LONI Pipeline Environment Releases

pipeline Pipeline V.5.9.1

jvanhorn@stage.nitrcce.org (John Van Horn) — Fri, 01 Nov 2013 14:59:00 GMT

http://pipeline.loni.usc.edu/products-services/pipeline-software/

pipeline LONI Pipeline V.5.4

iwaterpolo@stage.nitrcce.org (I Dinov) — Wed, 14 Mar 2012 22:06:00 GMT

See this site for compelte Release Notes ([url=http://pipeline.loni.ucla.edu/features/pipeline-5-4/]http://pipeline.loni.ucla.edu/features/pipeline-5-4/[/url])

pipeline Pipeline V.5.3.1

jvanhorn@stage.nitrcce.org (John Van Horn) — Tue, 22 Nov 2011 23:12:00 GMT

See http://users.loni.usc.edu/~pipeline/pipeline_releases/ReleaseNotes

pipeline Pipeline V5.2.1

jvanhorn@stage.nitrcce.org (John Van Horn) — Wed, 18 May 2011 22:34:00 GMT

<pre>Changes in build 3665 ( v5.2.1 )
---[ Pipeline Client / Server ]
* Added: New feature for hiding/showing all annotations in a module group and all nested module groups
* Added: the option to automatically export sessions and communicators information from database to a directory. When a directory is given with HistoryLogPath tag in the preferences xml, the server will save old information (that are more than two times of DaysToPersistStatus) from database to the directory and remove them from the database.

* Fixed: to not create links when there are multiple data sinks connected to one module, instead files will be copied to all connected data sinks.
* Fixed: "Cancelled" module bugs. In some cases when module was incomplete child modules were cancelled. Also, sometimes when the node needed to be cancelled, it wasn't.
* Fixed: To properly open a file when Pipeline already is running and user double clicks on the file.
* Fixed bug when user clicks OK on edit module dialog with exported parameters, the parameters will be saved properly like before (pre-5.2).
* Fixed to stage local metadata files for study modules on local-remote workflows.
* Fixed: bug of copy with input when input file type has needs files, the copied data source will not include those need files as input.
* Fixed: bug which was not terminating those jobs which are not monitored by Pipeline.
* Made optimizations and improvements

---[ Server Monitor Terminal ]
* Changed: "Show Running Workflow" checkbox status to be selected by default.
</pre>

pipeline Pipeline V.5.1

jvanhorn@stage.nitrcce.org (John Van Horn) — Thu, 16 Sep 2010 18:11:00 GMT

Pipeline 5.1

* Array Job Submission
The Pipeline server now supports array job submission via JGDI plugin. Array job improves the total processing time of a workflow by combining repeated jobs into one job. Everything is transparent to the users, with individual job’s output and error logs displayed as before. The total processing time on workflows with large number of instances will be improved dramatically.

* User Management
User management is supported for Pipeline server. Once enabled, user’s job slot allocation will be based on the number of free slots on submission time and percentage allowed per user. This value is dynamically calculated and updated. User will also be able to monitor their own usage by clicking the server status label on the lower right corner.

* XNAT Database
Pipeline now supports XNAT database. Collections on any XNAT server can be integrated as a module with output, by providing an XNAT catalog file and your XNAT credential. The module can be connected to any input processing modules. When executing, the compute nodes will download the data, convert to desired file type and proceed into the subsequent module. For more information, please refer to user guide – XNAT.

* Server Configuration Tool
Server configuration tool lets Pipeline server administrators easily configure Pipeline server’s preferences. The tool includes all the preferences required and provides brief description for each field. It has five categories, General, Grid, Access, Packages and Advanced.

* MPI and Special Queue Support
Pipeline server supports MPI for SGE and a special queue with external network access enabled. With server support, user can right click on module and under Execution tab’s Advanced Options, provide MPI parameters or check the checkbox to enable external network access queue.

pipeline Pipeline V5.0.1

jvanhorn@stage.nitrcce.org (John Van Horn) — Tue, 25 May 2010 0:00:00 GMT

Changes in build 2800 ( v5.0.1 )

* Fixed the bug which was hiding SGE stack size options from Execution Panel. Also added some GUI flexibility for the components of same panel.
* Fixed bug when copying a module with exported a parameter inside a module group, the new exported parameter was not shown from the parent module group.
* Fixed several validation bugs: now validation will properly report validation errors, including multiple server error and the bug reported on revision 2654.
* Fixed bug on edit study module > import data's local file browser, it will show correctly the selected file by local file chooser.
* Fixed the wrong number of backlogged issue reported in Pipeline client when there are stopped workflows which contain backlogged instances.
* Fixed to prepend "_ " (unbderscore) to job names of those executables which names start with digit. SGE does not allow job submission with name which starts with digit.
* Fixed bug on rerun module on running workflow, it will properly start from the module. Also any errorred data sink children will be reset.
* Fixed to trim Filetypes when they are created from comma seperated extension type.
* Fixed bug using data sink with type directory and directory dump not enabled, it will not report error. It was because sudo copy tries to preserve sticky bit on temp directory and failed.
* Fixed Provenance Bug, which was showing only one module in the final module's provenance.
* Fixed $username validation bug when the module is newly created.
* Fixed to not include $username variable in XML file when saving the workflow. And also added to remove $username variable from workflow which has been saved before this version and includes $username variable.
* Fixed bug when running local workflows using command line interface (CLI), it will complete as expected.
* Fixed to report an error on validation when a file is given to Directory source.
* Fixed a bug that interpreted a String parameter that happens to be a valid URL as a URL instead of a String.
* Fixed to put default icon when the icon is not found for downloading files. This fixed the problem of empty dialog appearing after user tried to download some kinds of output files.

* Changed: Created two subpanels for the Concrete Module's Execution panel. The Execution Environment panel is the previous Execution panel and holds information about the execution environment for the module. The new Looping Conditions panel specifies whether to run the module in a repeat until loop and the conditions for completing the loop.
* Changed smartline color to have standard line color.
* Changed Repeat Until looping GUI flag from icon to small circle intersecting the main concrete module GUI circle.
* Changed "New loop..." string to "Loop" when on insert new loop action.

Changes in build 2699 ( v5.0.0 )
* Added: Help Buttons to almost all Pipeline dialogs
* Added: Search when selecting Filetypes for all module types.
* Added: columns in File Type table.
* Added: converter of comma seperated file types, which converts
single comma seperated file type to multiple filetypes.
* Added 3 rules for automatically creating/building a study module:
filename matching, derived from metadata, and derived from csv file.
* Added: number of backlogged jobs in server status of client. Also
changed % busy calculation, now it is the total number of backlogged,
queued and running jobs divided by total number of slots.
* Added sortable tables under study module's matrix tab. User can define columns, and generate table that can be sorted by any column. Also added export to CSV feature, where you can export the whole table in CSV file format.
* Added: support for IDA shared collections. Now user can download any shared collections as well as their own collections.
* Added: bug report dialog to have a confirmation message when user doesn't provide an email address.
* Added support for static loop groups. The loop index is currently initialized only through a Study module query.
* Added support for dynamic repeat until looping for concrete modules.

