Module rename : added - Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/3aa91bf8 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/3aa91bf8 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/3aa91bf8
Branch: refs/heads/master Commit: 3aa91bf883dc3b112a7e7b9a8b2154c43c8e3957 Parents: 66a8cfd Author: Menaka Madushanka <menaka12...@gmail.com> Authored: Tue Feb 2 11:59:55 2016 +0530 Committer: Menaka Madushanka <menaka12...@gmail.com> Committed: Tue Feb 2 11:59:55 2016 +0530 ---------------------------------------------------------------------- taverna-tavlang-tool/.gitignore | 1 + taverna-tavlang-tool/README.md | 425 +++++ taverna-tavlang-tool/pom.xml | 213 +++ taverna-tavlang-tool/src/main/java/.gitignore | 0 .../apache/taverna/tavlang/CommandLineTool.java | 350 ++++ .../taverna/tavlang/TavernaCommandline.java | 29 + .../org/apache/taverna/tavlang/tools/Tools.java | 88 + .../tavlang/tools/convert/Scufl2Convert.java | 206 +++ .../taverna/tavlang/tools/convert/ToJson.java | 298 ++++ .../tavlang/tools/convert/ToRobundle.java | 66 + .../tavlang/tools/inspect/ProcessorNames.java | 169 ++ .../tavlang/tools/inspect/ServiceTypes.java | 112 ++ .../taverna/tavlang/tools/stats/GetWfStat.java | 193 ++ .../tavlang/tools/validate/Validate.java | 151 ++ .../src/main/resources/.gitignore | 0 .../src/main/resources/META-INF/NOTICE | 7 + taverna-tavlang-tool/src/test/java/.gitignore | 0 .../taverna/tavlang/test/CommandLineTest.java | 43 + .../taverna/tavlang/test/TestConvert.java | 34 + .../apache/taverna/tavlang/test/TestStats.java | 34 + .../apache/taverna/tavlang/test/TestTools.java | 80 + .../taverna/tavlang/test/TestValidate.java | 49 + .../src/test/resources/.gitignore | 0 .../test/resources/workflows/t2flow/as.t2flow | 1674 ++++++++++++++++++ 24 files changed, 4222 insertions(+) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/.gitignore ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/.gitignore b/taverna-tavlang-tool/.gitignore new file mode 100644 index 0000000..916e17c --- /dev/null +++ b/taverna-tavlang-tool/.gitignore @@ -0,0 +1 @@ +dependency-reduced-pom.xml http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/README.md ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/README.md b/taverna-tavlang-tool/README.md new file mode 100644 index 0000000..e76cbcd --- /dev/null +++ b/taverna-tavlang-tool/README.md @@ -0,0 +1,425 @@ +<!-- + Licensed to the Apache Software Foundation (ASF) under one or more + contributor license agreements. See the NOTICE file distributed with + this work for additional information regarding copyright ownership. + The ASF licenses this file to You under the Apache License, Version 2.0 + (the "License"); you may not use this file except in compliance with + the License. You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +--> + +# Apache Taverna Language Command Line + + +This is planned as a command line for the +[Apache Taverna Language](https://github.com/apache/incubator-taverna-language/), +an API for the +[Apache Taverna](http://taverna.incubator.apache.org/) workflows. + +This module is a **work in progress** as part of Google Summer of Code 2015. + + + +## License + +(c) 2015 Apache Software Foundation + +This product includes software developed at The [Apache Software +Foundation](http://www.apache.org/). + +Licensed under the [Apache License +2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file +[../LICENSE](../LICENSE) for details. + +The file [NOTICE](src/main/resources/NOTICE) contains any additional attributions and +details about embedded third-party libraries and source code. + + +# Contribute + +Please subscribe to and contact the +[dev@taverna](http://taverna.incubator.apache.org/community/lists#dev%20mailing%20list) +for any questions, suggestions and discussions about +Apache Taverna Language Commandline. + +Bugs and planned features are tracked in the Jira +[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326903) +under the `TAVERNA` component _GSOC Taverna Language Command line_. Feel free +to add an issue! + +To suggest changes to this source code, feel free to raise a +[GitHub pull request](https://github.com/apache/incubator-taverna-mobile/pulls). +Any contributions received are assumed to be covered by the [Apache License +2.0](https://www.apache.org/licenses/LICENSE-2.0). We might ask you +to sign a [Contributor License Agreement](https://www.apache.org/licenses/#clas) +before accepting a larger contribution. + + +# Building and install requirements + +## Requisites + +* Java 1.7 or newer +* [Apache Maven](https://maven.apache.org/download.html) 3.2.5 or newer (older + versions probably also work) + + +## Building + +To build, run: + + mvn clean install + + +# Usage + + usage: tavlang <command> [<args>] + + The most commonly used tavlang commands are: + convert Convert the given workflow + help Display help information about Tvarna + inspect Inspect the given workflow and show the results on the terminal + validate Validate the given workflow + version Show version informantion + + See 'tavlang help <command>' for more information on a specific command. + +# Documentation + +The Taverna language command line tool is for accessing the features of the Taverna language modules. +The tool has the following functions: + +* Conversion +* Inspection +* Validation +* Viewing workflow statistics. + +## Command line structure + + $tavlang <command> <options> [arguments and parameters] + +Each command has its own set of options. + +###Commands and Options +The tool has the following major commands: + +* convert: Options {-r -- recursive, -i --input, -o --output,} +* inspect: Options {-l --log} +* validate: Options {-l --log, -v --verbose} +* stats: Options {-l --log, -v --verbose} + +## Commands in detail + +### convert ------------------------------------------------------ + +Convert the given workflow file/s into a specified output format. + +Usage: + + tavlang convert (--output_fomat) ([[options] [arguments]]|files...) + + Supported output formats are, + + * wfbundle + * iwir + * json + * robundle + * structure + +Options: + + * -r, --recursive : Convert all workflow files in a given directory recursively + * -i, --input : Used with recursive case. Specify the input directory + * -o, --output : Specify the out put directory + +*The tool can only convert into one format at a time + +There are two methods for using the conversion command. + +#### 1. Non-recursive method + +Usage: + + $tavlang convert (--output_format) [options] [arguments] + +####### Example 1: Without specifying any options + + $tavlang convert --structure /helloworld.t2flow + +Output: + + /converted/helloworld.structure is created + +Convert the helloworld.t2flow into helloworld.structure format and store in the /converted directory + +###### Example 2: Convert multiple workflows + + $tavlang convert --json /helloworld.t2flow /hello.t2flow + +Output: + + /converted/helloworld.json is created + /converted/hello.json is created + +Convert both workflow files and store them in /converted directory + +###### Example 3: with options and arguments + + $tavlang convert --wfbundle /helloworld.t2flow -o /output/workflows + +Output: + + /output/workflows/helloworld.wfbundle is created + +Convert the workflow file/s and store them in the specified output directory + +#### 2. Recursive method + +If there are many workflows in a directory, which are needed to be converted into one single format use this method. + +Usage: + + $tavlang convert -r (--output_format) -i workflow_src_dir <options> [arguments] + +###### Example 4: Without options and arguments + + $tavlang convert -r --json -i /home/user/workflows + +Convert all the workflows in the input directory into the specified format and store them in the "/home/user/workflows/converted" directory. + +Output: Suppose that there are 2 workflow files in the dir 1.t2flow and 2.t2flow + + /home/workflows/converted/1.json is created + /home/workflows/converted/2.json is created + +###### Example 5: with output dir is specified + + $tavlang convert -r --iwir -i /home/workflows -o /home/final + +Convert all the workflows in the input directory and store them in /home/final directory + +Output: + + /home/final/1.iwir is created + /home/final/2.iwir is created + +### inspect ----------------------------------------------------------------- + +Inspect the given workflow file/s and give the inspection report. +Supported workflow bundle formats: .wfbundle, .t2flow + +Usage:- + + $tavlang inspect (--inspection_options) <-other-options> [arguments] workflow_undles_to_be_inspected + +Inspection options: + + * --servicetypes :- List all the service-types used in the workflow + * --processornames :- List the tree of the processor names used in the workflow + +Other Options: + + * -l, --log :- save the inspection report in a text file + +###### Example 1: Without any other-options + +1. Inspection result for Service types + + + $tavlang inspect --servicetypes helloworld.wfbundle + Service types used in helloworld.wfbundle : + + http://ns.taverna.org.uk/2010/activity/constant + ************************************************** + +2. inspection result for Processor names + + + $tavlang inspect --processornames helloworld.wfbundle + Processor tree of helloworld.wfbundle + + Hello_World + - hello + +###### Example 2: With other options +The output is the same but the results will be saved in the given file. + + $tavlang inspect --processornames helloworld.wfbundle -l results.txt + Processor tree of helloworld.wfbundle + + Hello_World + - hello + + +The output will be saved in results.txt in the same format. + +### validate ---------------------------------------------------------------------- + +Validates the given workflow file or files and gives the validation report. +Validate tool checks for the following problematic conditions. + + * Empty Iteration Strategy Top-Node Problems + * Mismatch Configurable Type Problems + * Non-Absolute URI Problems + * Null Field Problems + * Out-Of-Scope Value Problems + * Port Mentioned Twice Problems + * Port Missing From Iteration Strategy Stack Problems + * Wrong Parent Problems + * Incompatible Granular Depth Problems + +Usage:- + + $tavlang validate [options][arguments] input_files + +Options:- + + * -l, --log: Save the validation report in a text file + * -v, --verbose: Verbose mode + +Supported workflow bundle formats: .t2flow and .wfbundle + +###### Example 1: Normal mode + + Validate one workflow bundle + + $tavlang validate helloworld.t2flow + +Output: + + Validation started.... + Validating helloworld.t2flow + The workflow helloworld.t2flow has no errors. + + Validation completed....... + + Validate more than one workflow bundles + + $tavlang validate ../../workflow2.t2flow ../../workflow3.wfbundle + + Validation started.... + Validating ../../workflow2.t2flow + The workflow workflow2.t2flow has no errors. + + Validating ../../workflow3.wfbundle + The workflow workflow3.t2flow has no errors. + + Validation completed....... + + +###### Example 2: Verbose mode + +The report is more explanatory. + + $tavlang validate -v ../../workflow2.t2flow + + Validation started.... + Validating ../../workflow2.t2flow + The workflow workflow2.t2flow has no errors. + + The validation report for defaultActivitiesTaverna2.wfbundle...... + -------------------------------------------------------------------------------- + -->NegativeValueProblems:- null + + -->EmptyIterationStrategyTopNodeProblems:- null + + -->MismatchConfigurableTypeProblems:- null + + -->NonAbsoluteURIProblems:- null + + -->NullFieldProblems:- null + + -->OutOfScopeValueProblems:- null + + -->PortMentionedTwiceProblems:- null + + -->PortMissingFromIterationStrategyStackProblems:- null + + -->WrongParentProblems:- null + + -->IncompatibleGranularDepthProblems:- null + + --------------------------------------------------------------------------------- + +###### Example 3: Saving results to a file + + $tavlang validate workflow2.t2flow -l log2.txt + Validation started.... + Validating workflow2.t2flow + The workflow helloworld.wfbundle has no errors. + Validation completed....... + + Results were saved into log2.txt + +### stats ---------------------------------------------------------------------------------- + +A workflow contains several resources. + +* Processors +* Input ports +* Output ports +* Data links +* Control links + +The stats command gives a report of the resources used in the workflow. + +Usage:- + + $tavlang stats <options>[arguments] input_files... + +Options:- + + * -l, â â log : Save results in a log file + * -v, â â verbose : verbose mode + +Supported workflow bundle formats:- .t2flow, .wfbundle + +###### Example 1: Normal mode + + $tavlang helloworld.wfbundle + >>> Statistics of the workflow bundle: helloworld.wfbundle <<< + Name of the workflow = Hello_World + |--> Number of Processors = 1 + |--> Number of Data Links = 1 + |--> Number of Control Links = 0 + |--> Number of Input ports = 0 + |--> Number of Output Ports = 1 + +###### Example 2: Verbose mode + + $tavlang -v ../../../helloworld.wfbundle + >>> Statistics of the workflow bundle: helloworld.wfbundle <<< + Name of the workflow = Hello_World + |--> Number of Processors = 1 + | |--> Processors: + | |--> hello + | + |--> Number of Data Links = 1 + | |--> Data Links + | |--> DataLink value=>greeting + | + |--> Number of Control Links = 0 + |--> Number of Input ports = 0 + |--> Number of Output Ports = 1 + | |--> Output Ports + | |--> OutputWorkflowPort "greeting" + +###### Example 3: Saving results in a file + + $tavlang -l ../../results.txt ../../../helloworld.wfbundle + >>> Statistics of the workflow bundle: helloworld.wfbundle <<< + Name of the workflow = Hello_World + |--> Number of Processors = 1 + |--> Number of Data Links = 1 + |--> Number of Control Links = 0 + |--> Number of Input ports = 0 + |--> Number of Output Ports = 1 + + Results were saved into ../../results.txt + +----------------------------------------------------------------------------------------------------------------------------------------- \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/pom.xml b/taverna-tavlang-tool/pom.xml new file mode 100644 index 0000000..369dbf4 --- /dev/null +++ b/taverna-tavlang-tool/pom.xml @@ -0,0 +1,213 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- + Licensed to the Apache Software Foundation (ASF) under one or more + contributor license agreements. See the NOTICE file distributed with + this work for additional information regarding copyright ownership. + The ASF licenses this file to You under the Apache License, Version 2.0 + (the "License"); you may not use this file except in compliance with + the License. You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +--> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> + <modelVersion>4.0.0</modelVersion> + <parent> + <groupId>org.apache.taverna.language</groupId> + <artifactId>taverna-language</artifactId> + <version>0.15.1-incubating-SNAPSHOT</version> + </parent> + <artifactId>taverna-tavlang-tool</artifactId> + <name>Apache Taverna Language Commandline</name> + <description>Command line for Taverna Language (experimental)</description> + + + <dependencies> + + <dependency> + <groupId>commons-io</groupId> + <artifactId>commons-io</artifactId> + </dependency> + + <dependency> + <groupId>${project.parent.groupId}</groupId> + <artifactId>taverna-scufl2-api</artifactId> + <version>${project.parent.version}</version> + </dependency> + + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>taverna-scufl2-wfbundle</artifactId> + <version>${project.version}</version> + </dependency> + + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>taverna-scufl2-t2flow</artifactId> + <version>${project.version}</version> + </dependency> + +<!-- <dependency> --> +<!-- <groupId>org.shiwa.iwir</groupId> --> +<!-- <artifactId>iwir</artifactId> --> +<!-- <version>1.1.4</version> --> +<!-- <scope>optional</scope> --> +<!-- <systemPath>${project.build.directory}/taverna-language-commandline/lib/</systemPath> --> +<!-- </dependency> --> + + <dependency> + <groupId>no.s11.scufl2</groupId> + <artifactId>scufl2-iwir</artifactId> + <version>0.2-SNAPSHOT</version> + <optional>true</optional> + </dependency> + + + + <dependency> + <groupId>com.thoughtworks.xstream</groupId> + <artifactId>xstream</artifactId> + <version>1.4.8</version> + </dependency> + + + <!-- <dependency> <groupId>${project.groupId}</groupId> <artifactId>taverna-scufl2-wfdesc</artifactId> + <version>${project.version}</version> <optional>true</optional> </dependency> --> + <!