some provenance refactoring Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/550b5992 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/550b5992 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/550b5992
Branch: refs/heads/master Commit: 550b59920cfa5e4f6139192a28e9d734309b4a1e Parents: 49cd7de Author: Dmitry Repchevsky <redmi...@list.ru> Authored: Mon Mar 30 15:46:46 2015 +0200 Committer: Dmitry Repchevsky <redmi...@list.ru> Committed: Mon Mar 30 15:46:46 2015 +0200 ---------------------------------------------------------------------- .../sf/taverna/t2/provenance/Provenance.java | 316 --- .../provenance/ProvenanceConnectorFactory.java | 8 - .../taverna/t2/provenance/api/NativeAnswer.java | 66 - .../t2/provenance/api/ProvenanceAccess.java | 725 ------ .../provenance/api/ProvenanceConnectorType.java | 16 - .../net/sf/taverna/t2/provenance/api/Query.java | 105 - .../taverna/t2/provenance/api/QueryAnswer.java | 47 - .../connector/AbstractProvenanceConnector.java | 646 ------ .../t2/provenance/connector/ProvenanceSQL.java | 5 - .../lineageservice/AnnotationsLoader.java | 86 - .../provenance/lineageservice/Dependencies.java | 127 -- .../lineageservice/EventProcessor.java | 1547 ------------- .../LineageQueryResultRecord.java | 243 -- .../lineageservice/LineageSQLQuery.java | 82 - .../provenance/lineageservice/Provenance.java | 199 -- .../lineageservice/ProvenanceAnalysis.java | 1200 ---------- .../lineageservice/ProvenanceQuery.java | 2069 ------------------ .../lineageservice/ProvenanceWriter.java | 676 ------ .../provenance/lineageservice/URIGenerator.java | 58 - .../lineageservice/WorkflowDataProcessor.java | 453 ---- .../lineageservice/types/ActivityType.java | 87 - .../lineageservice/types/DataDocumentType.java | 75 - .../lineageservice/types/IterationType.java | 96 - .../lineageservice/types/LiteralType.java | 55 - .../lineageservice/types/PortType.java | 96 - .../lineageservice/types/PortsSequenceType.java | 64 - .../lineageservice/types/ProcessType.java | 105 - .../lineageservice/types/ProcessorType.java | 83 - .../types/ProvenanceEventType.java | 30 - .../lineageservice/utils/Activity.java | 63 - .../lineageservice/utils/Collection.java | 68 - .../lineageservice/utils/DDRecord.java | 149 -- .../lineageservice/utils/DataBinding.java | 82 - .../lineageservice/utils/DataLink.java | 127 -- .../utils/DataValueExtractor.java | 23 - .../utils/DataflowInvocation.java | 118 - .../lineageservice/utils/NestedListNode.java | 107 - .../provenance/lineageservice/utils/Port.java | 198 -- .../lineageservice/utils/PortBinding.java | 258 --- .../lineageservice/utils/ProcessorBinding.java | 127 -- .../utils/ProcessorEnactment.java | 151 -- .../utils/ProvenanceProcessor.java | 115 - .../lineageservice/utils/ProvenanceUtils.java | 128 -- .../lineageservice/utils/QueryPort.java | 119 - .../lineageservice/utils/ServiceInvocation.java | 161 -- .../lineageservice/utils/Workflow.java | 37 - .../lineageservice/utils/WorkflowRun.java | 72 - .../lineageservice/utils/WorkflowTree.java | 73 - .../taverna/t2/provenance/opm/OPMImporter.java | 541 ----- .../taverna/t2/provenance/opm/OPMManager.java | 414 ---- .../apache/taverna/provenance/Provenance.java | 316 +++ .../provenance/ProvenanceConnectorFactory.java | 8 + .../taverna/provenance/api/NativeAnswer.java | 66 + .../provenance/api/ProvenanceAccess.java | 725 ++++++ .../provenance/api/ProvenanceConnectorType.java | 16 + .../apache/taverna/provenance/api/Query.java | 105 + .../taverna/provenance/api/QueryAnswer.java | 47 + .../connector/AbstractProvenanceConnector.java | 646 ++++++ .../provenance/connector/ProvenanceSQL.java | 5 + .../lineageservice/AnnotationsLoader.java | 86 + .../provenance/lineageservice/Dependencies.java | 127 ++ .../lineageservice/EventProcessor.java | 1547 +++++++++++++ .../LineageQueryResultRecord.java | 243 ++ .../lineageservice/LineageSQLQuery.java | 82 + .../provenance/lineageservice/Provenance.java | 199 ++ .../lineageservice/ProvenanceAnalysis.java | 1200 ++++++++++ .../lineageservice/ProvenanceQuery.java | 2069 ++++++++++++++++++ .../lineageservice/ProvenanceWriter.java | 676 ++++++ .../provenance/lineageservice/URIGenerator.java | 58 + .../lineageservice/WorkflowDataProcessor.java | 453 ++++ .../lineageservice/types/ActivityType.java | 87 + .../lineageservice/types/DataDocumentType.java | 75 + .../lineageservice/types/IterationType.java | 96 + .../lineageservice/types/LiteralType.java | 55 + .../lineageservice/types/PortType.java | 96 + .../lineageservice/types/PortsSequenceType.java | 64 + .../lineageservice/types/ProcessType.java | 105 + .../lineageservice/types/ProcessorType.java | 83 + .../types/ProvenanceEventType.java | 30 + .../lineageservice/utils/Activity.java | 63 + .../lineageservice/utils/Collection.java | 68 + .../lineageservice/utils/DDRecord.java | 149 ++ .../lineageservice/utils/DataBinding.java | 82 + .../lineageservice/utils/DataLink.java | 127 ++ .../utils/DataValueExtractor.java | 23 + .../utils/DataflowInvocation.java | 118 + .../lineageservice/utils/NestedListNode.java | 107 + .../provenance/lineageservice/utils/Port.java | 198 ++ .../lineageservice/utils/PortBinding.java | 258 +++ .../lineageservice/utils/ProcessorBinding.java | 127 ++ .../utils/ProcessorEnactment.java | 151 ++ .../utils/ProvenanceProcessor.java | 115 + .../lineageservice/utils/ProvenanceUtils.java | 128 ++ .../lineageservice/utils/QueryPort.java | 119 + .../lineageservice/utils/ServiceInvocation.java | 161 ++ .../lineageservice/utils/Workflow.java | 37 + .../lineageservice/utils/WorkflowRun.java | 72 + .../lineageservice/utils/WorkflowTree.java | 73 + .../taverna/provenance/opm/OPMImporter.java | 541 +++++ .../taverna/provenance/opm/OPMManager.java | 414 ++++ .../spring/provenance-connector-context.xml | 8 +- 101 files changed, 12500 insertions(+), 12500 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/Provenance.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/Provenance.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/Provenance.java deleted file mode 100644 index f6009ca..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/Provenance.java +++ /dev/null @@ -1,316 +0,0 @@ -package net.sf.taverna.t2.provenance; - -import java.sql.SQLException; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import net.sf.taverna.t2.invocation.InvocationContext; -import net.sf.taverna.t2.provenance.api.Query; -import net.sf.taverna.t2.provenance.api.QueryAnswer; -import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector; -import net.sf.taverna.t2.provenance.lineageservice.Dependencies; -import net.sf.taverna.t2.provenance.lineageservice.LineageQueryResultRecord; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceQuery; -import net.sf.taverna.t2.provenance.lineageservice.utils.Collection; -import net.sf.taverna.t2.provenance.lineageservice.utils.DataLink; -import net.sf.taverna.t2.provenance.lineageservice.utils.DataflowInvocation; -import net.sf.taverna.t2.provenance.lineageservice.utils.Port; -import net.sf.taverna.t2.provenance.lineageservice.utils.PortBinding; -import net.sf.taverna.t2.provenance.lineageservice.utils.ProcessorEnactment; -import net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor; -import net.sf.taverna.t2.provenance.lineageservice.utils.Workflow; -import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowRun; -import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowTree; -import net.sf.taverna.t2.