TAVERNA-971 Use our own jarcache.json as a workaround and set Thread context class loader to the taverna-commandline-common classloader.
contexts/bundle.jsonld copied from taverna-robundle Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/1f97dd0a Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/1f97dd0a Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/1f97dd0a Branch: refs/heads/master Commit: 1f97dd0a4ea24231c7405286baa6b2e309190045 Parents: 9786332 Author: Stian Soiland-Reyes <[email protected]> Authored: Thu May 26 16:21:19 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Thu May 26 16:35:05 2016 +0100 ---------------------------------------------------------------------- .../taverna/commandline/CommandLineTool.java | 83 ++++++----- .../src/main/resources/contexts/bundle.jsonld | 140 +++++++++++++++++++ .../src/main/resources/jarcache.json | 11 ++ 3 files changed, 198 insertions(+), 36 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/1f97dd0a/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java ---------------------------------------------------------------------- diff --git a/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java index 5133f21..90a6d47 100644 --- a/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java +++ b/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java @@ -33,6 +33,12 @@ import java.util.Set; import javax.naming.NamingException; +import org.apache.log4j.Level; +import org.apache.log4j.LogManager; +import org.apache.log4j.Logger; +import org.apache.log4j.PatternLayout; +import org.apache.log4j.PropertyConfigurator; +import org.apache.log4j.RollingFileAppender; import org.apache.taverna.commandline.data.DatabaseConfigurationHandler; import org.apache.taverna.commandline.data.InputsHandler; import org.apache.taverna.commandline.data.SaveResultsHandler; @@ -42,16 +48,19 @@ import org.apache.taverna.commandline.exceptions.InvalidOptionException; import org.apache.taverna.commandline.exceptions.OpenDataflowException; import org.apache.taverna.commandline.exceptions.ReadInputException; import org.apache.taverna.commandline.options.CommandLineOptions; -import org.apache.taverna.security.credentialmanager.CMException; -import org.apache.taverna.security.credentialmanager.CredentialManager; - -import org.apache.log4j.Level; -import org.apache.log4j.LogManager; -import org.apache.log4j.Logger; -import org.apache.log4j.PatternLayout; -import org.apache.log4j.PropertyConfigurator; -import org.apache.log4j.RollingFileAppender; +import org.apache.taverna.configuration.database.DatabaseConfiguration; +import org.apache.taverna.configuration.database.DatabaseManager; import org.apache.taverna.databundle.DataBundles; +import org.apache.taverna.platform.execution.api.ExecutionEnvironment; +import org.apache.taverna.platform.execution.api.InvalidExecutionIdException; +import org.apache.taverna.platform.execution.api.InvalidWorkflowException; +import org.apache.taverna.platform.report.State; +import org.apache.taverna.platform.report.WorkflowReport; +import org.apache.taverna.platform.run.api.InvalidRunIdException; +import org.apache.taverna.platform.run.api.RunProfile; +import org.apache.taverna.platform.run.api.RunProfileException; +import org.apache.taverna.platform.run.api.RunService; +import org.apache.taverna.platform.run.api.RunStateException; import org.apache.taverna.robundle.Bundle; import org.apache.taverna.scufl2.api.common.NamedSet; import org.apache.taverna.scufl2.api.container.WorkflowBundle; @@ -65,19 +74,10 @@ import org.apache.taverna.scufl2.validation.correctness.CorrectnessValidator; import org.apache.taverna.scufl2.validation.correctness.ReportCorrectnessValidationListener; import org.apache.taverna.scufl2.validation.structural.ReportStructuralValidationListener; import org.apache.taverna.scufl2.validation.structural.StructuralValidator; +import org.apache.taverna.security.credentialmanager.CMException; +import org.apache.taverna.security.credentialmanager.CredentialManager; -import org.apache.taverna.configuration.database.DatabaseConfiguration; -import org.apache.taverna.configuration.database.DatabaseManager; -import