From 763d9ae546d450518e226b410a67826f7921ac96 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 15 Apr 2025 07:45:01 -0700 Subject: [PATCH 1/3] Long identifier truncation improvements --- flow/src/org/labkey/flow/reports/FilterFlowReport.java | 3 ++- flow/src/org/labkey/flow/reports/PositivityFlowReport.java | 5 +++-- ms2/src/org/labkey/ms2/ProteinProphetImporter.java | 6 +++--- .../api-src/org/labkey/api/protein/fasta/FastaDbHelper.java | 6 +++--- 4 files changed, 11 insertions(+), 9 deletions(-) diff --git a/flow/src/org/labkey/flow/reports/FilterFlowReport.java b/flow/src/org/labkey/flow/reports/FilterFlowReport.java index f710b25766..7c7e6921aa 100644 --- a/flow/src/org/labkey/flow/reports/FilterFlowReport.java +++ b/flow/src/org/labkey/flow/reports/FilterFlowReport.java @@ -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; @@ -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(); } diff --git a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java index 74f8e05358..77c6844783 100644 --- a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java +++ b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java @@ -41,6 +41,7 @@ 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; @@ -137,7 +138,7 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde for (FieldKey fieldKey : getMetadataColumns(metadata)) { - String alias = AliasManager.makeLegalName(fieldKey, null, false); + String alias = AliasManager.makeLegalName(fieldKey, FlowManager.get().getSchema().getSqlDialect()); query.append(" ").append(tableName).append(".").append(toSQL(fieldKey)).append(" AS ").append(alias).append(",\n"); } @@ -145,7 +146,7 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde 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"); diff --git a/ms2/src/org/labkey/ms2/ProteinProphetImporter.java b/ms2/src/org/labkey/ms2/ProteinProphetImporter.java index 35e56c2c6e..a5deb86a66 100644 --- a/ms2/src/org/labkey/ms2/ProteinProphetImporter.java +++ b/ms2/src/org/labkey/ms2/ProteinProphetImporter.java @@ -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 @@ -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(); diff --git a/protein/api-src/org/labkey/api/protein/fasta/FastaDbHelper.java b/protein/api-src/org/labkey/api/protein/fasta/FastaDbHelper.java index 53d7ece91a..3f74d3aae1 100644 --- a/protein/api-src/org/labkey/api/protein/fasta/FastaDbHelper.java +++ b/protein/api-src/org/labkey/api/protein/fasta/FastaDbHelper.java @@ -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, " + @@ -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) " + From 84163646012860863fdf8283a4c831c40c8a50d4 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 15 Apr 2025 17:15:32 -0700 Subject: [PATCH 2/3] Move all key AliasManager methods to SqlDialect --- .../src/org/labkey/flow/reports/PositivityFlowReport.java | 8 +------- ms2/src/org/labkey/ms2/compare/CompareQuery.java | 2 +- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java index 77c6844783..7c8d75719c 100644 --- a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java +++ b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java @@ -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; @@ -51,10 +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"; @@ -138,7 +132,7 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde for (FieldKey fieldKey : getMetadataColumns(metadata)) { - String alias = AliasManager.makeLegalName(fieldKey, FlowManager.get().getSchema().getSqlDialect()); + String alias = FlowManager.get().getSchema().getSqlDialect().makeLegalName(fieldKey); query.append(" ").append(tableName).append(".").append(toSQL(fieldKey)).append(" AS ").append(alias).append(",\n"); } diff --git a/ms2/src/org/labkey/ms2/compare/CompareQuery.java b/ms2/src/org/labkey/ms2/compare/CompareQuery.java index 1ccd331322..c5b8806d1a 100644 --- a/ms2/src/org/labkey/ms2/compare/CompareQuery.java +++ b/ms2/src/org/labkey/ms2/compare/CompareQuery.java @@ -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()); From 6072efd7824dc0326c22330b6666ee9749be29ec Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Sat, 19 Apr 2025 17:14:47 -0700 Subject: [PATCH 3/3] StorageNameGenerator --- flow/src/org/labkey/flow/reports/PositivityFlowReport.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java index 7c8d75719c..0ea120ff95 100644 --- a/flow/src/org/labkey/flow/reports/PositivityFlowReport.java +++ b/flow/src/org/labkey/flow/reports/PositivityFlowReport.java @@ -132,7 +132,7 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde for (FieldKey fieldKey : getMetadataColumns(metadata)) { - String alias = FlowManager.get().getSchema().getSqlDialect().makeLegalName(fieldKey); + String alias = FlowManager.get().getSchema().getSqlDialect().makeLegalName(fieldKey, 0); query.append(" ").append(tableName).append(".").append(toSQL(fieldKey)).append(" AS ").append(alias).append(",\n"); }