Changes in build 1545 (v4.1 Release) * Fixed: Fixed command line switch and multiple arguments bug * Fixed: When user decreases argument count extra filled values will be removed * Fixed: Changing to List file when parameter type is changed from File to String. * Fixed: Ctrl+E (Command+E) to open edit Module window Changes in build 1528 (v4.1 Alpha) * Added: New visualization tool called "Viewer" * Fixed: Stop workflow command stops local executions too, but not Viewers * Fixed: Workflow continues execution on reconnect, even if it has local and remote executions * Fixed: Execution logs dialog updates Changes in build 1500 (v4.1 Alpha) * Added: Find and Replace functions in Data Modules dialog * Changed: Variables are now inherited to child module groups * Fixed some bugs Changes in build 1476 (v4.1 Alpha) * Added: New tool Server Changer at Tools menu which helps to change server addresses of multiple modules and parameters * Fixed: Module groups wasn't showing execution time * Fixed: Data modules now have correct cardinality value * Fixed: Wrap validation error message * Fixed: Execution of local module with remote parameters and otherwise Changes in build 1455 (v4.1 Alpha) * Added: Workflows may involve modules that run either on grid server or on local host * Added: Pipelines validates global environmental variables * Added: Validation now includes acceptance of the workflow * Added: "Save connection" button in the Connection Credentials dialog * Added: Font styles in annotations * Added: Data module editor now shows argument count for input/output data * Added: Cut,copy, paste operations for annotations * Added: Alias for Redo operation. Now Redo has Ctrl+Y and Ctrl+Shift+Z shortcuts on all platforms * Added: Remove icon button in Edit module dialog which appears only when icon is set to module * Added: Copy icon, paste icon, remove icon functions in module's popup menu * Changed: Pipeline messaging. This version can't connect to old version servers * Changed: Make module group darker when it is selected * Changed: Create module group command now includes annotations too * Changed: Top level menus * Changed: Modules which execution stopped by stop button show Incomplete state * Changed: Select all command now selects annotations too * Changed: Pause button replaced with grey (not clickable) play button, because pause function is not still supported * Changed: Cloning of module groups to non XML dependent * Changed: In Output files panel paths became selectable, users are able to select them * Changed: selectionBox includes annotations too * Changed: Now pipeline uses system's temporary location for its temp files * Changed: Module's parameter tooltip and description box to show parameter values and file types * Changed: default port from 8000 to 8001 * Changed: Pipeline's XML files will be smaller because they keep module icon resized info not the whole icon * Fixed bug: Main workflow timer roll-back problem when finishing file transfers * Fixed bug: Undo for the group from library now works properly in case if user was inside the group at undo time * Fixed bug: Show validation error message for every (not only for one) module with cardinality error * Fixed bug: Active sessions dialog now updates active sessions at runtime * Fixed bug: Execution log dialog now responds to keyboard shortcuts such as Command + W * Fixed bug: Get Files button in Output files dialog becomes enabled after execution completes for every instance * Fixed bug: Update passing messages to allow data transfers for Server Terminal GUI * Fixed bug: Changed default execution status times to be 0 instaed of -1 at XML serialization * Fixed some minor bugs as well Changes in build 1359 (v4.0.5) * IDA library has been updated * Added support for serializing/deserializing binary provenance information into workflows * updated execution engine to support DRMAA 1.0 * removed a thread race in the execution engine * the Pipeline log file location can be changed in the preferences.xml file * privilege escalation copying now uses a single cp command instead of many smaller ones * fixed a bug that sometimes prevented a user from connecting two parameters Changes in build 1322 (v4.0.4) * empty modules do not appear in the personal library anymore * fixed a bug where selecting a different workflow tab would try to open a recent workflow * fixed a copy/paste issue on module groups with connections * fixed a bug where modules saved with exported params, were still exported when dragged in from the personal lib. * updated the hsqldb library Changes in build 1314 (v4.0.3) * revamped IDA back end * data sources/sinks are now separated from regular modules in the personal/server library Changes in build 1307 (v4.0.2) * changed the IDA hostname Changes in build 1296 (v4.0.1) * fixed a bug in the active sessions dialog when trying to remove multiple sessions at once * fixed a translation issue with side effect outputs * fixed a bug in the execution log window * added the Pipeline logo to the main frame icon Changes in build 1255 (V4.0 Release) * fixed a bug with hyper links that was introduced in the last build * new JavaApplicationStub for OS X Changes in build 1242 * Minor GUI fixes everywhere * The Personal Library is loaded dynamically * Valication now checks for invalid user defined variables * Program start time should be faster in all OSes * Added more support for Pipeline server administration * Validation now checks for misuse of base