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Add DomainUtil.getNamesAndLabels utility method for use in reserving variants of column names #930

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Merged
labkey-susanh merged 3 commits into from
Sep 23, 2025
Merged

Add DomainUtil.getNamesAndLabels utility method for use in reserving variants of column names #930

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2e853dd
More consistency in reserving names and labels of fields
labkey-susanh Sep 18, 2025
de0fd83
Merge remote-tracking branch 'origin/develop' into fb_reservedFields
labkey-susanh Sep 22, 2025
520a7f2
Reduce number of sets we are constructing
labkey-susanh Sep 22, 2025
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3 changes: 2 additions & 1 deletion elispotassay/src/org/labkey/elispot/query/ElispotAntigenDomainKind.java
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Expand Up @@ -15,6 +15,7 @@
*/
package org.labkey.elispot.query;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.assay.AssayDomainKind;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.JdbcType;
Expand Down Expand Up @@ -87,7 +88,7 @@ public String getStorageSchemaName()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
return getAssayReservedPropertyNames();
}
Expand Down
42 changes: 22 additions & 20 deletions luminex/src/org/labkey/luminex/LuminexAnalyteDomainKind.java
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Expand Up @@ -15,10 +15,14 @@
*/
package org.labkey.luminex;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.assay.AssayDomainKind;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainUtil;
import org.labkey.api.security.User;

import java.util.List;
import java.util.Set;

/**
Expand All @@ -27,6 +31,22 @@
*/
public class LuminexAnalyteDomainKind extends AssayDomainKind
{
private static final Set<String> RESERVED_NAMES;
static {
RESERVED_NAMES = DomainUtil.getNamesAndLabels(
List.of("Name",
"FitProb",
"RegressionType",
"ResVar",
"StdCurve",
"MinStandardRecovery",
"MaxStandardRecovery",
LuminexDataHandler.POSITIVITY_THRESHOLD_COLUMN_NAME,
LuminexDataHandler.NEGATIVE_BEAD_COLUMN_NAME
)
);
RESERVED_NAMES.addAll(getAssayReservedPropertyNames());
}
public LuminexAnalyteDomainKind()
{
super(LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Expand All @@ -39,27 +59,9 @@ public String getKindName()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
Set<String> result = getAssayReservedPropertyNames();
result.add("Name");
result.add("FitProb");
result.add("Fit Prob");
result.add("RegressionType");
result.add("Regression Type");
result.add("ResVar");
result.add("Res Var");
result.add("StdCurve");
result.add("Std Curve");
result.add("MinStandardRecovery");
result.add("Min Standard Recovery");
result.add("MaxStandardRecovery");
result.add("Max Standard Recovery");
result.add(LuminexDataHandler.POSITIVITY_THRESHOLD_COLUMN_NAME);
result.add(LuminexDataHandler.POSITIVITY_THRESHOLD_DISPLAY_NAME);
result.add(LuminexDataHandler.NEGATIVE_BEAD_COLUMN_NAME);
result.add(LuminexDataHandler.NEGATIVE_BEAD_DISPLAY_NAME);
return result;
return RESERVED_NAMES;
}

@Override
Expand Down
36 changes: 22 additions & 14 deletions luminex/src/org/labkey/luminex/LuminexDataDomainKind.java
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Expand Up @@ -15,12 +15,16 @@
*/
package org.labkey.luminex;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.assay.AssayDomainKind;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainUtil;
import org.labkey.api.security.User;
import org.labkey.luminex.query.LuminexDataTable;
import org.labkey.luminex.query.LuminexProtocolSchema;

import java.util.HashSet;
import java.util.Map;
import java.util.Set;

Expand All @@ -30,6 +34,22 @@
*/
public class LuminexDataDomainKind extends AssayDomainKind
{
public static final Set<String> RESERVED_NAMES;

static {
// Standard reserved names
Set<String> names = new HashSet<>(getAssayReservedPropertyNames());
// All from the basic Luminex data table
names.addAll(LuminexProtocolSchema.getTableInfoDataRow().getColumnNameSet());
// Also reserve the aliased names of the columns
for (Map.Entry<String,String> entry : LuminexDataTable.REMAPPED_SCHEMA_COLUMNS.entrySet())
{
names.add(entry.getKey());
names.add(entry.getValue());
}

RESERVED_NAMES = DomainUtil.getNamesAndLabels(names);
}
public LuminexDataDomainKind()
{
super(LuminexAssayProvider.ASSAY_DOMAIN_CUSTOM_DATA);
Expand All @@ -42,20 +62,8 @@ public String getKindName()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
// Standard reserved names
Set<String> result = getAssayReservedPropertyNames();

// All from the basic Luminex data table
result.addAll(LuminexProtocolSchema.getTableInfoDataRow().getColumnNameSet());

// Also reserve the aliased names of the columns
for (Map.Entry<String,String> entry : LuminexDataTable.REMAPPED_SCHEMA_COLUMNS.entrySet())
{
result.add(entry.getKey());
result.add(entry.getValue());
}
return result;
return RESERVED_NAMES;
}
}
16 changes: 9 additions & 7 deletions nab/src/org/labkey/nab/query/NabVirusDomainKind.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,24 +15,29 @@
*/
package org.labkey.nab.query;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.assay.AssayDomainKind;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.JdbcType;
import org.labkey.api.data.PropertyStorageSpec;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainUtil;
import org.labkey.api.security.User;
import org.labkey.nab.NabAssayProvider;
import org.labkey.nab.NabManager;

import java.util.Collections;
import java.util.LinkedHashSet;
import java.util.Set;
import java.util.stream.Collectors;

public class NabVirusDomainKind extends AssayDomainKind
{
public static final String VIRUS_LSID_COLUMN_NAME = "virusLsid";
public static final String DATLSID_COLUMN_NAME = "dataLsid";
private static final Set<PropertyStorageSpec> _baseFields;
private static final Set<String> RESERVED_PROPERTY_NAMES;

static
{
Expand All @@ -42,6 +47,8 @@ public class NabVirusDomainKind extends AssayDomainKind
baseFields.add(new PropertyStorageSpec(DATLSID_COLUMN_NAME, JdbcType.VARCHAR));

_baseFields = Collections.unmodifiableSet(baseFields);
RESERVED_PROPERTY_NAMES = DomainUtil.getNamesAndLabels(_baseFields.stream().map(PropertyStorageSpec::getName).collect(Collectors.toSet()));
RESERVED_PROPERTY_NAMES.addAll(getAssayReservedPropertyNames());
}

public NabVirusDomainKind()
Expand Down Expand Up @@ -74,13 +81,8 @@ public String getStorageSchemaName()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
Set<String> names = getAssayReservedPropertyNames();

for (PropertyStorageSpec spec : getBaseProperties(domain))
names.add(spec.getName());

return names;
return RESERVED_PROPERTY_NAMES;
}
}