Merge from develop

Author: labkey-adam

resources/queries/targetedms/PeptideIds.query.xml

@@ -17,6 +17,7 @@
                                 <property name="showNextAndPrevious">true</property>
                                 <property name="useParens">true</property>
                                 <property name="exportFormatted">true</property>
+                                <property name="highlightFixed">false</property>
                             </properties>
                         </displayColumnFactory>
                     </column>

resources/schemas/dbscripts/postgresql/targetedms-0.000-24.000.sql

@@ -1455,7 +1455,7 @@ CREATE TABLE targetedms.QCMetricConfiguration
     CONSTRAINT UQ_QCMetricConfig_Name_Container UNIQUE (Name, Container)
 );
 
-
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName) VALUES
     ((select theIdentity from rootIdentity), 'Retention Time','Retention Time','targetedms','QCMetric_retentionTime',NULL , NULL , NULL ),
@@ -1466,6 +1466,7 @@ INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Serie
     ((select theIdentity from rootIdentity), 'Transition/Precursor Area Ratio','Transition/Precursor Area Ratio','targetedms','QCMetric_transitionPrecursorRatio',NULL , NULL , NULL ),
     ((select theIdentity from rootIdentity), 'Transition/Precursor Areas','Transition Area','targetedms','QCMetric_transitionArea','Precursor Area','targetedms','QCMetric_precursorArea'),
     ((select theIdentity from rootIdentity), 'Mass Accuracy','Mass Accuracy','targetedms','QCMetric_massAccuracy',NULL , NULL , NULL );
+-- @SkipOnEmptySchemasEnd
 
 -- Add column to ReplicateAnnotation to store the source of the annotation (e.g. Skyline or AutoQC)
 ALTER TABLE targetedms.ReplicateAnnotation ADD COLUMN Source VARCHAR(20) NOT NULL DEFAULT 'Skyline';
@@ -1800,9 +1801,11 @@ ALTER TABLE targetedms.MeasuredDriftTime ADD IonMobilityUnits VARCHAR(30);
 
 ALTER TABLE targetedms.Runs ADD COLUMN AuditLogEntriesCount INT4 DEFAULT 0 NOT NULL;
 
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
     INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName,PrecursorScoped) VALUES
     ((select theIdentity from rootIdentity), 'TIC Area','TIC Area','targetedms','QCRunMetric_ticArea',NULL , NULL , NULL , FALSE );
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE targetedms.SampleFile ADD COLUMN TicArea DOUBLE PRECISION;
 
@@ -1860,6 +1863,7 @@ CREATE TABLE targetedms.ListItemValue
 ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN EnabledQueryName VARCHAR(200);
 ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN EnabledSchemaName VARCHAR(200);
 
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName,PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
   ((select theIdentity from rootIdentity), 'Isotopologue LOD', 'LOD','targetedms', 'QCMetric_IsotopologuePrecursorLOD', NULL, NULL, NULL, TRUE, 'QCMetricEnabled_IsotopologuePrecursorLOD', 'targetedms');
@@ -1877,6 +1881,7 @@ INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Serie
   ((select theIdentity from rootIdentity), 'Isotopologue Regression RSquared', 'Coefficient', 'targetedms', 'QCMetric_IsotopologuePrecursorRSquared', NULL, NULL, NULL, TRUE, 'QCMetricEnabled_IsotopologuePrecursorRSquared', 'targetedms');
 
 UPDATE targetedms.QCMetricConfiguration SET EnabledQueryName = 'QCMetricEnabled_lhRatio', EnabledSchemaName ='targetedms' WHERE Series1QueryName = 'QCMetric_lhRatio';
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE targetedms.runs ALTER COLUMN SoftwareVersion TYPE VARCHAR(200);
 
@@ -2229,6 +2234,7 @@ CREATE TABLE targetedms.keywords (
     CONSTRAINT keywords_keywordid_key UNIQUE (keywordid)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO targetedms.keywordcategories VALUES (1, 'KW-9999', 'Biological process');
 INSERT INTO targetedms.keywordcategories VALUES (2, 'KW-9998', 'Cellular component');
 INSERT INTO targetedms.keywordcategories VALUES (3, 'KW-9997', 'Coding sequence diversity');
@@ -3423,6 +3429,7 @@ INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1268', 'Autism spectrum di
 INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1269', 'Autism', 'KW-9995');
 INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1270', 'Asperger syndrome', 'KW-9995');
 INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1271', 'Inflammasome', 'KW-9998');
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE targetedms.Runs ALTER COLUMN Id TYPE bigint;
 
