Item #6862: provenance loadRun API

api/schemas/expTypes.xsd

@@ -230,6 +230,18 @@
  <xs:attribute ref="rdf:parseType" fixed="Collection"/>
  </xs:complexType>
  </xs:element>
+ <xs:element name="ProvenanceMap" minOccurs="0">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="ObjectRefs" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="from" type="string" use="optional"/>
+ <xs:attribute name="to" type="string" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
  <xs:element name="Properties" type="exp:PropertyCollectionType" minOccurs="0"/>
  </xs:sequence>
  <xs:attribute ref="rdf:about" use="required"/>

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

@@ -1533,10 +1533,56 @@ public String getRunLSIDPrefix()
  return "urn:lsid:" + Lsid.encodePart(AppProps.getInstance().getDefaultLsidAuthority()) + ":" + Lsid.encodePart(getResultRowLSIDPrefix());
  }
 
+ @Override
+ public Pair<ExpProtocol, Integer> getAssayResultRowIdFromLsid(Container container, Lsid assayResultRowLsid)
+ {
+ assert getResultRowLSIDPrefix().equals(assayResultRowLsid.getNamespacePrefix());
+ String namespaceSuffix = assayResultRowLsid.getNamespaceSuffix();
+
+ // LSID namespace suffix format expected to be: "Protocol-" + <protocol-row-id>
+ ExpProtocol protocol = null;
+ if (namespaceSuffix.startsWith("Protocol-"))
+ {
+ try
+ {
+ int protocolId = Integer.parseInt(namespaceSuffix.substring("Protocol-".length()));
+ if (protocolId > 0)
+ protocol = ExperimentService.get().getExpProtocol(protocolId);
+ }
+ catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+
+ if (protocol == null)
+ return null;
+
+ // LSID object id expected to be rowId
+ int rowId = -1;
+ try
+ {
+ rowId = Integer.parseInt(assayResultRowLsid.getObjectId());
+ }
+ catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+
+ if (rowId <= 0)
+ return null;
+
+ return Pair.of(protocol, rowId);
+ }
+
  @Override
  public @Nullable ActionURL getResultRowURL(Container container, Lsid lsid)
  {
- return PageFlowUtil.urlProvider(AssayUrls.class).getAssayResultRowURL(this, container, lsid);
+ var pair = getAssayResultRowIdFromLsid(container, lsid);
+ if (pair == null)
+ return null;
+
+ return PageFlowUtil.urlProvider(AssayUrls.class).getAssayResultRowURL(this, container, pair.first, pair.second);
  }
 
  @Override

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

@@ -234,8 +234,10 @@ else if (mvIndicatorColumns.contains(column.name))
  }
  else
  {
- // It's not an expected column. Is it an MV indicator column?
- if (!settings.isAllowUnexpectedColumns() && !mvIndicatorColumns.contains(column.name))
+ // It's not an expected column. Is it an MV indicator column or prov:objectInput column?
+ if (!settings.isAllowUnexpectedColumns() &&
+ !mvIndicatorColumns.contains(column.name) &&
+ !column.name.equalsIgnoreCase(ProvenanceService.PROVENANCE_INPUT_PROPERTY))
  {
  column.load = false;
  }

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

@@ -311,6 +311,12 @@ enum Scope
  */
  @Nullable String getResultRowLSIDExpression();
 
+ /**
+ * Extract the ExpProtocol and rowId from an assay result row LSID.
+ */
+ @Nullable
+ Pair<ExpProtocol, Integer> getAssayResultRowIdFromLsid(Container container, Lsid assayResultRowLsid);
+
  /**
  * Get the URL for an assay result row's LSID.
  */

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

@@ -55,7 +55,7 @@ public interface AssayUrls extends UrlProvider
  ActionURL getAssayResultsURL(Container container, ExpProtocol protocol);
  ActionURL getAssayResultsURL(Container container, ExpProtocol protocol, int... runIds);
  ActionURL getAssayResultsURL(Container container, ExpProtocol protocol, ContainerFilter containerFilter, int... runIds);
- @Nullable ActionURL getAssayResultRowURL(AssayProvider provider, Container container, Lsid assayResultRowLsid);
+ @Nullable ActionURL getAssayResultRowURL(AssayProvider provider, Container container, ExpProtocol protocol, int rowId);
 
