diff --git a/ms2/src/org/labkey/ms2/MS2Run.java b/ms2/src/org/labkey/ms2/MS2Run.java index 12ccf2e66..ddfd0f44e 100644 --- a/ms2/src/org/labkey/ms2/MS2Run.java +++ b/ms2/src/org/labkey/ms2/MS2Run.java @@ -18,10 +18,12 @@ import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerManager; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SqlSelector; import org.labkey.api.protein.MassType; import org.labkey.api.query.FieldKey; +import org.labkey.api.util.GUID; import org.labkey.api.util.MemTracker; import org.labkey.api.util.logging.LogHelper; import org.labkey.api.view.ViewContext; @@ -41,7 +43,7 @@ public abstract class MS2Run implements Serializable protected final static String[] EMPTY_STRING_ARRAY = new String[0]; protected int run; - protected Container container; + protected GUID containerId; protected String description; protected String path; protected String fileName; @@ -252,13 +254,13 @@ public void setRun(int run) public Container getContainer() { - return container; + return ContainerManager.getForId(containerId); } public void setContainer(Container container) { - this.container = container; + this.containerId = container.getEntityId(); } diff --git a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java index 02b180f7a..ad349fa94 100644 --- a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java +++ b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java @@ -48,8 +48,7 @@ public class MascotRun extends MS2Run public void adjustScores(Map map) { // Mascot exported pepXML can exclude "homologyscore" - if (null == map.get("homologyscore")) - map.put("homologyscore", "-1"); + map.putIfAbsent("homologyscore", "-1"); // Issue 30322 - ProteomeDiscoverer pep.xml files use a different name for the score value if (null == map.get("ionscore") && map.containsKey("Ions Score")) map.put("ionscore", map.get("Ions Score")); diff --git a/nab/src/org/labkey/nab/NabAssayController.java b/nab/src/org/labkey/nab/NabAssayController.java index b2bff20eb..2f70bfdc3 100644 --- a/nab/src/org/labkey/nab/NabAssayController.java +++ b/nab/src/org/labkey/nab/NabAssayController.java @@ -331,8 +331,6 @@ private DilutionAssayRun _getNabAssayRun(ExpRun run, StatsService.CurveFitType f return assay; } - private static final String LAST_NAB_RUN_KEY = NabAssayController.class.getName() + "/LastNAbRun"; - @RequiresPermission(ReadPermission.class) @ContextualRoles(RunDatasetContextualRoles.class) public class DetailsAction extends RunDetailsAction @@ -504,12 +502,6 @@ protected DilutionAssayRun getAssayRun(ExpRun run, StatsService.CurveFitType fit { return _getNabAssayRun(run, fit, user); } - - @Override - public void addNavTrail(NavTree root) - { - throw new UnsupportedOperationException(); - } } public static class SampleSpreadsheetForm diff --git a/nab/src/org/labkey/nab/NabAssayRun.java b/nab/src/org/labkey/nab/NabAssayRun.java index de05334cd..f05445f41 100644 --- a/nab/src/org/labkey/nab/NabAssayRun.java +++ b/nab/src/org/labkey/nab/NabAssayRun.java @@ -42,12 +42,6 @@ import java.util.Map; import java.util.Set; -/* - * User: brittp - * Date: Dec 9, 2008 - * Time: 5:43:01 PM - */ - public abstract class NabAssayRun extends DilutionAssayRun { public NabAssayRun(DilutionAssayProvider provider, ExpRun run, @@ -119,7 +113,7 @@ else if (null != dataWithHandlerType) if (null == outputObject) throw new IllegalStateException("Expected a single data file output for this NAb run, but none matching the expected datatype found. Found a total of " + outputDatas.size()); - AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _run.getContainer(), _protocol, null); + AssayProtocolSchema schema = _provider.createProtocolSchema(getUser(), _run.getContainer(), _protocol, null); TableInfo virusTable = schema.createTable(DilutionManager.VIRUS_TABLE_NAME, null); Map> samplePropertiesMap = getSampleProperties(); diff --git a/nab/src/org/labkey/nab/NabDataHandler.java b/nab/src/org/labkey/nab/NabDataHandler.java index 16b49b01c..17f61a318 100644 --- a/nab/src/org/labkey/nab/NabDataHandler.java +++ b/nab/src/org/labkey/nab/NabDataHandler.java @@ -55,10 +55,6 @@ import java.util.List; import java.util.Map; -/** - * User: klum - * Date: May 15, 2009 - */ public abstract class NabDataHandler extends DilutionDataHandler { public static final Logger LOG = LogManager.getLogger(NabDataHandler.class); @@ -146,7 +142,7 @@ public void recalculateDilutionStats(ExpData data, ExpRun run, ExpProtocol proto * Calculates cutoff and AUC information from the passed in raw data and optionally saves the data to the * specific tables. * - * @param commitData true to persist dilution and well level data + * @param commitData true to persist dilution and well-level data * @param specimenRows if commitData is false, then specimen data will be returned in this collection * @param cutoffRows if commitData is false, then cutoff data will be returned in this collection */ @@ -268,7 +264,7 @@ public void beforeDeleteData(List datas, User user) throws ExperimentEx { NabManager.get().deleteRunData(datas); } - catch(SQLException e) + catch (SQLException e) { throw new ExperimentException(e); } diff --git a/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java b/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java index 2b65260b3..96e783da7 100644 --- a/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java +++ b/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java @@ -323,7 +323,7 @@ protected String getVirusName(String virusWellGroupName) if (!outputDatas.isEmpty()) { Lsid virusLsid = DilutionDataHandler.createVirusWellGroupLsid(outputDatas.get(0), virusWellGroupName); - AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _run.getContainer(), _protocol, null); + AssayProtocolSchema schema = _provider.createProtocolSchema(getUser(), _run.getContainer(), _protocol, null); TableInfo virusTable = schema.createTable(DilutionManager.VIRUS_TABLE_NAME, null); if (null != virusTable) {