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Posted to commits@taverna.apache.org by br...@apache.org on 2015/02/24 11:32:09 UTC
svn commit: r1661881 -
/incubator/taverna/site/trunk/content/documentation/command-line/index.md
Author: brenninc
Date: Tue Feb 24 10:32:09 2015
New Revision: 1661881
URL: http://svn.apache.org/r1661881
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incubator/taverna/site/trunk/content/documentation/command-line/index.md
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+Title: Command Line Tool
+Notice: 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.
+
+Command Line Tool is a script that runs Taverna workflows from a terminal.
+It comes in a form of a command line script called *executeworkflow*
+ (*executeworkflow.bat* on Windows and *executeworkflow.sh* on Linux/UNIX).
+
+You can [download the Command Line Tool](download/command-line-tool) from the Taverna Web site
+ or use the *executeworkflow.sh* or *executeworkflow.bat* that comes
+ bundled with the Taverna Workbench installation.
+
+- [Extended version](http://dev.mygrid.org.uk/wiki/display/tav250/Extended+version)
+
+##What is the difference between the bundled and standalone executeworkflow?
+
+ - The standalone command line tool has a **separate configuration**
+ [home directory](http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory),
+ called *taverna-cmdline-2.x.x* - while the bundled tool uses the same configuration from
+ *taverna* as the Taverna Workbench.
+
+ - Any [proxy settings](http://dev.mygrid.org.uk/wiki/display/tav250/HTTP+proxy+preferences)
+ have to be configured manually - copy
+ *conf/HttpProxy-B307A902-F292-4D2F-B8E7-00CC983982B6.config* from a configured
+ Workbench home directory.
+
+ - The bundled tool will load all the <strong>plugins</strong> installed for the workbench,
+ including third-party plugins.
+ However it will also load various GUI-supporting functions which might consume extra memory.
+
+ - To install service plugins for the command line tool, one will have to manually edit the
+ *plugins/plugins.xml* of the installation or home directory.
+ The *<plugin>... </plugin>* block can be copied from the *plugins/plugins.xml* from
+ the [home directory](http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory)
+ of a Workbench installation where the plugin is installed.
+
+ - The standalone installation and download is smaller than the workbench - but keeping both
+ installed will use more disk space.
+ (Note: the command line tool could use the {repository}} folder from the workbench using
+ symlinks or modifiying *plugins/plugins.xml*
+
+ - The standalone tool can easily be installed and used on remote servers without GUI access.
+
+ - Running the embedded tool with the database and provenance enabled allows the command line
+ runs to show up in the workbench
+ "[Workflow runs](http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective)".
+
+ - On the other hand the tool will have to use *-clientserver* if the workbench is already
+ running, or if shut down either a standalone *-startdb* database server process or
+ *-embedded*.
+
+ - The standalone tool would not be in conflict with the database of the workbench
+ (as it's in a different home directory) - but could be in conflict with parallel runs of
+ the command line tool - in which case a separate *-startdb* process should be started with
+ the other calls using *-clientserver* - see
+ [#Running the script with database](#CommandLineTool-Runningthescriptwithdatabase)
+
+<h2 id="CommandLineTool-ExecuteworkflowScript">Executeworkflow Script</h2>
+
+<p>To get help and a full set of options for the executeworkflow script type the following in the command prompt:</p>
+
+<div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent">
+<script type="syntaxhighlighter" class="theme: Eclipse; brush: java; gutter: false"><![CDATA[$ sh executeworkflow.sh -help]]></script>
+</div></div>
+
+<p>It will give the following usage options:</p>
+
+<div class="preformatted panel" style="border-width: 1px;"><div class="preformattedContent panelContent">
+<pre>usage: executeworkflow [options] [workflow]
+ -clientserver connects as a client to a
+ derby server instance.
+ -cmdir <Credential Manager's directory path> Absolute path to the
+ directory on the disk
+ where Credential Manager's
+ files are located
+ -cmpassword Indicates that the master
+ password for Credential
+ Manager will be provided
+ on standard input
+ -dbproperties <filename> loads a properties file to
+ configure the database
+ -embedded connects to an embedded
+ Derby database. This can
+ prevent mulitple
+ invocations
+ -help displays comprehensive
+ help information
+ -inmemory runs the workflow with
+ data stored in-memory
+ rather than in a database.