  ActionURL getShowUploadJobsURL(Container container, ExpProtocol protocol, ContainerFilter containerFilter);
 

api/src/org/labkey/api/data/FilterInfo.java

@@ -16,10 +16,14 @@
 
 package org.labkey.api.data;
 
+import org.json.JSONObject;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.util.URLHelper;
 
 import java.io.Serializable;
+import java.util.Map;
+
+import static org.labkey.api.util.PageFlowUtil.encode;
 
 /**
  * Bean to capture a single filter on a single column.
@@ -94,4 +98,18 @@ public void applyToURL(URLHelper url, String regionName, FieldKey fieldKey)
  String valueStr = value != null ? value : "";
  url.addParameter(regionName + "." + fieldKey.toString() + "~" + opStr, valueStr);
  }
+
+ public Map<String, String> toMap()
+ {
+ return Map.of(
+ "fieldKey", this.field.toString(),
+ "op", this.op != null ? this.op.getPreferredUrlKey() : "",
+ "value", this.value
+ );
+ }
+
+ public String toString()
+ {
+ return encode(field.toString()) + "~" + (this.op != null ? this.op.getPreferredUrlKey() : "") + "=" + encode(value);
+ }
 }

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

@@ -15,7 +15,10 @@
  */
 package org.labkey.api.exp;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.query.QueryRowReference;
+import org.labkey.api.view.ActionURL;
 
 /**
  * Base functionality for objects that have an LSID.
@@ -34,4 +37,14 @@ default String getLSIDNamespacePrefix()
  String getName();
 
  Container getContainer();
+
+ default @Nullable ActionURL detailsURL()
+ {
+ return null;
+ }
+
+ default @Nullable QueryRowReference getQueryRowReference()
+ {
+ return null;
+ }
 }

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

@@ -39,13 +39,11 @@ public IdentifiableBase()
 
  public IdentifiableBase(String lsid)
  {
- this();
  _lsid = lsid;
  }
 
  public IdentifiableBase(OntologyObject oo)
  {
- this();
  _lsid = oo.getObjectURI();
  objectId = oo.getObjectId();
  container = oo.getContainer();
@@ -97,6 +95,7 @@ public void setContainer(Container container)
  this.container = container;
  }
 
+
  @Override
  public boolean equals(Object o)
  {

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

@@ -693,7 +693,7 @@ public void testBuilder()
  assertEquals(b.toString(), lsid3.toString());
  Lsid lsid4 = b.setObjectId("OBJ").build();
 
- Lsid.LsidBuilder t = new Lsid.LsidBuilder(lsid1);
+ Lsid.LsidBuilder t = lsid1.edit();
  assertEquals(lsid1,t.build());
  assertEquals(lsid1.toString(),t.toString());
  t.setVersion("3");

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

@@ -18,6 +18,7 @@
 import org.apache.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.AssayProtocolSchema;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayUrls;
 import org.labkey.api.data.Container;
@@ -29,11 +30,14 @@
 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.query.FieldKey;
+import org.labkey.api.query.QueryRowReference;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.Pair;
 import org.labkey.api.view.ActionURL;
 
 import java.util.HashMap;
@@ -67,9 +71,9 @@ public static LsidManager get()
  return INSTANCE;
  }
 
- public interface LsidHandler
+ public interface LsidHandler<I extends Identifiable>
  {
-Identifiable getObject(Lsid lsid);
+I getObject(Lsid lsid);
 
  @Nullable
  ActionURL getDisplayURL(Lsid lsid);
@@ -79,13 +83,13 @@ public interface LsidHandler
  boolean hasPermission(Lsid lsid, @NotNull User user, @NotNull Class<? extends Permission> perm);
  }
 
- public abstract static class ExpObjectLsidHandlerimplements LsidHandler
+ public abstract static class ExpObjectLsidHandler<I extends ExpObject> implements LsidHandler<I>
  {
- public abstract ExpObject getObject(Lsid lsid);
+ public abstract I getObject(Lsid lsid);
 
  public Container getContainer(Lsid lsid)
  {
-ExpObject run = getObject(lsid);
+I run = getObject(lsid);
  return run == null ? null : run.getContainer();
  }
 
@@ -96,7 +100,7 @@ public boolean hasPermission(Lsid lsid, @NotNull User user, @NotNull Class<? ext
  }
  }
 
- public static class ExpRunLsidHandler extends ExpObjectLsidHandler
+ public static class ExpRunLsidHandler extends ExpObjectLsidHandler<ExpRun>
  {
  public ExpRun getObject(Lsid lsid)
  {
@@ -123,22 +127,23 @@ protected ActionURL getDisplayURL(Container c, ExpProtocol protocol, ExpRun run)
 