org.apache.taverna.platform.execution.api.ExecutionEnvironment; -import org.apache.taverna.platform.execution.api.InvalidExecutionIdException; -import org.apache.taverna.platform.execution.api.InvalidWorkflowException; -import org.apache.taverna.platform.report.State; -import org.apache.taverna.platform.report.WorkflowReport; -import org.apache.taverna.platform.run.api.InvalidRunIdException; -import org.apache.taverna.platform.run.api.RunProfile; -import org.apache.taverna.platform.run.api.RunProfileException; -import org.apache.taverna.platform.run.api.RunService; -import org.apache.taverna.platform.run.api.RunStateException; +import com.github.jsonldjava.utils.JsonUtils; /** * A utility class that wraps the process of executing a workflow, allowing workflows to be easily @@ -87,6 +87,7 @@ import org.apache.taverna.platform.run.api.RunStateException; * @author Alex Nenadic */ public class CommandLineTool { + private static final String BUNDLE_CONTEXT = "https://w3id.org/bundle/context";; private static boolean BOOTSTRAP_LOGGING = false; private static Logger logger = Logger.getLogger(CommandLineTool.class); @@ -160,25 +161,22 @@ public class CommandLineTool { } } } - + public int setupAndExecute() throws InputMismatchException, InvalidOptionException, CMException, OpenDataflowException, ReaderException, IOException, ValidationException, ReadInputException, InvalidWorkflowException, RunProfileException, InvalidRunIdException, RunStateException, InvalidExecutionIdException, DatabaseConfigurationException { - - if (!commandLineOptions.askedForHelp()) { + + if (commandLineOptions.askedForHelp()) { + commandLineOptions.displayHelp(); + return 0; + } setupDatabase(commandLineOptions); - + setupJarCache(); + + if (commandLineOptions.getWorkflow() != null) { - /* Set context class loader to us, - * so that things such as JSON-LD caching of - * robundle works. - */ - - Thread.currentThread().setContextClassLoader(getClass().getClassLoader()); - - /* * Initialise Credential Manager and SSL stuff quite early as * parsing and validating the workflow may require it @@ -309,9 +307,7 @@ public class CommandLineTool { System.out.println("Workflow completed."); } - } - } else { - commandLineOptions.displayHelp(); + } // wait until user hits CTRL-C before exiting @@ -329,6 +325,21 @@ public class CommandLineTool { return 0; } + private void setupJarCache() { + // TAVERNA-xx workaround - we'll have our own jarcache.json and + // our own bundle.jsonld + Thread.currentThread().setContextClassLoader(getClass().getClassLoader()); + + // Verify: + try { + JsonUtils.fromURL(new URL(BUNDLE_CONTEXT)); + } catch (Exception e) { + System.err.println("Can't load " + BUNDLE_CONTEXT + ""); + e.printStackTrace(); + + } + } + private boolean workflowFinished(WorkflowReport report) { State state = report.getState(); if (state == State.CANCELLED || state == State.COMPLETED || state == State.FAILED) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/1f97dd0a/taverna-commandline-common/src/main/resources/contexts/bundle.jsonld ---------------------------------------------------------------------- diff --git a/taverna-commandline-common/src/main/resources/contexts/bundle.jsonld b/taverna-commandline-common/src/main/resources/contexts/bundle.jsonld new file mode 100644 index 0000000..cadb9ff --- /dev/null +++ b/taverna-commandline-common/src/main/resources/contexts/bundle.jsonld @@ -0,0 +1,140 @@ +{ + "http://purl.org/dc/terms/license"; : + "Licensed to the Apache Software Foundation (ASF) under one or more\n contributor license agreements. See the NOTICE file distributed with\n this work for additional information regarding copyright ownership.\n The ASF licenses this file to You under the Apache License, Version 2.0\n (the \"License\"); you may not use this file except in compliance with\n the License. You may obtain a copy of the License at\n \n http://www.apache.org/licenses/LICENSE-2.0\n \n Unless required by applicable law or agreed to in writing, software\n distributed under the License is distributed on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n See the License for the specific language governing permissions and\n limitations under the License.