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); - -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/ProvenanceConnectorFactory.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/ProvenanceConnectorFactory.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/ProvenanceConnectorFactory.java deleted file mode 100644 index 0de22c2..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/ProvenanceConnectorFactory.java +++ /dev/null @@ -1,8 +0,0 @@ -package net.sf.taverna.t2.provenance; - -import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector; - -public interface ProvenanceConnectorFactory { - public AbstractProvenanceConnector getProvenanceConnector(); - public String getConnectorType(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/NativeAnswer.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/NativeAnswer.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/NativeAnswer.java deleted file mode 100644 index 65454cc..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/NativeAnswer.java +++ /dev/null @@ -1,66 +0,0 @@ -/** - * - */ -package net.sf.taverna.t2.provenance.api; - -import java.util.List; -import java.util.Map; - -import net.sf.taverna.t2.provenance.lineageservice.Dependencies; -import net.sf.taverna.t2.provenance.lineageservice.utils.QueryPort; -import net.sf.taverna.t2.provenance.lineageservice.LineageQueryResultRecord; - -/** - * Java bean used to encapsulate the results of a provenance query. <br/> - * This takes the form of a nested map, see {@link #getAnswer} for details on - * its structure. - * - * @author Paolo Missier - */ -public class NativeAnswer { - Map<QueryPort, Map<String, List<Dependencies>>> answer; - - /** - * @return a Map of the form: {@link QueryPort} --> ( <path> --> [ - * {@link Dependencies} ]) where - * <ul> - * <li> {@link QueryVar} denotes one of the ports in the <select> - * element of the input query, for example: - * <em>converter:atlasSlice</em> - * <li><path> is the index within the value associated to the - * port, for instance [1,2,3] or []. The inner Map structure - * accounts for multiple paths, so for example if the query asked - * for the provenance of elements [1,2] and [2,3] of the value bound - * to <em>converter:atlasSlice</em>, then the inner Map structure - * contains two entries, one for each of the two paths. - * <li>for each such path, the corresponding [{@link Dependencies}] - * is a list of {@link Dependencies}, each associated with one - * <it>target processor and port</it> mentioned in the input query. - * For example, for path [1,2] of value bound to - * <em>converter:atlasSlice</em>, you may see the following list of - * Dependencies: - * <ul> - * <li>converter:atlasSlice:[2] - * <li>slicer:atlasAverage[2] - * <li>slicer:atlasAverage[0] - * </ul> - * etc. <br/> - * Each of these elements is described by a Java bean, - * {@link LineageQueryResultRecord}, which represents a single - * provenance data record. This means that the particular value - * depends on each of these other values that are mentioned in the - * Dependencies list. - */ - public Map<QueryPort, Map<String, List<Dependencies>>> getAnswer() { - return answer; - } - - /** - * @param sets - * the query answer, in the format described in - * {@link #getAnswer()} - */ - public void setAnswer(Map<QueryPort, Map<String, List<Dependencies>>> answer) { - this.answer = answer; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceAccess.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceAccess.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceAccess.java deleted file mode 100644 index f3d6df9..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceAccess.java +++ /dev/null @@ -1,725 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2009 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * - ******************************************************************************/ -package net.sf.taverna.t2.provenance.api; - -import static java.sql.Connection.TRANSACTION_READ_UNCOMMITTED; -import static javax.naming.Context.INITIAL_CONTEXT_FACTORY; - -import java.sql.SQLException; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; -import java.util.Set; - -import javax.naming.InitialContext; -import javax.naming.NamingException; - -import net.sf.taverna.t2.invocation.InvocationContext; -import net.sf.taverna.t2.invocation.impl.InvocationContextImpl; -import net.sf.taverna.t2.provenance.Provenance; -import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory; -import net.sf.taverna.t2.provenance.connector.AbstractProvenanceConnector; -import net.sf.taverna.t2.provenance.lineageservice.Dependencies; -import net.sf.taverna.t2.provenance.lineageservice.LineageQueryResultRecord; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceQuery; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter; -import net.sf.taverna.t2.provenance.lineageservice.utils.Collection; -import net.sf.taverna.t2.provenance.lineageservice.utils.DataLink; -import net.sf.taverna.t2.provenance.lineageservice.utils.DataflowInvocation; -import net.sf.taverna.t2.provenance.lineageservice.utils.PortBinding; -import net.sf.taverna.t2.provenance.lineageservice.utils.ProcessorEnactment; -import net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor; -import net.sf.taverna.t2.provenance.lineageservice.utils.Port; -import net.sf.taverna.t2.provenance.lineageservice.utils.Workflow; -import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowRun; -import net.sf.taverna.t2.provenance.lineageservice.utils.WorkflowTree; -import net.sf.taverna.t2.reference.ReferenceService; -import net.sf.taverna.t2.reference.T2Reference; - -import org.apache.commons.dbcp.BasicDataSource; -import org.apache.log4j.Logger; - -/** - * 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 class ProvenanceAccess implements Provenance { - private static Logger logger = Logger.getLogger(ProvenanceAccess.class); - - private AbstractProvenanceConnector connector = null; - private ProvenanceAnalysis analyser = null; - private ProvenanceQuery querier; - private ProvenanceWriter writer; - - private String connectorType; - private final List<ProvenanceConnectorFactory> provenanceConnectorFactories; - - public ProvenanceAccess(String connectorType, - List<ProvenanceConnectorFactory> provenanceConnectorFactories) { - this.connectorType = connectorType; - this.provenanceConnectorFactories = provenanceConnectorFactories; - init(); - } - - public ProvenanceAccess(String connectorType, InvocationContext context, - List<ProvenanceConnectorFactory> provenanceConnectorFactories) { - this.connectorType = connectorType; - this.provenanceConnectorFactories = provenanceConnectorFactories; - init(context); - } - - /** - * The recommended data source intitialisation method, where only a driver - * name and jdbc url are required.