-- <dependency> <groupId>org.purl.wf4ever</groupId> <artifactId>scufl2-wfdesc</artifactId> + <version>0.3.7</version> </dependency> --> + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-core</artifactId> + </dependency> + + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-databind</artifactId> + </dependency> + + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>taverna-scufl2-ucfpackage</artifactId> + <version>${project.version}</version> + </dependency> + + <dependency> + <groupId>${project.groupId}</groupId> + <artifactId>taverna-robundle</artifactId> + <version>${project.version}</version> + </dependency> + + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <scope>test</scope> + </dependency> + + <dependency> + <groupId>io.airlift</groupId> + <artifactId>airline</artifactId> + <!-- <version>${io.airlift.airline.version}</version> --> + <version>0.7</version> + </dependency> + + + </dependencies> + + <build> + <!-- TODO: plugins for launchers and executable jar files? --> + <plugins> + + <plugin> + <groupId>org.codehaus.mojo</groupId> + <artifactId>appassembler-maven-plugin</artifactId> + <version>1.1.1</version> + <executions> + <execution> + <id>assemble</id> + <phase>package</phase> + <goals> + <goal>assemble</goal> + </goals> + </execution> + </executions> + <configuration> + <repositoryLayout>flat</repositoryLayout> + <repositoryName>lib</repositoryName> + <assembleDirectory>${project.build.directory}/${project.artifactId}</assembleDirectory> + <programs> + <program> + <mainClass>org.apache.taverna.tavlang.TavernaCommandline</mainClass> + <name>tavlang</name> + </program> + </programs> + </configuration> + </plugin> + + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-shade-plugin</artifactId> + <version>2.3</version> + <executions> + <execution> + <phase>package</phase> + <goals> + <goal>shade</goal> + </goals> + <configuration> + <transformers> + <transformer + implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" /> + <transformer + implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> + <mainClass>org.apache.taverna.tavlang.TavernaCommandline</mainClass> + </transformer> + <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer"> + <addHeader>false</addHeader> + </transformer> + </transformers> + </configuration> + </execution> + </executions> + </plugin> + + + </plugins> + </build> + + <repositories> + <repository> + <releases> + <enabled>false</enabled> + </releases> + <snapshots /> + <id>mygrid-repository</id> + <name>myGrid Repository</name> + <url>http://www.mygrid.org.uk/maven/repository</url> + </repository> + + <repository> + <id>mygrid-snapshot-repository</id> + <name>myGrid Snapshot Repository</name> + <url>http://www.mygrid.org.uk/maven/snapshot-repository</url> + <releases> + <enabled>false</enabled> + </releases> + <snapshots /> + </repository> + + <repository> + <id>apache.snapshots</id> + <name>Apache Snapshot Repository</name> + <url>http://repository.apache.org/snapshots</url> + <releases> + <enabled>false</enabled> + </releases> + </repository> + </repositories> + +</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/.gitignore ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/.gitignore b/taverna-tavlang-tool/src/main/java/.gitignore new file mode 100644 index 0000000..e69de29 http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java new file mode 100644 index 0000000..068c933 --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java @@ -0,0 +1,350 @@ +package org.apache.taverna.tavlang; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import io.airlift.airline.Arguments; +import io.airlift.airline.Cli; +import io.airlift.airline.Cli.CliBuilder; +import io.airlift.airline.Command; +import io.airlift.airline.Help; +import io.airlift.airline.Option; + +import java.io.IOException; +import java.util.List; + +import javax.inject.Inject; +import javax.xml.bind.JAXBException; + +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.tavlang.tools.convert.Scufl2Convert; +import org.apache.taverna.tavlang.tools.convert.ToRobundle; +import org.apache.taverna.tavlang.tools.inspect.ProcessorNames; +import org.apache.taverna.tavlang.tools.inspect.ServiceTypes; +import org.apache.taverna.tavlang.tools.stats.GetWfStat; +import org.apache.taverna.tavlang.tools.validate.Validate; + +import com.google.common.collect.Lists; + +/* + * The command line options for convert, validate and inspect workflows. + * Use the airlift/airline library + * */ + +public class CommandLineTool { + + private static Cli<TvnLangTool> parser() { + CliBuilder<TvnLangTool> build = Cli.<TvnLangTool> builder("tavlang") + .withDescription("Convert, manage workflows") + .withDefaultCommand(HelpCommand.class) + .withCommand(CommandConvert.class) // Conversion + .withCommand(HelpCommand.class) // Help + .withCommand(CommandInspect.class) // Inspect + .withCommand(CommandValidate.class) // Validate + .withCommand(CommandVersion.class) // Version + .withCommand(CommandStat.class); // Statistics + + return build.build(); + } + + public CommandLineTool() { + }; + + public void parse(String... args) { + TvnLangTool command = parser().parse(args); + command.execute(); + System.out.println(); + } + + public static abstract class TvnLangTool { + + public abstract void execute(); + } + + // placeholder for output file types + public static class Filetypes { + @Option(name = "--wfdesc", description = "Convert the workflow file to wfdesc-turtle") + public static boolean isWfdesc = false; + + @Option(name = "--wfbundle", description = "Convert the workflow file to wfbundle") + public static boolean isWfbundle = false; + + @Option(name = "--robundle", description = "Convert given bundle in to Research Object bundle") + public static boolean isRo = false; + + @Option(name = "--structure", description = "Convert the workflow into *.structure") + public static boolean isStructure = false; + + @Option(name = "--json", description = "Convert the workflow into json") + public static boolean isJson = false; + + + @Option(name = "--iwir", description = "Convert scufl2 workflows into IWIR 1.1 specification") + public static boolean isIwir = false; + + + // The tool can only handle one output format at a time. + // Return the file type which is selected + public static String isTrue() { + if (isWfdesc) + return "wfdesc"; + else if (isWfbundle) + return "wfbundle"; + else if (isRo) + return "robundle"; + else if (isStructure) + return "structure"; + else if (isJson) + return "json"; + + else if (isIwir) + return "iwir"; + + + else{ + System.out.println("Invalid argument...."); + TvnLangTool command = parser().parse("help", "convert"); + command.execute(); + return null; + } + + } + + } + + public static class Inspect { + @Option(name = "--servicetypes", description = "List the service types used in workflow") + public static boolean servicetypes = false; + + @Option(name = "--processornames", description = "List a tree of processor names used in workflow") + public static boolean processor = false; + + public String getWay() { + if (servicetypes) + return "servicetypes"; + else if (processor) + return "processornames"; + else{ + System.out.println("Invalid argument...."); + TvnLangTool command = parser().parse("help", "inspect"); + command.execute(); + return null; + + } + + } + + } + + // Placeholder for optional parameters: Ex: -i, -o + public static class Optional { + + // The input file or directory + @Option(name = { "-i", "--input" }, description = "Input file/ file dir for conversion") + public static String in_file_dir; + + // The out put file or directory. When this is set, all the converted + // files will be saved into the directory that specified. + @Option(name = { "-o", "--output" }, description = "Output file/ directory") + public static String out_file_dir; + + public static String getInFile() { + return in_file_dir; + } + + public static String getOutFile() { + return out_file_dir; + } + + } + + @Command(name = "help", description = "Display help information about Tvarna") + public static class HelpCommand extends TvnLangTool { + @Inject + public Help help; + + @Override + public void execute() { + help.call(); + } + } + + // Command for convert workflows + @Command(name = "convert", description = "Convert the given workflow") + public static class CommandConvert extends TvnLangTool { + @Inject + Optional optional = new Optional(); + + @Inject + Filetypes filetypes = new Filetypes(); + + @Arguments(usage = "<output format> <input files> ", description = "List of files to be converted.