* Changed pipe to script (save as script/makefile) from Python hosted by LONI's web server to Java code. User doesn't need to send the workflow to our server to do the conversion.
* Changed: to have local smartline execution if parent and child modules are both local. If either of the modules is remote, smartline will be executed remotely.
* Changed smartline's color slightly.

* Fixed: validation bug for conditional module when the conditional source contains source with one byte length arguments. For example String.contains("1") would not work with previous code.
* Fixed: for connections dialog, when user tries to connect but it returns with error, the Connect button will not be disabled.
* Fixed: when making a connection, and the input parameter already has one value (double-clicked on the node), it will remove that single value. Undo the connection will put the value back.
* Fixed: missing validation error when open a workflow (with validation errors), delete some modules, then validate, it will show validation passed. But if we execute instead of validate, it will show validation error. Now validation will catch that.
* Fixed: to allow string and number output parameter to connect to enumerated input parameter. Added validaiton check for each string and number values, they must be defined in the enumerated parameter's possible values.
* Fixed: to not attempt to make a connection to localhost when server library refers to localhost and in that case update from local filesystem when user presses update library.
* Fixed: smartline module to have parameter orders and the type of predefined input to "File"
* Fixed: to hide connection line portion that runs over connection nodes.
* Fixed: Export to script to support Workflow Variables
* Fixed: Export to Makedile and Script to support inner & outer product dependent of module's parameter cardinalities.
* Fixed: to ignore duplicated values for enumeration file type. Also fixed to generate unique enumeration value when user clicks Add.
* Fixed: removed Enumerated file type for data source, study and conditional modules. Added validation error when user runs a workflow with enumerated output connected to enumerated input. Also added error message when user tries to connect these.
* Fixed: multiple smartline format suggestion dialog not properly working when user clicks cancel. Changed when user holds shift key when making connections, it will override to have the opposite smartline option than user's preference.
* Fixed: to keep existing grouping members and matrix table when user click OK to close study module dialog, then double-click to reopen. Also fixed Double comparison/sorting on matrix table bug.
* Fixed: the issue with not visible "+" button which creates a new workflow. Now a new "+" button will be created if there will not be space for "+" Tab in workflow tabs. This change will be affected also in Pipeline Window resize.
* Fixed bug on output files tab when click Download on an xml file, download manager will appear just like downloading other files.
* Fixed bug now download manager will auto-scroll to the bottom to display the active download whenever user downloads a new file. Before it was fixed so user may not realize the activity below.
* Fixed: Edit study grouping panel, when user changes a grouping
criteria and click OK or Reload, the new criteria will be saved.
* Fixed: to not include Empty Workflow in Bug Report which represents
the "+" Tab.
* Fixed: bug when a Pipeline client submits a workflow on a Pipeline
server which is running on the same machine, it's stuck at validation
forever. *Fixed: Fixed to hide workflow overview pane, when opening
Pipeline menu.
* Fixed: bug on edit study module dialog, if user makes changes, and switches tabs then clicks cancel, it will not save any changes.
* Fixed: Fixed to create server library monitor file dirs in case they do not exist.

Changes in build 2618 (v4.5.2)
* Added Open From URL feature which allows to open Workflows which are
located on the Web.
* Added support to open Extended RDF files.
* Added preference to specify manual monitoring file for Server Library. This is useful when updating multiple packages in the library at the same time. With Automatic monitoring it forces to load library multiple times during the multiple package update. Manual monitoring file solves this issue.

* Fixed bug when user cancel on remote file browser, then choose
remote browse and cancel again, the dialog did not show up.
* Fixed a bug which was allowing to save on already existed file, when
new file was created and saved. Removed fileDialog for OSX, instead it
will use fileChooser as other operating systems do.
* Fixed the bug which was making LONI Viewer to open JAR file
instead of actual data when it has multiple instances.
* Fixed bug the PMID link in module citations is updated. The old
link did not work under Windows.
* Fixed validation error issue when concrete module executable
location is surrounded with spaces.
* Fixed the issue when the command of the module was not complete
when the module has multiple parents.
* Fixed variables interpreted as 'null' when user copy a workflow
with variables and run the original workflow.
* Fixed LONI Viewer's default input parameter will have file types
it supports, instead of type File(*), which caused missing header
problems when trying to connect to analyze image output.
* Fixed: In module's parameter type editor, when checking and
unchecking random file types rapidly, then finally click OK, the saved
result had more file types than it displayed.
* Fixed the problem which was making Server Library to disappear
when multiple clients are started together.
* Fixed validation bug: when server's port is not default,
validation will not give "file not exists" error on data sink.
* Fixed to show the absolute path of the workflow when hovering on the workflow tab even if the path is a URL.
* Fixed Out of Memory exception when loading server library for multiple servers.
* Fixed bug on output files panel, when multiple instances are selected, download button is sometimes disabled.
* Fixed bug which was causing "Update Library" action to not work for the first time and only after second call it was working.
* Fixed other bugs

Changes in build 2481 (v4.5.1)
* Fixed: Remote File Browser and Directory Sources to properly recognize symbolic links.
* Fixed: 'Download files' button on output files tab for local module works.
* Fixed: when restart a remote-local workflow's local module, it will restart from this exact local module, not from the first local module.
* Fixed: not to update the node with old events which have been occurred before the "Restart Module" action.
* Fixed: not to submit new local processes when workflow is already closed. Also fixed to not submit new local processes when module's parent has been restarted.
* Fixed: LONI Viewer to have valid predefined parameter and executable Location when reconnecting from another client.
* Fixed: execution state of the local module when it has been interrupted and connected with another client.
* Fixed: bug causing complete local modules to show incomplete after reconnection.
* Fixed: validation not to give error for non-existing output files, fixed null pointer exception when there are duplicated files.
* Fixed: to select the first instance in execution log dialog.
* Fixed: "argument too long" error when restart a module.
* Fixed: after restart module, only the statuses of the rerun module and its children are reset.

Changes in build 2390 (v4.5)
* Added: Smartline feature to suggest preferred output file format, if there is one.
* Added: Filetype extension and needs information when selecting parameter filetypes.