parameters * Command Line Interface rewrite Changes in build 1216 * You can set environment variables in your preferences * Reconnecting to workflows is much easier now. (They won't all explode onto your screen) * Reduced memory footprint * Commands and output files are loaded dynamically in the GUI * You can now download outputs that are directories after execution * Some validation bug fixes * Validation now checks that base and cardinality parameters are valid * Bug fixes for GUI drawing * Fixed a couple issues with the Connections Dialog * Updates to the command line interface * Added support for OS X 10.5 (Leopard) * Fixed a bug that would sometimes affect list generation * Fixed a race condition that occurred when hitting stop and reset back to back * Local system execution errors are now displayed in the error stream tab (in red) * Lots of back end work Changes in build 1156 * Sever library now animates during execution or when its empty (can be disabled) * Validation is again more thorough than before * Bug fixes in Copy/Paste for data sinks and sources * Fixed where data modules show up in the library panels * Personal Library and Variables Dialog remain on top of the main frame * A bug fix when staging local files for remote execution on Windows * Server side authentication is now synchronized to 1 thread at a time * Fixed a problem with too many open file descriptors for non-grid execution * Also fixed an issue with execution stops Changes in build 1127 * Great improvements in network speed and stability * Validation is much faster, and more thorough * Fixed several GUI bugs relating to execution, validation and general screen updates * Fixed a bug that wouldn't allow a specific filetype to connect to a 'File' input * Resolved some issues with Windows execution * Icons are now stored inside the .pipe files * Fixed a bug in selecting all modules through the edit menu * Added some keyboard shortcuts * Fixed prestaging bugs * Fixed a bug in execution when a command only had 1 argument Changes in build 1062 * Added a splash screen * Progress of file copying is now drawn to the screen when a module completes * Another revision of the variables dialog * Many dialogs now have keyboard listeners, and the personal library and variables dialogs remember their positions * Validation catches many more errors now (including file type checking) * This may cause problems for workflows that had improperly connected input/outputs before * Validation status is drawn to the screen more accurately * Added support for dragging and dropping .pipe files from the desktop to the workflow area * Fixed several issues with the server and personal libraries * Known issue * Some executables that are executed locally in Windows Vista can be problematic. Changes in build 1027 * Fixed bug with communicator not sending problem messages * DownloadManager is more informative on failure * PipelineControlBar no longer defaults to "Validating Workflow" during execution * Preference dialog tweaks * Changed the dmg mounting name to LONI Pipeline, added optimization * Fixed memory leak when workflows close * Fixed bug in UNIX release scripts * Changed the transformations list in the edit advanced parameter dialog to be drag-able * Optimizations in the Java2D rendering * Fixed high CPU usage bug * Increased WorkflowAnimator action period to save CPU cycles * Moved update checker off Swing thread * Animator now stops processing updates after workflow is complete * Validation error is now thrown for input parameters that have no file types selected * Added JDOM to About Box * Pipeline Server Utility GUI added Changes in build 980 * many small bug fixes Changes in build 967 * FEATURE: New searchable Server and Personal Library * FEATURE: Tagging, Modules can be tag with any information which is searchable * FEATURE: The Pipeline will check for program updates at startup * FEATURE: Workflow can now be paused and stopped at anytime * FEATURE: User definable file types * FEATURE: Inputs can now accept multiple file types * FEATURE: Bug Reporter, please submit your bugs * FEATURE: Feedback for pre-execution events * validation now has a more robust check for the correct number of files going from one module to another * module groups resizes correctly after having a parameter exported * fixed annotations loading * fixed a bug with editing infinite cardinality file parameters * module groups edit dialog can be reached by right clicking * fixed a bug where some needs file did not get uploaded * added a new download download dialog * status message is optimized to save the amount of information going across the network * fixed a bug where connections can be made even if that exact one exist already * file transfers can now be stopped while in progress * data sinks can be marked as directory dumps, all outputs connect to a directory dump will be placed at the dump location * Recent files now displays the correct number of files defined in the Preferences * fixed the file finder on windows * validation will now check to make sure that all input values in an enumerated list are defined in the module definition * job times now displays the correct time after a reconnect * commands.log file is now in XML format and is printed out in order * annotations will now load properly * new Log Viewer Dialog * data sent across the network will now be compressed to increase transfer speed * validation now checks for malformed variables * fixed a bug