+ This can give performance
+ inprovements, at the cost
+ of overall memory usage
+ -inputdelimiter <inputname delimiter> causes an inputvalue or
+ inputfile to be split into
+ a list according to the
+ delimiter. The associated
+ workflow input must be
+ expected to receive a list
+ -inputdoc <document> load inputs from a Baclava
+ document
+ -inputfile <inputname filename> load the named input from
+ file or URL
+ -inputvalue <inputname value> directly use the value for
+ the named input
+ -janus <file> saves Janus RDF/XML trace
+ of execution to FILE or
+ 'provenance-janus.rdf'
+ -logfile <filename> the logfile to which more
+ verbose logging will be
+ written to
+ -opm <file> saves Open Provenance
+ Model (OPM) RDF/XML trace
+ of execution to FILE or
+ 'provenance-opm.rdf'
+ -outputdir <directory> save outputs as files in
+ directory, default is to
+ make a new directory
+ workflowName_output
+ -outputdoc <document> save outputs to a new
+ Baclava document
+ -port <portnumber> the port that the database
+ is running on. If set
+ requested to start its own
+ internal server, this is
+ the start port that will
+ be used.
+ -provenance generates provenance
+ information and stores it
+ in the database.
+ -startdb automatically starts an
+ internal Derby database
+ server.
+
+(..)
+
+</pre>
+</div></div>
+
+
+<p>If this directory already exists then an new directory is created, and appended with <code>_<n></code>, where <code>n</code> is incremented to the next available index.</p>
+
+<p>Results are written out to files named after the output port for that result. If a result is composed of lists, then a directory is created for the output port and individual list items are named after the list element index (with 1 being the first index). The the output is the result of an error, the filename is appended with â.errorâ.</p>
+
+<p>You can provide your own output directory with the <code>-outputdir</code> option. There will be an error if the directory already exists.</p>
+
+<p>You can <a href="http://dev.mygrid.org.uk//wiki/display/tav250/Provenance+export+to+OPM+and+Janus">export the provenance</a> using the <code>-opm</code> or <code>-janus</code> options.</p>
+
+<p>You can also record your results to a Baclava document using <code>-outputdoc</code> option. The document will be overwritten if it already exists. You can use the <a href="http://dev.mygrid.org.uk/wiki/display/tav250/DataViewer+Tool">DataViewer Tool</a> to view Baclava files.</p>
+
+<p>Inputs can be provided in three ways. Both <code>-inputfile</code> and <code>-inputvalue</code> options can be used together; <code>-inputdoc</code> option must be used on its own. <code>-inputfile</code> and <code>-inputvalue</code> options both take two additional arguments, the name of the port for the input, and either a file containing the input data, or the input value itself respectively.</p>
+
+<p>If one of more of you workflow inputs is described as a list, you can create a list by using the <code>-inputdelimiter</code> option, which may be used with either <code>-inputfile</code> or <code>-inputvalue</code>. This option takes two parameters â an input name and the delimiter by which to split the input into a list.</p>
+
+<p>The delimiter may be a simple character, such as a comma or a new-line character, or a regular expression. The input string, or file, will then be converted into a list being split by the delimiter specified.</p>
+
+<p>If a list of greater depth (i.e. a list or lists or deeper) is required then you will need to use the <code>-inputdocoption</code> to pass data from a Baclava file. However, if you provide an input of lower depth to that required, then it will automatically be wrapped in one or more lists up to the required depth. Providing an input of greater depth than that required will result in an error.</p>
+
+<h3 id="CommandLineTool-Runningthescriptwithdatabase">Running the script with database</h3>
+
+<p>If a workflow has a high memory requirement, then it may be better to run it using a database to store data rather than storing it in memory, which is the default option. There are three options for using a database:</p>
+<ul>
+ <li><code>-embedded</code> option, runs with an embedded database. This is slightly faster than -clientserver option (below), but has the limitation that only one <code>executeworkflow</code> script may be executed simultaneously.</li>
+ <li><code>-clientserver</code> option allows the workflow to be executed backed by the database running as a server. By default a database is not started for you, but may be started using <code>-startdb</code> option.</li>
+ <li><code>-startdb</code> option starts a database. It may be used without providing a workflow to allow a database to be started separately, allowing multiple simultaneous <code>executeworkflow</code> script runs.</li>
+</ul>
+
+
+<p>More advanced database configurations can be specified using <code>-dbproperties</code> option, allowing you to take full control over the database used. This takes a second argument, the filename of the propeties file, for which the following example contains the default settings used:</p>
+
+<div class="preformatted panel" style="border-width: 1px;"><div class="preformattedContent panelContent">