* Fixed: bug when populating instances execution log dialog. It improves the performance for large number of instances.
* Fixed: validation to report multiple servers error when more than one remote server is used in a workflow.
* Fixed: to ignore square brackets when creating unique ids.
* Fixed: to set instance as errored when it is not found in ARCo database.
* Fixed: bug on submission when the name of the module contains comma in it.
* Fixed: to trim whitespace in front and at the end of values of parameter type file and directory.
* Fixed: rerun bugs when rerun on running workflows.
* Fixed: incorrect smartline output file type description when PL make preference suggestion or let user choose among multiple types.
* Fixed: bug which was preventing to report local validation errors.
* Fixed: missing connections when make a module group. Also fixed another grouping bug about incorrect connections.
* Fixed: the design of getting info about completed jobs while server synchronizing list of jobs with plugin's list jobs.
* Fixed: bug when resubmitting a job, the same job was requested many times.
* Fixed: bug when resubmitting a job the grid job sync stopped working.
* Fixed: bug sometimes after rerun, some modules do not show correct status.
* Fixed: when user pauses the workflow and waiting for server to response, the workflow will show "pausing" instead of "paused". Also changed stop button to reset when workflow is paused.

Changes in build 2345 (v4.5 beta)
* Added: support for user-owned temporary files and directories.
* Added: workflow pause and module rerun functions.
* Added: tab User in preference that stores user information, which is used to automatically set module author when user creates a module.
* Added: to show command line switch in Module Overview Box.
* Added: series ID and series count information on IDA dialog.

* Fixed: pipeline server bug when the server was running in local mode (No grid plugin was specified).
* Fixed: remote browser bug for data sinks and sources.
* Fixed: Command+E shortcut is working.
* Fixed: IDA connection timeout and out of memory problems when it tries to download a large collection of data.
* Fixed: validation will not give validation error about cardinality when the parameter has infinite number of arguments.
* Fixed: validation will not validate the same file multiple times in a workflow.
* Fixed: several memory leaks on client.
* Fixed: bug that causes some module's status not shown.
* Fixed: under output file tab of execution log dialog, when user downloading .img file, it will only donwload the .img file.
* Fixed: edit enumeration parameter type bug. Also fixed its dialog to show a combobox for server address, instead of text field.
* Fixed: to move the viewport to the selected module after the module overview box is closed.
* Fixed: to show animation when module is running but has failed instances.
* Fixed: disconnecting from the server will display a message on completed open workflows as well, and execution log dialog will be disabled.
* Fixed: bug of Module Group status which appeared when moduleGroup had several cancelled modules.
* Fixed: not show the percentage of workflow complete when it is 100% and there are errors.
* Fixed: to remove from queued jobs list those restored jobs which have state "running".
* Fixed: to show change instance status to queued when server restarts and find that current instance is still queued.
* Fixed: when reconnecting open workflows with remote-local modules, the message "Connection to server was lost" will go away properly.
* Fixed: bug when a workflow with data sink has error (the error could come from any module), the finish time is not properly set.
* Fixed: When login dialog is opened from remote browser and then cancelled, it reopens that dialog which opened Remote File Browser.

Changes in build 2257 (v4.4)
* Added: JGDI support on server, which enables job submission as the user instead of user 'pipelnvr.'
* Added: Grid Plugins support. An API is now provided to allow developers to implement their own plugin for Pipeline Server to be able to communicate with various grid managers.
* Added: % Complete for running workflow in Pipeline status bar.
* Added: Local and remote .scene file support for the LONI Viewer.
* Added: "View Data" button to the Output Files panel of the LONI Viewer to allow the user to easily open files supported by LONIViewer.
* Added: Additional information and features in Server Terminal GUI, including submitting instances report, updated time, etc.
* Added: Support for grid-specific complex resource attributes.
* Added: FailoverPostScript option in Preferences. This is a string argument for the path to a script to be called after a Pipeline Server failover procedure completes.
* Added: Staging error visual indicator for data sinks.
* Added: The ability to connect a data source to a data sink.
* Added: option in server preference. If this is enabled, temporary directories older than 2 * will be deleted on Pipeline server startup.
* Added: Copying modules will copy all variables defined in module group.

* Optimized: Library Updater will not hold same Modules/Workflows in memory which saves time and memory.
* Optimized: Queries to Pipeline's persistence Database when retrieving workflow info. This significantly speeds up workflow reconnection and overall workflow status monitoring.
* Optimized: Running jobs are no longer terminated after a server restart.
* Optimized: User management through SGE should now work as expected. Job priorities will be based on historical usage.

* Modified: GridEngine will no longer issue multiple queries to Pipeline's Persistence database for the same data. This improves the speed of restarting workflow execution after a server restart.
* Modified: Cardinality of error module when exceeding 3000 is now shown on the GUI. The Pipeline server will throw a validation error in this case.
* Modified: Job submission now creates threads to submit jobs. Parallelization is improved and Pipeline server responsiveness is faster.
* Modified: "Change Parameters" checkbox checked by default in Server Changer tool.
* Modified: "Disable Smartline" option when user right-clicks a smartline module is now hidden IF the modules cannot be connected by a regular line.
* Modified: Data Sinks panel will no longer hide file type selection area when directory dump mode is enabled.

* Fixed: Bug where instance errors were not properly shown when reconnecting to workflow.
* Fixed: Bug where files with filenames containing spaces weren't copied properly to data sink destination.
* Fixed: Bug where the calculation of dynamic cardinality was wrong when "infinite argument" parameter exists in the node.
* Fixed: Bug where copy module group with variables defined in parent module group failed. Added checking for duplicate variable name in variables dialog.
* Fixed: Bug where grouping did not work when coping a module group and pasting it to another module group.
* Fixed: Bug when deleting certain module groups and saving the workflow will cause it not to open in the GUI.
* Fixed: Missing menu bar bug on Mac OS X Leopard, after a dialog is open and closed. This bug appeared after the recent Java update on Leopard.
* Fixed: Memory leaks, when opening and closing workflows.
* Fixed: Bug in Copy Citations when Data Module, Viewer Module, Smartline, Study Module, Conditional Module are copied.
* Fixed: Other minor bugs

Changes in build 2073 (v4.3.3)
* Fixed: Selecting one concrete module with smartline modules will not enable "Group selected items" option.
* Fixed server changer to have first server selected by default, and changed "All servers" to "All components".
* Fixed bug where user double-clicks parameter node with directory type, and uses local file browser, directory selected will not be shown on the text field.
* Fixed bug which was crashing Pipeline server when executable location or some other arguments were transferring as null to DRMAA.
* Fixed problem when parameter's description is very long, edit numerator and infinite file/string/number dialog goes out of range. Added scrollbar for these dialogs.
* Fixed: Pipeline updater will work in Windows Vista. Also added current version information on updater dialog.
* Fixed: IDA File Conversions feature for Windows

Changes in build 2037 (v4.3.2)
* Added: support to specify stack size for SGE and DRMAA, user can specify from 10-256 MB of stack size per module, default will be empty (not specified).
* Added: support for directory as input type of smartline, it can be a series of dicom files.
* Added: to show message "Authenticating", which will appear after "Handshake done".

