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Merged
bbimber merged 7 commits into from
Mar 15, 2025
Merged

Improve handling of generated queries when dealing with a container-scoped list #41

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4135db4
Improve handling of generated queries when dealing with a container-s…
bbimber Mar 14, 2025
6646ed0
Explicitly set keyField to false
bbimber Mar 15, 2025
745b925
Set col name
bbimber Mar 15, 2025
69d734b
Set calculated=true
bbimber Mar 15, 2025
fa845fa
Set setShownInInsertView/setShownInUpdateView
bbimber Mar 15, 2025
37b3a15
Update URL
bbimber Mar 15, 2025
5cdcedc
Code cleanup
bbimber Mar 15, 2025
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2 changes: 1 addition & 1 deletion LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ public DataIteratorBuilder persistRows(DataIteratorBuilder data, DataIteratorCon

protected class UpdateService extends SimpleQueryUpdateService
{
private KeyManager _keyManager = new KeyManager();
private final KeyManager _keyManager = new KeyManager();

public UpdateService(SimpleUserSchema.SimpleTable<?> ti)
{
Expand Down
8 changes: 2 additions & 6 deletions LDK/src/org/labkey/ldk/LDKController.java
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Expand Up @@ -847,14 +847,10 @@ public ModelAndView getView(QueryForm form, BindException errors) throws Excepti

if (keyField != null)
{
// Note: the ContainerContext will need to be set within QueryView
DetailsURL importUrl = DetailsURL.fromString("/query/importData.view?schemaName=" + schemaName + "&query.queryName=" + queryName + "&keyField=" + keyField);
importUrl.setContainerContext(getContainer());

DetailsURL updateUrl = DetailsURL.fromString("/ldk/manageRecord.view?schemaName=" + schemaName + "&query.queryName=" + queryName + "&keyField=" + keyField + "&key=${" + keyField + "}");
updateUrl.setContainerContext(getContainer());

DetailsURL deleteUrl = DetailsURL.fromString("/query/deleteQueryRows.view?schemaName=" + schemaName + "&query.queryName=" + queryName);
deleteUrl.setContainerContext(getContainer());

url.addParameter("importURL", importUrl.toString());
url.addParameter("updateURL", updateUrl.toString());
Expand All @@ -866,7 +862,7 @@ public ModelAndView getView(QueryForm form, BindException errors) throws Excepti
url.addParameter("queryName", queryName);
url.addParameter("allowChooseQuery", false);

WebPartFactory factory = Portal.getPortalPartCaseInsensitive("Query");
WebPartFactory factory = Portal.getPortalPart("Query");
Portal.WebPart part = factory.createWebPart();
part.setProperties(url.getQueryString());

Expand Down
2 changes: 1 addition & 1 deletion laboratory/api-src/org/labkey/api/laboratory/query/ContainerIncrementingTable.java
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Expand Up @@ -59,7 +59,7 @@ public ContainerIncrementingTable(UserSchema us, TableInfo st, ContainerFilter c
}

@Override
public SimpleUserSchema.SimpleTable init()
public SimpleUserSchema.SimpleTable<?> init()
{
super.init();

Expand Down
123 changes: 86 additions & 37 deletions laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.BaseColumnInfo;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
Expand All @@ -18,7 +19,7 @@
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.TableCustomizer;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.WrappedColumn;
import org.labkey.api.data.WrappedColumnInfo;
import org.labkey.api.gwt.client.FacetingBehaviorType;
import org.labkey.api.laboratory.LaboratoryService;
import org.labkey.api.ldk.LDKService;
Expand Down Expand Up @@ -183,13 +184,16 @@ public void customizeColumns(AbstractTableInfo ti)
{
container.setHidden(true);

