You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2016/02/02 22:58:01 UTC
[05/11] incubator-taverna-language git commit: Command line module
removed
Command line module removed
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/66a8cfd1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/66a8cfd1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/66a8cfd1
Branch: refs/heads/master
Commit: 66a8cfd1fb33925c99a24c8b63a1cc9dda9e8c0f
Parents: 021fcd5
Author: Menaka Madushanka <me...@gmail.com>
Authored: Tue Feb 2 11:49:46 2016 +0530
Committer: Menaka Madushanka <me...@gmail.com>
Committed: Tue Feb 2 11:49:46 2016 +0530
----------------------------------------------------------------------
taverna-language-commandline/.gitignore | 1 -
taverna-language-commandline/README.md | 425 -----
taverna-language-commandline/pom.xml | 213 ---
.../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 -
.../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 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66a8cfd1/taverna-language-commandline/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/.gitignore b/taverna-language-commandline/.gitignore
deleted file mode 100644
index 916e17c..0000000
--- a/taverna-language-commandline/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-dependency-reduced-pom.xml
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66a8cfd1/taverna-language-commandline/README.md
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/README.md b/taverna-language-commandline/README.md
deleted file mode 100644
index e76cbcd..0000000
--- a/taverna-language-commandline/README.md
+++ /dev/null
@@ -1,425 +0,0 @@
-<!--
- 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, – – log : Save results in a log file
- * -v, – – 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/66a8cfd1/taverna-language-commandline/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/pom.xml b/taverna-language-commandline/pom.xml
deleted file mode 100644
index 2da63ff..0000000
--- a/taverna-language-commandline/pom.xml
+++ /dev/null
@@ -1,213 +0,0 @@
-<?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-language-commandline</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/66a8cfd1/taverna-language-commandline/src/main/java/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/.gitignore b/taverna-language-commandline/src/main/java/.gitignore
deleted file mode 100644
index e69de29..0000000
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java
deleted file mode 100644
index 068c933..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java
+++ /dev/null
@@ -1,350 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java
deleted file mode 100644
index 016488c..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java
+++ /dev/null
@@ -1,29 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/Tools.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/Tools.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/Tools.java
deleted file mode 100644
index c78c7a2..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/Tools.java
+++ /dev/null
@@ -1,88 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java
deleted file mode 100644
index da4dff0..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java
+++ /dev/null
@@ -1,206 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java
deleted file mode 100644
index f11424c..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToJson.java
+++ /dev/null
@@ -1,298 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java
deleted file mode 100644
index 6ab14bc..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/ToRobundle.java
+++ /dev/null
@@ -1,66 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java
deleted file mode 100644
index f93aadc..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ProcessorNames.java
+++ /dev/null
@@ -1,169 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java
deleted file mode 100644
index ddff2ab..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/inspect/ServiceTypes.java
+++ /dev/null
@@ -1,112 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java
deleted file mode 100644
index 7daa38e..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/stats/GetWfStat.java
+++ /dev/null
@@ -1,193 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java b/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java
deleted file mode 100644
index fc05e3b..0000000
--- a/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/validate/Validate.java
+++ /dev/null
@@ -1,151 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/main/resources/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/resources/.gitignore b/taverna-language-commandline/src/main/resources/.gitignore
deleted file mode 100644
index e69de29..0000000
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66a8cfd1/taverna-language-commandline/src/main/resources/META-INF/NOTICE
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/resources/META-INF/NOTICE b/taverna-language-commandline/src/main/resources/META-INF/NOTICE
deleted file mode 100644
index 370a8fc..0000000
--- a/taverna-language-commandline/src/main/resources/META-INF/NOTICE
+++ /dev/null
@@ -1,7 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/test/java/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/.gitignore b/taverna-language-commandline/src/test/java/.gitignore
deleted file mode 100644
index e69de29..0000000
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/66a8cfd1/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java b/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java
deleted file mode 100644
index 6beaa8e..0000000
--- a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java
+++ /dev/null
@@ -1,43 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java b/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java
deleted file mode 100644
index a920db2..0000000
--- a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java
+++ /dev/null
@@ -1,34 +0,0 @@
-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/66a8cfd1/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestStats.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestStats.java b/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestStats.java
deleted file mode 100644
index 4c22377..0000000
--- a/taverna-language-commandline/src/test/java/org/apache/taverna/tavlang/test/TestStats.java
+++ /dev/null
@@ -1,34 +0,0 @@
-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");
- }
-
-}