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 <[email protected]> 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 <[email protected]> > 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>
