Experiment: Run graph details for steps, inputs, and outputs

api/src/org/labkey/api/assay/AssayRunType.java

@@ -48,7 +48,7 @@ public class AssayRunType extends ExperimentRunType
 
  public AssayRunType(ExpProtocol protocol, Container c)
  {
- super(protocol.getName(), SchemaKey.fromParts(AssaySchema.NAME, AssayService.get().getProvider(protocol).getResourceName(), protocol.getName()).toString(), AssayProtocolSchema.RUNS_TABLE_NAME);
+ super(protocol.getName(), AssayProtocolSchema.schemaName(AssayService.get().getProvider(protocol), protocol), AssayProtocolSchema.RUNS_TABLE_NAME);
  _protocol = protocol;
  }
 

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

@@ -0,0 +1,28 @@
+package org.labkey.api.exp;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.exp.api.ExpProtocol;
+import org.labkey.api.exp.api.ExpProtocolApplication;
+import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.query.QueryRowReference;
+
+/**
+ * Provides some basic recognition for protocols of a particular type.
+ */
+public interface ExperimentProtocolHandler extends Handler<ExpProtocol>
+{
+ /**
+ * Get a query reference for the protocol type.
+ */
+ public @Nullable QueryRowReference getQueryRowReference(ExpProtocol protocol);
+
+ /**
+ * Get a query reference for the run of the protocol type.
+ */
+ public @Nullable QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpRun run);
+
+ /**
+ * Get a query reference for the protocol application of the protocol type.
+ */
+ public @Nullable QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpProtocolApplication app);
+}

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

@@ -16,11 +16,22 @@
 
 package org.labkey.api.exp;
 
-import org.labkey.api.data.*;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.ButtonBar;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpProtocol;
+import org.labkey.api.exp.api.ExpProtocolApplication;
+import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.exp.query.ExpProtocolApplicationTable;
+import org.labkey.api.exp.query.ExpRunTable;
 import org.labkey.api.exp.query.ExpSchema;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.query.QueryService;
+import org.labkey.api.query.SchemaKey;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
 import org.labkey.api.view.DataView;
@@ -37,20 +48,29 @@
  * User: jeckels
  * Date: Sep 25, 2006
  */
-public abstract class ExperimentRunType implements Comparable<ExperimentRunType>, Handler<ExpProtocol>
+public abstract class ExperimentRunType implements Comparable<ExperimentRunType>, ExperimentProtocolHandler
 {
- private final String _description;
- private final String _schemaName;
- private final String _tableName;
- public static final ExperimentRunType ALL_RUNS_TYPE = new ExperimentRunType("All Runs", ExpSchema.SCHEMA_NAME, ExpSchema.TableType.Runs.toString())
+ public static final ExperimentRunType ALL_RUNS_TYPE = new ExperimentRunType("All Runs", ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Runs.toString())
  {
- public Priority getPriority(ExpProtocol object)
+ public Priority getPriority(ExpProtocol protocol)
  {
- return Priority.LOW;
+ if (protocol.getApplicationType() == ExpProtocol.ApplicationType.ExperimentRun)
+ return Priority.LOW;
+
+ return null;
  }
  };
 
+ private final String _description;
+ private final SchemaKey _schemaName;
+ private final String _tableName;
+
  public ExperimentRunType(String description, String schemaName, String tableName)
+ {
+ this(description, SchemaKey.fromString(schemaName), tableName);
+ }
+
+ public ExperimentRunType(String description, SchemaKey schemaName, String tableName)
  {
  _description = description;
  _schemaName = schemaName;
@@ -62,7 +82,7 @@ public String getDescription()
  return _description;
  }
 
- public String getSchemaName()
+ public SchemaKey getSchemaName()
  {
  return _schemaName;
  }
@@ -72,6 +92,33 @@ public String getTableName()
  return _tableName;
  }
 
+ /**
+ * Reference to the row that represents the protocol for this run type.
+ */
+ @Nullable
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol)
+ {
+ return new QueryRowReference(protocol.getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.Protocols.name(), ExpProtocolApplicationTable.Column.RowId, protocol.getRowId());
+ }
+
+ /**
+ * Reference to the row that represents the run of for this run type.
+ */
+ @Nullable
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpRun run)
+ {
+ return new QueryRowReference(run.getContainer(), SchemaKey.fromParts(_schemaName), _tableName, ExpRunTable.Column.RowId, run.getRowId());
+ }
+
+ /**
+ * Reference to the row that represents the protocol application for this run type.
+ */
+ @Nullable
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpProtocolApplication app)
+ {
+ return new QueryRowReference(app.getContainer(), ExpSchema.SCHEMA_EXP, ExpSchema.TableType.ProtocolApplications.name(), ExpProtocolApplicationTable.Column.RowId, app.getRowId());
+ }
+
  public long getRunCount(User user, Container c)
  {
  UserSchema schema = QueryService.get().getUserSchema(user, c, _schemaName);