WrappedColumn wrappedContainer = new WrappedColumn(container, "workbook");
wrappedContainer.setLabel("Workbook");
BaseColumnInfo wrappedContainer = WrappedColumnInfo.wrapAsCopy(ti, FieldKey.fromString("workbook"), container, "Workbook", null);
wrappedContainer.setName("workbook");
wrappedContainer.setCalculated(true);
wrappedContainer.setShownInInsertView(false);
wrappedContainer.setShownInUpdateView(false);
wrappedContainer.setFk(QueryForeignKey
.from(ti.getUserSchema(), ti.getContainerFilter())
.schema(us)
.to("workbooks", LaboratoryWorkbooksTable.WORKBOOK_COL, "workbookId"));
wrappedContainer.setURL(DetailsURL.fromString("/project/start.view"));
wrappedContainer.setURL(DetailsURL.fromString("/project/begin.view"));
wrappedContainer.setShownInDetailsView(true);
wrappedContainer.setFacetingBehaviorType(FacetingBehaviorType.ALWAYS_OFF);
wrappedContainer.setDisplayColumnFactory(new DisplayColumnFactory()
Expand Down Expand Up @@ -290,11 +294,15 @@ private void appendDemographicsCols(final UserSchema us, AbstractTableInfo ti, C
if (ti.getColumn(name) != null)
continue;

WrappedColumn col = new WrappedColumn(subjectCol, name);
col.setLabel(qd.getLabel());
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ti, FieldKey.fromString(name), subjectCol, qd.getLabel(), null);
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
col.setShownInUpdateView(false);
col.setReadOnly(true);
col.setIsUnselectable(true);
col.setUserEditable(false);
col.setKeyField(false);

UserSchema targetSchema = qd.getTableInfo(targetContainer, us.getUser()).getUserSchema();
col.setFk(new QueryForeignKey(us, ti.getContainerFilter(), targetSchema, null, qd.getQueryName(), qd.getTargetColumn(), qd.getTargetColumn())
Expand Down Expand Up @@ -366,12 +374,16 @@ private void appendMajorEventsCol(final UserSchema us, AbstractTableInfo ds, fin
final String pkColSelectName = pk.getFieldKey().toSQLString();
final String pkColRawName = pk.getName();

MutableColumnInfo col = new WrappedColumn(pk, name);
col.setLabel("Major Events");
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Major Events", null);
col.setDescription("This column shows all major events recorded in this subject's history and will calculate the time elapsed between the current sample and these dates.");
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
col.setShownInUpdateView(false);
col.setReadOnly(true);
col.setIsUnselectable(true);
col.setUserEditable(false);
col.setKeyField(false);

final String schemaName = ds.getUserSchema().getSchemaPath().toSQLString();
final String subjectSelectName = ds.getSqlDialect().makeLegalIdentifier(subjectColName);
Expand All @@ -384,11 +396,10 @@ private void appendMajorEventsCol(final UserSchema us, AbstractTableInfo ds, fin
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
UserSchema effectiveUs = us.getContainer().isWorkbookOrTab() ? QueryService.get().getUserSchema(us.getUser(), target, us.getSchemaPath()) : us;
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, effectiveUs, colName);
Container parentContainer = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
QueryDefinition qd = createQueryDef(us, colName);

qd.setSql(getMajorEventsSql(target, schemaName, querySelectName, pkColSelectName, subjectSelectName, dateSelectName));
qd.setSql(getMajorEventsSql(parentContainer, schemaName, querySelectName, pkColSelectName, subjectSelectName, dateSelectName));
qd.setIsTemporary(true);

List<QueryException> errors = new ArrayList<>();
Expand Down Expand Up @@ -444,21 +455,24 @@ private void appendOverlapingProjectsCol(final UserSchema us, AbstractTableInfo
final String subjectSelectName = ds.getSqlDialect().makeLegalIdentifier(subjectColName);
final String dateSelectName = dateColName == null ? null : ds.getSqlDialect().makeLegalIdentifier(dateColName);