\n", + "@context": { + "ao": "http://purl.org/ao/";, + "oa": "http://www.w3.org/ns/oa#";, + "dc": "http://purl.org/dc/elements/1.1/";, + "dct": "http://purl.org/dc/terms/";, + "ore": "http://www.openarchives.org/ore/terms/";, + "ro": "http://purl.org/wf4ever/ro#";, + "roterms": "http://purl.org/wf4ever/roterms#";, + "bundle": "http://purl.org/wf4ever/bundle#";, + "prov": "http://www.w3.org/ns/prov#";, + "pav": "http://purl.org/pav/";, + "xsd": "http://www.w3.org/2001/XMLSchema#";, + "foaf": "http://xmlns.com/foaf/0.1/";, + "owl": "http://www.w3.org/2002/07/owl#";, + + "uri": "@id", + "id": { + "@id": "owl:sameAs", + "@type": "@id" }, + "file": { + "@id": "owl:sameAs", + "@type": "@id" }, + "annotation": { + "@id": "owl:sameAs", + "@type": "@id" }, + + "manifest": { + "@id": "ore:isDescribedBy", + "@type": "@id" + }, + + "createdOn": { + "@id": "pav:createdOn", + "@type": "xsd:dateTime" + }, + "createdBy": { + "@id": "pav:createdBy", + "@type": "@id" + }, + "aggregatedOn": { + "@id": "pav:createdOn", + "@type": "xsd:dateTime" + }, + "aggregatedBy": { + "@id": "pav:createdBy", + "@type": "@id" + }, + "authoredOn": { + "@id": "pav:authoredOn", + "@type": "xsd:dateTime" + }, + "authoredBy": { + "@id": "pav:authoredBy", + "@type": "@id" + }, + "curatedOn": { + "@id": "pav:curatedOn", + "@type": "xsd:dateTime" + }, + "curatedBy": { + "@id": "pav:curatedBy", + "@type": "@id" + }, + "contributedOn": { + "@id": "pav:contributedOn", + "@type": "xsd:dateTime" + }, + "contributedBy": { + "@id": "pav:contributedBy", + "@type": "@id" + }, + "retrievedOn": { + "@id": "pav:retrievedOn", + "@type": "xsd:dateTime" + }, + "retrievedBy": { + "@id": "pav:retrievedBy", + "@type": "@id" + }, + "retrievedFrom": { + "@id": "pav:retrievedFrom", + "@type": "@id" + }, + "name": { + "@id": "foaf:name" + }, + "orcid": { + "@id": "roterms:orcid", + "@type": "@id" + }, + + "history": { + "@id": "prov:has_provenance", + "@type": "@id" + }, + "aggregates": { + "@id": "ore:aggregates", + "@type": "@id" + }, + "mediatype": { + "@id": "dc:format" + }, + "folder": { + "@id": "bundle:inFolder", + "@type": "@id" + }, + "filename": { + "@id": "ro:entryName" + }, + "proxy": { + "@id": "bundle:hasProxy", + "@type": "@id" + }, + "bundledAs": { + "@id": "bundle:bundledAs", + "@type": "@id" + }, + "conformsTo": { + "@id": "dct:conformsTo", + "@type": "@id" + }, + "annotations": { + "@id": "bundle:hasAnnotation", + "@type": "@id" + }, + "content": { + "@id": "oa:hasBody", + "@type": "@id" + }, + "about": { + "@id": "oa:hasTarget", + "@type": "@id" + } + + }, + "http://purl.org/pav/retrievedFrom": { "@id": "https://raw.githubusercontent.com/wf4ever/ro/61b563e7e9941485ff6e7b338875d4015d734b6f/bundle/draft/context.json"; } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/1f97dd0a/taverna-commandline-common/src/main/resources/jarcache.json ---------------------------------------------------------------------- diff --git a/taverna-commandline-common/src/main/resources/jarcache.json b/taverna-commandline-common/src/main/resources/jarcache.json new file mode 100644 index 0000000..64aa4d3 --- /dev/null +++ b/taverna-commandline-common/src/main/resources/jarcache.json @@ -0,0 +1,11 @@ +[ + { + "X-License" : + "Licensed to the Apache Software Foundation (ASF) under one or more\n contributor license agreements. See the NOTICE file distributed with\n this work for additional information regarding copyright ownership.\n The ASF licenses this file to You under the Apache License, Version 2.0\n (the \"License\"); you may not use this file except in compliance with\n the License. You may obtain a copy of the License at\n \n http://www.apache.org/licenses/LICENSE-2.0\n \n Unless required by applicable law or agreed to in writing, software\n distributed under the License is distributed on an \"AS IS\" BASIS,\n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n See the License for the specific language governing permissions and\n limitations under the License.\n", + + "Content-Location": "https://w3id.org/bundle/context";, + "X-Classpath": "contexts/bundle.jsonld", + "Content-Type": "application/ld+json" + } +] +
