working notes.txt

Overlord Simulator: add argument parsing for -r, -c, -m, -v

Overlord Simulator: add scrollbars to ovp xml textbox

Overlord Simulator: add ListView to display Overlord input variables

Overlord Simulator: add test Dictionary object to display to variables ListView

Overlord Simulator: add code to display variables set from command line to ListView

Overlord Simulator: Add animation to progress bar for simTime

Overlord Simulator: Add Pause/Resume button for simulation time; Implement -c option (close when done)

Overlord Simulator: Add Stop Now button for simulation time;

Overlord Simulator: Implement -r (run immediately), and -m (run minimized) options

Overlord Simulator: Implement code to handle when no command line arguments are passed

Overlord Simulator: Disable Pause button when sim progress finishes (if -c option not given)

Overlord Simulator: Add LMSF icon


LMSF Scheduler: Setup App layout, menu bar, and tool bar

LMSF Scheduler: Add ListView and Panel to display experiment steps, and buttons (Add, Duplicate, Delete, Move Up, Move Down) to organize steps

LMSF Scheduler: Add AutomationStep class to hold info about each automation step

LMSF Scheduler: Add ListOfSteps ObservableCollection and have it displayed in the ListBox with a DataTemplate

LMSF Scheduler: Add StepIcon as property for AutomationStep class and display icon in ListBox w/ DataTemplate

LMSF Scheduler: Add event handling for addStep Button with place-holder ListOfSteps.Add()

LMSF Scheduler: Add ContentControl on right hand side of main Window to display details of selected text, and implement place-holder code for data Binding

LMSF Scheduler: Add INotifyPropertyChanged interface to Main Window class, also add test buttons and text boxes to test data binding

LMSF Scheduler: Change Add Step code to add step after selected step )instead of at end of Collection 

LMSF Scheduler: Implement code for Duplicate Step button 

LMSF Scheduler: Add wait and dialog icons to AutomationStep class 

LMSF Scheduler: Implement code for Delete Step, Move Up, and Move Down buttons 

LMSF Scheduler: Add Dialog box for Add New Step 

LMSF Scheduler: Add Rodio buttons to select step type for Add New Step 

LMSF Scheduler: Take out temporary ListOfSteps initialization code, and edit Add, Duplicate, Delete, ect methods to deal appropriately with empty list

LMSF Scheduler: Add LMSF icon bitmap as default image for steps

LMSF Scheduler: Switch to purely text-based step editing and specification; make new branch, graphicStepEditor, for old GUI
                  In new method, replace ListBox with TextBox, and remove buttons for manipulating steps (Add, Duplicate, etc.)

LMSF Scheduler: Add code for Open/Save/SaveAs, and deal with Focus issue for menu items (IsFocusScope="False")

LMSF Scheduler: Add button and code for "Insert File Path" - to insert the selected file path into the InputText

LMSF Scheduler: Make input and output Text Boxes accept enter, nowrap, auto scroll bars; fix Binding/Focus issue for Toolbar items (IsFocusScope="False")

LMSF Scheduler: Finish File menu functions, and add code to prompt for file save when inputText has changed as appropriately

LMSF Scheduler: Fix code for "Insert File Path" so that file path string is inserted at the textBox caret location; 
    insert ParseSteps() method to break up inputText into lines; Add Rewind button; Add blank button click handlers for Play, Step, Pause, etc.

LMSF Scheduler: Add inputTextBox.Focus() at the end of each menu item action to return focus to the text box

LMSF Scheduler: Add filename to main window title, with * to indicate unsaved changes

LMSF Scheduler: Rename "startButton" -> "playButton"; add fields for parsing and running steps; and add test code for line/step parsing

LMSF Scheduler: Add validate button to test string parsing; fix tooltip text for other buttons

LMSF Scheduler: Add Overlord to step parser; Add basic validation method run when validateButton clicked (same as Play, but sets isValidating flag so actual actions can be turned off)

LMSF Scheduler: Add System.Diagnostics.Process code to run Overlord.Main.exe

Overlord Simulator: Set Main window icon =  LMSF icon

LMSF Scheduler: Switch path to Ovderlord.Main.exe to actual location (C:\Program Files (x86)\PAA\Overlord3)

Overlord Simulator: Capitalize method names to conform with reccomended C# style

LMSF Scheduler: Add code to wait between steps (clunky right now since it runs on the main thread, TODO: set it up to run steps on a separate thread)

LMSF Scheduler: Wrap waitingForStepCompletion in a propety with getter and setter

LMSF Scheduler: Run Steps on separate (BackgroundWorker) thread so that GUI updates are maintained

