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Merged
cnathe merged 4 commits into from
Jun 17, 2025
Merged

Misc assay issues fixes for 25.7 #6760

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90efe28
GH Issue #755: Field type conversion from Boolean to String fails if …
cnathe Jun 16, 2025
6d45412
GH Issue 778: exp.materialInput error inserting row with Role > 50 ch…
cnathe Jun 16, 2025
b884d41
Merge branch 'develop' into fb_cory257fixes
cnathe Jun 17, 2025
1e5e969
add GH Issue number
cnathe Jun 17, 2025
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2 changes: 2 additions & 0 deletions experiment/resources/schemas/dbscripts/postgresql/exp-25.002-25.003.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
--GH Issue 778: materialinput Role can be a field name, which has a max length of 200 characters
ALTER TABLE exp.MaterialInput ALTER COLUMN Role TYPE VARCHAR(200);
4 changes: 4 additions & 0 deletions experiment/resources/schemas/dbscripts/sqlserver/exp-25.002-25.003.sql
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@@ -0,0 +1,4 @@
--GH Issue 778: materialinput Role can be a field name, which has a max length of 200 characters
EXECUTE core.fn_dropifexists 'MaterialInput', 'exp', 'INDEX', 'IDX_MaterialInput_Role';
ALTER TABLE exp.MaterialInput ALTER COLUMN Role NVARCHAR(200) NOT NULL;
CREATE INDEX IDX_MaterialInput_Role ON exp.MaterialInput(Role);
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/ExperimentModule.java
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Expand Up @@ -183,7 +183,7 @@ public String getName()
@Override
public Double getSchemaVersion()
{
return 25.002;
return 25.003;
}

@Nullable
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16 changes: 8 additions & 8 deletions experiment/src/org/labkey/experiment/api/property/DomainPropertyImpl.java
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Expand Up @@ -26,6 +26,7 @@
import org.labkey.api.data.ConditionalFormat;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.DatabaseIdentifier;
import org.labkey.api.data.JdbcType;
import org.labkey.api.data.PHI;
import org.labkey.api.data.SQLFragment;
Expand Down Expand Up @@ -839,6 +840,7 @@ else if (newType.getJdbcType().isDateOrTime() && oldType.getJdbcType().isDateOrT
OntologyManager.ensurePropertyDomain(_pd, dd, sortOrder);

boolean hasProvisioner = null != getDomain().getDomainKind() && null != getDomain().getDomainKind().getStorageSchemaName() && dd.getStorageTableName() != null;
SqlDialect dialect = OntologyManager.getExpSchema().getSqlDialect();

if (hasProvisioner)
{
Expand All @@ -860,7 +862,7 @@ else if (newType.getJdbcType().isDateOrTime() && oldType.getJdbcType().isDateOrT
if (_pdOld.getJdbcType() == JdbcType.BOOLEAN && _pd.getJdbcType().isText())
{
updateBooleanValue(_domain.getDomainKind().getStorageSchemaName() + "." + _domain.getStorageTableName(),
_pd.getStorageColumnName(), _pdOld.getFormat(), null);
_pd.getLegalSelectName(dialect), _pdOld.getFormat(), null); // GH Issue 755
}
}
else if (propResized)
Expand Down Expand Up @@ -889,7 +891,6 @@ else if (!oldType.getJdbcType().isText() && newType.getJdbcType().isText())
}
else if (oldType.getJdbcType().isDateOrTime() && newType.getJdbcType().isDateOrTime())
{
SqlDialect dialect = OntologyManager.getExpSchema().getSqlDialect();
String sqlTypeName = dialect.getSqlTypeName(newType.getJdbcType());
String update = String.format("CAST(DateTimeValue AS %s)", sqlTypeName);
if (newType.getJdbcType() == JdbcType.TIME)
Expand All @@ -915,7 +916,7 @@ else if (oldType.getJdbcType().isDateOrTime() && newType.getJdbcType().isDateOrT

if (changedType && _pdOld.getJdbcType() == JdbcType.BOOLEAN && _pd.getJdbcType().isText())
{
updateBooleanValue(OntologyManager.getTinfoObjectProperty().getSelectName(), "StringValue", _pdOld.getFormat(), new SQLFragment("PropertyId = ?", _pdOld.getPropertyId()));
updateBooleanValue(OntologyManager.getTinfoObjectProperty().getSelectName(), dialect.makeDatabaseIdentifier("StringValue"), _pdOld.getFormat(), new SQLFragment("PropertyId = ?", _pdOld.getPropertyId()));
}
}
else
Expand Down Expand Up @@ -943,17 +944,16 @@ else if (oldType.getJdbcType().isDateOrTime() && newType.getJdbcType().isDateOrT
* Postgres will now have 'true' and 'false', and SQLServer will have '0' and '1'. Use the format string to use the
* preferred format, and standardize on 'true' and 'false' in the absence of an explicitly configured format.
*/
private void updateBooleanValue(String schemaTable, String column, String formatString, @Nullable SQLFragment whereClause)
private void updateBooleanValue(String schemaTable, DatabaseIdentifier column, String formatString, @Nullable SQLFragment whereClause)
{
column = OntologyManager.getExpSchema().getSqlDialect().makeLegalIdentifier(column);
BooleanFormat f = BooleanFormat.getInstance(formatString);
String trueValue = StringUtils.trimToNull(f.format(true));
String falseValue = StringUtils.trimToNull(f.format(false));
String nullValue = StringUtils.trimToNull(f.format(null));
SQLFragment sql = new SQLFragment("UPDATE ").append(schemaTable).append(" SET ").
append(column).append(" = CASE WHEN ").
append(column).append(" IN ('1', 'true') THEN ? WHEN ").
append(column).append(" IN ('0', 'false') THEN ? ELSE ? END");
appendIdentifier(column).append(" = CASE WHEN ").
appendIdentifier(column).append(" IN ('1', 'true') THEN ? WHEN ").
appendIdentifier(column).append(" IN ('0', 'false') THEN ? ELSE ? END");
sql.add(trueValue);
sql.add(falseValue);
sql.add(nullValue);
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