<p/> - * If the driver supports multiple connections, then a pool will be created - * of 10 min idle, 50 max idle, and 50 max active connections. - * - * @param driverClassName - * @param jdbcUrl - */ - public static void initDataSource(String driverClassName, String jdbcUrl) { - initDataSource(driverClassName, jdbcUrl, null, null, 10, 50, 50); - } - - /** - * Initialises a named JNDI DataSource if not already set up externally. The - * DataSource is named jdbc/taverna - * - * @param driverClassName - * - the classname for the driver to be used. - * @param jdbcUrl - * - the jdbc connection url - * @param username - * - the username, if required (otherwise null) - * @param password - * - the password, if required (oteherwise null) - * @param minIdle - * - if the driver supports multiple connections, then the - * minumum number of idle connections in the pool - * @param maxIdle - * - if the driver supports multiple connections, then the - * maximum number of idle connections in the pool - * @param maxActive - * - if the driver supports multiple connections, then the - * minumum number of connections in the pool - */ - public static void initDataSource(String driverClassName, String jdbcUrl, - String username, String password, int minIdle, int maxIdle, - int maxActive) { - System.setProperty(INITIAL_CONTEXT_FACTORY, - "org.osjava.sj.memory.MemoryContextFactory"); - System.setProperty("org.osjava.sj.jndi.shared", "true"); - - BasicDataSource ds = new BasicDataSource(); - ds.setDriverClassName(driverClassName); - ds.setDefaultTransactionIsolation(TRANSACTION_READ_UNCOMMITTED); - ds.setMaxActive(maxActive); - ds.setMinIdle(minIdle); - ds.setMaxIdle(maxIdle); - ds.setDefaultAutoCommit(true); - if (username != null) - ds.setUsername(username); - if (password != null) - ds.setPassword(password); - ds.setUrl(jdbcUrl); - - try { - new InitialContext().rebind("jdbc/taverna", ds); - } catch (NamingException ex) { - logger.error("Problem rebinding the jdbc context", ex); - } - } - - /** - * 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 - */ - @Override - public InvocationContext initDefaultReferenceService() { - // FIXME - return initReferenceService("hibernateReferenceServiceContext.xml"); - } - - /** - * 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 - */ - @Override - public InvocationContext initReferenceService(String hibernateContext) { - // FIXME - return new InvocationContextImpl(refService, connector); - } - - private ReferenceService refService; - /** - * Set the Reference Service for the connector of this ProvenanceAccess - * if you do not 'like' the default one created when ProvenanceAccess is created. - */ - public void setReferenceService(ReferenceService refService) { - this.refService = refService; - if (connector != null) - connector.setReferenceService(refService); - } - - @Override - public void init() { - init(initDefaultReferenceService()); - } - - @Override - public void init(InvocationContext context) { - for (ProvenanceConnectorFactory factory : provenanceConnectorFactories) - if (connectorType.equalsIgnoreCase(factory.getConnectorType())) - connector = factory.getProvenanceConnector(); - logger.info("Provenance being captured using: " + connector); - - //slight change, the init is outside but it also means that the init call has to ensure that the dbURL - //is set correctly - connector.init(); - - connector.setReferenceService(context.getReferenceService()); // CHECK context.getReferenceService()); - connector.setInvocationContext(context); - - analyser = connector.getProvenanceAnalysis(); - analyser.setInvocationContext(context); - - querier = connector.getQuery(); - writer = connector.getWriter(); - writer.setQuery(querier); - - logger.info("using writer of type: " + writer.getClass()); - } - - /* - * main provenance query methods - */ - - /** - * Executes a provenance query. Please see separate doc. for the XML query language schema. - * @throws SQLException - */ - @Override - public QueryAnswer executeQuery(Query pq) throws SQLException { - return analyser.lineageQuery(pq.getTargetPorts(), pq.getRunIDList().get(0), - pq.getSelectedProcessors()); - } - - /** - * 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 - */ - @Override - public Dependencies fetchPortData(String workflowRunId, String workflowId, - String processorName, String portName, String iteration) { - logger.info("running fetchPortData on instance " + workflowRunId - + " workflow " + workflowId + " processor " + processorName - + " port " + portName + " iteration " + iteration); - // TODO add context workflowID to query - try { - return analyser.fetchIntermediateResult(workflowRunId, workflowId, - processorName, portName, iteration); - } catch (SQLException e) { - logger.error("Problem with fetching intermediate results", e); - return null; - } - } - - /** - * @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 - */ - @Override - public String getContainingCollection(LineageQueryResultRecord record) { - return querier.getContainingCollection(record); - } - - /* - * manage instances - */ - - /** - * @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 - */ - @Override - public List<WorkflowRun> listRuns(String workflowId, - Map<String, String> conditions) { - try { - return querier.getRuns(workflowId, conditions); - } catch (SQLException e) { - logger.error("Problem with listing runs", e); - return null; - } - } - - @Override - public boolean isTopLevelDataflow(String workflowId) { - return querier.isTopLevelDataflow(workflowId); - } - - @Override - public boolean isTopLevelDataflow(String workflowId, String workflowRunId) { - return querier.isTopLevelDataflow(workflowId, workflowRunId); - } - - @Override - public String getLatestRunID() throws SQLException { - return querier.getLatestRunID(); - } - - /** - * 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 - */ - @Override - public Set<String> removeRun(String runID) { - // implement using clearDynamic() method or a variation. Collect references and forward - try { - Set<String> danglingDataRefs = writer.clearDBDynamic(runID); - - if (logger.isDebugEnabled()) - logger.debug("references collected during removeRun: " + danglingDataRefs); - - // TODO send the list of dangling refs to the Data manager for removal of the corresponding data values - return danglingDataRefs; - } catch (SQLException e) { - logger.error("Problem while removing run : " + runID, e); - return null; - } - } - - /** - * 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 - */ - @Override - public void removeWorkflow(String workflowId) { - try { - writer.clearDBStatic(workflowId); - } catch (SQLException e) { - logger.error("Problem with removing static workflow: " + workflowId, e); - } - } - - /** - * 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 - */ - @Override - public List<String> getWorkflowID(String runID) { - try { - return querier.getWorkflowIdsForRun(runID); - } catch (SQLException e) { - logger.error("Problem getting workflow ID: " + runID, e); - return null; - } - } - - /** - * @param runID - * the internal ID for a specific workflow run - * @return the ID of the top-level workflow that executed during the input - * run - */ - @Override - public String getTopLevelWorkflowID(String runID) { - try { - return querier.getTopLevelWorkflowIdForRun(runID); - } catch (SQLException e) { - logger.error("Problem getting top level workflow: " + runID, e); - return null; - } - } - - @Override - public List<Workflow> getWorkflowsForRun(String runID) { - try { - return querier.getWorkflowsForRun(runID); - } catch (SQLException e) { - logger.error("Problem getting workflows