* Changed: default order of exported parameter will be decided on the position of linked module, from left to right then top to bottom. Added "Arrange Export Order" when right click exported parameter nodes, which will list all exported parameters and let user to arrange. Also added module name column on Module Group dialog's Parameter tab.
* Changed: cancellation design, now it has following rule. Node becomes canceled whenever all its parents are canceled or Failed. When it has parameter which is Optional and parent of that parameter is canceled/failed, node won't be canceled.
* Changed: remote files validation design. Validation will gather all remote files information into a list and then when files are needed the list will be as a source not remote server. This will save time and make validation to pass faster.
* Changed: to send an email to Pipeline Email Recipients when server fails over.

* Fixed: bug for data source where "directory source" and "use filter" is checked then unchecked, some components of "use filter" did not hide properly.
* Fixed: to not give validation error for paths which have spaces before or after it.
* Fixed: directory staging will have correct status information displayed on GUI.
* Fixed: IDA download to server will be owned by the user with proper permissions. Added feature to have one directory per series as data sink, smartline will convert the input to other image formats.
* Fixed: IDA download, create data source as directory will be an option only when download as archived.
* Fixed: the overlapping issue on Windows with data modules: number of input/output items count label and replace, browse, clear buttons will take two separate lines.
* Fixed: the order of exported parameters for module groups will be user configurable. In addition, the default order of exported parameters will be the order of parameters within each module.
* Fixed: the bug when parameter has a space at the beginning or at the end of its name, transformation base couldn't find it.
* Fixed: validation will not show duplicate error messages for the same module.
* Fixed: validation will get correct cardinality value for directory source of data module. And mismatched inputs producing more than 3000 instances will be caught.
* Fixed: bug which was preventing to close the EditConcreteModule panel when a parameter which was a dependent of some other parameter has been removed.
* Fixed: to clone Citations and Executable version as well when module is copied.
* Fixed: to not redraw the connection lines which are connected to those parameters which do not exist anymore when parameter is removed from Edit Module dialog.
* Fixed: to show the "Show Results" link in Control bar.
* Fixed: bug when smartline is connected to data sink and user wants to disable only smartline, it was deleting whole connection line.
* Fixed: bug about grouping involving smartline modules. Smartline module will be grouped to a new module group only when its parent and child are in this new group as well.
* Fixed: some other minor bugs.

Changes in build 1995 (v4.3.1)
* Fixed update of server library bug
* Fixed command line validation
* Fixed IDA selected directory by remote browser to not append any type of slash because server and client OSs can be different
* Fixed when parameter has a long description or large number of arguments, EditParameterValue dialog didn't render correctly, it was smaller than necessary. Now it shows proper size.

Changes in build 1988 (v4.3)
* Added Smartline. An automatic file conversion tool.
* Added support for Directory Sources, which will allow users to specify directory from where Pipeline will read needed files and add as values for specified parameters.
* Added Pipeline Updater, which will download and launch new versions of Pipeline installer automatically.
* Added user can now make a screenshot of the entire workflow, it will be saved as an image file (.png)
* Added support to specify maximum memory limit per module when using SGE
* Added to the Pipeline functionality for retrieving the metadata of Ida collections.
* Added active sessions table sorted by column values.
* Added default icon and other default information for LONI Viewer. Added LONI Viewer under top menu Tools.
* Added timeout for server connections
* Added counts for workflows and users in Server Terminal GUI Tool, also added sorting by column.
* Added new Parameter type "Flow Control" for ConcreteModules. This type of parameter will allow module to be started without transferring any data from parents
* Added file conversion for local IDA download, added IDA download to include metadata.
* Added validation status messages for modules and added more information in control bar's status about validation. Added support to navigate the ViewPort to those dataSinks which have 20+ instances.

* Fixed "infinite waiting module" bug, where a module is completed but the child module waits forever.
* Changed the GUI design of number of arguments which has more clear interface for users and will allow user to make module to have up to 99 arguments.
* Updated Help Menu. Now it contains following items What's New, FAQ, Quick Start Guide, Video Tutorials, User Guide, Server Guide, Glossary, Pipe XML Overview, Pipeline Forum instead of only "Contents".
* Fixed XSD document for Pipe file format. Optimized the Pipe XML file to decrease its size.
* Fixed bug when a node is connected, user should not edit the parameter value by double click or right click.
* Fixed to stop validation when user hits Stop button. Also added more feedback about validating modules and remote files which can be useful for big workflows which take more time for validation.
* Fixed Personal Library which was freezing whole Pipeline when refreshing.
* Fixed remote Browse button in Infinite dialog to open Remote File Browser instead of local file browser.
* Fixed server manager to get active jobs and queued jobs count directly from drmaa engine
* Fixed to moduleGroup to display accurate status instead of just showing waiting for some cases.
* Fixed bug for Mac OS X Leopard which was hiding all content of dialog when Remote checkbox was clicked to be selected. Also fixed the width of browse button for Leopard.
* Fixed bug where a module is incomplete, clicking "show details" in pipeline control bar returns information about first errored module.
* Fixed to remove parameter's base when parameter doesn't have tranformation.
* Fixed to show more than 10 argument inputs in Edit Parameter Values Dialog. Added Parameter number on appropriate labels.
* Fixed user will be able to add, delete and edit annotations when workflow is in execution status.
* Fixed active sessions drop down will be scrollable if the list is long, and it will be ordered by start time.
* Changed textfield to combobox to help users easily select base parameter instead of typing it.
* Fixed IDA will create folders as series' collection name, data sink for each download only contains files in that download; if there are more than one type of files downloaded, data sink will select all applicable types
* Fixed remote browser will select the current path if no item is selected, added remote browse to IDA.
* Fixed found memory leaks
* Minimized number of requests to DB. In previous versions Pipeline was creating multiple times connections to DB server to put data there. Now Pipeline uses one connection for multiple columns of the same DB table.
* Fixed to shutdown DRMAA Engine properly when Pipeline shuts down
* Improved Server Sweeper to stop the running workflows before resetting them. Also added interrupt calls to release submitLocks if they are acquired at reset time.
* Fixed cancelled event to support modules which have multiple connections and local/remote executions.
* Fixed bug when save as script/makefile, the output file's line separator should be line return "\n"
* Fixed bug where input of a module has multiple types, the parent module will output to the most common type between input and output, instead of the first type from output.
* Fixed validation will get correct number of cardinality of modules with .list files, and validation will report error if cardinality exceeds 3000. Server changer will change the server of .list files as well.
* Included in IDA: refresh list button after connected. Fixed IDA bugs: it properly gives an error when user downloads invalid series, it will delete partially downloaded files when user hit cancel, also file translation will stop sooner.

