schemas/dbscripts/sqlserver/exp-25.013-25.014.sql	Drops FK_Run_WorfklowTask constraint
experiment/resources/schemas/dbscripts/postgresql/exp-25.013-25.014.sql	Drops FK_Run_WorfklowTask constraint
assay/src/org/labkey/assay/plate/query/PlateTable.java	Adds import for relocated NamePlusIdDataIterator
assay/src/org/labkey/assay/plate/query/PlateSetTable.java	Adds import for relocated NamePlusIdDataIterator
assay/src/org/labkey/assay/actions/ImportRunApiAction.java	Renames workflowTask variables to workflowTaskId
api/src/org/labkey/api/util/PageFlowUtil.java	Introduces AppUrls base class for application URL generation
api/src/org/labkey/api/query/AbstractQueryUpdateService.java	Adds overridable permission check methods for insert/update/delete operations
api/src/org/labkey/api/qc/TsvDataExchangeHandler.java	Removes unused getWorkflowTask method override
api/src/org/labkey/api/exp/api/ExpRun.java	Replaces workflow task object methods with ID-based methods
api/src/org/labkey/api/dataiterator/NamePlusIdDataIterator.java	Relocates from assay.plate.query package to api.dataiterator
api/src/org/labkey/api/dataiterator/NameExpressionDataIteratorBuilder.java	Adds parameterized constructor for custom column names
api/src/org/labkey/api/dataiterator/NameExpressionDataIterator.java	Adds parameterized constructor for custom column names
api/src/org/labkey/api/data/NameGeneratorState.java	Adds nameField parameter for flexible name field lookup
api/src/org/labkey/api/data/NameGenerator.java	Adds createState overload with nameField parameter
api/src/org/labkey/api/data/CreatedModified.java	Adds Date and User convenience getters, and int-based setters
api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java	Updates to use getWorkflowTaskId method
api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java	Renames field and methods from workflowTask to workflowTaskId
api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java	Renames field and methods from workflowTask to workflowTaskId
api/src/org/labkey/api/assay/DefaultAssayRunCreator.java	Updates to use getWorkflowTaskId method
api/src/org/labkey/api/assay/AssayRunUploadContextImpl.java	Renames field from workflowTask to workflowTaskId
api/src/org/labkey/api/assay/AssayRunUploadContext.java	Renames method from getWorkflowTask to getWorkflowTaskId
api/src/org/labkey/api/assay/AssayRunDatabaseContext.java	Simplifies to directly return workflow task ID
api/src/org/labkey/api/announcements/EmailOption.java	Renames enum constants from SAMPLEMANAGER_* to WORKFLOW_*

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XingY · 2025-11-24T22:04:56Z

isSampleWorkflowProtocol and related utils in ExpProtocol are still being used. I believe those should be removed.

@labkey-susanh My main comment for this PR is updating/removing usages of isSampleWorkflowProtocol and related.

labkey-susanh · 2025-11-25T00:07:11Z

isSampleWorkflowProtocol and related utils in ExpProtocol are still being used. I believe those should be removed.

@labkey-susanh My main comment for this PR is updating/removing usages of isSampleWorkflowProtocol and related.

Yes, sorry. Asked for re-review too early.

labkey-susanh · 2025-11-25T02:55:11Z

isSampleWorkflowProtocol and related utils in ExpProtocol are still being used. I believe those should be removed.

I have removed references to this except where currently in use by the folder writer/reader. Those will get excised when we do the folder export/import part but I am choosing to leave them for now as a trail to follow in that next story.

…d of the User object

labkey-susanh added 16 commits October 27, 2025 15:26

More helper methods for getting and setting createdBy/modifiedBy

1a39739

Parameterize NameExpressionDataIterator with column names

b8a2bb2

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

8ac2eab

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

e7ecdbd

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

5b31ebd

Add method for overriding hasInsertRowsPermission

31581d3

Fixes for job deletion

e7eb759

Allow update permission check to be overridden too

9cd40cd

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

f4d200f

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

ffc0be8

Rename EmailOption for workflow notifications

db30ede

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

18795fa

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

92c548f

Create a base class for App controller URL providers

0e9638b

Getter for date version of longs

66682b6

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

532ea97

labkey-susanh requested a review from XingY November 12, 2025 17:50

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cnathe and others added 6 commits November 13, 2025 08:18

Rename assay run workflowTask to workflowTaskId since it holds a RowId

f34ed63

Change exp.ExperimentRun WorkflowTask column to reference workflow.ta…

b3bbeaa

…sk RowId instead of exp.ProtocolApplication

Comment out XarExporter and XarReader handling of workflowTask for now

3577a8d

update comments

a5b13d7

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

a3c426a

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

d0de03d

labkey-susanh mentioned this pull request Nov 18, 2025

Reimplement Workflow with its own schema LabKey/labkey-ui-components#1897

Merged

labkey-susanh added 2 commits November 19, 2025 08:19

Generalize NameGenerator to work with other fields

b710e83

Move NamePlusIdDataIterator to API for general use

d74a452

labkey-susanh and others added 4 commits November 19, 2025 08:42

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

fa5448c

Merge branch 'develop' into fb_moveWorkflowCode

97a4e1d

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

82eefc2

Merge branch 'develop' into fb_moveWorkflowCode

5365cf4

XingY reviewed Nov 24, 2025

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labkey-susanh requested a review from XingY November 24, 2025 21:54

Use this

5376be8

labkey-susanh added 2 commits November 24, 2025 16:12

Remove check for isSampleWorkflow in run deletion

771597d

Add TODO reminder for code removal

51463d1

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

46160d8

XingY approved these changes Nov 25, 2025

View reviewed changes

labkey-susanh and others added 3 commits November 25, 2025 12:49

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

cc8992f

ExpObject getCreatedById() and getModifiedById() to get the id instea…

3815a73

…d of the User object

Merge remote-tracking branch 'origin/develop' into fb_moveWorkflowCode

8851a78

labkey-susanh merged commit 0fa8c2e into develop Dec 1, 2025
6 of 14 checks passed

labkey-susanh deleted the fb_moveWorkflowCode branch December 1, 2025 23:29

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Reimplement Workflow with its own schema #7203

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labkey-susanh commented Nov 12, 2025 •

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labkey-susanh commented Nov 12, 2025 •

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