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

@@ -16,11 +16,12 @@
 
 package org.labkey.api.exp.api;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.AbstractAssayProvider;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ObjectProperty;
 import org.labkey.api.exp.ProtocolParameter;
 import org.labkey.api.security.User;
-import org.labkey.api.assay.AbstractAssayProvider;
 
 import java.util.Collection;
 import java.util.List;
@@ -105,7 +106,8 @@ enum ApplicationType
  ApplicationType getApplicationType();
  void setApplicationType(ApplicationType type);
 
- ProtocolImplementation getImplementation();
+ @Nullable String getImplementationName();
+ @Nullable ProtocolImplementation getImplementation();
 
  String getDescription();
  void setDescription(String description);

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

@@ -60,13 +60,16 @@ public class ExperimentJSONConverter
  // General experiment object properties
  public static final String ID = "id";
  public static final String ROW_ID = "rowId";
+ public static final String CONTAINER = "container";
  public static final String CREATED = "created";
  public static final String CREATED_BY = "createdBy";
  public static final String MODIFIED = "modified";
  public static final String MODIFIED_BY = "modifiedBy";
  public static final String NAME = "name";
  public static final String LSID = "lsid";
  public static final String CPAS_TYPE = "cpasType";
+ // Matches the expType parameter used in the linage api: "Data", "Material", "ExperimentRun", "Object"
+ public static final String EXP_TYPE = "expType";
  public static final String URL = "url";
  public static final String PROPERTIES = "properties";
  public static final String COMMENT = "comment";
@@ -153,6 +156,11 @@ public Settings withIncludeInputsAndOutputs(boolean b)
  {
  return new Settings(includeProperties, b, includeRunSteps);
  }
+
+ public Settings withIncludeRunSteps(boolean b)
+ {
+ return new Settings(includeProperties, includeInputsAndOutputs, b);
+ }
  }
 
  @NotNull
@@ -176,12 +184,14 @@ public static JSONObject serializeRunGroup(ExpExperiment runGroup, Domain domain
  {
  JSONObject jsonObject = serializeExpObject(runGroup, domain != null ? domain.getProperties() : Collections.emptyList(), settings);
  jsonObject.put(COMMENT, runGroup.getComments());
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "Experiment");
  return jsonObject;
  }
 
  public static JSONObject serializeRun(ExpRun run, Domain domain, User user, @NotNull Settings settings)
  {
  JSONObject jsonObject = serializeExpObject(run, domain == null ? null : domain.getProperties(), settings);
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "ExperimentRun");
  if (settings.isIncludeProperties())
  {
  jsonObject.put(COMMENT, run.getComments());
@@ -252,6 +262,7 @@ public static JSONObject serializeProtocol(ExpProtocol protocol, User user)
  // Just include basic protocol properties for now.
  // See GetProtocolAction and GWTProtocol for serializing an assay protocol with domain fields.
  JSONObject jsonObject = serializeExpObject(protocol, null, DEFAULT_SETTINGS.withIncludeProperties(false));
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "Protocol");
  return jsonObject;
  }
 
@@ -344,6 +355,7 @@ else if (runInput instanceof ExpMaterialRunInput)
  protected static JSONObject serializeRunProtocolApplication(@NotNull ExpProtocolApplication protApp, ExpRun run, User user, Settings settings)
  {
  JSONObject json = serializeExpObject(protApp, null, settings);
+ json.put(ExperimentJSONConverter.EXP_TYPE, "ProtocolApplication");
 
  json.put(ACTION_SEQUENCE, protApp.getActionSequence());
  json.put(APPLICATION_TYPE, protApp.getApplicationType().toString());
@@ -474,6 +486,8 @@ private static JSONObject serializeIdentifiableBean(@NotNull Identifiable obj)
  if (url != null)
  json.put(URL, url);
 
+ json.put(CONTAINER, obj.getContainer().getId());
+
  QueryRowReference rowRef = obj.getQueryRowReference();
  if (rowRef != null)
  {
@@ -492,6 +506,7 @@ private static JSONObject serializeIdentifiableBean(@NotNull Identifiable obj)
  public static JSONObject serializeIdentifiable(@NotNull Identifiable obj, Settings settings)
  {
  JSONObject json = serializeIdentifiableBean(obj);
+ json.put(ExperimentJSONConverter.EXP_TYPE, (Object)null);
 
  if (settings.isIncludeProperties())
  {
@@ -516,6 +531,8 @@ public static JSONObject serializeExpObject(@NotNull ExpObject object, @Nullable
  // instead and use serializeOntologyProperties(ExpObject) so the object properties will be
  // fetched using ExpObject.getProperty().
  JSONObject jsonObject = serializeIdentifiableBean(object);
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "Object");
+
  int rowId = object.getRowId();
  if (rowId != 0)
  {
@@ -634,6 +651,7 @@ public static JSONObject serializeData(@NotNull ExpData data, @Nullable User use
  final ExpDataClass dc = data.getDataClass(user);
 