\n " + + "Give the list of files to be converted without -i/-o and the converted files will be saved in to /converted folder in the same dir") + public final List<String> files = Lists.newArrayList(); + + // When this is true, the command will run recursively in a directory. + @Option(name = { "-r", "--recursive" }, description = "Execute the command recursively") + public boolean recurse = false; + + // Option for validate the given workflow when converting + @Option(name = { "-V", "--validate" }, description = "Validate the workflow before convert") + public boolean validate = false; + + @Override + public void execute() { + + //Validate before convert + if(validate){ + Validate validate = new Validate(files, null, false); + if(validate.getCheck()){ + System.out.println("Conversion failed...! Workflow bundle has errors"); + return; + }else{ + runcommand(); + } + } + } + + public void runcommand(){ + if (Filetypes.isRo) { + try { + new ToRobundle(files, Optional.getOutFile()); + } catch (Exception e) { + e.printStackTrace(); + } +// else if(Filetypes.isIwir || Filetypes.isJson || Filetypes.isStructure || Filetypes.isWfbundle || Filetypes.isWfdesc) + } else if(Filetypes.isIwir || Filetypes.isJson || Filetypes.isStructure || Filetypes.isWfbundle || Filetypes.isWfdesc){ + if (recurse) { + new Scufl2Convert(Filetypes.isTrue(), + Optional.getInFile(), Optional.getOutFile()); + } else { + new Scufl2Convert(Filetypes.isTrue(), files, + Optional.getOutFile()); + } + }else{ + System.out.println("Invalid argument...."); + TvnLangTool command = parser().parse("help", "convert"); + command.execute(); + } + + } + + + + } + + // Version command + @Command(name = "version", description = "Show version informantion") + public static class CommandVersion extends TvnLangTool { + + @Override + public void execute() { + System.out.print(getClass().getPackage().getImplementationTitle()); + System.out.println(" " + getClass().getPackage().getImplementationVersion()); + } + + } + + // Command for inspection of workflows....!! + @Command(name = "inspect", description = "Inspect the given workflow and show the results on the terminal") + public static class CommandInspect extends TvnLangTool { + + @Inject + Inspect inspect = new Inspect(); + + @Option(name = { "-l", "--log" }, description = "Specify the file name where results should be stored ([some dir]/log.txt)") + public String file; + + @Arguments(usage = "<option> <input files>", description = "Inspect the given workflow") + public List<String> toInspect = Lists.newArrayList(); + + @Override + public void execute() { + if (Inspect.processor) { + try { + new ProcessorNames(toInspect, file); + + } catch (ReaderException | IOException | JAXBException e) { + e.printStackTrace(); + } + } else if (Inspect.servicetypes) { + try { + new ServiceTypes(toInspect, file); + } catch (IOException | ReaderException e) { + e.printStackTrace(); + } + + }else{ + System.out.println("Invalid argument...."); + TvnLangTool command = parser().parse("help", "inspect"); + command.execute(); + } + + } + + } + + // Command for validation + @Command(name = "validate", description = "validate the given workflow") + public static class CommandValidate extends TvnLangTool{ + + @Option(name = { "-l", "--log" }, description = "Specify the file name where results should be stored ([some dir]/log.txt)") + public String file; + + @Option(name = {"-v", "--verbose"}, description = "Verbose mode") + public boolean verbose; + +// @Arguments(usage = "<option> <input files> <output dir>", description = "Validate the given workflow file/s") + @Arguments(usage = "input files", description = "Validate the given workflow file/s") + public List<String> toValidate = Lists.newArrayList(); + + @Override + public void execute() { + + Validate validate = new Validate(toValidate, file, verbose); + + + } + + } + + //Command for getting workflow stats + @Command (name = "stats", description = "Shows the workflow statistics") + public static class CommandStat extends TvnLangTool{ + + + @Option(name = {"-l", "--log"}, description ="Save the workflow statictics in a file") + public String file; + + @Option(name = {"-v", "--verbose"}, description = "Verbose mode") + public boolean verbose; + + @Arguments(usage="input files", description = "Enter the workflow bundle files") + public List<String> files; + + @Override + public void execute() { + + GetWfStat stat = new GetWfStat(files, file, verbose); + + } + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java new file mode 100644 index 0000000..016488c --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java @@ -0,0 +1,29 @@ +package org.apache.taverna.tavlang; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +public class TavernaCommandline { + + public static void main(String args[]){ + CommandLineTool tool = new CommandLineTool(); + tool.parse(args); + + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/Tools.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/Tools.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/Tools.java new file mode 100644 index 0000000..c78c7a2 --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/Tools.java @@ -0,0 +1,88 @@ +package org.apache.taverna.tavlang.tools; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + + +public class Tools { + + public static enum ConvertionTools { + wfbundle{ + public String mediaType = "application/vnd.taverna.scufl2.workflow-bundle"; + + + @Override + public String getMediaType(ConvertionTools t) { + return this.mediaType; + } + }, + json{ + public String mediaType = "application/ld+json"; + + + @Override + public String getMediaType(ConvertionTools t) { + return mediaType; + } + }, + wfdesc{ + public String mediaType = "text/vnd.wf4ever.wfdesc+turtle"; + + + @Override + public String getMediaType(ConvertionTools t) { + // TODO Auto-generated method stub +// System.out.println(mediaType); + return mediaType; + } + }, + robundle{ + + @Override + public String getMediaType(ConvertionTools t) { + return null; + } + + }, + structure{ + public String mediaType = "text/vnd.taverna.scufl2.structure"; + + @Override + public String getMediaType(ConvertionTools t) { + return mediaType; + } + }, + + iwir{ + public String mediaType = "application/vnd.shiwa.iwir+xml"; + + @Override + public String getMediaType(ConvertionTools t) { + return mediaType; + } + }; + + ConvertionTools(){} + + public abstract String getMediaType(ConvertionTools t); + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java new file mode 100644 index 0000000..da4dff0 --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java @@ -0,0 +1,206 @@ +package org.apache.taverna.tavlang.tools.convert; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import java.io.File; +import java.io.IOException; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.FilenameUtils; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.io.WriterException; +import org.apache.taverna.tavlang.tools.Tools.ConvertionTools; + + +/* + * Converts + * .t2flow --> .wfbundle + * .t2flow --> .structure + * .wfbundle --> .structure + * .wfbundle/ .t2flow -> .iwir + * two constructors. + * Scufl2Convert(List<String> list, String out) --> will save the converted files in 'out folder or a directory named /converted in the same folder. + * Scufl2Convert(String in, String out) --> Will convert all the files in the 'in' folder and save them in 'out' folder --> -r must be true. + * + * */ +public class Scufl2Convert{ + + private ConvertionTools t; + private String MEDIA_TYPE; + private String input; + private String output; + private String type; + private List<String> filesList; + + public Scufl2Convert(String type, List<String> files, String out){ + this.filesList = files; + this.output = out; + this.type = type.equals("wfdesc")?".wfdesc.ttl":"."+type; + this.MEDIA_TYPE = ConvertionTools.valueOf(type).getMediaType(t); + this.convert(); + } + + //When recursive case is on.... + public Scufl2Convert(String type, String in, String out){ + this.input = in; + this.output = out; + this.type = type.equals("wfdesc")?".wfdesc.ttl":"."