Issue 41014: fix flagging of flow FCSAnalysis wells

api/src/org/labkey/api/exp/Identifiable.java

@@ -17,6 +17,7 @@
 
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.view.ActionURL;
 
@@ -47,4 +48,12 @@ default String getLSIDNamespacePrefix()
  {
  return null;
  }
+
+ /**
+ * Get the corresponding ExpObject for this Identifiable, if there is one.
+ */
+ default @Nullable ExpObject getExpObject()
+ {
+ return null;
+ }
 }

api/src/org/labkey/api/exp/api/ExpObject.java

@@ -75,4 +75,11 @@ public interface ExpObject extends Identifiable, Comparable<ExpObject>
  * @return Map from PropertyURI to ObjectProperty
  */
  Map<String, ObjectProperty> getObjectProperties();
+
+ @Override
+ @Nullable
+ default ExpObject getExpObject()
+ {
+ return this;
+ }
 }

experiment/src/org/labkey/experiment/api/Data.java

@@ -17,6 +17,7 @@
 
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
@@ -123,4 +124,10 @@ public boolean equals(Object o)
 
  return !(getRowId() == 0 || getRowId() != data.getRowId());
  }
+
+ @Override
+ public @Nullable ExpDataImpl getExpObject()
+ {
+ return new ExpDataImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/DataClass.java

@@ -17,6 +17,7 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpDataClass;
 import org.labkey.api.view.ActionURL;
 import org.labkey.experiment.controllers.exp.ExperimentController;
 
@@ -104,4 +105,10 @@ public int compareTo(@NotNull DataClass o)
  {
  return getName().compareToIgnoreCase(o.getName());
  }
+
+ @Override
+ public @Nullable ExpDataClassImpl getExpObject()
+ {
+ return new ExpDataClassImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/DataInput.java

@@ -16,8 +16,10 @@
 
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.LsidType;
 import org.labkey.api.exp.api.ExpDataRunInput;
+import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.settings.AppProps;
 
 import static org.labkey.api.util.PageFlowUtil.encode;
@@ -67,4 +69,10 @@ protected int getInputKey()
  {
  return _dataId;
  }
+
+ @Override
+ public @Nullable ExpDataRunInputImpl getExpObject()
+ {
+ return new ExpDataRunInputImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/DataProtocolInput.java

@@ -1,20 +1,23 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+/*
+ * Copyright (c) 2018 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpObject;
+
 public class DataProtocolInput extends AbstractProtocolInput
 {
  protected Integer _dataClassId;
@@ -34,4 +37,10 @@ public String getObjectType()
  {
  return ExpDataImpl.DEFAULT_CPAS_TYPE;
  }
+
+ @Override
+ public @Nullable ExpDataProtocolInputImpl getExpObject()
+ {
+ return new ExpDataProtocolInputImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/Experiment.java

@@ -15,6 +15,9 @@
  */
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpExperiment;
+
 import java.io.Serializable;
 
 /**
@@ -101,4 +104,10 @@ public void setBatchProtocolId(Integer batchProtocolId)
  {
  _batchProtocolId = batchProtocolId;
  }
+
+ @Override
+ public @Nullable ExpExperimentImpl getExpObject()
+ {
+ return new ExpExperimentImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/ExperimentRun.java

@@ -16,11 +16,9 @@
 package org.labkey.experiment.api;
 
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.assay.AssayUrls;
 import org.labkey.api.data.Container;
-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.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.experiment.controllers.exp.ExperimentController;
 
@@ -137,4 +135,10 @@ public int hashCode()
  result = 31 * result + (protocolLSID != null ? protocolLSID.hashCode() : 0);
  return result;
  }
+
+ @Override
+ public @Nullable ExpRunImpl getExpObject()
+ {
+ return new ExpRunImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java

@@ -1273,11 +1273,10 @@ public String generateLSID(@NotNull Container container, @NotNull DataType type,
  public ExpObject findObjectFromLSID(String lsid)
  {
  Identifiable id = LsidManager.get().getObject(lsid);
- if (id instanceof ExpObject)
- {
- return (ExpObject) id;
- }
- return null;
+ if (id == null)
+ return null;
+
+ return id.getExpObject();
  }
 
  @Override

experiment/src/org/labkey/experiment/api/Material.java

@@ -15,7 +15,9 @@
  */
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.api.ExpMaterial;
+import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.experiment.controllers.exp.ExperimentController;
@@ -55,4 +57,10 @@ public int hashCode()
  {
  return getRowId();
  }
+
+ @Override
+ public @Nullable ExpMaterialImpl getExpObject()
+ {
+ return new ExpMaterialImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/MaterialInput.java

@@ -16,6 +16,7 @@
 
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.LsidType;
 import org.labkey.api.exp.api.ExpMaterialRunInput;
 import org.labkey.api.settings.AppProps;
@@ -64,4 +65,10 @@ protected int getInputKey()
  {
  return _materialId;
  }
+
+ @Override
+ public @Nullable ExpMaterialRunInputImpl getExpObject()
+ {
+ return new ExpMaterialRunInputImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/MaterialProtocolInput.java

@@ -15,6 +15,9 @@
  */
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpObject;
+
 public class MaterialProtocolInput extends AbstractProtocolInput
 {
  protected Integer _materialSourceId;
@@ -34,4 +37,10 @@ public String getObjectType()
  {
  return ExpMaterialImpl.DEFAULT_CPAS_TYPE;
  }
+
+ @Override
+ public @Nullable ExpMaterialProtocolInputImpl getExpObject()
+ {
+ return new ExpMaterialProtocolInputImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/MaterialSource.java

@@ -17,6 +17,8 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpObject;
+import org.labkey.api.exp.api.ExpSampleType;
 import org.labkey.api.exp.query.ExpSampleTypeTable;
 import org.labkey.api.exp.query.ExpSchema;
 import org.labkey.api.query.FieldKey;
@@ -169,4 +171,9 @@ public int compareTo(@NotNull MaterialSource o)
  return getName().compareToIgnoreCase(o.getName());
  }
 
+ @Override
+ public @Nullable ExpSampleTypeImpl getExpObject()
+ {
+ return new ExpSampleTypeImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/Protocol.java

@@ -16,14 +16,15 @@
 package org.labkey.experiment.api;
 
 import org.apache.commons.beanutils.BeanUtils;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.ObjectProperty;
 import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.exp.ProtocolParameter;
+import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpProtocolInput;
 
 import java.lang.reflect.InvocationTargetException;
-import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -411,4 +412,9 @@ public List<? extends ExpProtocolInputImpl> retrieveProtocolInputs()
  return _protocolInputs;
  }
 
+ @Override
+ public @Nullable ExpProtocolImpl getExpObject()
+ {
+ return new ExpProtocolImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/api/ProtocolApplication.java

@@ -15,6 +15,8 @@
  */
 package org.labkey.experiment.api;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpObject;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.IdentifiableBase;
 
@@ -155,4 +157,9 @@ public void setEndTime(Date endTime)
 
  }
 
+ @Override
+ public @Nullable ExpProtocolApplicationImpl getExpObject()
+ {
+ return new ExpProtocolApplicationImpl(this);
+ }
 }

experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java

@@ -4627,10 +4627,6 @@ public boolean handlePost(SetFlagForm form, BindException errors) throws Excepti
  throw new UnauthorizedException();
  }
 
- if (!container.hasPermission(getUser(), UpdatePermission.class))
- {
- throw new UnauthorizedException();
- }
  obj.setComment(getUser(), form.getComment());
 
  if (form.isRedirect())