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labkey-adam wants to merge 4 commits into from
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Long identifier truncation improvements #876

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763d9ae
Long identifier truncation improvements
labkey-adam Apr 15, 2025
8416364
Move all key AliasManager methods to SqlDialect
labkey-adam Apr 16, 2025
6072efd
StorageNameGenerator
labkey-adam Apr 20, 2025
785c4db
Merge remote-tracking branch 'origin/develop' into fb_long_identifiers
labkey-adam Apr 29, 2025
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3 changes: 2 additions & 1 deletion flow/src/org/labkey/flow/reports/FilterFlowReport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
import org.labkey.flow.controllers.well.WellController;
import org.labkey.flow.data.FlowProtocol;
import org.labkey.flow.data.ICSMetadata;
import org.labkey.flow.persist.FlowManager;
import org.labkey.flow.query.FlowSchema;
import org.labkey.flow.query.FlowTableType;
import org.springframework.beans.PropertyValue;
Expand Down Expand Up @@ -195,7 +196,7 @@ void addScriptProlog(ViewContext context, StringBuffer sb)
// Copied from ScriptEngineReport.
private String oldLegalName(FieldKey fkey)
{
String r = AliasManager.makeLegalName(StringUtils.join(fkey.getParts(), "_"), null, false, false);
String r = AliasManager.makeLegalName(StringUtils.join(fkey.getParts(), "_"), FlowManager.get().getSchema().getSqlDialect(), false);
return ColumnInfo.propNameFromName(r).toLowerCase();
}

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11 changes: 3 additions & 8 deletions flow/src/org/labkey/flow/reports/PositivityFlowReport.java
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Expand Up @@ -23,11 +23,9 @@
import org.labkey.api.data.ContainerManager;
import org.labkey.api.exp.PropertyDescriptor;
import org.labkey.api.exp.PropertyType;
import org.labkey.api.query.AliasManager;
import org.labkey.api.query.FieldKey;
import org.labkey.api.reports.report.ReportDescriptor;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Tuple3;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
Expand All @@ -41,6 +39,7 @@
import org.labkey.flow.controllers.protocol.ProtocolController;
import org.labkey.flow.data.FlowProtocol;
import org.labkey.flow.data.ICSMetadata;
import org.labkey.flow.persist.FlowManager;
import org.springframework.beans.PropertyValues;
import org.springframework.validation.BindException;

Expand All @@ -50,10 +49,6 @@
import java.util.Collections;
import java.util.List;

/**
* User: kevink
* Date: 5/26/11
*/
public class PositivityFlowReport extends FilterFlowReport
{
public static final String TYPE = "Flow.PositivityReport";
Expand Down Expand Up @@ -137,15 +132,15 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde

for (FieldKey fieldKey : getMetadataColumns(metadata))
{
String alias = AliasManager.makeLegalName(fieldKey, null, false);
String alias = FlowManager.get().getSchema().getSqlDialect().makeLegalName(fieldKey, 0);
query.append(" ").append(tableName).append(".").append(toSQL(fieldKey)).append(" AS ").append(alias).append(",\n");
}

SubsetSpec subset = getSubset();
SubsetSpec subsetParent = getSubsetParent();

String stat = subset + ":Count";
String parentStat = subsetParent == null ? "Count" : subsetParent.toString() + ":Count";
String parentStat = subsetParent == null ? "Count" : subsetParent + ":Count";

query.append(" ").append(tableName).append(".Statistic(").append(toSQL(stat)).append(") AS stat,\n");
query.append(" ").append(tableName).append(".Background(").append(toSQL(stat)).append(") AS stat_bg,\n");
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6 changes: 3 additions & 3 deletions ms2/src/org/labkey/ms2/ProteinProphetImporter.java
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Expand Up @@ -210,7 +210,7 @@ public MS2Run importFile(ViewBackgroundInfo info, Logger log) throws SQLExceptio
long insertStartTime = System.currentTimeMillis();
log.info("Starting to move data into ms2.PeptidesMemberships");

peptideIndexStmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(peptidesTempTableName,null) + " ON " + peptidesTempTableName + "(TrimmedPeptide, Charge)");
peptideIndexStmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(peptidesTempTableName, _dialect) + " ON " + peptidesTempTableName + "(TrimmedPeptide, Charge)");
peptideIndexStmt.execute();