+type; + this.MEDIA_TYPE = ConvertionTools.valueOf(type).getMediaType(t); //Determine the writer media type + + this.createdir(); + } + + //Create the dir if not exists + public void createdir(){ + if(output == null){ + File outFile = new File(this.input, "converted"); + try { + FileUtils.forceMkdir(outFile); + this.output = outFile.getAbsolutePath(); + } catch (IOException e1) { + System.err.println("Error: The directory cannot be created...!!!!"); + e1.printStackTrace(); + } + }else{ + File outFile = new File(this.output); + try { + FileUtils.forceMkdir(outFile); + + } catch (IOException e1) { + System.err.println("Error: The directory cannot be created...!!!!"); + e1.printStackTrace(); + } + } + this.rec_convert(this.input); + } + + //Convert the given file. Return in case of an exception. + public boolean convert(){ + + boolean check = false; + // If the output folder is given, save the converted files in to that folder. + + if(this.filesList.size()>0 && this.output != null){ + File outFile = new File(this.output); + try { + FileUtils.forceMkdir(outFile); + } catch (IOException e1) { + System.err.println("Error: The directory cannot be created...!!!"); + } + for(String file : this.filesList){ + File t2File = new File(file); + + convertFile(t2File, outFile); + + } + + } + + /* If the output file is not given, save the converted files in + * '/converted' folder. + */ + + else if(this.filesList.size()>0 && this.output == null){ + for(String file : this.filesList){ + File t2File = new File(file); + + File outFile = new File(t2File.getParentFile(), "converted"); + try { + FileUtils.forceMkdir(outFile); + } catch (IOException e1) { + System.err.println("Error: The directory cannot be created...!!!"); + } + + convertFile(t2File, outFile); + + } + }else{ + System.err.println("Error: Argument mismatch"); + check = false; + } + + return check; + } + + //Convert the files in a given directory and save the converted files in to specified dir or /converted folder. + //Recursive conversion + public void rec_convert(String dir){ + + File parent = new File(this.input); + if(!parent.exists()){ + System.err.println("Error: Input directory not found"); + }else{ + for(File file : parent.listFiles()){ + if(!file.isDirectory()) + { + File outFile = new File(this.output); + convertFile(file, outFile); + } + } + } + } + + //Convert the file + public void convertFile(File t2File, File outFile){ + + //Check weather the input files are in valid format...!!! + String ext = FilenameUtils.getExtension(t2File.getName()); + if(!ext.equalsIgnoreCase("t2flow")&&!ext.equalsIgnoreCase("wfbundle")){ + System.err.println("Error: Invalid input file format...!!!"); + return; + } + + WorkflowBundleIO wfbio = new WorkflowBundleIO(); + String filename = t2File.getName(); + filename = filename.replaceFirst("\\..*", this.type); + File scufl2File = new File(outFile.getAbsolutePath(), filename); + + WorkflowBundle wfBundle; + try { + wfBundle = wfbio.readBundle(t2File, null);// null --> will guess the media type for reading. + +// if(this.type.equals(".iwir")){ +// IwirWriter iww = new IwirWriter(); +// iww.writeBundle(wfBundle, scufl2File, this.MEDIA_TYPE); +// }else + + if(this.type.equals(".json")){ + ToJson toJ = new ToJson(); + toJ.convert(t2File, outFile); + } + else{ + wfbio.writeBundle(wfBundle, scufl2File, this.MEDIA_TYPE); + } + System.out.println(scufl2File.getPath() + " is created."); + }catch (ReaderException e){ + System.err.println("Error: Connot read the file"); + }catch(IOException e){ + System.err.println("Error: File not found"); + }catch(WriterException e) { + System.err.println("Error: Cannot write to the file"); +// e.printStackTrace(); + } + } + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java new file mode 100644 index 0000000..f11424c --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java @@ -0,0 +1,298 @@ +package org.apache.taverna.tavlang.tools.convert; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import java.io.File; +import java.io.IOException; +import java.io.OutputStream; +import java.net.URI; +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.taverna.scufl2.api.annotation.Annotation; +import org.apache.taverna.scufl2.api.annotation.Revision; +import org.apache.taverna.scufl2.api.common.Child; +import org.apache.taverna.scufl2.api.common.Ported; +import org.apache.taverna.scufl2.api.common.Scufl2Tools; +import org.apache.taverna.scufl2.api.common.URITools; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.core.BlockingControlLink; +import org.apache.taverna.scufl2.api.core.ControlLink; +import org.apache.taverna.scufl2.api.core.DataLink; +import org.apache.taverna.scufl2.api.core.Processor; +import org.apache.taverna.scufl2.api.core.Workflow; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.io.WorkflowBundleWriter; +import org.apache.taverna.scufl2.api.io.WriterException; +import org.apache.taverna.scufl2.api.port.DepthPort; +import org.apache.taverna.scufl2.api.port.GranularDepthPort; +import org.apache.taverna.scufl2.api.port.Port; +import org.apache.taverna.scufl2.api.profiles.Profile; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import com.fasterxml.jackson.databind.node.ArrayNode; +import com.fasterxml.jackson.databind.node.ObjectNode; +import com.fasterxml.jackson.databind.util.ISO8601DateFormat; + +public class ToJson { + public class JsonWriter implements WorkflowBundleWriter { + + @Override + public Set<String> getMediaTypes() { + return new HashSet<String>(Arrays.asList("application/ld+json", + "application/json")); + } + + @Override + public void writeBundle(WorkflowBundle wfBundle, File destination, + String mediaType) throws WriterException, IOException { + ObjectNode json = toJson(wfBundle); + mapper.writeValue(destination, json); + } + + @Override + public void writeBundle(WorkflowBundle wfBundle, OutputStream output, + String mediaType) throws WriterException, IOException { + ObjectNode json = toJson(wfBundle); + mapper.writeValue(output, json); + } + + } + + + private WorkflowBundleIO io = new WorkflowBundleIO();; + + private WorkflowBundleWriter jsonWriter = new JsonWriter(); + + private ObjectMapper mapper = new ObjectMapper(); + + private Scufl2Tools scufl2Tools = new Scufl2Tools(); + + private URITools uriTools = new URITools(); + + public ToJson() { + mapper.enable(SerializationFeature.INDENT_OUTPUT); + mapper.disable(SerializationFeature.FAIL_ON_EMPTY_BEANS); + mapper.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS); + + mapper.setDateFormat(new ISO8601DateFormat()); + + // Adding custom writer dynamically + List<WorkflowBundleWriter> writers = io.getWriters(); + writers.add(jsonWriter); + io.setWriters(writers); + } + + protected void addPorts(Ported ported, ObjectNode p) { + ArrayNode inputs = mapper.createArrayNode(); + for (Port port : ported.getInputPorts()) { + inputs.add(toJson(port)); + } + p.put("inputs", inputs); + + ArrayNode outputs = mapper.createArrayNode(); + for (Port port : ported.getOutputPorts()) { + outputs.add(toJson(port)); + // FIXME: Do we need the id for ports? Needed if we add datalinks + } + p.put("outputs", outputs); + } + + protected ObjectNode annotations(Child<?> bean) { + ObjectNode node = mapper.createObjectNode(); + for (Annotation ann : scufl2Tools.annotationsFor(bean)) { + URI annUri = uriTools.uriForBean(ann); + + // TODO: include annotation body? + } + return node; + } + + public void convert(File in, File out) throws ReaderException, IOException, + WriterException { + String filename = in.getName(); + filename = filename.replaceFirst("\\..*", ".json"); + File workflowFile = new File(out.getAbsolutePath(), filename); + + WorkflowBundle wfBundle = io.readBundle(in, null); + io.writeBundle(wfBundle, workflowFile, "application/ld+json"); +// System.out.println(workflowFile); + + } + + protected ObjectNode toJson(Port port) { + ObjectNode p = mapper.createObjectNode(); + p.put("name", port.getName()); + p.putPOJO("id", + uriTools.relativeUriForBean(port, scufl2Tools.findParent( + WorkflowBundle.class, ((Child<?