@@ -3924,6 +3931,7 @@ ALTER TABLE targetedms.SampleFile ADD IRTSlope REAL;
 ALTER TABLE targetedms.SampleFile ADD IRTIntercept REAL;
 ALTER TABLE targetedms.SampleFile ADD IRTCorrelation REAL;
 
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
     ((select theIdentity from rootIdentity), 'iRT Slope', 'iRT Slope', 'targetedms', 'QCRunMetric_iRTSlope', false, 'QCRunMetricEnabled_iRTSlope', 'targetedms');
@@ -3943,7 +3951,6 @@ WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped) VALUES
     ((select theIdentity from rootIdentity), 'Precursor Area', 'Precursor Area', 'targetedms', 'QCMetric_precursorArea', true);
 
-
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
     ((select theIdentity from rootIdentity), 'Transition Area', 'Transition Area', 'targetedms', 'QCMetric_transitionArea', true, 'QCMetricEnabled_transitionArea', 'targetedms');
@@ -3970,6 +3977,7 @@ SET
     EnabledQueryName = 'QCMetricEnabled_transitionArea',
     EnabledSchemaName = 'targetedms'
 WHERE Name = 'Transition & Precursor Areas';
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE targetedms.PrecursorChromInfo
     ADD COLUMN TotalAreaMs1 REAL,
@@ -4025,13 +4033,15 @@ SELECT core.fn_dropifexists('AuditLogEntry', 'targetedms', 'CONSTRAINT', 'fk_aud
 ALTER TABLE targetedms.AuditLogEntry
 DROP COLUMN VersionId;
 
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
     ((select theIdentity from rootIdentity), 'Library dotp', 'Library dotp', 'targetedms', 'QCMetric_libraryDotp', true, 'QCMetricEnabled_libraryDotp', 'targetedms');
 
 WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
     ((select theIdentity from rootIdentity), 'Isotope dotp', 'Isotope dotp', 'targetedms', 'QCMetric_isotopeDotp', true, 'QCMetricEnabled_isotopeDotp', 'targetedms');
+-- @SkipOnEmptySchemasEnd
 
 -- Reparent table if it exists in PanoramaPremium schema
 ALTER TABLE IF EXISTS PanoramaPremium.QCEmailNotifications SET SCHEMA targetedms;

resources/schemas/dbscripts/postgresql/targetedms-24.000-24.001.sql

@@ -6,7 +6,8 @@ UPDATE targetedms.QCMetricConfiguration SET
                                             YAxisLabel1 = 'Mass Error PPM'
 WHERE Name = 'Mass Accuracy';
 
+-- @SkipOnEmptySchemasBegin
 WITH rootIdentity AS (SELECT EntityId AS theIdentity FROM core.Containers WHERE Parent IS NULL)
 INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, EnabledSchemaName, EnabledQueryName, YAxisLabel1) VALUES
-    ((SELECT theIdentity FROM rootIdentity), 'Transition Mass Error','Transition Mass Error','targetedms','QCMetric_massErrorTransition', 'targetedms', 'QCMetricEnabled_massErrorTransition', 'Mass Error PPM')
-;
+    ((SELECT theIdentity FROM rootIdentity), 'Transition Mass Error','Transition Mass Error','targetedms','QCMetric_massErrorTransition', 'targetedms', 'QCMetricEnabled_massErrorTransition', 'Mass Error PPM');
+-- @SkipOnEmptySchemasEnd

src/org/labkey/targetedms/TargetedMSUpgradeCode.java

@@ -54,21 +54,27 @@ public class TargetedMSUpgradeCode implements UpgradeCode
     @SuppressWarnings({"UnusedDeclaration"})
     public void populateDefaultAnnotationTypes(final ModuleContext moduleContext)
     {
-        insertAnnotationType("Instrumentation Change", "FF0000", moduleContext.getUpgradeUser());
-        insertAnnotationType("Reagent Change", "00FF00", moduleContext.getUpgradeUser());
-        insertAnnotationType("Technician Change", "0000FF", moduleContext.getUpgradeUser());
+        if (ModuleLoader.getInstance().shouldInsertData())
+        {
+            insertAnnotationType("Instrumentation Change", "FF0000", moduleContext.getUpgradeUser());
+            insertAnnotationType("Reagent Change", "00FF00", moduleContext.getUpgradeUser());
+            insertAnnotationType("Technician Change", "0000FF", moduleContext.getUpgradeUser());
 
