Merge remote-tracking branch 'gale/patch-1'
Conflicts:
taverna-tavlang-tool/README.md
This closes #27
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
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Branch: refs/heads/master
Commit: 755469c59026a897081b4a2c757f2409dc98d16e
Parents: 41f0349 17bc19b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 2 22:16:08 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 2 22:16:08 2016 +0000
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+<!--
+ 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 tavlang tool
+
+
+This is 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.
+
+
++See below for [Building and Install
Requirements](#building-and-install-requirements), [Usage](#usage), and
[Documentation](#documentation).
+
+## 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 1.8 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
++ help Display help information about Taverna
+ 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
+
+-----------------------------------------------------------------------------------------------------------------------------------------