Changes in build 1835 (v4.2.1)
* Added: Number of queued jobs in server status
* Added: Dynamic server preferences for Pipeline server
* Added: Modes for directory based access control

* Fixed: new provenance file format
* Fixed: provenance file will be generated only if it is enabled in the workflow
* Fixed: empty server status on Windows bug
* Fixed: password dialog not rendered on Windows for connections window
* Fixed: "Authentication done" message not changed even when it is connected
* Fixed: correct staging status after reconnect
* Fixed: to show Module name and ID always when opening popup description box of the module
* Fixed: to show ModuleGroup Live information in PopupBox which was implemented only for ConcreteModules
* Fixed: to show proper count of connections when connected to new (not saved ) connections
* Fixed: to change URL compatibility when switching the Type of parameter from File to String or vice versa

Changes in build 1808 (v4.2)
* Added: Provenance
* Added: Scripting
* Added: Intelligence
* Added: Remote File Browser
* Added: Server status which displays server's queue utilization as a percentage
* Added: Support to resume all running jobs after server restart
* Added: Directory-based executable access control
* Added: Server fail-over support
* Added: New module statuses: Initializing, Staging, Backlogged, Cancelled
* Added: Ability to show speed and estimated time when staging files
* Added: Staging status message for Data Modules
* Added: More detailed information for modules in their popup info boxes
* Added: Hostname and port on data modules
* Added: Support for multiple server libraries and its status messages.
* Added: Popup menu in Data Modules dialog for Cut,Copy,Paste,Select All functions
* Added: Data module usability. Added undo & redo and shortcut keys for Find & Replace.
* Added: Refresh button on active sessions dialog
* Added: Ability to save and open to/from Personal library
* Added: Default connection to LONI's default server
* Added: Ring notations for exported parameters in workflow's UI
* Added: 3 state buttons in module overview box
* Added: Ability to select multiple inputs when parameter has multiple arguments
* Added: Link to execution logs dialog on control bar when execution is done
* Added: More information about workflows in server terminal manager ( for administrators only )

* Removed: Saving password feature. Passwords will not be saved.

* Fixed: Transformations
* Fixed: Connections to be unique
* Fixed: to not allow more than one connections with data sink when it is not dir dump
* Fixed: to continue workflow execution when one of instances failed
* Fixed: to not send email when user manually stops the workflow execution.
* Fixed: to automatically find the file type when parameter type is any type of file
* Fixed: to create personal library directory if it doesn't exist or has been removed
* Fixed: to not freeze Pipeline UI while loading server library
* Fixed: to send server library updates to all connected users when there is a library change
* Fixed: variables to work properly on local executions
* Fixed: increased maximum number of simultaneous IDA download
* Fixed: leading spaces in executable path of modules to execute properly
* Fixed: to reconnect properly when user changed IP address.
* Fixed: server changer tool to keep user defined variables as they are
* Fixed: connections to exported parameter to be copied
* Fixed: to show job id when job is queued
* Fixed: to show appropriate icon for connected and disconnected status
* Fixed: command line run locally only if executable location is localhost, sync is enabled automatically
* Fixed: active sessions quick reconnect to reload open workflows with lost connections

Changes in build 1545 (v4.1)
* 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)
* 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

pipeline Pipeline V5.0

jvanhorn@stage.nitrcce.org (John Van Horn) — Fri, 02 Apr 2010 0:02:00 GMT

Changes in build 2699 ( v5.0.0 )
* Added: Help Buttons to almost all Pipeline dialogs
* Added: Search when selecting Filetypes for all module types.
* Added: columns in File Type table.
* Added: converter of comma seperated file types, which converts
single comma seperated file type to multiple filetypes.
* Added 3 rules for automatically creating/building a study module:
filename matching, derived from metadata, and derived from csv file.
* Added: number of backlogged jobs in server status of client. Also
changed % busy calculation, now it is the total number of backlogged,
queued and running jobs divided by total number of slots.
* Added sortable tables under study module's matrix tab. User can define columns, and generate table that can be sorted by any column. Also added export to CSV feature, where you can export the whole table in CSV file format.
* Added: support for IDA shared collections. Now user can download any shared collections as well as their own collections.
* Added: bug report dialog to have a confirmation message when user doesn't provide an email address.
* Added support for static loop groups. The loop index is currently initialized only through a Study module query.
* Added support for dynamic repeat until looping for concrete modules.

* Changed pipe to script (save as script/makefile) from Python hosted by LONI's web server to Java code. User doesn't need to send the workflow to our server to do the conversion.
* Changed: to have local smartline execution if parent and child modules are both local. If either of the modules is remote, smartline will be executed remotely.
* Changed smartline's color slightly.

* Fixed: validation bug for conditional module when the conditional source contains source with one byte length arguments. For example String.contains("1") would not work with previous code.
* Fixed: for connections dialog, when user tries to connect but it returns with error, the Connect button will not be disabled.
* Fixed: when making a connection, and the input parameter already has one value (double-clicked on the node), it will remove that single value. Undo the connection will put the value back.
* Fixed: missing validation error when open a workflow (with validation errors), delete some modules, then validate, it will show validation passed. But if we execute instead of validate, it will show validation error. Now validation will catch that.
* Fixed: to allow string and number output parameter to connect to enumerated input parameter. Added validaiton check for each string and number values, they must be defined in the enumerated parameter's possible values.
* Fixed: to not attempt to make a connection to localhost when server library refers to localhost and in that case update from local filesystem when user presses update library.
* Fixed: smartline module to have parameter orders and the type of predefined input to "File"
* Fixed: to hide connection line portion that runs over connection nodes.
* Fixed: Export to script to support Workflow Variables
* Fixed: Export to Makedile and Script to support inner & outer product dependent of module's parameter cardinalities.
* Fixed: to ignore duplicated values for enumeration file type. Also fixed to generate unique enumeration value when user clicks Add.
* Fixed: removed Enumerated file type for data source, study and conditional modules. Added validation error when user runs a workflow with enumerated output connected to enumerated input. Also added error message when user tries to connect these.
* Fixed: multiple smartline format suggestion dialog not properly working when user clicks cancel. Changed when user holds shift key when making connections, it will override to have the opposite smartline option than user's preference.
* Fixed: to keep existing grouping members and matrix table when user click OK to close study module dialog, then double-click to reopen. Also fixed Double comparison/sorting on matrix table bug.
* Fixed: the issue with not visible "+" button which creates a new workflow. Now a new "+" button will be created if there will not be space for "+" Tab in workflow tabs. This change will be affected also in Pipeline Window resize.
* Fixed bug on output files tab when click Download on an xml file, download manager will appear just like downloading other files.
* Fixed bug now download manager will auto-scroll to the bottom to display the active download whenever user downloads a new file. Before it was fixed so user may not realize the activity below.
* Fixed: Edit study grouping panel, when user changes a grouping
criteria and click OK or Reload, the new criteria will be saved.
* Fixed: to not include Empty Workflow in Bug Report which represents
the "+" Tab.
* Fixed: bug when a Pipeline client submits a workflow on a Pipeline
server which is running on the same machine, it's stuck at validation
forever. *Fixed: Fixed to hide workflow overview pane, when opening
Pipeline menu.
* Fixed: bug on edit study module dialog, if user makes changes, and switches tabs then clicks cancel, it will not save any changes.
* Fixed: Fixed to create server library monitor file dirs in case they do not exist.