  // This is different from ExpObjectLsidHandler in that it supports generic
  // OntologyObjects that don't fit into the ExpObject class hierarchy.
- public static class OntologyObjectLsidHandlerimplements LsidHandler
+ public static class OntologyObjectLsidHandler<I extends IdentifiableBase> implements LsidHandler<I>
  {
  @Override
- public Identifiable getObject(Lsid lsid)
+ public I getObject(Lsid lsid)
  {
  OntologyObject oo = OntologyManager.getOntologyObject(null, lsid.toString());
  if (oo == null)
  return null;
 
- return new IdentifiableBase(oo);
+ return (I)new IdentifiableBase(oo);
  }
 
  @Override
- public @Nullable ActionURL getDisplayURL(Lsid lsid)
+ public final @Nullable ActionURL getDisplayURL(Lsid lsid)
  {
- return null;
+ I obj = getObject(lsid);
+ return obj == null ? null : obj.detailsURL();
  }
 
  @Override
@@ -159,32 +164,76 @@ public boolean hasPermission(Lsid lsid, @NotNull User user, @NotNull Class<? ext
  }
  }
 
- public static class AssayResultLsidHandler extends OntologyObjectLsidHandler
+ /**
+ * Represents a single row in the assay results table.
+ */
+ public static class AssayResultIdentifiable extends IdentifiableBase
  {
  private final AssayProvider _provider;
+ private final ExpProtocol _protocol;
+ private int _rowId;
 
- public AssayResultLsidHandler(AssayProvider provider)
+ public AssayResultIdentifiable(AssayProvider provider, OntologyObject oo, ExpProtocol protocol, int rowId)
  {
+ super(oo);
  _provider = provider;
- assert _provider.getResultRowLSIDPrefix() != null;
+
+ Pair<ExpProtocol, Integer> pair = provider.getAssayResultRowIdFromLsid(oo.getContainer(), new Lsid(oo.getObjectURI()));
+ if (pair != null)
+ {
+ _protocol = pair.first;
+ _rowId = pair.second;
+ }
+ else
+ {
+ _protocol = null;
+ _rowId = 0;
+ }
  }
 
  @Override
- public Identifiable getObject(Lsid lsid)
+ public @Nullable ActionURL detailsURL()
  {
- assert _provider.getResultRowLSIDPrefix().equals(lsid.getNamespacePrefix());
- return super.getObject(lsid);
+ var urls = PageFlowUtil.urlProvider(AssayUrls.class);
+ if (urls == null)
+ return null;
+
+ return urls.getAssayResultRowURL(_provider, getContainer(), _protocol, _rowId);
  }
 
  @Override
- public @Nullable ActionURL getDisplayURL(Lsid lsid)
+ public @Nullable QueryRowReference getQueryRowReference()
  {
- Container c = getContainer(lsid);
- if (c == null)
+ var schemaKey = AssayProtocolSchema.schemaName(_provider, _protocol);
+ return new QueryRowReference(getContainer(), schemaKey, AssayProtocolSchema.DATA_TABLE_NAME, FieldKey.fromParts("rowId"), _rowId);
+ }
+ }
+
+ public static class AssayResultLsidHandler extends OntologyObjectLsidHandler<AssayResultIdentifiable>
+ {
+ private final AssayProvider _provider;
+
+ public AssayResultLsidHandler(AssayProvider provider)
+ {
+ _provider = provider;
+ assert _provider.getResultRowLSIDPrefix() != null;
+ }
+
+ @Override
+ public AssayResultIdentifiable getObject(Lsid lsid)
+ {
+ assert _provider.getResultRowLSIDPrefix().equals(lsid.getNamespacePrefix());
+ OntologyObject oo = OntologyManager.getOntologyObject(null, lsid.toString());
+ if (oo == null)
+ return null;
+
+ Pair<ExpProtocol, Integer> pair = _provider.getAssayResultRowIdFromLsid(oo.getContainer(), lsid);
+ if (pair == null)
  return null;
 
- return PageFlowUtil.urlProvider(AssayUrls.class).getAssayResultRowURL(_provider, c, lsid);
+ return new AssayResultIdentifiable(_provider, oo, pair.first, pair.second);
  }
+
  }
 
  public void registerHandlerFinder(LsidHandlerFinder finder)