LabKey · labkey-kevink · Mar 27, 2020 · Mar 3, 2020 · Mar 14, 2020 · Mar 24, 2020
diff --git a/flow/src/org/labkey/flow/data/FlowCompensationControl.java b/flow/src/org/labkey/flow/data/FlowCompensationControl.java
@@ -17,6 +17,10 @@
 package org.labkey.flow.data;
 
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
+import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 public class FlowCompensationControl extends FlowWell
 {
@@ -27,4 +31,10 @@ public FlowCompensationControl(ExpData data)
  {
  super(data);
  }
+
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.CompensationControls.name(), FieldKey.fromParts("RowId"), getRowId());
+ }
 }
diff --git a/flow/src/org/labkey/flow/data/FlowCompensationMatrix.java b/flow/src/org/labkey/flow/data/FlowCompensationMatrix.java
@@ -20,6 +20,8 @@
 import org.labkey.api.data.DbScope;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.FlowSettings;
@@ -30,6 +32,8 @@
 import org.labkey.flow.persist.AttributeSet;
 import org.labkey.flow.persist.AttributeSetHelper;
 import org.labkey.flow.persist.FlowDataHandler;
+import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 import javax.servlet.http.HttpServletRequest;
 import java.io.File;
@@ -141,6 +145,12 @@ public ActionURL urlDownload()
  return urlFor(CompensationController.DownloadAction.class);
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.CompensationMatrices.name(), FieldKey.fromParts("RowId"), getRowId());
+ }
+
  public void addParams(Map<FlowParam, Object> map)
  {
  map.put(FlowParam.compId, getCompId());

diff --git a/flow/src/org/labkey/flow/data/FlowDataObject.java b/flow/src/org/labkey/flow/data/FlowDataObject.java
@@ -24,6 +24,9 @@
 import org.labkey.api.exp.api.ExpProtocolApplication;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.exp.query.ExpSchema;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.flow.persist.AttrObject;
 import org.labkey.flow.persist.AttributeSet;
 import org.labkey.flow.persist.AttributeSetHelper;
@@ -283,4 +286,9 @@ public AttributeSet getAttributeSet(boolean includeGraphBytes)
  return AttributeSetHelper.fromData(getData(), includeGraphBytes);
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Data.name(), FieldKey.fromParts("RowId"), getRowId());
+ }
 }
diff --git a/flow/src/org/labkey/flow/data/FlowDataType.java b/flow/src/org/labkey/flow/data/FlowDataType.java
@@ -16,16 +16,20 @@
 
 package org.labkey.flow.data;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
 import org.labkey.api.exp.Lsid;
 import org.labkey.api.exp.LsidManager;
 import org.labkey.api.exp.api.DataType;
 import org.labkey.api.exp.api.ExpDataRunInput;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.query.QueryRowReference;
+import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.assay.AssayDataType;
-import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.persist.ObjectType;
 
@@ -47,33 +51,37 @@ private FlowDataType(String type, String label, ObjectType objType, boolean requ
  _objType = objType;
  _requireAttrObject = requireAttrObject;
 
- LsidManager.get().registerHandler(getNamespacePrefix(), new LsidManager.ExpObjectLsidHandler()
+ LsidManager.get().registerHandler(getNamespacePrefix(), new FlowDataObjectLsidHandler());
+ }
+
+ static final class FlowDataObjectLsidHandler implements LsidManager.LsidHandler<FlowDataObject>
+ {
+ @Override
+ public FlowDataObject getObject(Lsid lsid)
+ {
+ return FlowDataObject.fromLSID(lsid.toString());
+ }
+
+ @Override
+ public @Nullable ActionURL getDisplayURL(Lsid lsid)
  {
- @Override
- public ExpData getObject(Lsid lsid)
- {
- FlowDataObject fdo = FlowDataObject.fromLSID(lsid.toString());
- if (fdo != null)
- return fdo.getData();
-
- return null;
- }
-
- @Nullable
- @Override
- public ActionURL getDisplayURL(Lsid lsid)
- {
- FlowDataObject fdo = FlowDataObject.fromLSID(lsid.toString());
- if (fdo != null)
- {
- ActionURL url = fdo.urlShow();
- if (url != null)
- return url;
- }
-
- return null;
- }
- });
+ FlowDataObject fdo = getObject(lsid);
+ return fdo != null ? fdo.urlShow() : null;
+ }
+
+ @Override
+ public Container getContainer(Lsid lsid)
+ {
+ FlowDataObject fdo = getObject(lsid);
+ return fdo != null ? fdo.getContainer() : null;
+ }
+
+ @Override
+ public boolean hasPermission(Lsid lsid, @NotNull User user, @NotNull Class<? extends Permission> perm)
+ {
+ FlowDataObject fdo = getObject(lsid);
+ return fdo != null ? fdo.getContainer().hasPermission(user, perm) : null;
+ }
  }
 
  static final public FlowDataType FCSFile = new FlowDataType("FCSFile", "FCS File", ObjectType.fcsKeywords, true)
@@ -146,7 +154,7 @@ public String getName()
  }
 
  @Override
- public URLHelper getDetailsURL(ExpData dataObject)
+ public ActionURL getDetailsURL(ExpData dataObject)
  {
  FlowDataObject fdo = FlowDataObject.fromData(dataObject);
  if (fdo != null)
@@ -164,6 +172,16 @@ public ActionURL getDownloadURL(ExpData dataObject)
  return null;
  }
 