for run:" + runID, e); - return null; - } - } - - /** - * @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) - */ - @Override - public List<WorkflowRun> getAllWorkflowIDs() { - try { - return querier.getRuns(null, null); - } catch (SQLException e) { - logger.error("Problem getting all workflow IDs", e); - return null; - } - } - -// / access static workflow structure - - /** - * @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) - */ - @Override - public Map<String, List<ProvenanceProcessor>> getProcessorsInWorkflow( - String workflowID) { - return querier.getProcessorsDeep(null, workflowID); - } - - @Override - public List<Collection> getCollectionsForRun(String wfInstanceID) { - return querier.getCollectionsForRun(wfInstanceID); - } - - @Override - public List<PortBinding> getPortBindings(Map<String, String> constraints) - throws SQLException { - return querier.getPortBindings(constraints); - } - - /** - * 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 - */ - @Override - public List<Port> getPortsForDataflow(String workflowID) { - return querier.getPortsForDataflow(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 - */ - @Override - public List<Port> getAllPortsInDataflow(String workflowID) { - return querier.getAllPortsInDataflow(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 - */ - @Override - public List<Port> getPortsForProcessor(String workflowID, - String processorName) { - return querier.getPortsForProcessor(workflowID, processorName); - } - - // PM added 5/2010 - @Override - public String getWorkflowNameByWorkflowID(String workflowID) { - return querier.getWorkflow(workflowID).getExternalName(); - } - - @Override - public WorkflowTree getWorkflowNestingStructure(String workflowID) - throws SQLException { - return querier.getWorkflowNestingStructure(workflowID); - } - -// public List<ProvenanceProcessor> getSuccessors(String workflowID, String processorName, String portName) { -// return null; // TODO -// } - -// public List<String> getActivities(String workflowID, String processorName) { -// return null; // TODO -// } - -// / configure provenance query functionality - - /** - * include valus of output ports in the query result? input port values are - * always included<br> - * default is FALSE - */ - @Override - public void toggleIncludeProcessorOutputs(boolean active) { - analyser.setReturnOutputs(active); - } - - @Override - public boolean isIncludeProcessorOutputs() { - return analyser.isReturnOutputs(); - } - - /** - * @return an instance of {@link InvocationContext} that can be used by a - * client to deref a Taverna data reference - */ - @Override - public InvocationContext getInvocationContext() { - return getProvenanceConnector().getInvocationContext(); - } - -// / OPM management - - /** - * should an OPM graph be generated in response to a query?<br> - * default is TRUE - */ - @Override - public void toggleOPMGeneration(boolean active) { - analyser.setGenerateOPMGraph(active); - } - - /** - * - * @return true if OPM is set to be generated in response to a query - */ - @Override - public boolean isOPMGenerationActive() { - return analyser.isGenerateOPMGraph(); - } - - /** - * should actual artifact values be attached to OPM artifact nodes?<br> - * default is FALSE<br/> - * THIS IS CURRENTLY UNSUPPORTED -- DEFAULTS TO FALSE - * - * @param active - */ - @Override - public void toggleAttachOPMArtifactValues(boolean active) { - analyser.setRecordArtifactValues(active); - } - - /** - * @return true if the OPM graph artifacts are annotated with actual values - */ - @Override - public boolean isAttachOPMArtifactValues() { - return analyser.isRecordArtifactValues(); - } - - /** - * @deprecated as workflow 'names' are not globally unique, this method - * should not be used! - * @param workflowName - * @return - */ - @Override - public String getWorkflowIDForExternalName(String workflowName) { - return querier.getWorkflowIdForExternalName(workflowName); - } - - @Override - public List<ProvenanceProcessor> getProcessorsForWorkflowID( - String workflowID) { - return querier.getProcessorsForWorkflow(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} - */ - @Override - public AbstractProvenanceConnector getProvenanceConnector() { - return connector; - } - - /** - * @param provenanceConnector - * a specific provenanceConnector used by the API - */ - public void setProvenanceConnector( - AbstractProvenanceConnector provenanceConnector) { - this.connector = provenanceConnector; - } - - /** - * @return - */ - @Override - public ProvenanceAnalysis getAnalysis() { - return analyser; - } - - /** - * @param pa - * the pa to set - */ - public void setPa(ProvenanceAnalysis pa) { - this.analyser = pa; - } - - /** - * @return the pq - */ - @Override - public ProvenanceQuery getQuery() { - return querier; - } - - /** - * @param pq - * the pq to set - */ - public void setPq(ProvenanceQuery pq) { - this.querier = pq; - } - - @Override - public List<ProcessorEnactment> getProcessorEnactments( - String workflowRunId, String... processorPath) { - return querier.getProcessorEnactments(workflowRunId, processorPath); - } - - @Override - public ProcessorEnactment getProcessorEnactmentByProcessId( - String workflowRunId, String processIdentifier, String iteration) { - return querier.getProcessorEnactmentByProcessId(workflowRunId, - processIdentifier, iteration); - } - - @Override - public ProcessorEnactment getProcessorEnactment(String processorEnactmentId) { - return querier.getProcessorEnactment(processorEnactmentId); - } - - @Override - public ProvenanceProcessor getProvenanceProcessor(String workflowId, - String processorNameRef) { - return querier.getProvenanceProcessorByName(workflowId, processorNameRef); - } - - @Override - public ProvenanceProcessor getProvenanceProcessor(String processorId) { - return querier.getProvenanceProcessorById(processorId); - } - - @Override - public Map<Port, T2Reference> getDataBindings(String dataBindingId) { - Map<Port, T2Reference> references = new HashMap<>(); - for (Entry<Port, String> entry : querier.getDataBindings(dataBindingId) - .entrySet()) - references.put(entry.getKey(), getProvenanceConnector() - .getReferenceService() - .referenceFromString(entry.getValue())); - return references; - } - - @Override - public DataflowInvocation getDataflowInvocation(String workflowRunId) { - return querier.getDataflowInvocation(workflowRunId); - } - - @Override - public DataflowInvocation getDataflowInvocation( - ProcessorEnactment processorEnactment) { - return querier.getDataflowInvocation(processorEnactment); - } - - @Override - public List<DataflowInvocation> getDataflowInvocations(String workflowRunId) { - return querier.getDataflowInvocations(workflowRunId); - } - - @Override - public List<DataLink> getDataLinks(String workflowId) { - try { - Map<String, String> queryConstraints = new HashMap<>(); - queryConstraints.put("workflowId", workflowId); - return querier.getDataLinks(queryConstraints); - } catch (SQLException e) { - logger.error( - "Problem getting datalinks for workflow:" + workflowId, e); - return null; - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceConnectorType.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceConnectorType.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceConnectorType.java deleted file mode 100644 index 5c32d42..