| /* |
| * Licensed to the Apache Software Foundation (ASF) under one |
| * or more contributor license agreements. See the NOTICE file |
| * distributed with this work for additional information |
| * regarding copyright ownership. The ASF licenses this file |
| * to you 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.apache.taverna.provenance; |
| |
| import java.sql.SQLException; |
| import java.util.List; |
| import java.util.Map; |
| import java.util.Set; |
| |
| import org.apache.taverna.invocation.InvocationContext; |
| import org.apache.taverna.provenance.api.Query; |
| import org.apache.taverna.provenance.api.QueryAnswer; |
| import org.apache.taverna.provenance.connector.AbstractProvenanceConnector; |
| import org.apache.taverna.provenance.lineageservice.Dependencies; |
| import org.apache.taverna.provenance.lineageservice.LineageQueryResultRecord; |
| import org.apache.taverna.provenance.lineageservice.ProvenanceAnalysis; |
| import org.apache.taverna.provenance.lineageservice.ProvenanceQuery; |
| import org.apache.taverna.provenance.lineageservice.utils.Collection; |
| import org.apache.taverna.provenance.lineageservice.utils.DataLink; |
| import org.apache.taverna.provenance.lineageservice.utils.DataflowInvocation; |
| import org.apache.taverna.provenance.lineageservice.utils.Port; |
| import org.apache.taverna.provenance.lineageservice.utils.PortBinding; |
| import org.apache.taverna.provenance.lineageservice.utils.ProcessorEnactment; |
| import org.apache.taverna.provenance.lineageservice.utils.ProvenanceProcessor; |
| import org.apache.taverna.provenance.lineageservice.utils.Workflow; |
| import org.apache.taverna.provenance.lineageservice.utils.WorkflowRun; |
| import org.apache.taverna.provenance.lineageservice.utils.WorkflowTree; |
| import org.apache.taverna.reference.T2Reference; |
| |
| /** |
| * This API is the single access point into the Taverna provenance database. Its |
| * main functionality is to let clients query the content of the DB, either |
| * using dedicated methods that retrieve specific entity values from the DB, or |
| * through a more general XML-based query language. Examples of XML provenance |
| * queries can be found in the external package |
| * {@link net.sf.taverna.t2.provenance.apic.client.resources}. Class |
| * {@link net.sf.taverna.t2.provenance.api.client.ProvenanceAPISampleClient} |
| * provides an example of API client that third parties would use to interact |
| * with this API. |
| * <p/> |
| * The XML schema for the XML query language is {@code pquery.xsd} in |
| * {@link net.sf.taverna.t2.provenance.apic.client.resources} |
| * |
| * @author Paolo Missier |
| * @author Stuart Owen |
| */ |
| public interface Provenance { |
| |
| /** |
| * Initialises a default Reference Service for storing data and their associated references. |
| * This creates a reference service using the named JNDI Data Source 'jdbc/taverna'.<br/> |
| * the new Reference Service is associated to the {@link AbstractProvenanceConnector}, enabling data references to be resolved |
| */ |
| InvocationContext initDefaultReferenceService(); |
| |
| /** |
| * Initialises the Reference Service for a given hibernate context definition. |
| * This mapping file must be available in the root of the classpath. |
| * @see #initDefaultReferenceService() |
| * @param hibernateContext |
| */ |
| InvocationContext initReferenceService(String hibernateContext); |
| |
| void init(); |
| |
| void init(InvocationContext context); |
| |
| /** |
| * Executes a provenance query. Please see separate doc. for the XML query language schema. |
| * @throws SQLException |
| */ |
| QueryAnswer executeQuery(Query pq) throws SQLException; |
| |
| /** |
| * Returns individal records from the provenance DB in response to a query |
| * that specifies specific elements within values associated with a |
| * processor port, in the context of a specific run of a workflow. <br/> |
| * This is used in the workbench to retrieve the "intermediate results" at |