LMSF Scheduler: Modifiy ValidateButton_Click() to work with new multi-thread methods (validation runs like play but on main thread)

LMSF Scheduler: Add code to check for existence of ovp files during validation/running

LMSF Scheduler: Add Validation before every run

LMSF Scheduler: Change output text box to have line wrapping

LMSF Scheduler: Add Wait step to step parser; also add RunWaitStep() method, TODO: re-write RunWaitStep() with pop-up progress bar + cancel button

LMSF Scheduler: Rearange RunWaitStep() method; move WaitingForStepCompletion = false to OutsideProcessMonitor_RunWorkerCompleted; Rename ovWorker -> ovMonitorWorker

LMSF Scheduler: Move Background worker that waits for Overlord into a different step.
    So now, Overlord steps start Overord and go on to the next step;
	The new "WaitFor" step is then used to specifically wait for the Overlord step to finish; 
	Also included code to prevent two Overlord processes from running at the same time

Add new LMSF_Utilities library to solution

LMSF_Utilities: Add TimerDialog
LMSF Scheduler: Add test code for TimerDialog (on TestButton_Click)

LMSF_Utilities.TimerDialog: Add IsClosed Property to allow Scheduler to check if the TimerDialog has closed.

LMSF Scheduler: In StepParser(), replace Wait step with Timer step; Also replace RunWaitStep() with RunTimer()

Switch from "BackgroundWorker runStepsWorker" to "Thread runStepsThread" to create the thread that handles running steps,
    Why? Since I thought "thread.SetApartmentState(ApartmentState.STA)" would be necessary to access GUI components (like the TimerDialog)
	    from the step-runner thread. It turns out that is not true (program seems to run just fin with the SetApartmentState commented out).
		What is actually needed is to use a Dispatcher for lines of code in the step-runner methods that interact with the GUI,
    		e.g., this.Dispatcher.Invoke(() => { IsRunning = false; });  
			    "IsRunning" calls "UpdateEnabledState" which sets the enabled state of GUI components appropriatly
	Anyway, I'm not sure if the Dispatcher thing would have worked in a background thread, and I don't want to take the time to find out, since the code now works.
	
	Notes added later: the Dispatcher things works from a background worker; I used it to display the time remaining in the TimerDialog class.

LMSF Scheduler: Make play, pause, etc. buttons not focusable, and then insert "inputTextBox.GetBindingExpression(TextBox.TextProperty).UpdateSource();"
    at the beginning of each button clicked method to makse sure the inputText gets updated appropriately.

LMSF Scheduler: Finish single-step button method, and implement abort button method

LMSF Scheduler: On main page, add visual indicator of run/paused state and abort called - with red/yellow/green colors

LMSF Scheduler: Add WaitForTimer() method and code to ParseSteps()

LMSF_Utilities: Add SharedParameters Class for storage of constants used by Utility methods

LMSF_Utilities: Add MetaItem class; and SharedParameters.GetMetaList() method to parse meta-item lists

LMSF_Utilities: Add SharedParameters.SortMetaList() method

LMSF_Utilities: Add SharedParameters.SortAndSaveMetaList() method; fix encoding issue that caused problems with Hamilton Venus (use default encoding instead of UTF8)

LMSF_Utilities: Add new class: SelectMetaIdentDialog, with placeholder code for CreateNewIdentier() methods

LMSF_Utilities: Finish GetMetaIdentifier(), and most of CreateNewIdentier() (still has some TODO commetns in it)

LMSF_Utilities: Add RegexValidationRule() and bindings to enforce validity of short identifiers in NewMetaIdentDialog

LMSF_Utilities: Add NewLongNameDialog, NotesDialog

LMSF_Utilities: Add NotesDialog and finish code for CreateNewIdentier()

LMSF_Utilities: Set up Combo boxes to initially have slectedIndex = -1 (no item selected)

LMSF_Utilities.GetMetaIdentifier: On cancel, make sure GetMetaIdentifier returns empty string.