// Move the peptide information of the temp table into the real table
Expand All @@ -231,11 +231,11 @@ public MS2Run importFile(ViewBackgroundInfo info, Logger log) throws SQLExceptio
log.info("Starting to move data into ms2.ProteinGroupMemberships");

// Create an index to use for the join with prot.fastasequences
proteinIndexStmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(proteinsTempTableName,null) + " ON " + proteinsTempTableName + "(LookupString)");
proteinIndexStmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(proteinsTempTableName, _dialect) + " ON " + proteinsTempTableName + "(LookupString)");
proteinIndexStmt.execute();

// Create an index to use for the GROUP BY
proteinIndex2Stmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(proteinsTempTableName,null) + "2 ON " + proteinsTempTableName + "(ProteinGroupId, Probability)");
proteinIndex2Stmt = connection.prepareStatement("CREATE INDEX idx_" + AliasManager.makeLegalName(proteinsTempTableName, _dialect) + "2 ON " + proteinsTempTableName + "(ProteinGroupId, Probability)");
proteinIndex2Stmt.execute();

int[] fastaIds = run.getFastaIds();
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2 changes: 1 addition & 1 deletion ms2/src/org/labkey/ms2/compare/CompareQuery.java
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Expand Up @@ -496,7 +496,7 @@ public CompareDataRegion getCompareGrid(boolean export)
protected DisplayColumn createColumn(ActionURL linkURL, RunColumn column, String columnName, TableInfo ti, ResultSetMetaData md, CompareDataRegion rgn)
throws SQLException
{
var ci = new BaseColumnInfo(columnName);
var ci = new BaseColumnInfo(columnName, ti, null);
ci.setParentTable(ti);
ci.setSqlTypeName(md.getColumnTypeName(rgn.getResultSet().findColumn(columnName)));
ci.setLabel(column.getLabel());
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6 changes: 3 additions & 3 deletions protein/api-src/org/labkey/api/protein/fasta/FastaDbHelper.java
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Expand Up @@ -119,8 +119,8 @@ public FastaDbHelper(Connection c) throws SQLException
"entry_date " + _dialect.getDefaultDateTimeDataType() + " NULL" +
")");

c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_seqTableName,null) + "_HASH_ORGID_SROWID ON " + _seqTableName + "(hash, orgId, srowid)");
c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_seqTableName,null) + "_ORGID ON " + _seqTableName + "(orgId)");
c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_seqTableName, _dialect) + "_HASH_ORGID_SROWID ON " + _seqTableName + "(hash, orgId, srowid)");
c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_seqTableName, _dialect) + "_ORGID ON " + _seqTableName + "(orgId)");

c.createStatement().execute("CREATE " + _dialect.getTempTableKeyword() + " TABLE " + _identTableName + " ( " +
"Identifier varchar(50) NOT NULL, " +
Expand All @@ -130,7 +130,7 @@ public FastaDbHelper(Connection c) throws SQLException
"entry_date " + _dialect.getDefaultDateTimeDataType() + " NULL" +
")");

c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_identTableName,null) + " ON " + _identTableName + "(Identifier,IdentTypeId,SeqId)");
c.createStatement().execute("CREATE INDEX IX_" + AliasManager.makeLegalName(_identTableName, _dialect) + " ON " + _identTableName + "(Identifier,IdentTypeId,SeqId)");

_addSeqStmt = c.prepareStatement("INSERT INTO " + _seqTableName +
" (ProtSequence,hash,description,mass,length,best_name,fname,lookup,genus,species,fullOrg,entry_date) " +
Expand Down