Skip to content

GitHub Issue 1117: sample type and dataclass foreign keys #7804

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
XingY merged 8 commits into from
Jul 3, 2026
Merged

GitHub Issue 1117: sample type and dataclass foreign keys #7804

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
df1c733
GitHub Issue 1117: sample type and dataclass foreign keys
XingY Jul 1, 2026
238671b
CC code review
XingY Jul 1, 2026
b3587cd
Revert "CC code review"
XingY Jul 1, 2026
87320c9
Scope changes to samples and dataclass
XingY Jul 1, 2026
4dd4963
Make change generic, remove unused assay FK
XingY Jul 2, 2026
01fce09
clean
XingY Jul 2, 2026
bbcfbab
scale back change scope
XingY Jul 2, 2026
b175f96
spell
XingY Jul 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 0 additions & 9 deletions assay/api-src/org/labkey/api/assay/AssayResultDomainKind.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,15 +100,6 @@ public Set<PropertyStorageSpec.Index> getPropertyIndices(Domain domain)
return PageFlowUtil.set(new PropertyStorageSpec.Index(false, AbstractTsvAssayProvider.DATA_ID_COLUMN_NAME));
}

@Override
public Set<PropertyStorageSpec.ForeignKey> getPropertyForeignKeys(Container container)
{
return new HashSet<>(Arrays.asList(
new PropertyStorageSpec.ForeignKey(SpecialColumn.CreatedBy.name(), "core", "users", "userid", null, false),
new PropertyStorageSpec.ForeignKey(SpecialColumn.ModifiedBy.name(), "core", "users", "userid", null, false)
));
}

@Override
public DbScope getScope()
{
Expand Down
5 changes: 5 additions & 0 deletions experiment/src/org/labkey/experiment/XarReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,7 @@
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.api.SampleTypeService;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainKind;
import org.labkey.api.exp.property.DomainProperty;
import org.labkey.api.exp.property.PropertyService;
import org.labkey.api.exp.query.ExpMaterialTable;
Expand Down Expand Up @@ -893,6 +894,10 @@ private Domain loadDomain(DomainDescriptorType xDomain) throws ExperimentExcepti

try
{
DomainKind<?> kind = domain.getDomainKind();
if (kind != null)
domain.setPropertyForeignKeys(kind.getPropertyForeignKeys(getContainer())); // GitHub Issue 1117

domain.save(getUser());
DefaultValueService.get().setDefaultValues(domain.getContainer(), newDefaultValues);
}
Expand Down
4 changes: 4 additions & 0 deletions experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -835,7 +835,11 @@ public ExpSampleTypeImpl createSampleType(Container c, User u, String name, Stri
Domain domain = PropertyService.get().createDomain(c, lsid, name, templateInfo);
DomainKind<?> kind = domain.getDomainKind();
if (kind != null)
{
domain.setDisabledSystemFields(kind.getDisabledSystemFields(disabledSystemField));
domain.setPropertyForeignKeys(kind.getPropertyForeignKeys(c)); // GitHub Issue 1117
}

Set<String> reservedNames = kind.getReservedPropertyNames(domain, u);
Set<String> reservedPrefixes = kind.getReservedPropertyNamePrefixes();
Set<String> lowerReservedNames = reservedNames.stream().map(String::toLowerCase).collect(Collectors.toSet());
Expand Down
9 changes: 9 additions & 0 deletions experiment/src/org/labkey/experiment/api/property/StorageProvisionerImpl.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -213,6 +213,15 @@ private String _create(DbScope scope, DomainKind<?> kind, Domain domain, boolean
indices.addAll(domain.getPropertyIndices());
change.setIndexedColumns(domain, indices);

/*
* TODO:
* GitHub Issue 1117: Consider the generic fix below for develop. See https://github.com/LabKey/platform/pull/7804
* Tests may need updates and domains FKs (for example, issues) maybe need to adjusted.
*
* Set<PropertyStorageSpec.ForeignKey> foreignKeys = new LinkedHashSet<>(kind.getPropertyForeignKeys(domain.getContainer()));
* foreignKeys.addAll(domain.getPropertyForeignKeys());
* change.setForeignKeys(foreignKeys);
*/
change.setForeignKeys(domain.getPropertyForeignKeys());

try
Expand Down