LMSF_Utilities: Finish CreateNewMediaIdentifier() and MediaIngredientsDialog class

LMSF_Utilities: Add ConcentrationDialog class

LMSF Scheduler: Reorganize ParseSteps() method with Local functions to parse each step type

LMSF Scheduler: Fix Bug: Output does not show/update text for variables passed to Overlord

LMSF Scheduler: Add/midify code to properly deal with Main Window closing - either through the red 'X' or the File.Close()

LMSF Scheduler: Fix Bug: inputTextBox.GetBindingExpression(TextBox.TextProperty).UpdateSource(); - causes InputChanged <- true, even when it has not changed;
    slight change in Setter to fix

LMSF Scheduler: Fix Bug: Will not Validate after Aborted run;

LMSF Scheduler: display validation result prominently with gree/red colr to indicate success/fail

LMSF Scheduler: Put DateTime info in Output text;

LMSF Scheduler: Add Running/Validating and ExperimentFileName to beginning of OutputText

LMSF Scheduler: Add saving of output text to log file

LMSF Scheduler: Add ComboBox on toolbar for shortcuts to insert Command into InputText

LMSF Scheduler: Move InsertFileButton to tool bar

LMSF Scheduler: Change WaitForOverlord() output to "... waiting for Overlord to finish and exit."

LMSF Scheduler: Add code to create log file directory if it does not exist, also changed the log file directory to: "C:\\Shared Files\\LMSF Scheduler\\LogFiles\\"

LMSF Scheduler: Change format for log file name to , "yyyy-MM-dd HH.mm.ss"

LMSF Scheduler: Turn play and step buttons yellow when waiting to resume from pause; also use predefined Brushes everywhere else: Brushes.NamedBrush

LMSF Scheduler: Add "Method Aborted." to log file

LMSF Scheduler: "project" to metadata type (same dialogs as additive/antibiotic)

LMSF Scheduler: Add local method, ParseGenericStep(), in ParseSteps(), as a template for new local parse methods

LMSF Scheduler: NewXML and SaveXML steps to ParseSteps(); and RunNewXml() and RunSaveXml() methods

LMSF Scheduler: Add  AddXmlStep() method, and argument handling in ParseNewXml() to assign value to experimentStep attribute in XML aoutput

LMSF_Utilities: Add GetDateTimeString() method for consistent formatting of DateTime string: "yyyy-MM-dd HH:mm:ss", for everything except log file names

LMSF Scheduler: Add  AddXmlStep() method, and argument handling in ParseNewXml() to assign value to experimentStep attribute in XML aoutput

LMSF Scheduler: Change code for RunNewXml() so that if 'Cancel' is selected at the "select project" dialog, the run will abort

LMSF Scheduler: Allow commenting input lines with "//"

LMSF Scheduler: Change XML schema a bit: metadata/project/protocol/<step> instead of metadata/project/experimentStep/<step>

LMSF Scheduler: Fix "procedure started" and "procedure finished" bugs 

LMSF Scheduler: AddDateTimeNodes(XmlNode parentNode)

LMSF Scheduler: Add datetime info to protocol start/finish in XML;

LMSF Scheduler: Change signature of RunTimer() method to RunTimer(int num, string[] args) to be consistent with other RunXxxx() methods

LMSF Scheduler: Add command: WaitFor, DateTime

LMSF Scheduler: Add command: AppendXML

LMSF Scheduler: Add command: UserPrompt; make shortcut drop-down box a bit wider

LMSF Scheduler: Change command-argument separator to foreward slash "/" - to allow use of commas and semicolons in arguments.

LMSF Scheduler: Add key syntax to arguments: any {keyString}, inclosed with "{" and "}", in an inputText argument will be replaced with the corresponding value from the metaDictionary

LMSF Scheduler: Add Set command to directly set entries in metaDictionary

LMSF Scheduler: Add Get command, calls up a user dialog to get a metadata type and saves the result in the metaDictionary

LMSF_Utilities: Fix Bug; "none" not showing up in parent list for create new identifier

LMSF Scheduler: Add "Validate with User Input" check box - when checked, the validate method goes through all the user dialogs

LMSF Scheduler: Add XML metadata output at end of RunGet() method

LMSF Scheduler: Add concDictionary (Dictionary<string, Concentration>) to store user input concentrations

LMSF Scheduler: Add Get/ concentration/... command, with automated XML output

LMSF Scheduler: Change default prompt on Get/ command to use the "key" instead of "type"

LMSF Scheduler: Add code to NewXML/ command: automatically add the protocol type to the metadata dictionary, metaDictionary["protocol type"] = protocolType;

LMSF Scheduler: Add "default" as prompt parameter in Get/ command; update help file

LMSF Scheduler: Fix bug: When 'Cancel' selected in Get/ concentration/..., the run needs to abort before trying to reference the concentration object, which is null.