WrappedColumn col = new WrappedColumn(pk, name);
col.setLabel("Overlapping Groups");
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Overlapping Groups", null);
col.setDescription("This column shows all groups to which this subject belonged at the time of this sample.");
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
col.setShownInUpdateView(false);
col.setReadOnly(true);
col.setIsUnselectable(true);
col.setUserEditable(false);
col.setKeyField(false);
col.setFk(new LookupForeignKey(){
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
UserSchema effectiveUs = us.getContainer().isWorkbookOrTab() ? QueryService.get().getUserSchema(us.getUser(), target, us.getSchemaPath()) : us;
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, effectiveUs, colName);
Container parentContainer = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
QueryDefinition qd = createQueryDef(us, colName);

qd.setSql(getOverlapSql(target, schemaName, querySelectName, pkColSelectName, subjectSelectName, dateSelectName));
qd.setSql(getOverlapSql(parentContainer, schemaName, querySelectName, pkColSelectName, subjectSelectName, dateSelectName));
qd.setIsTemporary(true);

List<QueryException> errors = new ArrayList<>();
Expand Down Expand Up @@ -490,20 +504,24 @@ public TableInfo getLookupTableInfo()

//add pivot column
String pivotColName = "overlappingProjectsPivot";
WrappedColumn col2 = new WrappedColumn(pk, pivotColName);
col2.setLabel("Overlapping Group List");
BaseColumnInfo col2 = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(pivotColName), pk, "Overlapping Group List", null);
col2.setName(pivotColName);
col2.setCalculated(true);
col2.setShownInInsertView(false);
col2.setShownInUpdateView(false);
col2.setDescription("Shows groups to which this subject belonged at the time of this sample.");
col2.setHidden(true);
col2.setReadOnly(true);
col2.setIsUnselectable(true);
col2.setUserEditable(false);
col2.setKeyField(false);
final String lookupColName = ds.getName() + "_overlappingProjectsPivot";
col2.setFk(new LookupForeignKey(){
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, us, lookupColName);
QueryDefinition qd = createQueryDef(us, lookupColName);

qd.setSql(getOverlapPivotSql(target, schemaName, querySelectName, pkColSelectName, subjectColName, dateColName));
qd.setIsTemporary(true);
Expand Down Expand Up @@ -555,21 +573,24 @@ public void appendProjectsCol(final UserSchema us, AbstractTableInfo ds, final S
final String publicTableName = ds.getPublicName();

final String colName = ds.getName() + "_allProjects";
WrappedColumn col = new WrappedColumn(pk, name);
col.setLabel("Groups");
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Groups", null);
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
col.setShownInUpdateView(false);
col.setDescription("This column shows all groups to which this subject has ever been a member, regardless of whether that assignment overlaps with the current data point");
col.setReadOnly(true);
col.setIsUnselectable(true);
col.setUserEditable(false);
col.setKeyField(false);
col.setFk(new LookupForeignKey(){
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
UserSchema effectiveUs = us.getContainer().isWorkbookOrTab() ? QueryService.get().getUserSchema(us.getUser(), target, us.getSchemaPath()) : us;
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, effectiveUs, colName);
Container parentContainer = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
QueryDefinition qd = createQueryDef(us, colName);

qd.setSql(getOverlapSql(target, schemaName, querySelectName, pkColSelectName, subjectSelectName, null));
qd.setSql(getOverlapSql(parentContainer, schemaName, querySelectName, pkColSelectName, subjectSelectName, null));
qd.setIsTemporary(true);

List<QueryException> errors = new ArrayList<>();
Expand Down Expand Up @@ -602,20 +623,23 @@ public TableInfo getLookupTableInfo()
//add pivot column
String pivotColName = "allProjectsPivot";
final String lookupName = ds.getName() + "_allProjectsPivot";
WrappedColumn col2 = new WrappedColumn(pk, pivotColName);
col2.setLabel("Group Summary List");
BaseColumnInfo col2 = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(pivotColName), pk, "Group Summary List", null);
col2.setName(pivotColName);
col2.setCalculated(true);
col2.setShownInInsertView(false);
col2.setShownInUpdateView(false);
col2.setDescription("Shows groups to which this subject belonged at any point in time.");
col2.setHidden(true);
col2.setReadOnly(true);
col2.setIsUnselectable(true);
col2.setUserEditable(false);
col2.setKeyField(false);
col2.setFk(new LookupForeignKey(){
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
UserSchema effectiveUs = us.getContainer().isWorkbookOrTab() ? QueryService.get().getUserSchema(us.getUser(), target, us.getSchemaPath()) : us;
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, effectiveUs, lookupName);
QueryDefinition qd = createQueryDef(us, lookupName);

qd.setSql(getOverlapPivotSql(target, schemaName, querySelectName, pkColSelectName, subjectSelectName, null));
qd.setIsTemporary(true);
Expand Down Expand Up @@ -749,11 +773,15 @@ private void appendRelativeDatesCol(final UserSchema us, AbstractTableInfo ds, f
final String pkColSelectName = pk.getFieldKey().toSQLString();
final String pkColRawName = pk.getName();