+<pre>in_memory = true
+provenance = false
+connector = derby
+port = 1527
+dialect = org.hibernate.dialect.DerbyDialect
+start_derby = false
+driver = org.apache.derby.jdbc.EmbeddedDriver
+jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
+</pre>
+</div></div>
+
+
+<p>If you want to run the Derby database with client/server setting instead of with the embedded driver, change the properties in the <code>-dbproperties</code> file (described above) as follows:</p>
+
+<div class="preformatted panel" style="border-width: 1px;"><div class="preformattedContent panelContent">
+<pre>driver=org.apache.derby.jdbc.ClientDriver
+start_derby=true
+</pre>
+</div></div>
+
+<p>If you wish to run your own separate Derby server instance, then do not define the <code>start_derby</code> option and define the port on which you are running you Derby server as <code>port=<port></code>.</p>
+
+<p>If you want to use MySQL database rather than Derby, first you need to drop the mysql-connector-java-5.1.5.jar file from the <a href="http://dev.mysql.com/downloads/connector/j/" class="external-link" rel="nofollow">mySQL</a> website into the lib folder of the Taverna installation directory (Taverna installation directory if where you are running the script from).</p>
+
+<p>You need to edit the <code>-dbproperties</code> file as follows:</p>
+
+<div class="preformatted panel" style="border-width: 1px;"><div class="preformattedContent panelContent">
+<pre>connector=mysql
+jdbcuri=jdbc:mysql://localhost/T2Provenance
+dialect=org.hibernate.dialect.MySQLDialect
+driver=com.mysql.jdbc.Driver
+username=<username>
+password=<password>
+port=<port>
+</pre>
+</div></div>
+<p>It is essential that the database name in the <code>jdbcuri</code> property is T2Provenance, as this database is hard-coded into the MySQL provenance SQL queries.</p>
+
+<p>If you do not specify the port, the script will try to connect to the default port for MySQL server, which is 3306.</p>
+
+
+<div class='panelMacro'><table class='noteMacro'><colgroup><col width='24'><col></colgroup><tr><td valign='top'><img src="/wiki/images/icons/emoticons/warning.png" width="16" height="16" align="absmiddle" alt="" border="0"></td><td><p>When using <code>-dbproperties</code> together with other options, the other options take precedence.</p></td></tr></table></div>
+
+<h2 id="CommandLineTool-Examples">Examples</h2>
+
+<p>Some examples on how the script can be invoked are shown below.</p>
+
+<div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent">
+<script type="syntaxhighlighter" class="theme: Eclipse; brush: java; gutter: false"><![CDATA[$ sh executeworkflow.sh "/Users/alex/Taverna Workflows/wf-1.t2flow"]]></script>
+</div></div>
+
+
+<p>The above line executes the workflow located in <code>/Users/alex/Taverna Workflows/wf-1.t2flow</code> that has no inputs and uses the memory for data storage (the default option). Make sure to enclose the file path in quotes if it contains spaces. The <code><workflowName>_outputdirectory</code> will be created in the current directory and outputs will be written to it.</p>
+
+<div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent">
+<script type="syntaxhighlighter" class="theme: Eclipse; brush: java; gutter: false"><![CDATA[
+$ sh executeworkflow.sh -embedded -inputvalue in1 aaa -inputvalue in2 "bb b" -outputdir /tmp/wf-2/ wf-2.t2flow
+
+]]></script>
+</div></div>
+
+
+<p>The above line executes the workflow <code>wf-2.t2flow</code> from the current directory passing the value âaaaâ to the input port <code>in1</code> and value âbb bâ to the input port <code>in2</code>. If input values contain spaces make sure to enclose them in quotes. Uses the embedded Derby database to store the data. Outputs will be written to the <code>/tmp/wf-2/</code> directory.</p>
+
+<div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent">
+<script type="syntaxhighlighter" class="theme: Eclipse; brush: java; gutter: false"><![CDATA[
+$ sh executeworkflow.sh -inputvalue in1 aaa -inputfile in2 input2.txt -inputdelimiter in2 "\n" wf-3.t2flow
+
+]]></script>
+</div></div>
+
+
+<p>The above line executes the workflow <code>wf-3.t2flow</code> from the current directory passing the value âaaaâ to the input port <code>in1</code> and splitting the content of file <code>input2.txt</code> using â\nâ (new line character) as the delimiter and passing the resulting list to the input port <code>in2</code>. Make sure to out the delimiter in quotes, even if it is just a single character, like â;â. The <code><workflowName>_outputdirectory</code> will be created in the current directory and outputs will be written to it.</p>
+
+<div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent">
+<script type="syntaxhighlighter" class="theme: Eclipse; brush: java; gutter: false"><![CDATA[
+$ sh executeworkflow.sh -inputdoc /tmp/input-doc.xml -outputdoc /tmp/output-doc.xml "/Users/alex/Taverna Workflows/wf-4.t2flow"
+
+]]></script>
+</div></div>
+
+
+<p>The above line executes the workflow <code>/Users/alex/Taverna Workflows/wf-4.t2flow</code>, loading inputs from the Baclava document in <code>/tmp/input-doc.xml</code>, and writing the outputs to a Baclava document <code>/tmp/output-doc.xml</code>.</p>