| * various points during workflow execution, as opposed to a set of |
| * dependencies in response to a full-fledged provenance query. |
| * |
| * @param workflowRunId |
| * lineage scope -- a specific instance |
| * @param processorName |
| * for a specific processor [required] |
| * @param a |
| * specific (input or output) variable [optional] |
| * @param iteration |
| * and a specific iteration [optional] |
| * @return a list of @ LineageQueryResultRecord} , encapsulated in a |
| * {@link Dependencies} object |
| * @throws SQLException |
| */ |
| Dependencies fetchPortData(String workflowRunId, String workflowId, |
| String processorName, String portName, String iteration); |
| |
| /** |
| * @param record a record representing a single value -- possibly within a list hierarchy |
| * @return the URI for topmost containing collection when the input record is within a list hierarchy, or null otherwise |
| */ |
| String getContainingCollection(LineageQueryResultRecord record); |
| |
| /** |
| * @param workflowId |
| * defines the scope of the query - if null then the query runs |
| * on all available workflows |
| * @param conditions |
| * additional conditions to be defined. This is a placeholder as |
| * conditions are currently ignored |
| * @return a list of workflowRunId, each representing one run of the input |
| * workflowID |
| */ |
| List<WorkflowRun> listRuns(String workflowId, Map<String, String> conditions); |
| |
| boolean isTopLevelDataflow(String workflowId); |
| |
| boolean isTopLevelDataflow(String workflowId, String workflowRunId); |
| |
| String getLatestRunID() throws SQLException; |
| |
| /** |
| * Removes all records that pertain to a specific run (but not the static |
| * specification of the workflow run) |
| * |
| * @param runID |
| * the internal ID of a run. This can be obtained using |
| * {@link #listRuns(String, Map)} |
| * @return the set of data references that pertain to the deleted run. This |
| * can be used by the Data Manager to ensure that no dangling |
| * references are left in the main Taverna data repositorry |
| */ |
| Set<String> removeRun(String runID); |
| |
| /** |
| * removes all records pertaining to the static structure of a workflow. |
| * |
| * @param workflowId |
| * the ID (not the external name) of the workflow whose static |
| * structure is to be deleted from the DB |
| */ |
| void removeWorkflow(String workflowId); |
| |
| /** |
| * returns a set of workflowIDs for a given runID. The set is a singleton if |
| * the workflow has no nesting, but in general the list contains one |
| * workflowID for each nested workflow involved in the run |
| * |
| * @param runID |
| * the internal ID for a specific workflow run |
| * @return a list of workflow IDs, one for each nested workflow involved in |
| * the input run |
| */ |
| List<String> getWorkflowID(String runID); |
| |
| /** |
| * @param runID |
| * the internal ID for a specific workflow run |
| * @return the ID of the top-level workflow that executed during the input |
| * run |
| */ |
| String getTopLevelWorkflowID(String runID); |
| |
| List<Workflow> getWorkflowsForRun(String runID); |
| |
| /** |
| * @return a list of {@link WorkflowRun} beans, each representing the |
| * complete description of a workflow run (note that this is not |
| * just the ID of the run) |
| */ |
| List<WorkflowRun> getAllWorkflowIDs(); |
| |
| /** |
| * @param workflowID |
| * @return a Map: workflowID -> [ @ link ProvenanceProcessor} ] Each entry |
| * in the list pertains to one composing sub-workflow (if no nesting |
| * then this contains only one workflow, namely the top level one) |
| */ |
| Map<String, List<ProvenanceProcessor>> getProcessorsInWorkflow( |
| String workflowID); |
| |
| List<Collection> getCollectionsForRun(String wfInstanceID); |
| |
| List<PortBinding> getPortBindings(Map<String, String> constraints) |
| throws SQLException; |
| |
| /** |
| * lists all ports for a workflow |
| * |
| * @param workflowID |
