* various notes from slips of papers: - why does a Reporter need to make another copy of a local file? - XSLT processing for Gowlab is not finished (check out also http://www.iopus.com/imacros/firefox - useful for us?) - Can we set maximum memory limit for the executables? For example running the EMBOSS dotpath application with wordsize 4 freezes a fedora 8 server with 1 GB memory. (LSF supports specifying maximum memory use for the submitted jobs) - walk through TBD's - empty protocol property should result in no protocol, not the default one (in ServiceLocator) - When the WEB-INF/classes/soaplab.properties file of a running soaplab web application is modified tomcat unloads the previous instance of the web application and then reloads the web application again. We have noticed that when tomcat unloads the previously running soaplab web application it doesn't automatically terminates the threads already spawned by that soaplab web application. However after unloading the web application, all(we observe) static fields available to the previously spawned threads become null. Based on this observation if the log fields of the ServiceCleaning and JobCleaning threads are null we decide the threads belong to an unloaded Soaplab web application and they are terminated. There should however be better ways of terminating the previously spawned threads when tomcat unloads a web application. - [full] format validation of inputs (use class Formatter for %f... formats) - is property runtime.dir really reloadable? (try in Tomcat) - perhaps do not show result_url if the original result is empty - display.showdb - how to send 'boolean false' (e.g. comment false) (perhaps problem with "calculated fields"? 0r, with not (yet) supporting -noXXX options?) - make sure that 'tagsepar' is well documented (why doe sit use '='?, why not just 'tagsepar +'? [then update MetadataGuide.html] ---- Testing, debugging: * more junit * some junit test for JobState and FileStorage synchronization ---- Documentation: - Gowlab.html - update DevelopersGuide.html - document user-defined parameters (see SERVER_CLASS in CmdLineJob..., an example can be a boolean argument with tags prefixed by '+' and '-') - examples of a simple implementation of a Job, and DataAdaptor, and Parameter - JobFactory is missing there - API * update javadoc, at least in the main interfaces * what should be in the generated API? better package.html's - activate _no_report.html cookies - create a Wikipedia article ---- Bug in gowlab: parameter: "Y" and query=oryze (only works with method?) * why list does not work in gowlab? * there is a problem with using the word 'format' in th method ---- - Maven - uploading to maven had problems ---- - 'method' problems: try [$greeting]... and it separate square brackets as separate argument... - also -m option in ExploreParameters did not work for me ======================================= * OMII * renew the idea of distributing war files with pre-packed services * what event filters for events? * channel notification & negotiation * an example how to extend JobState by my own states [low priority] * DB Storage handler - incl. new db connections pools * a BeanShell Job * derived services * Tom's comments: - analysis categories: more levels - input data (even paramneters) should be a structure: data and a type where type says "the data re direct" or "the data are a reference" * Gowlab with authentication? - would need a special input parameters (username, password) that would be treated differently from the other parameters * admin/ExploreMetadata - prints more than -ii; - also where are metadata read from, how old is its file, etc. * dependency rules * in the new version of ACD/XML generator: - specify the role of (or remove) options 'datatype', etc. - remove tag * to have a separate output adaptor for the URL-based results (in order to add there some hyperlinks) * patch war utility? * IOParameter - use ThreadLocal for List variable (but make this change only after creating junit tests) * input/output data adapter interfaces - add there feature to change direct data to indirect (e.g. input is a list of files - a byte[][] - and I need on the command-line a comma-separated list of these files; which means that for IOData the returned value from the adaptor should be a reference, so the IOData just puts in on the command-line, but the metadata still says that the input is direct data - that's how the input was given to the adaptor) * should we allow a direct_url for filelists? * listfile, dirlist... * truevalue? (in gowlab) * Open again the issue how to distinguish/send binary files as inputs (and also implications of binary outputs); how/if "comment: bindata" works * referring to the real values of other parameters in ACD file (e.g. graphics.dot: # the 'extension' works but it may be confusing # if the wanted format is different; the best # would be (TBD) to use: extension: ${format}) * JSP client to run services (not only o list them) * dealing with repeatables: - what env. vars create when ENVAR and more repetitions? - test ACD for repeatability (min should be 0 or 1?) - example ACD file for repeates - 'repeatibility' should be in AnalysesSpec - it is important for clients to know... - repeatable (min, max) are not always propagated from an ACD file to XML * perhaps to return to the idea to disribute war files * Metadata: - attribute 'datatype' should be also present by those inputs that are either only direct or only URL (as it is for inputs allowing both, direct data and reference) - and also for all emboss "additional" files (such as matrices) - type=long is lost (send, sbegin, etc.) - we should rectify it - re-write the whole XML parsing by using JAXB? - InputPropertyDef should also have 'allowed_values_shown_as' (this is now hidden in the analysis extension part; it will be easier to get it when JAXB is used) - when this is done, use it in Spinet to fill the select list with '...shown_as' texts - 'separator' in 'lists' (choice_list tag) is used correctly but it does not seem correct in the XML file (see testing.lists) * When calling ant axis1war target the service-list call using CmdLineClient uses the metadata directory property set for the war file being prepared and fails with errors as it could not find the metadata directory. This errors are also printed into the wsdd file being generated which should normally be printed on the screen so user aware of the problem. =============== * input files are written twice, test/debug using the following example input_direct_data testing12345 list ::data/file.list -protocol local * Is it possible to set in soaplab2 a queue size for runs? (Eric Perche) Because we have some workflows which call lot of web servcices in parallel and it could be critical for the stability of the OS. =============== These are notes that I am not anymore sure what I meant... ---------------------------------------------------------- * in CmdLineJob constructor, about sharedAttributes: "...|| jobRecreated" is correct? Why? I can perhaps have more recreated jbs in the same JVM, so why to call init() for each of them?... --- Sourceforge: You don't have an active shell at this time. For basic file transfers and management, use web.sourceforge.net -- it allows rsync, sftp, and scp access. If you would like to create a shell, use ssh to login using a USER,PROJECT username with the "create" command. If you tell ssh to allocate a tty (e.g. using -t), an interactive shell will be opened when the create is done. Otherwise, the create command will exit when the shell becomes ready for use. An example create that enters the shell when ready: ssh -t USER,PROJECT@shell.sourceforge.net create