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Move specimen module to customModules repository - #281

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labkey-tchad merged 522 commits into
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fb_specimenTestCleanup
Sep 29, 2026
Merged

labkey-tchad merged 522 commits into
developfrom
fb_specimenTestCleanup

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@labkey-tchad labkey-tchad commented Sep 25, 2026 •

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labkey-tchad and others added 30 commits November 9, 2017 17:40
SVN r54982 |2017-11-09 17:40:11 +0000
SVN r55556 |2017-12-19 17:44:29 +0000
SVN r55560 |2017-12-19 18:45:28 +0000
Remove unnecessary calls to 'setSourceTransformer(text -> text)'

SVN r56307 |2018-02-02 19:57:24 +0000
SVN r57023 |2018-03-16 21:23:15 +0000
SVN r58166 |2018-05-13 21:43:41 +0000
SVN r58189 |2018-05-14 20:32:31 +0000
SVN r58244 |2018-05-17 14:49:09 +0000
SVN r59267 |2018-07-17 18:16:50 +0000
…licking project menu expand link)

SVN r60690 |2018-10-17 17:40:40 +0000
  -- Update for November 2018
  -- Now scanning .tf and .tfvars files (Terraform)
  -- Deliberately leaving out SNPRC module (moving to Git very soon)

SVN r61088 |2018-11-13 00:57:49 +0000
  -- Update for November 2018
  -- Now scanning .tf and .tfvars files (Terraform)
  -- Deliberately leaving out SNPRC module (moving to Git very soon)
SVN r61403 |2018-12-11 19:04:37 +0000
SVN r61675 |2019-01-04 23:45:39 +0000
SVN r61964 |2019-01-22 20:01:31 +0000
…is present before trying to click it.

SVN r62140 |2019-01-30 15:06:23 +0000
SVN r62515 |2019-02-18 17:41:40 +0000
SVN r62619 |2019-02-21 22:58:45 +0000
…f you only care about the content of the alert message and not about format.

SVN r62627 |2019-02-22 15:11:54 +0000
…re put in the Study Specimens sample set.

SVN r62819 |2019-03-05 22:12:27 +0000
SVN r63550 |2019-05-02 22:32:50 +0000
SVN r63739 |2019-05-17 17:11:12 +0000
Will allow us to run against CAS-only servers in the future
Currently requires password authentication to be enabled on the server

SVN r63743 |2019-05-17 18:27:46 +0000
- use raw string in labkey:radio currentValue so Objects.equals in RadioTag.isChecked will return true
- add expected error message to test

fix SampleSetTest
- expected audit log message has changed
fix AliquotTest
- use raw string in labkey:radio currentValue so Objects.equals in RadioTag.isChecked will return true
- add expected error message to test

fix SampleSetTest
- expected audit log message has changed
labkey-tchad and others added 22 commits June 16, 2026 09:57
 Conflicts:
	api/src/org/labkey/api/mcp/McpService.java
	experiment/src/org/labkey/experiment/ExperimentModule.java
	specimen/src/org/labkey/specimen/actions/SpecimenController.java
Original PR: LabKey/platform#7749

#### Rationale
We can improve our parameter validation

#### Changes
- New test coverage
- Assorted scoping checks
 Conflicts:
	issues/src/org/labkey/issue/IssuesController.java
 Conflicts:
	announcements/src/org/labkey/announcements/AnnouncementsController.java
	announcements/src/org/labkey/announcements/ToursController.java
	announcements/src/org/labkey/announcements/announcementThread.jsp
	announcements/src/org/labkey/announcements/model/AnnouncementManager.java
	api/src/org/labkey/api/data/TableViewForm.java
	api/src/org/labkey/api/exp/api/ExperimentService.java
	api/src/org/labkey/api/util/XmlBeansUtil.java
	assay/api-src/org/labkey/api/assay/nab/view/MultiGraphAction.java
	core/src/org/labkey/core/CoreModule.java
	list/src/org/labkey/list/controllers/ListController.java
	list/src/org/labkey/list/model/ListAuditProvider.java
	study/src/org/labkey/study/StudyModule.java
	study/src/org/labkey/study/controllers/DatasetController.java
	study/src/org/labkey/study/model/ParticipantGroupManager.java
	studydesign/src/org/labkey/studydesign/StudyDesignModule.java
 Conflicts:
	src/org/labkey/test/tests/AttachmentFieldTest.java
	src/org/labkey/test/tests/nab/NabAssayTest.java
 Conflicts:
	announcements/src/org/labkey/announcements/AnnouncementsController.java
	api/src/org/labkey/api/data/TableViewForm.java
	api/src/org/labkey/api/security/permissions/AbstractContainerScopingTest.java
	assay/src/org/labkey/assay/AssayController.java
	core/src/org/labkey/core/CoreController.java
	core/src/org/labkey/core/admin/AdminController.java
	mothership/src/org/labkey/mothership/MothershipController.java
	pipeline/src/org/labkey/pipeline/api/PipelineStatusManager.java
	query/src/org/labkey/query/QueryModule.java
	study/src/org/labkey/study/model/ParticipantGroupManager.java
	studydesign/src/org/labkey/studydesign/StudyDesignController.java
	studydesign/src/org/labkey/studydesign/StudyDesignModule.java
	studydesign/src/org/labkey/studydesign/model/TreatmentManager.java
 Conflicts:
	api/src/org/labkey/api/data/TableViewForm.java
	api/src/org/labkey/api/webdav/FileSystemResource.java
	specimen/src/org/labkey/specimen/actions/SpecimenController.java
 Conflicts:
	assay/src/org/labkey/assay/actions/DeleteAction.java
	core/src/org/labkey/core/CoreController.java
	issues/src/org/labkey/issue/IssuesController.java
Original PR: LabKey/platform#7888

## Rationale
- Clean up some warnings and unused methods in `JspBase`
- Migrate uses of Commons Collections `Bag` to `MultiSet`. MultiSet is
the replacement for Bag that's fully compatible with the Collection
contract.

Note: Originally this was meant to update our CSPs to use report-to
exclusively (LabKey/internal-issues#900), but
we'll revisit that after confirming support for this directive on
TeamCity.
Original PR: LabKey/platform#7889

## Rationale
Move a few classes from study into specimen.

Also, on the study summary page, stop displaying a "Manage Study" link
to Specimen Coordinators when requests are disabled. This avoids leading
them to a Manage Study page that's completely blank.

#### Tasks
- [x] Dev
- [x] Claude code review
- [x] Code review
- [x] Manual testing - automated testing should be sufficient
- [x] TeamCity review and merge
Original PR: LabKey/platform#7969

## Rationale
We no longer support SQLServer as a primary DB

## Changes
- Remove schema upgrade scripts
- Remove SQLServer conditional code
- Remove `SupportedDatabases` in `module.properties`
- Remove uses of `PostgresOnlyTest`
Original PR: LabKey/platform#8073

## Rationale
Push containers into `ExperimentService` retrieval methods for
performance and reliability.
LabKey/kanban#1969
@labkey-tchad
labkey-tchad merged commit 8983de7 into develop Sep 29, 2026
5 of 6 checks passed
@labkey-tchad
labkey-tchad deleted the fb_specimenTestCleanup branch September 29, 2026 17:28
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