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From Menaka Madushanka <menaka12...@gmail.com>
Subject Re: GSOC 2015 - Taverna: Language command line tool
Date Wed, 11 Mar 2015 13:36:45 GMT
Hi Stain,

Relevant to my previous message....

For examinations, I'll try my best to do something.
Because, there is some possibility to negotiate with lecturers about this

But I'm not sure. :(
Lectures are friendly and they are supporting us.
I'll try.


On 11 March 2015 at 18:49, Menaka Madushanka <menaka12350@gmail.com> wrote:

> Hi Stain,
> For time factor, my main problem is examinations in our faculty :-).
> For MID Exams that is a minor case but for End semester examinations,
> study leave 1  week and exam 1 week.
> Now I'm facing for Mid semester examination.
> Our end exam of this semester will be in May.
> Other than that there are no any problems for me. :-)
> Thank you very much.
> Cheers.
> On 11 March 2015 at 16:44, Stian Soiland-Reyes <stain@apache.org> wrote:
>> ... Let's try to keep the technical bit of this thread on dev@taverna
>> - but feel free to contact me personally for private matters such as
>> your commitments.
>> On 10 March 2015 at 19:25, Menaka Madushanka <menaka12350@gmail.com>
>> wrote:
>> > If I understood correctly,
>> > I have to implement the generalized version of the command line tools
>> by the
>> > mid evaluation
>> >
>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-examples
>> >
>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-wfdesc
>> > https://github.com/stain/ro-combine-archive
>> Right - that sounds like a good plan. Once we have a prototype up and
>> running we can see better what fits well.
>> This should include writing some documentation on command line
>> options, example usage etc.
>> > After that update ExecuteWorkflow....
>> Perhaps we should flesh out a more detailed plan for ExecuteWorkflow.
>> Having some kind of -verbose mode with proper logging was mentioned -
>> I can help you show how to hook into the platform to get
>> notifications.  Perhaps this needs some kind of verbosity level as
>> some workflows can be very active and thus be very noisy if everything
>> is logged.
>> Have you got any other suggestions? For instance on simplifying the
>> command line options and perhaps moving some of these to a config
>> file? Making it a bit more unix-like perhaps.
>> stain@biggie-utopic
>> :~/src/taverna/incubator-taverna-commandline/taverna-commandline-product/target/apache-taverna-commandline-3.1.0.incubating-SNAPSHOT-dev/apache-taverna-commandline-3.1.0.incubating-SNAPSHOT$
>> ./executeworkflow.sh --help
>> OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=400m;
>> support was removed in 8.0
>> usage: executeworkflow [options] [workflow]
>>  -bundle <bundle>                        Save outputs to a new Workflow
>>                                          Run Bundle (zip).
>>  -clientserver                           Connect as a client to a derby
>>                                          server instance.
>>  -cmdir <directory path>                 Absolute path to a directory
>>                                          where Credential Manager's files
>>                                          (keystore and truststore) are
>>                                          located.
>>  -cmpassword                             Indicate that the master password
>>                                          for Credential Manager will be
>>                                          provided on standard input.
>>  -dbproperties <filename>                Load a properties file to
>>                                          configure the database.
>>  -embedded                               Connect to an embedded Derby
>>                                          database. This can prevent
>>                                          mulitple invocations.
>>  -help                                   Display comprehensive help
>>                                          information.
>>  -inmemory                               Run the workflow with data stored
>>                                          in-memory rather than in a
>>                                          database (this is the default
>>                                          option). This can give
>>                                          performance inprovements, at the
>>                                          cost of overall memory usage.
>>  -inputdelimiter <inputname delimiter>   Cause 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.
>>  -logfile <filename>                     The logfile to which more verbose
>>                                          logging will be written to.
>>  -outputdir <directory>                  Save outputs as files in
>>                                          directory, default is to make a
>>                                          new directory
>>                                          workflowName_output.
>>  -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                             Generate provenance information
>>                                          and store it in the database.
>>  -startdb                                Automatically start an internal
>>                                          Derby database server.
>> By default, the workflow is executed using the -inmemory option, and the
>> results are written out to a directory named after the workflow name.
>> If this directory already exists then a new directory is created, and
>> appended with _<n>, where n is incremented to the next available index.
>> 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 '.error'.
>> You can provide your own output directory with the -outputdir option.
>> There
>> will be an error if the directory already exists.
>> You can also record your results to a Baclava document using -outputdoc
>> option. The document will be overwritten if it already exists.
>> Inputs can be provided in three ways. Both -inputfile and -inputvalue
>> options
>> can be used together; -inputdoc option must be used on its own.
>> -inputfile and
>> -inputvalue 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.
>> If one of more of your workflow inputs is a list, you can create a list
>> input by using the -inputdelimiter option, which may be used with either
>> -inputfile or -inputvalue. This option takes two parameters - an input
>> name
>> and the delimiter by which to split the input into a list.
>> 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. Make sure to
>> put the delimiter character in quotes as it may be interpreted by the
>> shell
>> as a special character, e.g. ;.
>> If a list of greater depth (i.e. a list or lists or deeper) is required
>> then
>> you will need to use the -inputdoc option.  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.
>> 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:
>> -embedded option, runs with an embedded database. This is slightly faster
>> than
>> the -clientserver option (below), but has the limitation that only one
>> executeworkflow script may be executed simultaneously.
>> -clientserver 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 -startdb option.
>> -startdb option starts a database. It may be used without providing a
>> workflow
>> to allow a database to be started separately, allowing multiple
>> simultaneous
>> executeworkflow script runs.
>> More advanced database configurations can be specified using -dbproperties
>> option, allowing you to take full control over the database used. This
>> takes a
>> second argument, the filename of the properties file, for which the
>> following
>> example contains the default settings:
>> 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
>> Note that when using -dbproperties together with other options, the other
>> options take precedence.
>> -cmdir option lets you specify an absolute path to a directory where
>> Credential Manager's files (keystore and truststore - containing user's
>> credentials and trusted certificates for accessing secure services) are
>> stored.
>> If not specified and the workflow requires access to these files, Taverna
>> will
>> try to find them in the default location in <TAVERNA_HOME>/security
>> somewhere
>> inside user's home directory (depending on the platform).
>> -cmpassword option can be used to tell Taverna to expect the password for
>> the
>> Credential Manager on standard input. If the password is not piped in,
>> Taverna
>> will prompt you for it in the terminal and block until it is entered. Do
>> not
>> enter your password in the command line! If -cmpassword option is not
>> specified
>> and -cmdir option is used, Taverna will try to find the password in a
>> special
>> file password.txt in the directory specified with -cmdir option.
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>

Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>

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