WrappedColumn col = new WrappedColumn(pk, name);
col.setLabel("Relative Dates");
BaseColumnInfo col = WrappedColumnInfo.wrapAsCopy(ds, FieldKey.fromString(name), pk, "Relative Dates", null);
col.setName(name);
col.setCalculated(true);
col.setShownInInsertView(false);
col.setShownInUpdateView(false);
col.setReadOnly(true);
col.setIsUnselectable(true);
col.setUserEditable(false);
col.setKeyField(false);

final String colName = ds.getName() + "_relativeDates";
final String schemaName = ds.getUserSchema().getSchemaPath().toSQLString();
Expand All @@ -765,9 +793,8 @@ private void appendRelativeDatesCol(final UserSchema us, AbstractTableInfo ds, f
@Override
public TableInfo getLookupTableInfo()
{
Container target = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
UserSchema effectiveUs = us.getContainer().isWorkbookOrTab() ? QueryService.get().getUserSchema(us.getUser(), target, us.getSchemaPath()) : us;
QueryDefinition qd = QueryService.get().createQueryDef(us.getUser(), target, effectiveUs, colName);
Container parentContainer = us.getContainer().isWorkbookOrTab() ? us.getContainer().getParent() : us.getContainer();
QueryDefinition qd = createQueryDef(us, colName);

qd.setSql("SELECT\n" +
"t." + pkColSelectName + ",\n" +
Expand Down Expand Up @@ -795,7 +822,7 @@ public TableInfo getLookupTableInfo()
"ROUND(CONVERT(age_in_months(p.startdate, s." + dateSelectName + "), DOUBLE) / 12, 1) AS YearsPostStartDecimal,\n" +
"\n" +
"FROM " + schemaName + "." + publicTableName + " s\n" +
"JOIN \"" + target.getPath() + "\".laboratory.project_usage p\n" +
"JOIN \"" + parentContainer.getPath() + "\".laboratory.project_usage p\n" +
"ON (s." + subjectSelectName + " = p.subjectId AND CONVERT(p.startdate, DATE) <= CONVERT(s." + dateSelectName + ", DATE) AND CONVERT(s." + dateSelectName + ", DATE) <= CONVERT(COALESCE(p.enddate, {fn curdate()}), DATE))\n" +
"WHERE s." + dateSelectName + " IS NOT NULL and s." + subjectSelectName + " IS NOT NULL\n" +
"\n" +
Expand Down Expand Up @@ -830,6 +857,28 @@ public TableInfo getLookupTableInfo()
ds.addColumn(col);
}

private QueryDefinition createQueryDef(UserSchema us, String queryName)
{
if (!us.getContainer().isWorkbook())
{
return QueryService.get().createQueryDef(us.getUser(), us.getContainer(), us, queryName);
}

// The rationale is that if we are querying from a workbook, preferentially translate to the parent US
// However, there are situations like workbook-scoped lists, where that query might not exist on the parent
UserSchema parentUserSchema = QueryService.get().getUserSchema(us.getUser(), us.getContainer().getParent(), us.getSchemaPath());
assert parentUserSchema != null;

if (parentUserSchema.getTableNames().contains(queryName))
{
return QueryService.get().createQueryDef(parentUserSchema.getUser(), parentUserSchema.getContainer(), parentUserSchema, queryName);
}
else
{
return QueryService.get().createQueryDef(us.getUser(), us.getContainer(), us, queryName);
}
}

public UserSchema getUserSchema(AbstractTableInfo ds, String name)
{
UserSchema us = ds.getUserSchema();
Expand Down