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 matter. But I'm not sure. :( Lectures are friendly and they are supporting us. I'll try. Cheers. On 11 March 2015 at 18:49, Menaka Madushanka <[email protected]> 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 <[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> > -- Menaka Madushanka Jayawardena Faculty of Engineering, <http://www.pdn.ac.lk/eng> University of Peradeniyaya. LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