| * @return a list of {@link Port} beans, each representing an input or |
| * output port for the workflow |
| */ |
| List<Port> getPortsForDataflow(String workflowID); |
| |
| /** |
| * lists all ports for a workflow |
| * |
| * @param workflowID |
| * @return a list of {@link Port} beans, each representing an input or |
| * output port for the workflow or a processor in the workflow |
| */ |
| List<Port> getAllPortsInDataflow(String workflowID); |
| |
| /** |
| * list all ports for a specific processor within a workflow |
| * |
| * @param workflowID |
| * @param processorName |
| * @return a list of {@link Port} beans, each representing an input or |
| * output port for the input processor |
| */ |
| List<Port> getPortsForProcessor(String workflowID, String processorName); |
| |
| // PM added 5/2010 |
| String getWorkflowNameByWorkflowID(String workflowID); |
| |
| WorkflowTree getWorkflowNestingStructure(String workflowID) |
| throws SQLException; |
| |
| /** |
| * include valus of output ports in the query result? input port values are |
| * always included<br> |
| * default is FALSE |
| */ |
| void toggleIncludeProcessorOutputs(boolean active); |
| |
| boolean isIncludeProcessorOutputs(); |
| |
| /** |
| * @return an instance of {@link InvocationContext} that can be used by a |
| * client to deref a Taverna data reference |
| */ |
| InvocationContext getInvocationContext(); |
| |
| /** |
| * should an OPM graph be generated in response to a query?<br> |
| * default is TRUE |
| */ |
| void toggleOPMGeneration(boolean active); |
| |
| /** |
| * |
| * @return true if OPM is set to be generated in response to a query |
| */ |
| boolean isOPMGenerationActive(); |
| |
| /** |
| * should actual artifact values be attached to OPM artifact nodes?<br> |
| * default is FALSE<br/> |
| * THIS IS CURRENTLY UNSUPPORTED -- DEFAULTS TO FALSE |
| * |
| * @param active |
| */ |
| void toggleAttachOPMArtifactValues(boolean active); |
| |
| /** |
| * @return true if the OPM graph artifacts are annotated with actual values |
| */ |
| boolean isAttachOPMArtifactValues(); |
| |
| /** |
| * @deprecated as workflow 'names' are not globally unique, this method |
| * should not be used! |
| * @param workflowName |
| * @return |
| */ |
| String getWorkflowIDForExternalName(String workflowName); |
| |
| List<ProvenanceProcessor> getProcessorsForWorkflowID(String workflowID); |
| |
| /** |
| * @return the singleton {@link AbstractProvenanceConnector} used by the API |
| * to operate on the DB. Currently we support MySQL |
| * {@link MySQLProvenanceConnector} and Derby |
| * {@link DerbyProvenanceConnector} connectors. The set of supported |
| * connectors is extensible. The available connectors are discovered |
| * automatically by the API upon startup, and it includes all the |
| * connectors that are mentioned in the <dependencies> section of |
| * pom.xml for Maven module |
| * {@code net.sf.taverna.t2.core.provenanceconnector} |
| */ |
| AbstractProvenanceConnector getProvenanceConnector(); |
| |
| /** |
| * @return |
| */ |
| ProvenanceAnalysis getAnalysis(); |
| |
| /** |
| * @return the pq |
| */ |
| ProvenanceQuery getQuery(); |
| |
| List<ProcessorEnactment> getProcessorEnactments(String workflowRunId, |
| String... processorPath); |
| |
| ProcessorEnactment getProcessorEnactmentByProcessId(String workflowRunId, |
| String processIdentifier, String iteration); |
| |
| ProcessorEnactment getProcessorEnactment(String processorEnactmentId); |
| |
| ProvenanceProcessor getProvenanceProcessor(String workflowId, |
| String processorNameRef); |
| |
| ProvenanceProcessor getProvenanceProcessor(String processorId); |
| |
| Map<Port, T2Reference> getDataBindings(String dataBindingId); |
| |
| DataflowInvocation getDataflowInvocation(String workflowRunId); |
| |
| DataflowInvocation getDataflowInvocation( |
| ProcessorEnactment processorEnactment); |
| |
| List<DataflowInvocation> getDataflowInvocations(String workflowRunId); |
| |
| List<DataLink> getDataLinks(String workflowId); |
| |
| } |