TEST
XmlFiles.sql: changed so that the actual path is returned

RootPath.sql: RowId/FileId not included anymore

OpenCytoPreprocessing.r:
-added Rlibstree package and needed logic to be able to get the deepest common root folder of the passed in paths (where the data will be saved)
-logic added to parse a list of passed in workspaces and to then combine the resulting gating sets into a gating sets list
-name column of the pheno data is made a factor, so that it can be properly graphed in the Viz module
-satisfied the requirement so that rownames of the pheno data are the sample names
-saving/loading of the gating set replaced with saving/loading of the gating set list ('save' now includes the 'move' option, which quickly moves the underlying netcdf data file to the proper location)
-writeProjections() routine altered so that terminal leaf nodes are now included in the Projections table
-facility added, if an error occurs to pass to the UI the id of the gating set, so that a command can be dispatched to delete it
-if an error occurs, all of the 'temporary' netcdf data files are deleted

SampleGroups.r: modified to be able to handle multiple workspaces

begin.view.xml: added custom Ext.ux.tree.TreeFilterX.js dependency to be able to filter Ext.Tree

ExtendedComboBox.js: an important fix to make sure non-unique display values do not break anything

ExtendedLovCombo.js:
-When 'Select All' is clicked, now a 'select' event is also fired
-A fix in onTrigger2Click() method to properly handle allSelected boolean value

jquery.fancybox-buttons.css: modified the width of the controls panel to accomodate just 2 buttons (expand and close)

OpenCyto.css:
-modified spacing around a checkbox
-added various Ext.Tree fixes so that its appearance and behavior are uniform across browsers
-introduced fix for the numberer background not to look ugly for larger column widths

OpenCyto.js: introduced disallowMoveBefore config parameter along with necessary funcitons overrides that prevents columns being dragged-and-dropped to the first disallowMoveBefore positions

OpenCytoPreprocessing:js:
-the workspaces' paths are now decoded only once, once loaded
-in the grid table of the selected samples added 2 new columns: associated workspace and sample group
-in order to visualize several workspaces and their associated sample groups, added a tree widget
-modified the sample group control to be a search string input field
-changed parse web part into parse config of the new format for the new API
-added logic so that if errors are returned after parsing the incomplete data that was added is removed
OpenCytoPreprocessing.r : fix to make the 'name' column of the pheno-data a factor, so that it can be properly plotted

SampleGroups.r : lapply changed to mclapply and parallel package added to make use of parallel processing capabilities
OpenCytoPreprocessing.r : because of API change boolean gates were not filtered out, made a fix to filter them out once again

OpenCyto.js : minor fix to utility method

OpenCytoPreprocessing.js : minor fix to hide/show the tree widget
Files.sql : changed to look for files from runs of type 'Analysis' instead of 'Keywords'

RootPath.sql, GatingSet.sql : streamlined the queries

Population.sql : moved to Preprocessing module since used in both Visualization and QualityControl

Delete.r : modifications made to be in line with GatingSet.sql changes

OpenCytoPreprocessing.r :
- streamlined some variable names
- included logic to remove gating set row entry added to the corresponding table if the script did not successfully complete
- added a creation of a temporary file FOLDER_LOCKED_TEMP, which signifies that the folder is 'locked' and being worked on, so that no concurrent process can corrupt its structure

SampleGroups.r : qualified toJSON with the package name to get rid of some lurking issue

opencyto_preprocessing-0.00-0.01.sql :
- changed the tables definition for gating sets to make the row id globally unique
- added constraint to the same table to make the name unique to each study
- adjusted other related tables accordingly

begin.html : changed so that jQuery is only loaded if it's not already present

ExtendedComboBox.js, ExtendedLovCombo.js : resizeToFit() modified to only use the Element if it exists and has been rendered

OpenCyto.css :
- added icons for Import, Export and Update
- made rules specific to OpenCyto modules by adding an opencyto class qualifier
- added rules to make text in the grid selectable
- added a rule to display properly just 2 buttons for the full screen mode of FancyBox: 'full-screen' and 'close'

OpenCyto.js : time-out value increased to 6 hours

OpenCytoPreprocessing.js :
- added info masks, when there are no workspaces detected
- changed the SQL to fetch the table of file and associated meta data so that meaningful links can be displayed in the grid
- added customized renderers to 'Workspace' and 'File Name' columns - close #13
- added a custom check for the case when no files have been detected with the current settings to see if there are any files present at all, if not - add an info mask
- added the capability to be able to edit the table of existing analyses in place
- added a button to save the changes made to the table of existing analyses
- deleted the hack that used the Delete.r script to delete an analysis in case its creation did not succeed
- added 'opencyto' class to the custom grand panel, not to interfere with other modules CSS rules
- streamlined and made flow more robust
OpenCytoPreprocessing.r :
- an attempt made to suppress the output while parsing workspaces (through the use of sink(...) )
- refactored the code to insert a row into the gstbl tables after the parsing is done
- before parsing is done, a check is performed to see if there is already a row with the same name, if yes, do not continue with heavy lifting parsing

OpenCytoPreprocessing.js : disabled the icons
OpenCytoPreprocessing.r :
- changed the location, where the temporary ncdf files are written so that they don't get deleted if another process errors out
- changed when the 'lock' file is being deleted, so that the behavior is more robust

begin.html, OpenCyto.js, OpenCytoPreprocessing.js :
- added the LABKEY.ext.OpenCyto scoping namespace and changed the names of the methods accordingly

OpenCytoPreprocessing.js :
- eliminated the sessions management for both the 'Create' and 'Delete' UIs, so that a new session is created each time it is needed; the session also get deleted automatically as soon as it is done, that way we do not end up multiplying R sessions sitting in memory idle
- fixed, so that the console output is not displayed, if an info message shows up concerning another session already working on the same analysis folder
- filesIds string now is generated from a sorted array to prevent potential duplication of data
Renamed ./src to ./resources to be consistent with Labkey's conventions, adjusted mac version of flowJo workspace recognized.

OpenCytoPreprocessing.r : removed flowIncubator dependency

OpenCytoPreprocessing.js : added another filter to the keywords set
module.properties : changed the required server version to 13.2

OpenCytoPreprocessing.r : returned the requirement for flowIncubator erroneously removed

Ncdf.r : removed as it is no longer used