+ @Override
+ public @Nullable QueryRowReference getQueryRowReference(ExpData dataObject)
+ {
+ FlowDataObject fdo = FlowDataObject.fromData(dataObject);
+ if (fdo != null)
+ return fdo.getQueryRowReference();
+
+ return null;
+ }
+
  @Override
  public String getRole()
  {

diff --git a/flow/src/org/labkey/flow/data/FlowExperiment.java b/flow/src/org/labkey/flow/data/FlowExperiment.java
@@ -22,11 +22,14 @@
 import org.labkey.api.exp.api.ExpExperiment;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.controllers.FlowParam;
 import org.labkey.flow.controllers.run.RunController;
 import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 import javax.servlet.http.HttpServletRequest;
 import java.io.File;
@@ -241,6 +244,12 @@ public ActionURL urlDownload()
  throw new UnsupportedOperationException();
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.Analyses.name(), FieldKey.fromParts("RowId"), getExperimentId());
+ }
+
  public boolean hasRun(File filePath, @Nullable FlowProtocolStep step)
  {
  List<FlowRun> runs = getRuns(step);

diff --git a/flow/src/org/labkey/flow/data/FlowFCSAnalysis.java b/flow/src/org/labkey/flow/data/FlowFCSAnalysis.java
@@ -17,6 +17,10 @@
 package org.labkey.flow.data;
 
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
+import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 public class FlowFCSAnalysis extends FlowWell
 {
@@ -27,4 +31,10 @@ public FlowFCSAnalysis(ExpData data)
  {
  super(data);
  }
+
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.FCSAnalyses.name(), FieldKey.fromParts("RowId"), getRowId());
+ }
 }
diff --git a/flow/src/org/labkey/flow/data/FlowFCSFile.java b/flow/src/org/labkey/flow/data/FlowFCSFile.java
@@ -18,7 +18,11 @@
 
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
+import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 import java.util.ArrayList;
 import java.util.Date;
@@ -98,4 +102,9 @@ public void setFileDate(User user, Date date) throws Exception
  setProperty(user, FlowProperty.FileDate.getPropertyDescriptor(), date);
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.FCSFiles.name(), FieldKey.fromParts("RowId"), getRowId());
+ }
 }
diff --git a/flow/src/org/labkey/flow/data/FlowObject.java b/flow/src/org/labkey/flow/data/FlowObject.java
@@ -16,15 +16,18 @@
 
 package org.labkey.flow.data;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DataRegion;
+import org.labkey.api.exp.Identifiable;
 import org.labkey.api.exp.Lsid;
 import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.api.DataType;
 import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.exp.property.SystemProperty;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.ReadPermission;
@@ -45,7 +48,7 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
-abstract public class FlowObject<T extends ExpObject> implements Comparable<Object>, Serializable
+abstract public class FlowObject<T extends ExpObject> implements Comparable<Object>, Serializable, Identifiable
 {
  protected T _expObject;
  protected String _entityId;
@@ -68,6 +71,14 @@ public T getExpObject()
  abstract public ActionURL urlShow();
  abstract public ActionURL urlDownload();
 
+ @Override
+ public @Nullable ActionURL detailsURL()
+ {
+ return urlShow();
+ }
+
+ abstract public QueryRowReference getQueryRowReference();
+
  public String getLSID()
  {
  return _expObject.getLSID();

diff --git a/flow/src/org/labkey/flow/data/FlowProtocol.java b/flow/src/org/labkey/flow/data/FlowProtocol.java
@@ -45,12 +45,14 @@
 import org.labkey.api.exp.property.ExperimentProperty;
 import org.labkey.api.exp.query.ExpDataTable;
 import org.labkey.api.exp.query.ExpMaterialTable;
+import org.labkey.api.exp.query.ExpSchema;
 import org.labkey.api.exp.query.SamplesSchema;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.UserSchema;
@@ -225,6 +227,12 @@ public ActionURL urlDownload()
  throw new UnsupportedOperationException();
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Protocols.name(), FieldKey.fromParts("RowId"), getProtocol().getRowId());
+ }
+
  public FlowProtocolStep getStep()
  {
  return FlowProtocolStep.fromLSID(getContainer(), getLSID());

diff --git a/flow/src/org/labkey/flow/data/FlowProtocolImplementation.java b/flow/src/org/labkey/flow/data/FlowProtocolImplementation.java
@@ -21,9 +21,14 @@
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExpProtocol;
+import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.api.ProtocolImplementation;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
+import org.labkey.flow.query.FlowSchema;
+import org.labkey.flow.query.FlowTableType;
 
 import java.util.List;
 
@@ -66,4 +71,10 @@ public void onRunDeleted(Container container, User user)
 
  new SqlExecutor(ExperimentService.get().getSchema()).execute(sql);
  }
+
+ @Override
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpRun run)
+ {
+ return new QueryRowReference(run.getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.Runs.name(), FieldKey.fromParts("rowId"), run.getRowId());
+ }
 }
diff --git a/flow/src/org/labkey/flow/data/FlowRun.java b/flow/src/org/labkey/flow/data/FlowRun.java
@@ -31,6 +31,8 @@
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExpRunAttachmentParent;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
@@ -335,6 +337,12 @@ public ActionURL urlDownload()
  return urlFor(RunController.DownloadAction.class);
  }
 
+ @Override
+ public QueryRowReference getQueryRowReference()
+ {
+ return new QueryRowReference(getContainer(), FlowSchema.SCHEMAKEY, FlowTableType.Runs.name(), FieldKey.fromParts("RowId"), getRunId());
+ }
+
  public String getLabel()
  {
  return getName();