Changes in build 2618 (v4.5.2)
* Added Open From URL feature which allows to open Workflows which are
located on the Web.
* Added support to open Extended RDF files.
* Added preference to specify manual monitoring file for Server Library. This is useful when updating multiple packages in the library at the same time. With Automatic monitoring it forces to load library multiple times during the multiple package update. Manual monitoring file solves this issue.

* Fixed bug when user cancel on remote file browser, then choose
remote browse and cancel again, the dialog did not show up.
* Fixed a bug which was allowing to save on already existed file, when
new file was created and saved. Removed fileDialog for OSX, instead it
will use fileChooser as other operating systems do.
* Fixed the bug which was making LONI Viewer to open JAR file
instead of actual data when it has multiple instances.
* Fixed bug the PMID link in module citations is updated. The old
link did not work under Windows.
* Fixed validation error issue when concrete module executable
location is surrounded with spaces.
* Fixed the issue when the command of the module was not complete
when the module has multiple parents.
* Fixed variables interpreted as 'null' when user copy a workflow
with variables and run the original workflow.
* Fixed LONI Viewer's default input parameter will have file types
it supports, instead of type File(*), which caused missing header
problems when trying to connect to analyze image output.
* Fixed: In module's parameter type editor, when checking and
unchecking random file types rapidly, then finally click OK, the saved
result had more file types than it displayed.
* Fixed the problem which was making Server Library to disappear
when multiple clients are started together.
* Fixed validation bug: when server's port is not default,
validation will not give "file not exists" error on data sink.
* Fixed to show the absolute path of the workflow when hovering on the workflow tab even if the path is a URL.
* Fixed Out of Memory exception when loading server library for multiple servers.
* Fixed bug on output files panel, when multiple instances are selected, download button is sometimes disabled.
* Fixed bug which was causing "Update Library" action to not work for the first time and only after second call it was working.
* Fixed other bugs

Changes in build 2481 (v4.5.1)
* Fixed: Remote File Browser and Directory Sources to properly recognize symbolic links.
* Fixed: 'Download files' button on output files tab for local module works.
* Fixed: when restart a remote-local workflow's local module, it will restart from this exact local module, not from the first local module.
* Fixed: not to update the node with old events which have been occurred before the "Restart Module" action.
* Fixed: not to submit new local processes when workflow is already closed. Also fixed to not submit new local processes when module's parent has been restarted.
* Fixed: LONI Viewer to have valid predefined parameter and executable Location when reconnecting from another client.
* Fixed: execution state of the local module when it has been interrupted and connected with another client.
* Fixed: bug causing complete local modules to show incomplete after reconnection.
* Fixed: validation not to give error for non-existing output files, fixed null pointer exception when there are duplicated files.
* Fixed: to select the first instance in execution log dialog.
* Fixed: "argument too long" error when restart a module.
* Fixed: after restart module, only the statuses of the rerun module and its children are reset.

Changes in build 2390 (v4.5)
* Added: Smartline feature to suggest preferred output file format, if there is one.
* Added: Filetype extension and needs information when selecting parameter filetypes.

* Fixed: bug when populating instances execution log dialog. It improves the performance for large number of instances.
* Fixed: validation to report multiple servers error when more than one remote server is used in a workflow.
* Fixed: to ignore square brackets when creating unique ids.
* Fixed: to set instance as errored when it is not found in ARCo database.
* Fixed: bug on submission when the name of the module contains comma in it.
* Fixed: to trim whitespace in front and at the end of values of parameter type file and directory.
* Fixed: rerun bugs when rerun on running workflows.
* Fixed: incorrect smartline output file type description when PL make preference suggestion or let user choose among multiple types.
* Fixed: bug which was preventing to report local validation errors.
* Fixed: missing connections when make a module group. Also fixed another grouping bug about incorrect connections.
* Fixed: the design of getting info about completed jobs while server synchronizing list of jobs with plugin's list jobs.
* Fixed: bug when resubmitting a job, the same job was requested many times.
* Fixed: bug when resubmitting a job the grid job sync stopped working.
* Fixed: bug sometimes after rerun, some modules do not show correct status.
* Fixed: when user pauses the workflow and waiting for server to response, the workflow will show "pausing" instead of "paused". Also changed stop button to reset when workflow is paused.

Changes in build 2345 (v4.5 beta)
* Added: support for user-owned temporary files and directories.
* Added: workflow pause and module rerun functions.
* Added: tab User in preference that stores user information, which is used to automatically set module author when user creates a module.
* Added: to show command line switch in Module Overview Box.
* Added: series ID and series count information on IDA dialog.

* Fixed: pipeline server bug when the server was running in local mode (No grid plugin was specified).
* Fixed: remote browser bug for data sinks and sources.
* Fixed: Command+E shortcut is working.
* Fixed: IDA connection timeout and out of memory problems when it tries to download a large collection of data.
* Fixed: validation will not give validation error about cardinality when the parameter has infinite number of arguments.
* Fixed: validation will not validate the same file multiple times in a workflow.
* Fixed: several memory leaks on client.
* Fixed: bug that causes some module's status not shown.
* Fixed: under output file tab of execution log dialog, when user downloading .img file, it will only donwload the .img file.
* Fixed: edit enumeration parameter type bug. Also fixed its dialog to show a combobox for server address, instead of text field.
* Fixed: to move the viewport to the selected module after the module overview box is closed.
* Fixed: to show animation when module is running but has failed instances.
* Fixed: disconnecting from the server will display a message on completed open workflows as well, and execution log dialog will be disabled.
* Fixed: bug of Module Group status which appeared when moduleGroup had several cancelled modules.
* Fixed: not show the percentage of workflow complete when it is 100% and there are errors.
* Fixed: to remove from queued jobs list those restored jobs which have state "running".
* Fixed: to show change instance status to queued when server restarts and find that current instance is still queued.
* Fixed: when reconnecting open workflows with remote-local modules, the message "Connection to server was lost" will go away properly.
* Fixed: bug when a workflow with data sink has error (the error could come from any module), the finish time is not properly set.
* Fixed: When login dialog is opened from remote browser and then cancelled, it reopens that dialog which opened Remote File Browser.