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/ProvenanceConnectorType.java +++ /dev/null @@ -1,16 +0,0 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ - -package net.sf.taverna.t2.provenance.api; - -/** - * Defines names for the common Provenance Connector types - * - * @author Stuart Owen - */ -public class ProvenanceConnectorType { - public static final String MYSQL = "mysql"; - public static final String DERBY = "derby"; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/Query.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/Query.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/Query.java deleted file mode 100644 index e859c39..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/Query.java +++ /dev/null @@ -1,105 +0,0 @@ -/** - * - */ -package net.sf.taverna.t2.provenance.api; - -import java.util.List; - -import net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor; -import net.sf.taverna.t2.provenance.lineageservice.utils.QueryPort; - -/** - * Bean encapsulating one provenance query, consisting of the following - * elements: - * <ul> - * <li>static scope: the (single) name of the workflow whose run(s) are queried - * <li>dynamic scope: a list of workflow run IDs. - * <li>a list of <select> variables, encoded as List<{@link QueryPort}> - * <li>a list of <target> processors, encoded as List< - * {@link ProvenanceProcessor}> - * </ul> - * - * @author Paolo Missier - */ -public class Query { - private String workflowName; - private List<QueryPort> targetPorts; - private List<String> runIDList; - private List<ProvenanceProcessor> selectedProcessors; - - @Override - public String toString() { - StringBuilder sb = new StringBuilder(); - sb.append("\n **** QUERY SCOPE: ****\n").append("\tworkflow name: ") - .append(getWorkflowName()).append("\n\truns: "); - for (String r : getRunIDList()) - sb.append("\n\t").append(r); - sb.append("\n**** TARGET PORTS: ****\n"); - for (QueryPort v : getTargetPorts()) - sb.append("\n\t").append(v); - sb.append("\n\n**** SELECTED PROCESSORS: **** "); - for (ProvenanceProcessor pp : getSelectedProcessors()) - sb.append("\n\t").append(pp); - return sb.toString(); - } - - /** - * @return the targetVars - */ - public List<QueryPort> getTargetPorts() { - return targetPorts; - } - - /** - * @param targetVars - * the targetVars to set - */ - public void setTargetPorts(List<QueryPort> targetVars) { - this.targetPorts = targetVars; - } - - /** - * @return the selectedProcessors - */ - public List<ProvenanceProcessor> getSelectedProcessors() { - return selectedProcessors; - } - - /** - * @param selectedProcessors - * the selectedProcessors to set - */ - public void setFocus(List<ProvenanceProcessor> selectedProcessors) { - this.selectedProcessors = selectedProcessors; - } - - /** - * @return the runIDList - */ - public List<String> getRunIDList() { - return runIDList; - } - - /** - * @param runIDList - * the runIDList to set - */ - public void setRunIDList(List<String> runIDList) { - this.runIDList = runIDList; - } - - /** - * @return the workflowName - */ - public String getWorkflowName() { - return workflowName; - } - - /** - * @param workflowName - * the workflowName to set - */ - public void setWorkflowName(String workflowName) { - this.workflowName = workflowName; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/QueryAnswer.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/QueryAnswer.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/QueryAnswer.java deleted file mode 100644 index 1cc563c..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/api/QueryAnswer.java +++ /dev/null @@ -1,47 +0,0 @@ -/** - * - */ -package net.sf.taverna.t2.provenance.api; - -/** - * Encapsulates a native Java data structure as a well as a String that holds - * the OPM graph that represents the query answer - * - * @author Paolo Missier - * - */ -public class QueryAnswer { - private NativeAnswer nativeAnswer; - private String _OPMAnswer_AsRDF; - - /** - * @return the native Java part of the query answer - */ - public NativeAnswer getNativeAnswer() { - return nativeAnswer; - } - - /** - * @param sets - * the query answer - */ - public void setNativeAnswer(NativeAnswer a) { - this.nativeAnswer = a; - } - - /** - * @return the OPM graph as RDF/XML string, or null if OPM was inhibited - * {@see OPM.computeGraph in APIClient.properties} - */ - public String getOPMAnswer_AsRDF() { - return _OPMAnswer_AsRDF; - } - - /** - * @param set - * the OPM graph as RDF/XML string - */ - public void setOPMAnswer_AsRDF(String asRDF) { - _OPMAnswer_AsRDF = asRDF; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/AbstractProvenanceConnector.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/AbstractProvenanceConnector.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/AbstractProvenanceConnector.java deleted file mode 100644 index 1609efe..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/AbstractProvenanceConnector.java +++ /dev/null @@ -1,646 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.provenance.connector; - -import java.io.IOException; -import java.sql.Connection; -import java.sql.SQLException; -import java.util.List; -import java.util.Set; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.ScheduledThreadPoolExecutor; - -import net.sf.taverna.t2.invocation.InvocationContext; -import net.sf.taverna.t2.provenance.item.ProvenanceItem; -import net.sf.taverna.t2.provenance.item.WorkflowProvenanceItem; -import net.sf.taverna.t2.provenance.lineageservice.EventProcessor; -import net.sf.taverna.t2.provenance.lineageservice.LineageQueryResultRecord; -import net.sf.taverna.t2.provenance.lineageservice.Provenance; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceQuery; -import net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter; -import net.sf.taverna.t2.provenance.lineageservice.WorkflowDataProcessor; -import net.sf.taverna.t2.provenance.reporter.ProvenanceReporter; -import net.sf.taverna.t2.reference.ReferenceService; - -import org.apache.log4j.Logger; - -import uk.org.taverna.configuration.database.DatabaseManager; - -/** - * Collects {@link ProvenanceItem}s as it travels up and down the dispatch stack - * inside the InvocationContext - * - * @author Ian Dunlop - * @author Stuart Owen - * - */ -public abstract class AbstractProvenanceConnector implements ProvenanceReporter { - - public static enum ActivityTable { - Activity, activityId, activityDefinition, workflowId; - - public static String getCreateTable() { - return "CREATE TABLE " + Activity + "(\n" - + activityId + " varchar(36) NOT NULL,\n" - + activityDefinition + " blob NOT NULL,\n" - + workflowId + " varchar(100) NOT NULL, \n" - + "PRIMARY KEY (" + activityId + ")\n" + ")"; - } - } - - public static enum CollectionTable { - Collection, collID, parentCollIDRef, workflowRunId, processorNameRef, portName, iteration; - public static String getCreateTable() { - return "CREATE TABLE " + Collection + " (\n" - + collID + " varchar(100) NOT NULL,\n" - + parentCollIDRef + " varchar(100) NOT NULL ,\n" - + workflowRunId + " varchar(36) NOT NULL,\n" - + processorNameRef + " varchar(100) NOT NULL,\n" - + portName + " varchar(100) NOT NULL,\n" - + iteration + " varchar(2000) NOT NULL default '',\n" - + " PRIMARY KEY (\n" - + collID + "," + workflowRunId + "," + processorNameRef - + "," + portName + "," + parentCollIDRef + "," + iteration - + "))"; - } - } - - public static enum DataBindingTable { - DataBinding, dataBindingId, portId, t2Reference, workflowRunId; - - public static String getCreateTable() { - return "CREATE TABLE " + DataBinding + "(\n" - + dataBindingId + " varchar(36) NOT NULL,\n" - + portId + " varchar(36) NOT NULL,\n" - + t2Reference + " varchar(100) NOT NULL,\n" - + workflowRunId + " varchar(100) NOT NULL, \n" - + "PRIMARY KEY (" + dataBindingId + "," + portId + ")\n" + ")"; - } - } - - public static enum DataflowInvocationTable { - DataflowInvocation, dataflowInvocationId, - workflowId, - invocationStarted, invocationEnded, - inputsDataBinding, outputsDataBinding, - parentProcessorEnactmentId, workflowRunId, completed; - - public static String getCreateTable() { - return "CREATE TABLE " + DataflowInvocation + "(\n" - + dataflowInvocationId + " varchar(36) NOT NULL,\n" - + workflowId + " varchar(100) NOT NULL, \n" - + invocationStarted + " timestamp, \n" - + invocationEnded + " timestamp, \n" - + inputsDataBinding + " varchar(36),\n" - + outputsDataBinding + " varchar(36),\n" - + parentProcessorEnactmentId + " varchar(36), \n" - + workflowRunId + " varchar(100) NOT NULL, \n" - + completed + " smallint NOT NULL,\n" - + "PRIMARY KEY (" + dataflowInvocationId+ ")\n" + ")"; - } - } - - public static enum DataLinkTable { - Datalink, sourcePortName, sourcePortId, destinationPortId, - destinationPortName, sourceProcessorName, destinationProcessorName, workflowId; - public static String getCreateTable() { - return "CREATE TABLE " + Datalink + " (\n" - + sourcePortName + " varchar(100) NOT NULL ,\n" - + sourcePortId + " varchar(36) NOT NULL ,\n" - + destinationPortId + " varchar(36) NOT NULL ,\n" - + destinationPortName + " varchar(100) NOT NULL,\n" - + sourceProcessorName + " varchar(100) NOT NULL,\n" - + destinationProcessorName + " varchar(100) NOT NULL,\n" - + workflowId + " varchar(36) NOT NULL," - + " PRIMARY KEY (" - + sourcePortId + "," + destinationPortId + "," + workflowId - + "))"; - } - } - - public static enum PortBindingTable { - PortBinding, portName, workflowRunId, value, collIDRef, positionInColl, processorNameRef, valueType, ref, iteration, workflowId; - public static String getCreateTable() { - return "CREATE TABLE " + PortBinding + " (\n" - + portName + " varchar(100) NOT NULL,\n" - + workflowRunId + " varchar(100) NOT NULL,\n" - + value + " varchar(100) default NULL,\n" - + collIDRef + " varchar(100),\n" - + positionInColl + " int NOT NULL,\n" - + processorNameRef + " varchar(100) NOT NULL,\n" - + valueType + " varchar(50) default NULL,\n" - + ref + " varchar(100) default NULL,\n" - + iteration + " varchar(2000) NOT NULL,\n" - + workflowId + " varchar(36),\n" - + "PRIMARY KEY (\n" - + portName + "," + workflowRunId + "," - + processorNameRef + "," + iteration + ", " + workflowId - + "))"; - } - } - - public static enum PortTable { - Port, portId, processorId, portName, isInputPort, processorName, - workflowId, depth, resolvedDepth, iterationStrategyOrder; - public static String getCreateTable() { - return "CREATE TABLE " + Port + " (\n" - + portId + " varchar(36) NOT NULL,\n" - + processorId + " varchar(36),\n" - + portName + " varchar(100) NOT NULL,\n" - + isInputPort + " smallint NOT NULL ,\n" - + processorName + " varchar(100) NOT NULL,\n" - + workflowId + " varchar(36) NOT NULL,\n" - + depth + " int,\n" - + resolvedDepth + " int,\n" - + iterationStrategyOrder + " smallint, \n" - + "PRIMARY KEY (" + "portId" + "),\n" - + "CONSTRAINT port_constraint UNIQUE (\n" - + portName + "," + isInputPort + "," + processorName + "," + workflowId + "\n" - + "))"; - } - } - - public static enum ProcessorEnactmentTable { - ProcessorEnactment, processEnactmentId, workflowRunId, processorId, - processIdentifier, iteration, parentProcessorEnactmentId, - enactmentStarted, enactmentEnded, initialInputsDataBindingId, - finalOutputsDataBindingId; - - public static String getCreateTable() { - return "CREATE TABLE " + ProcessorEnactment + " (\n" - + processEnactmentId + " varchar(36) NOT NULL, \n" - + workflowRunId + " varchar(100) NOT NULL, \n" - + processorId + " varchar(36) NOT NULL, \n" - + processIdentifier + " varchar(2047) NOT NULL, \n" - + iteration + " varchar(100) NOT NULL, \n" - + parentProcessorEnactmentId + " varchar(36), \n" - + enactmentStarted + " timestamp, \n" - + enactmentEnded + " timestamp, \n" - + initialInputsDataBindingId + " varchar(36), \n" - + finalOutputsDataBindingId + " varchar(36), \n" - + " PRIMARY KEY (" + processEnactmentId + ")" + ")"; - } - } - - public static enum ProcessorTable { - Processor,processorId, processorName,workflowId,firstActivityClass,isTopLevel ; - public static String getCreateTable() { - return "CREATE TABLE "+ Processor +" (\n" - + processorId + " varchar(36) NOT NULL,\n" - + processorName + " varchar(100) NOT NULL,\n" - + workflowId + " varchar(36) NOT NULL ,\n\n" - + firstActivityClass + " varchar(100) default NULL,\n" - + isTopLevel + " smallint, \n" - + "PRIMARY KEY (" + processorId+ "),\n" - + "CONSTRAINT processor_constraint UNIQUE (\n" - + processorName + "," + workflowId + "))"; - } - } - - public static enum ServiceInvocationTable { - ServiceInvocation, processorEnactmentId, workflowRunId, - invocationNumber, invocationStarted, invocationEnded, - inputsDataBinding, outputsDataBinding, failureT2Reference, - activityId, initiatingDispatchLayer, finalDispatchLayer; - - public static String getCreateTable() { - return "CREATE TABLE " + ServiceInvocation + "(\n" - + processorEnactmentId + " varchar(36) NOT NULL,\n" - + workflowRunId + " varchar(100) NOT NULL, \n" - + invocationNumber + " bigint NOT NULL,\n" - + invocationStarted + " timestamp, \n" - + invocationEnded + " timestamp, \n" - + inputsDataBinding + " varchar(36),\n" - + outputsDataBinding + " varchar(36),\n" - + failureT2Reference + " varchar(100) default NULL,\n" - + activityId + " varchar(36),\n" - + initiatingDispatchLayer + " varchar(250) NOT NULL,\n" - + finalDispatchLayer + " varchar(250) NOT NULL,\n" - + "PRIMARY KEY (" + processorEnactmentId + ", " - + invocationNumber + "))"; - } - } - - public static enum WorkflowRunTable { - WorkflowRun, workflowRunId, workflowId, timestamp; - public static String getCreateTable() { - return "CREATE TABLE " + WorkflowRun + " (\n" - + workflowRunId + " varchar(36) NOT NULL,\n" - + workflowId + " varchar(36) NOT NULL,\n" - + timestamp + " timestamp NOT NULL default CURRENT_TIMESTAMP,\n" - + " PRIMARY KEY (" + workflowRunId + ", " + workflowId + "))"; - } - } - - public static enum WorkflowTable { - WorkflowTable, workflowId, parentWorkflowId, externalName, dataflow; - public static String getCreateTable() { - return "CREATE TABLE " + "Workflow (\n" + - workflowId + " varchar(36) NOT NULL,\n" - + parentWorkflowId + " varchar(100),\n" - + externalName + " varchar(100),\n" - + dataflow + " blob, \n" - + "PRIMARY KEY (" + workflowId + "))"; - } - } - - private static Logger logger = Logger.getLogger(AbstractProvenanceConnector.class); - private String saveEvents; - private ProvenanceAnalysis provenanceAnalysis; - private ExecutorService executor = Executors.newSingleThreadExecutor(); - private boolean finished = false; - private String sessionID; - private InvocationContext invocationContext; - private ReferenceService referenceService; - - private Provenance provenance; - private ProvenanceWriter writer; - private ProvenanceQuery query; - private WorkflowDataProcessor wfdp; - private EventProcessor eventProcessor; - private final DatabaseManager databaseManager; - - public AbstractProvenanceConnector(DatabaseManager databaseManager) { - this.databaseManager = databaseManager; - } - - /** - * Set up the the {@link EventProcessor}, {@link ProvenanceWriter} & - * {@link ProvenanceQuery}. Since it is an SPI you don't want any code - * cluttering the default constructor. Call this method after instantiation - * and after the dbURL has been set. - */ - public void init() { - createDatabase(); - try { - setWfdp(new WorkflowDataProcessor()); - getWfdp().setPq(getQuery()); - getWfdp().setPw(getWriter()); - - setEventProcessor(new EventProcessor()); - getEventProcessor().setPw(getWriter()); - getEventProcessor().setPq(getQuery()); - getEventProcessor().setWfdp(getWfdp()); - - setProvenanceAnalysis(new ProvenanceAnalysis(getQuery())); - setProvenance(new Provenance(getEventProcessor())); - } catch (InstantiationException | IllegalAccessException - | ClassNotFoundException | SQLException e) { - logger.error("Problem with provenance initialisation: ", e); - } - } - - /** - * @return the invocationContext - */ - @Override - public InvocationContext getInvocationContext() { - return invocationContext; - } - - /** - * @param invocationContext - * the invocationContext to set - */ - @Override - public void setInvocationContext(InvocationContext invocationContext) { - this.invocationContext = invocationContext; - } - - /** - * @return the referenceService - */ - @Override - public ReferenceService getReferenceService() { - return referenceService; - } - - /** - * @param referenceService - * the referenceService to set - */ - @Override - public void setReferenceService(ReferenceService referenceService) { - this.referenceService = referenceService; - } - - /** - * Uses a {@link ScheduledThreadPoolExecutor} to process events in a Thread - * safe manner - */ - @Override - public synchronized void addProvenanceItem( - final ProvenanceItem provenanceItem) { - -// Runnable runnable = new Runnable() { -// -// public void run() { - try { - - getProvenance().acceptRawProvenanceEvent( - provenanceItem.getEventType(), provenanceItem); - - } catch (SQLException e) { - logger.warn("Could not add provenance for " + provenanceItem.getEventType() + " " + provenanceItem.getIdentifier(), e); - } catch (IOException e) { - logger.error("Could not add provenance for " + provenanceItem.getEventType() + " " + provenanceItem.getIdentifier(), e); - } catch (RuntimeException e) { - logger.error("Could not add provenance for " + provenanceItem.getEventType() + " " + provenanceItem.getIdentifier(), e); - } -// -// } -// }; -// getExecutor().execute(runnable); - - } - - protected Connection getConnection() throws SQLException { - return databaseManager.getConnection(); - } - - /** - * Used by database backed provenance stores. Ask the implementation to - * create the database. Requires each datbase type to create all its own - * tables - */ - public abstract void createDatabase(); - - - public void clearDatabase() { clearDatabase(true); } - - /** - * Clear all the values in the database but keep the db there - */ - public void clearDatabase(boolean isClearDB) { - if (isClearDB) { - logger.info("clearing DB"); - try { - getWriter().clearDBStatic(); - - Set<String> danglingDataRefs = getWriter().clearDBDynamic(); - - logger.info("references collected during removeRun:"); - for (String s : danglingDataRefs) - logger.info(s); - } catch (SQLException e) { - logger.error("Problem clearing database", e); - } - } else { - logger.error("clearDB is FALSE: not clearing"); - } - -// String q = null; -// Connection connection = null; - -// Statement stmt = null; -// try { -// connection = getConnection(); -// stmt = connection.createStatement(); -// } catch (SQLException e) { -// logger.warn("Could not create database statement :" + e); -// } catch (InstantiationException e) { -// logger.warn("Could not create database statement :" + e); -// } catch (IllegalAccessException e) { -// logger.warn("Could not create database statement :" + e); -// } catch (ClassNotFoundException e) { -// logger.warn("Could not create database statement :" + e); -// } - -// q = "DELETE FROM Workflow"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM Processor"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM Datalink"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM Port"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM WorkflowRun"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM ProcBinding"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM PortBinding"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - -// q = "DELETE FROM Collection"; -// try { -// stmt.executeUpdate(q); -// } catch (SQLException e) { -// logger.warn("Could not execute statement " + q + " :" + e); -// } - - -// if (connection!=null) try { -// connection.close(); -// } catch (SQLException ex) { -// logger.error("Error closing connection",ex); -// } - } - - /** - * The name for this type of provenance connector. Is used by the workbench - * to ensure it adds the correct one to the InvocationContext - * - * @return - */ - public abstract String getName(); - - /** - * A unique identifier for this run of provenance, should correspond to the - * initial {@link WorkflowProvenanceItem} idenifier that gets sent through - * - * @param identifier - */ - @Override - public void setSessionID(String sessionID) { - this.sessionID = sessionID; - } - - /** - * What is the unique identifier used by this connector - * - * @return - */ - @Override - public String getSessionID() { - return sessionID; - } - - - public List<LineageQueryResultRecord> computeLineage(String workflowRun, - String port, String proc, String path, Set<String> selectedProcessors) { - return null; - } - - public String getDataflowInstance(String dataflowId) { - try { - return (getProvenance()).getPq().getRuns(dataflowId, null).get(0) - .getWorkflowRunId(); - } catch (SQLException e) { - logger.error("Error finding the dataflow instance", e); - return null; - } - } - - /** - * @return the saveEvents - */ - public String getSaveEvents() { - return saveEvents; - } - - /** - * @param saveEvents - * the saveEvents to set - */ - public void setSaveEvents(String saveEvents) { - this.saveEvents = saveEvents; - } - - public void setProvenance(Provenance provenance) { - this.provenance = provenance; - } - - public Provenance getProvenance() { - return provenance; - } - - public void setFinished(boolean finished) { - this.finished = finished; - } - - public boolean isFinished() { - return finished; - } - - public void setExecutor(ExecutorService executor) { - this.executor = executor; - } - - public synchronized ExecutorService getExecutor() { - return executor; - } - - public void setProvenanceAnalysis(ProvenanceAnalysis provenanceAnalysis) { - this.provenanceAnalysis = provenanceAnalysis; - } - - /** - * Use this {@link ProvenanceAnalysis} to carry out lineage queries on the - * provenance - * - * @return - */ - public ProvenanceAnalysis getProvenanceAnalysis() { - return provenanceAnalysis; - } - - /** - * @return the writer - */ - public ProvenanceWriter getWriter() { - return writer; - } - - /** - * @param writer the writer to set - */ - protected void setWriter(ProvenanceWriter writer) { - this.writer = writer; - } - - /** - * @return the query - */ - public ProvenanceQuery getQuery() { - return query; - } - - /** - * @param query the query to set - */ - protected void setQuery(ProvenanceQuery query) { - this.query = query; - } - - /** - * @return the wfdp - */ - public WorkflowDataProcessor getWfdp() { - return wfdp; - } - - /** - * @param wfdp the wfdp to set - */ - public void setWfdp(WorkflowDataProcessor wfdp) { - this.wfdp = wfdp; - } - - /** - * @return the eventProcessor - */ - public EventProcessor getEventProcessor() { - return eventProcessor; - } - - /** - * @param eventProcessor the eventProcessor to set - */ - public void setEventProcessor(EventProcessor eventProcessor) { - this.eventProcessor = eventProcessor; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/ProvenanceSQL.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/ProvenanceSQL.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/ProvenanceSQL.java deleted file mode 100644 index 628c80e..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/connector/ProvenanceSQL.java +++ /dev/null @@ -1,5 +0,0 @@ -package net.sf.taverna.t2.provenance.connector; - -public class ProvenanceSQL { - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/AnnotationsLoader.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/AnnotationsLoader.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/AnnotationsLoader.java deleted file mode 100644 index 203c168..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/AnnotationsLoader.java +++ /dev/null @@ -1,86 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.provenance.lineageservice; - -import java.io.FileReader; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.apache.log4j.Logger; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.input.SAXBuilder; - -/** - * @author Paolo Missier - * - */ -public class AnnotationsLoader { - private static Logger logger = Logger.getLogger(AnnotationsLoader.class); - - /** - * @param annotationFile - * by convention we use <workflow file name>+"annotations" - * @return a map pname -> annotation so that the lineage query alg can use - * the annotation when processing pname - */ - @SuppressWarnings("unchecked") - public Map<String,List<String>> getAnnotations(String annotationFile) { - Map<String, List<String>> procAnnotations = new HashMap<>(); - - // load XML file as doc -// parse the event into DOM - SAXBuilder b = new SAXBuilder(); - - try { - Document d = b.build(new FileReader(annotationFile)); - if (d == null) - return null; - - // look for all processor elements - for (Element el : (List<Element>) d.getRootElement().getChildren()) { - String pName = el.getAttributeValue("name"); - logger.info("processor name: " + pName); - - List<String> annotations = new ArrayList<>(); - // extract all annotations for this pname - - for (Element annotElement : (List<Element>) el.getChildren()) { - String annot = annotElement.getAttributeValue("type"); - logger.info("annotation: " + annot); - - // add this annotation - annotations.add(annot); - } - - procAnnotations.put(pName, annotations); - } - } catch (JDOMException | IOException e) { - logger.error("Problem getting annotations from: " + annotationFile, - e); - } - return procAnnotations; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/550b5992/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/Dependencies.java ---------------------------------------------------------------------- diff --git a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/Dependencies.java b/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/Dependencies.java deleted file mode 100644 index 3522dce..0000000 --- a/taverna-provenanceconnector/src/main/java/net/sf/taverna/t2/provenance/lineageservice/Dependencies.java +++ /dev/null @@ -1,127 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.provenance.lineageservice; - -import java.util.ArrayList; -import java.util.List; -import java.util.ListIterator; - -/** - * Java bean to hold a list of {@link LineageQueryResultRecord}, representing - * one record in the provenance DB at the finest possible level of granularity, - * i.e., a single value possibly within a collection, bound to a processor port - * and associated to a specific run of a specific workflow. - * - * @author Paolo Missier - * @see LineageQueryResultRecord - */ -public class Dependencies { - final public static String COLL_TYPE = "referenceSetCollection"; - final public static String ATOM_TYPE = "referenceSet"; - - boolean printResolvedValue; - - private List<LineageQueryResultRecord> records = new ArrayList<>(); - - public ListIterator<LineageQueryResultRecord> iterator() { - return getRecords().listIterator(); - } - - /** - * adds a single record to the list of dependencies - * - * @param workflowId - * @param pname - * @param vname - * @param workflowRun - * @param iteration - * @param collIdRef - * @param parentCollIDRef - * @param value - * @param resolvedValue - * @param type - * @param isInput - * @param isCollection - */ - public void addLineageQueryResultRecord(String workflowId, String pname, - String vname, String workflowRun, String iteration, - String collIdRef, String parentCollIDRef, String value, - String resolvedValue, String type, boolean isInput, - boolean isCollection) { - - LineageQueryResultRecord record = new LineageQueryResultRecord(); - - record.setWorkflowId(workflowId); - record.setWorkflowRunId(workflowRun); - record.setProcessorName(pname); - record.setValue(value); - record.setPortName(vname); - record.setIteration(iteration); - record.setResolvedValue(resolvedValue); - record.setIsInputPort(isInput); - record.setCollectionT2Reference(collIdRef); - record.setParentCollIDRef(parentCollIDRef); - record.setCollection(isCollection); - - getRecords().add(record); - } - - /** - * populates the bean with an entire list of {@link LineageQueryResultRecord} elements - * @param records - */ - public void setRecords(List<LineageQueryResultRecord> records) { - this.records = records; - } - - /** - * @return the entire set of records - */ - public List<LineageQueryResultRecord> getRecords() { - return records; - } - - @Override - public String toString() { - StringBuilder sb = new StringBuilder(); - for (LineageQueryResultRecord record : getRecords()) { - record.setPrintResolvedValue(printResolvedValue); - sb.append("*** record: ****\n"+record.toString()); - } - return sb.toString(); - } - - /** - * @return true is the records contain the actual values, in addition to the URI references to the values - * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version - */ - public boolean isPrintResolvedValue() { - return printResolvedValue; - } - - /** - * @param toggles insertion of values in addition to references to values in the records - * <br/>NOT YET SUPPORTED. This switch is currently ignored and no values are returned in the current version - */ - public void setPrintResolvedValue(boolean printResolvedValue) { - this.printResolvedValue = printResolvedValue; - } -}