  JSONObject jsonObject = serializeExpObject(data, null, settings);
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "Data");
 
  if (settings.isIncludeProperties())
  {
@@ -702,6 +720,7 @@ public static JSONObject serializeMaterial(@NotNull ExpMaterial material, @NotNu
  }
 
  jsonObject.put(CPAS_TYPE, material.getCpasType());
+ jsonObject.put(ExperimentJSONConverter.EXP_TYPE, "Material");
 
  return jsonObject;
  }

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

@@ -28,6 +28,7 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.ExperimentDataHandler;
 import org.labkey.api.exp.ExperimentException;
+import org.labkey.api.exp.ExperimentProtocolHandler;
 import org.labkey.api.exp.ExperimentRunListView;
 import org.labkey.api.exp.ExperimentRunType;
 import org.labkey.api.exp.ExperimentRunTypeSource;
@@ -760,9 +761,11 @@ ExpRun derive(Map<ExpMaterial, String> inputMaterials, Map<ExpData, String> inpu
 
  void registerProtocolImplementation(ProtocolImplementation impl);
 
+ void registerProtocolHandler(ExperimentProtocolHandler handler);
+
  void registerProtocolInputCriteria(ExpProtocolInputCriteria.Factory factory);
 
- ProtocolImplementation getProtocolImplementation(String name);
+@Nullable ProtocolImplementation getProtocolImplementation(String name);
 
  ExpProtocolApplication getExpProtocolApplication(int rowId);
 
@@ -827,6 +830,12 @@ ExpRun derive(Map<ExpMaterial, String> inputMaterials, Map<ExpData, String> inpu
 
  List<? extends ExpProtocol> getExpProtocolsUsedByRuns(Container c, ContainerFilter containerFilter);
 
+ @Nullable
+ ExperimentProtocolHandler getExperimentProtocolHandler(@NotNull ExpProtocol protocol);
+
+ @Nullable
+ ExperimentRunType getExperimentRunType(@NotNull ExpProtocol protocol);
+
  @Nullable
  ExperimentRunType getExperimentRunType(@NotNull String description, @Nullable Container container);
 

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

@@ -16,13 +16,15 @@
 
 package org.labkey.api.exp.api;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.exp.ExperimentProtocolHandler;
 import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
 
 import java.util.List;
 
-public class ProtocolImplementation
+public class ProtocolImplementation implements ExperimentProtocolHandler
 {
  final protected String _name;
  public ProtocolImplementation(String name)
@@ -60,8 +62,36 @@ public void onRunDeleted(Container container, User user)
  {
  }
 
+ @Override
+ public @Nullable Priority getPriority(ExpProtocol protocol)
+ {
+ if (getName().equals(protocol.getImplementationName()))
+ return Priority.HIGH;
+
+ return null;
+ }
+
+ /**
+ * Get a query reference for the protocol type.
+ */
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol)
+ {
+ return null;
+ }
+
+ /**
+ * Get a query reference for the run of the protocol type.
+ */
  public QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpRun run)
  {
  return null;
  }
+
+ /**
+ * Get a query reference for the protocol application of the protocol type.
+ */
+ public QueryRowReference getQueryRowReference(ExpProtocol protocol, ExpProtocolApplication app)
+ {
+ return null;
+ }
 }

api/src/org/labkey/api/exp/query/ExpProtocolApplicationTable.java

@@ -27,11 +27,17 @@ enum Column
  {
  RowId,
  Name,
+ Comments,
  LSID,
  Protocol,
  Run,
  ActionSequence,
- Type
+ Type,
+ ActivityDate,
+ StartTime,
+ EndTime,
+ RecordCount,
+ Properties
  }
 
  BaseColumnInfo createMaterialInputColumn(String alias, SamplesSchema schema, ExpSampleSet sampleSet, String... roleNames);

api/src/org/labkey/api/query/QueryRowReference.java

@@ -21,6 +21,11 @@ public class QueryRowReference
  final @NotNull String _queryName;
  final @NotNull List<Pair<FieldKey, Object>> _pkFilters;
 
+ public QueryRowReference(@NotNull Container c, @NotNull SchemaKey schemaKey, @NotNull String queryName, @NotNull Enum pkCol, int pkValue)
+ {
+ this(c, schemaKey, queryName, List.of(Pair.of(FieldKey.fromParts(pkCol), pkValue)));
+ }
+
  public QueryRowReference(@NotNull Container c, @NotNull SchemaKey schemaKey, @NotNull String queryName, @NotNull FieldKey pkCol, int pkValue)
  {
  this(c, schemaKey, queryName, List.of(Pair.of(pkCol, pkValue)));