Changes in build 2257 (v4.4)
* Added: JGDI support on server, which enables job submission as the user instead of user 'pipelnvr.'
* Added: Grid Plugins support. An API is now provided to allow developers to implement their own plugin for Pipeline Server to be able to communicate with various grid managers.
* Added: % Complete for running workflow in Pipeline status bar.
* Added: Local and remote .scene file support for the LONI Viewer.
* Added: "View Data" button to the Output Files panel of the LONI Viewer to allow the user to easily open files supported by LONIViewer.
* Added: Additional information and features in Server Terminal GUI, including submitting instances report, updated time, etc.
* Added: Support for grid-specific complex resource attributes.
* Added: FailoverPostScript option in Preferences. This is a string argument for the path to a script to be called after a Pipeline Server failover procedure completes.
* Added: Staging error visual indicator for data sinks.
* Added: The ability to connect a data source to a data sink.
* Added: option in server preference. If this is enabled, temporary directories older than 2 * will be deleted on Pipeline server startup.
* Added: Copying modules will copy all variables defined in module group.

* Optimized: Library Updater will not hold same Modules/Workflows in memory which saves time and memory.
* Optimized: Queries to Pipeline's persistence Database when retrieving workflow info. This significantly speeds up workflow reconnection and overall workflow status monitoring.
* Optimized: Running jobs are no longer terminated after a server restart.
* Optimized: User management through SGE should now work as expected. Job priorities will be based on historical usage.

* Modified: GridEngine will no longer issue multiple queries to Pipeline's Persistence database for the same data. This improves the speed of restarting workflow execution after a server restart.
* Modified: Cardinality of error module when exceeding 3000 is now shown on the GUI. The Pipeline server will throw a validation error in this case.
* Modified: Job submission now creates threads to submit jobs. Parallelization is improved and Pipeline server responsiveness is faster.
* Modified: "Change Parameters" checkbox checked by default in Server Changer tool.
* Modified: "Disable Smartline" option when user right-clicks a smartline module is now hidden IF the modules cannot be connected by a regular line.
* Modified: Data Sinks panel will no longer hide file type selection area when directory dump mode is enabled.

* Fixed: Bug where instance errors were not properly shown when reconnecting to workflow.
* Fixed: Bug where files with filenames containing spaces weren't copied properly to data sink destination.
* Fixed: Bug where the calculation of dynamic cardinality was wrong when "infinite argument" parameter exists in the node.
* Fixed: Bug where copy module group with variables defined in parent module group failed. Added checking for duplicate variable name in variables dialog.
* Fixed: Bug where grouping did not work when coping a module group and pasting it to another module group.
* Fixed: Bug when deleting certain module groups and saving the workflow will cause it not to open in the GUI.
* Fixed: Missing menu bar bug on Mac OS X Leopard, after a dialog is open and closed. This bug appeared after the recent Java update on Leopard.
* Fixed: Memory leaks, when opening and closing workflows.
* Fixed: Bug in Copy Citations when Data Module, Viewer Module, Smartline, Study Module, Conditional Module are copied.
* Fixed: Other minor bugs

Changes in build 2073 (v4.3.3)
* Fixed: Selecting one concrete module with smartline modules will not enable "Group selected items" option.
* Fixed server changer to have first server selected by default, and changed "All servers" to "All components".
* Fixed bug where user double-clicks parameter node with directory type, and uses local file browser, directory selected will not be shown on the text field.
* Fixed bug which was crashing Pipeline server when executable location or some other arguments were transferring as null to DRMAA.
* Fixed problem when parameter's description is very long, edit numerator and infinite file/string/number dialog goes out of range. Added scrollbar for these dialogs.
* Fixed: Pipeline updater will work in Windows Vista. Also added current version information on updater dialog.
* Fixed: IDA File Conversions feature for Windows

Changes in build 2037 (v4.3.2)
* Added: support to specify stack size for SGE and DRMAA, user can specify from 10-256 MB of stack size per module, default will be empty (not specified).
* Added: support for directory as input type of smartline, it can be a series of dicom files.
* Added: to show message "Authenticating", which will appear after "Handshake done".

* Changed: default order of exported parameter will be decided on the position of linked module, from left to right then top to bottom. Added "Arrange Export Order" when right click exported parameter nodes, which will list all exported parameters and let user to arrange. Also added module name column on Module Group dialog's Parameter tab.
* Changed: cancellation design, now it has following rule. Node becomes canceled whenever all its parents are canceled or Failed. When it has parameter which is Optional and parent of that parameter is canceled/failed, node won't be canceled.
* Changed: remote files validation design. Validation will gather all remote files information into a list and then when files are needed the list will be as a source not remote server. This will save time and make validation to pass faster.
* Changed: to send an email to Pipeline Email Recipients when server fails over.

* Fixed: bug for data source where "directory source" and "use filter" is checked then unchecked, some components of "use filter" did not hide properly.
* Fixed: to not give validation error for paths which have spaces before or after it.
* Fixed: directory staging will have correct status information displayed on GUI.
* Fixed: IDA download to server will be owned by the user with proper permissions. Added feature to have one directory per series as data sink, smartline will convert the input to other image formats.
* Fixed: IDA download, create data source as directory will be an option only when download as archived.
* Fixed: the overlapping issue on Windows with data modules: number of input/output items count label and replace, browse, clear buttons will take two separate lines.
* Fixed: the order of exported parameters for module groups will be user configurable. In addition, the default order of exported parameters will be the order of parameters within each module.
* Fixed: the bug when parameter has a space at the beginning or at the end of its name, transformation base couldn't find it.
* Fixed: validation will not show duplicate error messages for the same module.
* Fixed: validation will get correct cardinality value for directory source of data module. And mismatched inputs producing more than 3000 instances will be caught.
* Fixed: bug which was preventing to close the EditConcreteModule panel when a parameter which was a dependent of some other parameter has been removed.
* Fixed: to clone Citations and Executable version as well when module is copied.
* Fixed: to not redraw the connection lines which are connected to those parameters which do not exist anymore when parameter is removed from Edit Module dialog.
* Fixed: to show the "Show Results" link in Control bar.
* Fixed: bug when smartline is connected to data sink and user wants to disable only smartline, it was deleting whole connection line.
* Fixed: bug about grouping involving smartline modules. Smartline module will be grouped to a new module group only when its parent and child are in this new group as well.
* Fixed: some other minor bugs.

Changes in build 1995 (v4.3.1)
* Fixed update of server library bug
* Fixed command line validation
* Fixed IDA selected directory by remote browser to not append any type of slash because server and client OSs can be different
* Fixed when parameter has a long description or large number of arguments, EditParameterValue dialog didn't render correctly, it was smaller than necessary. Now it shows proper size.