>) port)))); + + if (port instanceof DepthPort) { + DepthPort depthPort = (DepthPort) port; + if (depthPort.getDepth() != null) { + p.put("depth", depthPort.getDepth()); + } + } + if (port instanceof GranularDepthPort) { + GranularDepthPort granularDepthPort = (GranularDepthPort) port; + if (granularDepthPort.getGranularDepth() != null + && !granularDepthPort.getGranularDepth().equals( + granularDepthPort.getDepth())) { + p.put("granularDepth", granularDepthPort.getGranularDepth()); + } + } + p.putAll(annotations((Child<?>) port)); + return p; + } + + protected JsonNode toJson(Processor proc) { + ObjectNode p = mapper.createObjectNode(); + p.putPOJO("id", + uriTools.relativeUriForBean(proc, proc.getParent().getParent())); + p.put("name", proc.getName()); + addPorts(proc, p); + p.putAll(annotations(proc)); + + List<Workflow> nested = scufl2Tools.nestedWorkflowsForProcessor(proc, + proc.getParent().getParent().getMainProfile()); + if (!nested.isEmpty()) { + if (nested.size() == 1) { + p.put("nestedWorkflow", toJson(nested.iterator().next())); + } else { + ArrayNode list = mapper.createArrayNode(); + for (Workflow w : nested) { + list.add(toJson(w)); + } + p.put("nestedWorkflow", list); + } + } + return p; + } + + protected JsonNode toJson(Revision currentRevision) { + ArrayNode revisions = mapper.createArrayNode(); + while (currentRevision != null) { + ObjectNode rev = mapper.createObjectNode(); + rev.putPOJO("id", currentRevision.getIdentifier()); + if (currentRevision.getGeneratedAtTime() != null) { + rev.putPOJO("generatedAtTime", + currentRevision.getGeneratedAtTime()); + } + currentRevision = currentRevision.getPreviousRevision(); + if (currentRevision != null) { + rev.putPOJO("wasRevisionOf", currentRevision.getIdentifier()); + } + revisions.add(rev); + } + return revisions; + } + + protected ObjectNode toJson(Workflow workflow) { + ObjectNode wf = mapper.createObjectNode(); + + wf.putPOJO("id", + uriTools.relativeUriForBean(workflow, workflow.getParent())); + + wf.put("name", workflow.getName()); + wf.put("revisions", toJson(workflow.getCurrentRevision())); + + ArrayNode processors = mapper.createArrayNode(); + for (Processor p : workflow.getProcessors()) { + processors.add(toJson(p)); + } + addPorts(workflow, wf); + wf.put("processors", processors); + + ArrayNode datalinks = mapper.createArrayNode(); + for (DataLink link : workflow.getDataLinks()) { + datalinks.add(toJson(link)); + } + wf.put("datalinks", datalinks); + + ArrayNode controlLinks = mapper.createArrayNode(); + for (ControlLink link : workflow.getControlLinks()) { + controlLinks.add(toJson(link)); + } + wf.put("controllinks", controlLinks); + + wf.putAll(annotations(workflow)); + + return wf; + } + + protected JsonNode toJson(ControlLink link) { + ObjectNode l = mapper.createObjectNode(); + if (link instanceof BlockingControlLink) { + BlockingControlLink controlLink = (BlockingControlLink) link; + l.putPOJO("block", uriTools.relativeUriForBean( + controlLink.getBlock(), link.getParent().getParent())); + l.putPOJO("untilFinished", uriTools.relativeUriForBean(controlLink + .getUntilFinished(), link.getParent().getParent())); + } + return l; + } + + protected JsonNode toJson(DataLink link) { + ObjectNode l = mapper.createObjectNode(); + l.putPOJO("receivesFrom", uriTools.relativeUriForBean( + link.getReceivesFrom(), link.getParent().getParent())); + l.putPOJO("sendsTo", uriTools.relativeUriForBean(link.getSendsTo(), + link.getParent().getParent())); + if (link.getMergePosition() != null) { + l.put("mergePosition", link.getMergePosition()); + } + return l; + } + + public ObjectNode toJson(WorkflowBundle wfBundle) { + + ObjectNode root = mapper.createObjectNode(); + ArrayNode contextList = root.arrayNode(); + root.put("@context", contextList); + ObjectNode context = root.objectNode(); + contextList.add("https://w3id.org/scufl2/context";); + contextList.add(context); + URI base = wfBundle.getGlobalBaseURI(); + context.put("@base", base.toASCIIString()); + root.put("id", base.toASCIIString()); + + // root.put("name", wfBundle.getName()); + // root.put("revisions", toJson(wfBundle.getCurrentRevision())); + + root.put("workflow", toJson(wfBundle.getMainWorkflow())); + root.put("profile", toJson(wfBundle.getMainProfile())); + + return root; + } + + private JsonNode toJson(Profile profile) { + ObjectNode pf = mapper.createObjectNode(); + + pf.putPOJO("id", + uriTools.relativeUriForBean(profile, profile.getParent())); + // TODO: Activities and configurations + return pf; + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java new file mode 100644 index 0000000..6ab14bc --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java @@ -0,0 +1,66 @@ +package org.apache.taverna.tavlang.tools.convert; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.List; +import java.util.logging.ConsoleHandler; +import java.util.logging.Level; +import java.util.logging.Logger; + +import org.apache.taverna.robundle.Bundle; +import org.apache.taverna.robundle.Bundles; + +public class ToRobundle{ + + public ToRobundle(List<String> files, String out) throws Exception{ + + Logger logger = Logger.getLogger(""); + //logger.setLevel(Level.FINER); + ConsoleHandler console = new ConsoleHandler(); + console.setLevel(Level.FINEST); + logger.addHandler(console); + Logger.getLogger("org.researchobject").setLevel(Level.FINEST); + + for(String f : files){ + Path file = Paths.get(f); + convert(file); + } + } + + //Recursive conversion + public ToRobundle(String type, String in, String out) { + + } + + public void convert(Path file) throws IOException{ + try (Bundle bundle = Bundles.openBundle(file)) { + +// System.out.println(bundle.getManifest().toString()); + bundle.getManifest().writeAsJsonLD(); + bundle.getManifest().writeAsCombineManifest(); + } + } + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java new file mode 100644 index 0000000..f93aadc --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java @@ -0,0 +1,169 @@ +package org.apache.taverna.tavlang.tools.inspect; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + +import javax.swing.tree.DefaultMutableTreeNode; +import javax.swing.tree.DefaultTreeModel; +import javax.swing.tree.TreeModel; +import javax.xml.bind.JAXBException; + +import org.apache.taverna.scufl2.api.common.Scufl2Tools; +import org.apache.taverna.scufl2.api.common.URITools; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.core.Processor; +import org.apache.taverna.scufl2.api.core.Workflow; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.profiles.Profile; + +/* + * list the processor names used in the workflow. + * Supported formats: .t2flow, .wfbundle + * */ + +public class ProcessorNames { + + private List<String> fileList; + + private String file2; + + private Scufl2Tools scufl2Tools = new Scufl2Tools(); + + private URITools uriTools = new URITools(); + + public ProcessorNames(List<String> fileList, String file) throws ReaderException, IOException, JAXBException{ + this.fileList = fileList; + this.file2 = file; + this.show(); + } + + public void show() throws ReaderException, IOException, JAXBException{ + WorkflowBundleIO io = new WorkflowBundleIO(); + StringBuilder sb = new StringBuilder(); + + for(String file : this.fileList){ + File file2 = new File(file); + if(file2.isDirectory()){ + for(File f : file2.listFiles()){ + WorkflowBundle wfb = io.readBundle(f, null); + System.out.println("Processor tree of "+ f.getName() +" \n" +this.showProcessorTree(wfb)); + sb.append("Processor tree of "+ f.getName() +" \n" +this.showProcessorTree(wfb) + "\n"); + } + }else{ + WorkflowBundle wfb = io.readBundle(new File(file), null); + System.out.println("Processor tree of "+ file +" \n" +this.showProcessorTree(wfb)); + sb.append("Processor tree of "+ file +" \n" +this.showProcessorTree(wfb) + "\n"); + } + + + } + + if(this.file2!