-        // Enable the module in the /Shared container so that it can be resolved
-        Set<Module> activeModules = new HashSet<>(ContainerManager.getSharedContainer().getActiveModules());
-        activeModules.add(ModuleLoader.getInstance().getModule(TargetedMSModule.class));
-        ContainerManager.getSharedContainer().setActiveModules(activeModules);
+            // Enable the module in the /Shared container so that it can be resolved
+            Set<Module> activeModules = new HashSet<>(ContainerManager.getSharedContainer().getActiveModules());
+            activeModules.add(ModuleLoader.getInstance().getModule(TargetedMSModule.class));
+            ContainerManager.getSharedContainer().setActiveModules(activeModules);
+        }
     }
 
     // initialization code called at 0.000-24.000 to add a new type. Can eventually be consolidated into the bootstrap insert above
     @SuppressWarnings({"UnusedDeclaration"})
     public void addInstrumentDowntimeAnnotationType(final ModuleContext moduleContext)
     {
-        insertAnnotationType(QCAnnotationTypeTable.INSTRUMENT_DOWNTIME, "CCCC00", moduleContext.getUpgradeUser());
+        if (ModuleLoader.getInstance().shouldInsertData())
+        {
+            insertAnnotationType(QCAnnotationTypeTable.INSTRUMENT_DOWNTIME, "CCCC00", moduleContext.getUpgradeUser());
+        }
     }
 
     private void insertAnnotationType(String name, String color, User user)

src/org/labkey/targetedms/parser/PeptideSettings.java

@@ -493,7 +493,7 @@ public Boolean getExplicitMod()
 
         public boolean isModExplicit()
         {
-            return _explicitMod == null ? false : _explicitMod;
+            return _explicitMod != null && _explicitMod;
         }
 
         public void setExplicitMod(Boolean explicitMod)

src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java

@@ -174,29 +174,29 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
             return new CrossLinkedPeptideDisplayColumn(colInfo, (match, sequence, modification) ->
             {
                 String label = match.protein().getLabel();
-                String suffix = getChainAbbreviation(label);
-                return (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification)) + suffix;
+                String prefix = getChainPrefix(label);
+                return prefix + (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification));
             });
         }
     }
 
-    public static @NotNull String getChainAbbreviation(String label)
+    public static @NotNull String getChainPrefix(String label)
     {
         String result = "";
         if (label != null)
         {
             label = label.toLowerCase();
             if (label.endsWith("_hc"))
             {
-                result = "HC";
+                result = "H";
             }
             if (label.endsWith("_hcstar"))
             {
-                result = "HC*";
+                result = "*";
             }
             if (label.endsWith("_lc"))
             {
-                result = "LC";
+                result = "L";
             }
         }
         return result;
@@ -222,7 +222,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
                         {
                             for (int linkIndex : sequence.getLinkIndices())
                             {
-                                bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainAbbreviation(match.protein().getLabel()));
+                                bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainPrefix(match.protein().getLabel()));
                             }
                         }
                         allBonds.add(bonds);

src/org/labkey/targetedms/query/ModificationManager.java

@@ -267,13 +267,15 @@ public static PeptideSettings.ModificationSettings getSettings(long runId)
     /**
      * @return    PeptideId -> (Set of indexes where the peptide has structural modifications)
      */
-    private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModIndexMap(long runId)
+    private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModIndexMap(long runId, boolean includeFixedMods)
     {
         SQLFragment sql = new SQLFragment();
         sql.append(" SELECT mod.PeptideId AS peptideId, mod.IndexAA AS indexAA, mod.PeptideIndex AS peptideIndex");
         sql.append(" FROM ");
         sql.append(TargetedMSManager.getTableInfoPeptideStructuralModification(), "mod");
         sql.append(" , ");
+        sql.append(TargetedMSManager.getTableInfoRunStructuralModification(), "runmod");
+        sql.append(" , ");
         sql.append(TargetedMSManager.getTableInfoGeneralMolecule(), "gm");
         sql.append(" , ");
         sql.append(TargetedMSManager.getTableInfoPeptideGroup(), "pg");
@@ -287,6 +289,15 @@ private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModInd
         sql.append(" gm.peptideGroupId = pg.id ");
         sql.append(" AND ");
         sql.append(" mod.peptideId = gm.id ");
+        sql.append(" AND ");
+        sql.append(" runmod.StructuralModId = mod.StructuralModId");
+        sql.append(" AND ");
+        sql.append(" runmod.RunId = run.Id");
+        if (!includeFixedMods)
+        {
+            sql.append(" AND (runmod.variable = ? OR runmod.ExplicitMod IS NOT NULL)");
+            sql.add(true);
+        }
 
         final Map<Long, Set<Pair<Integer, Integer>>> peptideModIndexMap = new LongHashMap<>();
 