Changes in build 1988 (v4.3)
* Added Smartline. An automatic file conversion tool.
* Added support for Directory Sources, which will allow users to specify directory from where Pipeline will read needed files and add as values for specified parameters.
* Added Pipeline Updater, which will download and launch new versions of Pipeline installer automatically.
* Added user can now make a screenshot of the entire workflow, it will be saved as an image file (.png)
* Added support to specify maximum memory limit per module when using SGE
* Added to the Pipeline functionality for retrieving the metadata of Ida collections.
* Added active sessions table sorted by column values.
* Added default icon and other default information for LONI Viewer. Added LONI Viewer under top menu Tools.
* Added timeout for server connections
* Added counts for workflows and users in Server Terminal GUI Tool, also added sorting by column.
* Added new Parameter type "Flow Control" for ConcreteModules. This type of parameter will allow module to be started without transferring any data from parents
* Added file conversion for local IDA download, added IDA download to include metadata.
* Added validation status messages for modules and added more information in control bar's status about validation. Added support to navigate the ViewPort to those dataSinks which have 20+ instances.

* Fixed "infinite waiting module" bug, where a module is completed but the child module waits forever.
* Changed the GUI design of number of arguments which has more clear interface for users and will allow user to make module to have up to 99 arguments.
* Updated Help Menu. Now it contains following items What's New, FAQ, Quick Start Guide, Video Tutorials, User Guide, Server Guide, Glossary, Pipe XML Overview, Pipeline Forum instead of only "Contents".
* Fixed XSD document for Pipe file format. Optimized the Pipe XML file to decrease its size.
* Fixed bug when a node is connected, user should not edit the parameter value by double click or right click.
* Fixed to stop validation when user hits Stop button. Also added more feedback about validating modules and remote files which can be useful for big workflows which take more time for validation.
* Fixed Personal Library which was freezing whole Pipeline when refreshing.
* Fixed remote Browse button in Infinite dialog to open Remote File Browser instead of local file browser.
* Fixed server manager to get active jobs and queued jobs count directly from drmaa engine
* Fixed to moduleGroup to display accurate status instead of just showing waiting for some cases.
* Fixed bug for Mac OS X Leopard which was hiding all content of dialog when Remote checkbox was clicked to be selected. Also fixed the width of browse button for Leopard.
* Fixed bug where a module is incomplete, clicking "show details" in pipeline control bar returns information about first errored module.
* Fixed to remove parameter's base when parameter doesn't have tranformation.
* Fixed to show more than 10 argument inputs in Edit Parameter Values Dialog. Added Parameter number on appropriate labels.
* Fixed user will be able to add, delete and edit annotations when workflow is in execution status.
* Fixed active sessions drop down will be scrollable if the list is long, and it will be ordered by start time.
* Changed textfield to combobox to help users easily select base parameter instead of typing it.
* Fixed IDA will create folders as series' collection name, data sink for each download only contains files in that download; if there are more than one type of files downloaded, data sink will select all applicable types
* Fixed remote browser will select the current path if no item is selected, added remote browse to IDA.
* Fixed found memory leaks
* Minimized number of requests to DB. In previous versions Pipeline was creating multiple times connections to DB server to put data there. Now Pipeline uses one connection for multiple columns of the same DB table.
* Fixed to shutdown DRMAA Engine properly when Pipeline shuts down
* Improved Server Sweeper to stop the running workflows before resetting them. Also added interrupt calls to release submitLocks if they are acquired at reset time.
* Fixed cancelled event to support modules which have multiple connections and local/remote executions.
* Fixed bug when save as script/makefile, the output file's line separator should be line return "\n"
* Fixed bug where input of a module has multiple types, the parent module will output to the most common type between input and output, instead of the first type from output.
* Fixed validation will get correct number of cardinality of modules with .list files, and validation will report error if cardinality exceeds 3000. Server changer will change the server of .list files as well.
* Included in IDA: refresh list button after connected. Fixed IDA bugs: it properly gives an error when user downloads invalid series, it will delete partially downloaded files when user hit cancel, also file translation will stop sooner.

Changes in build 1835 (v4.2.1)
* Added: Number of queued jobs in server status
* Added: Dynamic server preferences for Pipeline server
* Added: Modes for directory based access control

* Fixed: new provenance file format
* Fixed: provenance file will be generated only if it is enabled in the workflow
* Fixed: empty server status on Windows bug
* Fixed: password dialog not rendered on Windows for connections window
* Fixed: "Authentication done" message not changed even when it is connected
* Fixed: correct staging status after reconnect
* Fixed: to show Module name and ID always when opening popup description box of the module
* Fixed: to show ModuleGroup Live information in PopupBox which was implemented only for ConcreteModules
* Fixed: to show proper count of connections when connected to new (not saved ) connections
* Fixed: to change URL compatibility when switching the Type of parameter from File to String or vice versa

Changes in build 1808 (v4.2)
* Added: Provenance
* Added: Scripting
* Added: Intelligence
* Added: Remote File Browser
* Added: Server status which displays server's queue utilization as a percentage
* Added: Support to resume all running jobs after server restart
* Added: Directory-based executable access control
* Added: Server fail-over support
* Added: New module statuses: Initializing, Staging, Backlogged, Cancelled
* Added: Ability to show speed and estimated time when staging files
* Added: Staging status message for Data Modules
* Added: More detailed information for modules in their popup info boxes
* Added: Hostname and port on data modules
* Added: Support for multiple server libraries and its status messages.
* Added: Popup menu in Data Modules dialog for Cut,Copy,Paste,Select All functions
* Added: Data module usability. Added undo & redo and shortcut keys for Find & Replace.
* Added: Refresh button on active sessions dialog
* Added: Ability to save and open to/from Personal library
* Added: Default connection to LONI's default server
* Added: Ring notations for exported parameters in workflow's UI
* Added: 3 state buttons in module overview box
* Added: Ability to select multiple inputs when parameter has multiple arguments
* Added: Link to execution logs dialog on control bar when execution is done
* Added: More information about workflows in server terminal manager ( for administrators only )

* Removed: Saving password feature. Passwords will not be saved.

* Fixed: Transformations
* Fixed: Connections to be unique
* Fixed: to not allow more than one connections with data sink when it is not dir dump
* Fixed: to continue workflow execution when one of instances failed
* Fixed: to not send email when user manually stops the workflow execution.
* Fixed: to automatically find the file type when parameter type is any type of file
* Fixed: to create personal library directory if it doesn't exist or has been removed
* Fixed: to not freeze Pipeline UI while loading server library
* Fixed: to send server library updates to all connected users when there is a library change
* Fixed: variables to work properly on local executions
* Fixed: increased maximum number of simultaneous IDA download
* Fixed: leading spaces in executable path of modules to execute properly
* Fixed: to reconnect properly when user changed IP address.
* Fixed: server changer tool to keep user defined variables as they are
* Fixed: connections to exported parameter to be copied
* Fixed: to show job id when job is queued
* Fixed: to show appropriate icon for connected and disconnected status
* Fixed: command line run locally only if executable location is localhost, sync is enabled automatically
* Fixed: active sessions quick reconnect to reload open workflows with lost connections

Changes in build 1545 (v4.1)
* 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)
* 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