=null){ + File log = new File(file2); + FileWriter fw = new FileWriter(log); + BufferedWriter bw = new BufferedWriter(fw); + bw.write(sb.toString()); + bw.close(); + fw.close(); + System.out.println("Results were saved into " + file2); + } + } + + private Workflow findNestedWorkflow(Processor processor) { + Profile profile = processor.getParent().getParent().getMainProfile(); + return scufl2Tools.nestedWorkflowForProcessor(processor, profile); + } + + private void findProcessors(WorkflowBundle ro, Workflow workflow, + DefaultMutableTreeNode parent) { + for (Processor processor : workflow.getProcessors()) { + DefaultMutableTreeNode processorNode = new DefaultMutableTreeNode( + processor.getName()); + parent.add(processorNode); + Workflow wf = findNestedWorkflow(processor); + if (wf != null) { + findProcessors(ro, wf, processorNode); + } + } + + } + + public TreeModel makeProcessorTree(WorkflowBundle workflowBundle) + throws JAXBException, IOException { + Workflow workflow = workflowBundle.getMainWorkflow(); + TreeModel treeModel = new DefaultTreeModel(new DefaultMutableTreeNode( + workflow.getName())); + DefaultMutableTreeNode parent = (DefaultMutableTreeNode) treeModel + .getRoot(); + + findProcessors(workflowBundle, workflow, parent); + return treeModel; + } + + public List<String> showProcessorNames(WorkflowBundle ro) + throws JAXBException, IOException { + ArrayList<String> names = new ArrayList<String>(); + for (Processor processor : ro.getMainWorkflow().getProcessors()) { + names.add(processor.getName()); + } + Collections.sort(names); + return names; + } + + public String showProcessorTree(WorkflowBundle ro) throws JAXBException, + IOException { + TreeModel treeModel = makeProcessorTree(ro); + return treeModelAsString(treeModel); + } + + public String treeModelAsString(TreeModel treeModel) { + StringBuffer sb = new StringBuffer(); + Object root = treeModel.getRoot(); + treeModelAsString(treeModel, root, sb, ""); + return sb.toString(); + } + + protected void treeModelAsString(TreeModel treeModel, Object parent, + StringBuffer sb, String indentation) { + sb.append(indentation); + int childCount = treeModel.getChildCount(parent); + if (childCount == 0) { + sb.append("- "); + } else { + sb.append("+ "); + indentation = indentation + " "; + } + sb.append(parent); + sb.append("\n"); + for (int i = 0; i < childCount; i++) { + Object child = treeModel.getChild(parent, i); + treeModelAsString(treeModel, child, sb, indentation); + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java new file mode 100644 index 0000000..ddff2ab --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java @@ -0,0 +1,112 @@ +package org.apache.taverna.tavlang.tools.inspect; + + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Set; + +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.activity.Activity; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.profiles.Profile; + +/* + * List the service types used in workflow. + * Supported file formats : .wfbundle, .t2flow + * */ + +public class ServiceTypes { + + private List<String> filesList; + private Set<String> types = new LinkedHashSet<String>(); + private String save; + + public ServiceTypes(List<String> filesList, String file) throws IOException, ReaderException{ + this.filesList = filesList; + this.save = file; + this.service(); + + } + + public void service() throws ReaderException, IOException{ + WorkflowBundleIO io = new WorkflowBundleIO(); + StringBuilder sb = new StringBuilder(); + + for (String filepath : filesList) { + File file = new File(filepath); + + if(file.isDirectory()){ + for(File f : file.listFiles()){ + WorkflowBundle wfBundle = io.readBundle(f, null); + System.out.println("Service types used in " + f.getCanonicalPath() + " :" +"\n"); + sb.append("Service types used in " + f.getCanonicalPath() + " :"); + for (Profile profile : wfBundle.getProfiles()) { + for (Activity activity : profile.getActivities()) { + this.types.add(activity.getType().toASCIIString()); + } + } + for(String t : types){ + System.out.println(t); + sb.append(t + "\n"); + } + System.out.println("\n**************************************************\n"); + sb.append("\n**************************************************\n"); + } + }else{ + // mediaType = null --> guess + WorkflowBundle wfBundle = io.readBundle(file, null); + System.out.println("Service types used in " + file.getCanonicalPath() + " :" + "\n"); + sb.append("Service types used in " + file.getCanonicalPath() + " :"); + for (Profile profile : wfBundle.getProfiles()) { + for (Activity activity : profile.getActivities()) { + this.types.add(activity.getType().toASCIIString()); + } + } + for(String t : types){ + System.out.println(t); + sb.append(t + "\n"); + } + + System.out.println("\n**************************************************\n"); + sb.append("\n**************************************************\n"); + } + } + + if(save!=null){ + File log = new File(save); + FileWriter fw = new FileWriter(log); + BufferedWriter bw = new BufferedWriter(fw); + bw.write(sb.toString()); + bw.close(); + fw.close(); + System.out.println("Results were saved into " + save); + } + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java new file mode 100644 index 0000000..7daa38e --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java @@ -0,0 +1,193 @@ +package org.apache.taverna.tavlang.tools.stats; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.util.List; + +import org.apache.taverna.scufl2.api.common.NamedSet; +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.core.ControlLink; +import org.apache.taverna.scufl2.api.core.DataLink; +import org.apache.taverna.scufl2.api.core.Processor; +import org.apache.taverna.scufl2.api.core.Workflow; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.api.port.InputPort; +import org.apache.taverna.scufl2.api.port.OutputPort; + +public class GetWfStat { + + private NamedSet<Workflow> set; + private String logFile; + private boolean verbose; + private StringBuilder str_verb = new StringBuilder(); + private StringBuilder str_nverb = new StringBuilder(); + + + //If given file is a workflow file + public GetWfStat(List<String> wf_files, String log, boolean verbose){ + this.logFile = log; + this.verbose = verbose; + + for(String files : wf_files){ + File f = new File(files); + if(f.isFile()){ + this.read(f); + + }else{ + System.err.println("Error reading the file " + f.getName()); + } + } + + this.isVerbose(); + + if(log!=null){ + this.writefile(this.str_verb.toString(), this.logFile); + } + } + + //Read the workflow file and extract the resources. + //And append them to a String builder + public void read(File file){ + WorkflowBundleIO io = new WorkflowBundleIO(); + try { + WorkflowBundle wf = io.readBundle(file, null); + this.set = wf.getWorkflows(); + + //String to be written to a file. + this.str_nverb.append(">>> Statistics of the workflow bundle: " + file.getName() + " <<<\n"); + this.str_verb.append(">>> Statistics of the workflow bundle: " + file.getName() + " <<<\n"); + + for(Workflow wrf : set){ + //TODO :- Take each type of resource and make a system to view them to the user. + String name = "Name of the workflow = " + wrf.getName(); + this.str_verb.append(name + "\n"); + this.str_nverb.append(name + "\n"); + + + String noP = " |--> Number of Processors = " + wrf.getProcessors().size(); + this.str_verb.append(noP + "\n"); + this.str_nverb.append(noP + "\n"); + + if(this.verbose && wrf.getProcessors().size()!=0){ + this.str_verb.append(" | |--> Processors: " + "\n"); + + for(Processor p : wrf.getProcessors()){ + this.str_verb.append(" | |--> " + p.getName() + "\n"); + } + this.str_verb.append(" |" + "\n"); + } + + this.str_verb.append(" |--> Number of Data Links = " + wrf.getDataLinks().size() + "\n"); + this.str_nverb.append(" |--> Number of Data Links = " + wrf.getDataLinks().size() + "\n"); + + if(this.verbose && wrf.getDataLinks().size()!=0){ + this.str_verb.append(" | |--> Data Links" + "\n"); + + for(DataLink link : wrf.getDataLinks()){ + this.str_verb.append(" | |--> " + link + "\n"); + } + this.str_verb.append(" |" + "\n"); + } + + this.str_nverb.append(" |--> Number of Control Links = " + wrf.getControlLinks().size() + "\n"); + this.str_verb.append(" |--> Number of Control Links = " + wrf.getControlLinks().size() + "\n"); + + + if(this.verbose && wrf.getControlLinks().size()!=0){ + this.str_verb.append(" | |--> Control Links\n"); + for(ControlLink link : wrf.getControlLinks()){ + this.str_verb.append(" | |--> " + link + "\n"); + } + this.str_verb.append(" |\n"); + } + + this.str_nverb.append(" |--> Number of Input ports = " + wrf.getInputPorts().size()+"\n"); + this.str_verb.append(" |--> Number of Input ports = " + wrf.getInputPorts().size()+"\n"); + + + if(this.verbose && wrf.getInputPorts().size()!