where validation hangs if the server you're trying to connect to is down * added a GUI for selecting user defined filetypes * improved variables dialog * the about box is fixed * personal and server library has new icons to identify: data modules, modules, and module groups * some keyboard shortcuts has been updated Changes in build 822 * FEATURE: New icons for OS X builds and integration with Finder * FEATURE: New icons for pipe files * fixed a bug where directories before and after workflow execution were not being copied over correctly * fixed a bug where filetypes with multiple dots, eg someFileName.nifty.gz, were not being sent over to the server correctly * validation bug fix (validation will throw an error if the user puts in a directory for the executable path Changes in build 800 * FEATURE: IDA access * FEATURE: Validation can be called without executing the program * FEATURE: Module Groups * FEATURE: Data sources and sinks * FEATURE: Packages for OS X and Windows * FEATURE: Launch workflows in the GUI from the command line, example: java -jar Pipeline.jar myworkflow.pipe * FEATURE: Module definitions have support for two types of authors now (module and executable) and citation info as well * FEATURE: Once you submit a workflow to the server for execution, you can close the client. Reconnect later, and your workflow will reopen showing you its current status * FEATURE: The Pipeline now works on Windows Vista too * fixed parameters that output strings * more thorough validation including cardinality checks between modules * DRMAA native grid spec is now a preference (used to be hardcoded) * new preference for deleting workflow data after user resets workflow execution * commands.log file is now closed after writing * added citations to the module panel (removed metadata attributes) * fixed bug when trying to convert a parameter from an enumerated type to a string (bug 001693) * the browse button is back in the edit concrete module panel * validation checks enabled parameters in addition to required parameters * validation throws an error if a required parameter is not enabled * made copy/paste a little more robust * more detailed author information for modules * fixed a bug where users couldn't remove a base from the advanced parameter dialog * added a dialog that captures output and error streams and displays them to the user in the program * preferences dialog lets client users adjust thread pool size for execution * validation no longer checks output directories of type File for existence * validation fix, disabled parameters with values are no longer validated * fixed a regression that caused problems when editing enumerated parameter types * fixed the column size in the parameter table when editing module parameters * validation bug fix (no longer checks for needs files on List parameters) Changes in build 695 * bug fix for file transfer post processing * added logic to handle cycle detection in Validation * added several filetypes including some for the Brains2 application * fixed a Validation bug when checking extension that contain a dot * race condition in GUI updates at the end of workflows is now fixed * FEATURE: New tools available for monitoring a server's health * FEATURE: Annotations (notes) in a workflow. Use these to describe what different parts of your workflow do. * FEATURE: Program remembers its last size and position upon closing and opens up there (if possible) on the next run * Tons of bug fixes in the workflow editing area * FEATURE: You can download output files of parameters through the output log viewer * FEATURE: Thread pooling which allows limiting of the number of simultaneous threads/jobs that are running * FEATURE: Parameters added in the Edit Module dialog will now show up below the currently selected parameter * FEATURE: You can save output files after execution from the Log Viewer without having to bind a value. * personal library and variables dialog are now positioned inside the main frame (so they don't draw off screen) * removed old code and old libraries for a smaller binary and total package * bug fixed when trying to reorder parameters Known issue(s) in build 694 * Repainting of the workflow may leave artifacts sometimes Changes in build 661 * Many improvements in validation. It is much more strict now as well. * New dialogs for editing modules. Provenance attributes can be edited on workflows and module descriptions * Directory copying has been improved * Lots of little nice feature additions * Many bug fixes throughout the code. Changes in build 8 * Fixed a bug that would sometimes drop a network connection * Permissions on remote files are now handled by the server (no more chmod 777'ing destination folders) * Reduced the size of status updates * Improved the way status updates drawn to the GUI * Module and workflow timers that show you how long execution has taken * new log viewer * reorganized menu items * added Afni Brick, Afni Head and Nii.gz filetypes * the program will prompt you to make a connection to a server when you hit play, if the connection hasn't already been made * the workflow repaints in a smarter way (reduces CPU usage) * lots of bug fixes and robustness added throughout * the server's memory footprint has been significantly reduced Known issues in build 8 * Repainting of the workflow may leave artifacts sometimes * If a module has an error during execution, it will incorrectly turn green once the entire workflow completes