@@ -344,17 +355,25 @@ private static Map<Pair<Long,Long>, Set<Integer>> getPeptideIsotopeModIndexMap(l
         return Collections.unmodifiableMap(peptideModIndexMap);
     }
 
-    /** Pair is the index of the cross-linked peptide (or 0 for non-cross-linked peptides) and the amino acid index */
-    public static Set<Pair<Integer, Integer>> getStructuralModIndexes(long peptideId, Long runId)
+    /**
+     * Pair is the index of the cross-linked peptide (or 0 for non-cross-linked peptides) and the amino acid index
+     * @param includeFixedMods Whether to include fixed modifications
+     * @return Set of pairs of peptide index and amino acid index
+     */
+    public static Set<Pair<Integer, Integer>> getStructuralModIndexes(long peptideId, Long runId, boolean includeFixedMods)
     {
-        if(runId == null)
+        if (runId == null)
         {
+            if (!includeFixedMods)
+            {
+                throw new UnsupportedOperationException();
+            }
             Map<Pair<Integer, Integer>, Double> modMap = getPeptideStructuralModsMap(peptideId);
             return new HashSet<>(modMap.keySet());
         }
         else
         {
-            Map<Long, Set<Pair<Integer, Integer>>> modIndexesForRun = PEPTIDE_STR_MOD_INDEXES.get(String.valueOf(runId), null, (runId1, argument) -> getPeptideStructuralModIndexMap(Long.valueOf(runId1)));
+            Map<Long, Set<Pair<Integer, Integer>>> modIndexesForRun = PEPTIDE_STR_MOD_INDEXES.get(runId + "-" + includeFixedMods, null, (runId1, argument) -> getPeptideStructuralModIndexMap(runId, includeFixedMods));
             return modIndexesForRun.getOrDefault(peptideId, Collections.emptySet());
         }
     }

src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java

@@ -65,10 +65,15 @@ public abstract class ModifiedSequenceDisplayColumn extends IconColumn
     public static final String PRECURSOR_COLUMN_NAME = "ModifiedPrecursorDisplayColumn";
 
     public ModifiedSequenceDisplayColumn(ColumnInfo colInfo)
+    {
+        this(colInfo, true);
+    }
+
+    public ModifiedSequenceDisplayColumn(ColumnInfo colInfo, boolean highlightFixed)
     {
         super(colInfo);
 
-        _htmlMaker = new ModifiedPeptideHtmlMaker();
+        _htmlMaker = new ModifiedPeptideHtmlMaker(highlightFixed);
     }
 
     ModifiedPeptideHtmlMaker getHtmlMaker()
@@ -148,6 +153,7 @@ public static class PeptideDisplayColumnFactory implements DisplayColumnFactory
         private boolean _exportStrippedHtml = false;
         private boolean _showNextAndPrevious = false;
         private boolean _useParens = false;
+        private boolean _highlightFixed = true;
         /** Optionally, the name of the column that identifies the animo acid and index within the protein to highlight as modified */
         private String _modificationSite;
 
@@ -162,6 +168,7 @@ public PeptideDisplayColumnFactory(MultiValuedMap<String, String> map)
             _useParens = getBooleanProperty(map, "useParens", _useParens);
             _exportStrippedHtml = getBooleanProperty(map, "exportFormatted", _exportStrippedHtml);
             _modificationSite = map == null || map.get("modificationSite").isEmpty() ? null : map.get("modificationSite").iterator().next();
+            _highlightFixed = getBooleanProperty(map, "highlightFixed", _highlightFixed);
         }
 
         private boolean getBooleanProperty(MultiValuedMap<String, String> map, String propertyName, boolean defaultValue)
@@ -177,7 +184,7 @@ private boolean getBooleanProperty(MultiValuedMap<String, String> map, String pr
         @Override
         public DisplayColumn createRenderer(ColumnInfo colInfo)
         {
-            return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _modificationSite);
+            return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _highlightFixed, _modificationSite);
         }
     }
 
@@ -191,12 +198,12 @@ public static class PeptideCol extends ModifiedSequenceDisplayColumn
 
         public PeptideCol(ColumnInfo colInfo)
         {
-            this(colInfo, false, false, false, null);
+            this(colInfo, false, false, false, true, null);
         }
 
-        public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, String modificationSite)
+        public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, boolean highlightFixed, String modificationSite)
         {
-            super(colInfo);
+            super(colInfo, highlightFixed);
             _showNextAndPrevious = showNextAndPrevious;
             _useParens = useParens;
             _modificationSite = modificationSite;