=0){ + this.str_verb.append(" | |--> Input Ports\n"); + for(InputPort iport : wrf.getInputPorts()){ + this.str_verb.append(" | |--> " + iport.toString()+"\n"); + } + this.str_verb.append(" |\n"); + } + + this.str_nverb.append(" |--> Number of Output Ports = " + wrf.getOutputPorts().size()+"\n"); + this.str_verb.append(" |--> Number of Output Ports = " + wrf.getOutputPorts().size()+"\n"); + + if(this.verbose && wrf.getOutputPorts().size()!=0){ + this.str_verb.append(" | |--> Output Ports\n"); + for(OutputPort o_port : wrf.getOutputPorts()){ + this.str_verb.append(" | |--> " + o_port.toString()+"\n"); + } + + this.str_verb.append("\n"); + } + + this.str_nverb.append("\n"); + this.str_verb.append("\n"); + } + + } catch (ReaderException | IOException e) { + e.printStackTrace(); + } + } + + + //Saving the output into a log + public void writefile(String report, String url){ + + File file = new File(url); + + if(!file.isFile()){ + System.err.println("Error in writing the log file..."); + } + + FileWriter writer; + BufferedWriter bfw; + try { + writer = new FileWriter(file); + bfw = new BufferedWriter(writer); + bfw.write(report); + bfw.close(); + writer.close(); + System.out.println("Results were saved into " + file.getPath()); + } catch (IOException e) { + e.printStackTrace(); + } + + } + + public void isVerbose(){ + if(verbose) + System.out.println(this.str_verb.toString()); + else + System.out.println(this.str_nverb.toString()); + } + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java new file mode 100644 index 0000000..fc05e3b --- /dev/null +++ b/taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java @@ -0,0 +1,151 @@ +package org.apache.taverna.tavlang.tools.validate; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.util.List; + +import org.apache.taverna.scufl2.api.container.WorkflowBundle; +import org.apache.taverna.scufl2.api.io.ReaderException; +import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; +import org.apache.taverna.scufl2.validation.correctness.CorrectnessValidationListener; +import org.apache.taverna.scufl2.validation.correctness.CorrectnessValidator; +import org.apache.taverna.scufl2.validation.correctness.ReportCorrectnessValidationListener; + +/* + * Takes .wfbundle/ .t2flow as the input + * */ +public class Validate { + + private String logfile; + private String nonVerbose = ""; + private String finalrep = ""; + private boolean verbose; + private boolean check = false; + + + public Validate(List<String> files, String file, boolean verbose) { + this.verbose = verbose; + this.logfile = file; + System.out.println("Validation started...."); + for (String f : files) { + System.out.println("Validating " + f); + File wfile = new File(f); + read(wfile); + + } + System.out.println("Validation completed......."); + + + if (this.logfile != null) { + saveToLog(this.finalrep); + } + } + + public void read(File file) { + WorkflowBundleIO io = new WorkflowBundleIO(); + try { + this.finalrep += validate(io.readBundle(file, null), file.getName()); + + } catch (ReaderException e) { + System.err.println(e.getMessage()); + + } catch (IOException e) { + System.err.println("Workflow bundle not found!"); + System.err.println(e.getMessage()); + + } + } + + public String validate(WorkflowBundle wfb, String file) { + + StringBuilder report2 = new StringBuilder(); + CorrectnessValidationListener correctnessValidationListener = new ReportCorrectnessValidationListener(); + CorrectnessValidator correctnessValidator = new CorrectnessValidator(); + correctnessValidationListener = correctnessValidator.validate(wfb); + String report = correctnessValidationListener.toString().replace( + "ReportCorrectnessValidationListener [", ""); + + String[] sections = report.split(", "); + + + + boolean detect = correctnessValidationListener.detectedProblems(); + if (!detect){ + report2.append("The workflow " + file + " has no errors. \n\n"); + this.nonVerbose = "The workflow " + file + " has no errors. \n"; + } + + +// System.out.println("The validation report for " + file); + report2.append("The validation report for " + file + "......\n"); + report2.append("-------------------------------------------------------------------------------- \n"); + for (int i = 0; i < sections.length; i++) { + String line = "-->"+sections[i].split("=")[0].replace("()", "").replace( + "get", "") + + ":- "; + report2.append(line); + String line2 = sections[i].split("=")[1].replace("[", "").replace("]",""); + if(line2.equals("")) report2.append("null \n\n"); + else report2.append("\t").append(line2).append("\n"); + + + } + report2.append("--------------------------------------------------------------------------------- \n\n"); + + if(detect){ + System.out.println("The workflow bundle has following problems: \n"+report2.toString()); + check = true; + } + + if(verbose){ + System.out.println(report2.toString()); + }else{ + System.out.println(this.nonVerbose); + } + + return report2.toString(); + + } + + public void saveToLog(String s) { + File logFile = new File(this.logfile); + FileWriter logwriter; + try { + logwriter = new FileWriter(logFile); + BufferedWriter blw = new BufferedWriter(logwriter); + blw.write(s); + blw.close(); + logwriter.close(); + System.out.println("Results were saved into " + logFile.getPath()); + } catch (IOException e) { + System.err.println("Error writing to the file \n" + e.getMessage()); + } + + } + + public boolean getCheck(){ + return this.check; + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/resources/.gitignore ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/resources/.gitignore b/taverna-tavlang-tool/src/main/resources/.gitignore new file mode 100644 index 0000000..e69de29 http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/main/resources/META-INF/NOTICE ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/main/resources/META-INF/NOTICE b/taverna-tavlang-tool/src/main/resources/META-INF/NOTICE new file mode 100644 index 0000000..370a8fc --- /dev/null +++ b/taverna-tavlang-tool/src/main/resources/META-INF/NOTICE @@ -0,0 +1,7 @@ +Apache Taverna Language +Copyright 2010-2014 University of Manchester, UK +Copyright 2014-2015 The Apache Software Foundation + +This product includes software developed at +The Apache Software Foundation (http://www.apache.org/). + http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/test/java/.gitignore ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/test/java/.gitignore b/taverna-tavlang-tool/src/test/java/.gitignore new file mode 100644 index 0000000..e69de29 http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java new file mode 100644 index 0000000..6beaa8e --- /dev/null +++ b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java @@ -0,0 +1,43 @@ +package org.apache.taverna.tavlang.test; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + +import org.apache.taverna.tavlang.CommandLineTool; +import org.junit.Assert; +import org.junit.Test; + +public class CommandLineTest { + CommandLineTool commandLineTool = new CommandLineTool(); + + @Test + public void testHelp(){ + commandLineTool.parse(); + commandLineTool.parse("version"); + commandLineTool.parse("help"); + commandLineTool.parse("help", "convert"); + commandLineTool.parse("help", "inspect"); + commandLineTool.parse("help", "validate"); + commandLineTool.parse("help", "help"); + } + + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java new file mode 100644 index 0000000..a920db2 --- /dev/null +++ b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java @@ -0,0 +1,34 @@ +package org.apache.taverna.tavlang.test; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class TestConvert{ + + @Test + public void testConvertS() { +// fail("Not yet implemented"); + + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/3aa91bf8/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestStats.java ---------------------------------------------------------------------- diff --git a/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestStats.java b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestStats.java new file mode 100644 index 0000000..4c22377 --- /dev/null +++ b/taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestStats.java @@ -0,0 +1,34 @@ +package org.apache.taverna.tavlang.test; + +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class TestStats { + + @Test + public void test() { +// fail("Not yet implemented"); + } + +}