LMSF_Utilities: User prompt dialog open in center of screen

LMSF Scheduler: Fix Bug: "/" getting insterted when short-cut comboBox returns null

LMSF_Utilities: Add GetExperimentId Dialog and method

LMSF Scheduler: Implement GetExpID/ command and RunGetExpId()
        Also, modify signature of AddDateTimeNodes(DateTime dt, XmlNode parentNode, string statusStr) to take DateTime object as first argument (so it can add dateTime info other than DateTime.Now)

LMSF Scheduler: Fix Bug in "Get/ concentration" command- concentration node was being appended to the additives instead of the last additive node 

LMSF Scheduler: In GetExpID/ command, delete automatically created directory if it is not used (user choosed to same xml file somewhere else)

LMSF Scheduler: Add command: Get/ notes/ <key>/ <prompt>, to get notes from the user and append them as a notes node to the protocol node in the XML document

LMSF Scheduler: Add commands: Hamilton/ <method file>, and WaitFor/ Hamilton, to run Hamilton Venus methods (similar to Overlord/ command)

LMSF Scheduler: Add startDate to metaDictionary (same string as startDateTime, but without the time)

LMSF Scheduler: Add Get/ number/ - to get generic numberic input from user, with prompt

LMSF Scheduler: Add "Start/ <protocol title>/ <list file path>" command; Protocol Start Dialog, w/ list of requirements and 'OK' and 'Abort' buttons.

At start of RunHamilton, delete the schema.ini file from the Hamilton parameters directory;

Add abort button to UserPromptDialog

Experiment ID dialog: "choose XML file to save metadata:"

LMSF Scheduler: Add new command: AddXML/ <parentNode> / <newNode>/ <innerText>

LMSF Scheduler: In SaveXML/ add option argument "not finished" to not add "protocol finished" attribute

LMSF Scheduler: Change "Start/" command to "StartPrompt/"

LMSF Scheduler: Change "UserPrompt/ <title>/ <message>..." comand so that character escape sequences in the <message> are interpretted, this allows multi-line messages (\n) and tabs (\t). 

LMSF Scheduler: Add Get/ user/... - to get user ID for metadata; LMSF_Utilities: Add code to automatically create metaList.csv file if it does not exist 

LMSF_Utilities: Add saving MetaLists to XML document (MetaIdLists.xml); Protocol/experiment XML document, change projectID from Attribute to Element/Node 

LMSF_Utilities: Change GetMetaList() so that it gets the lists from the XML document, MetaIdLists.xml (instead of a bunch of .csv files)

Add parent info and notes (for strains and plasmids) to MetaIdLists.xml

LMSF Scheduler: Add code to better handle AppendXml/ command: SelectXmlDocForAppend() (called by RunAppendXml()); 
    also sets experimentId in dictionary automatically, so that GetExpID/ does not need to be called.
	
LMSF Scheduler: make sure projectId, experimentId, and data directory get saved to metaDictionary consistently

LMSF Scheduler: In RunAppendXml() check if protocol type already exists and prompt with warning (new AbortAppendOverwriteDialog)

LMSF Scheduler: Add "GetFile/ <file key>/ <file prompt>{/ <file filter>}" command; open user dialog to select file; add file path to dictionary

LMSF Scheduler: Add "If/ <logical test>/ <other valid command>" to step parser, for basic run-time decision making driven by user inputs

LMSF Scheduler: Add User yes/no choice, saves result to dictonary;

Switch Hamilton parameters to Dictionary


Add new projects for creating Gen5 reader: LMSF_Gen5_Reader.dll and LMSF_Gen5.exe (WFP Window)

LMSF_Gen5_Reader: Change PlateStartRead() to read plate in reverse orientation.

LMSF_Gen5_Reader: Add generic exception handling in NewExperiment().

LMSF_Gen5_Reader: Fix issue with folder browser window opening behind everything, by adding SetClientWindow(this) call.

LMSF_Gen5: Set Focusable Property to false for all buttons (to avoid accidental button pushing via keyboard)

LMSF_Gen5_Reader: Add IsReading Property

LMSF_Gen5_Reader: Add checks to make sure IsReading=false before any call to Gen5 methods that should not be called while a read in in progress.

Test over-writing previous experiment file

Move WaitForFinishThenExport() to Gen5Window - so it can more easily manipulate GUI; Add "Read In Progress"/"Reader Idle" status indicator to GUI

On pressing NewExp Button: disable experimentId text box, file/folder buttons, and NewExp button; 
    add "Close Experiment" button; re-enable controls at end of read;
    rename CarrierIn and CarrierOut buttons (previously were openButton and closeButton)
	
LMSF_Gen5_Reader.CarrierIn(): Retry 3 times on carrier bump error

LMSF_Gen5: Move NewExp, RunExp, CarrierIn, and CarrierOut to stand-alone methods (instead of button click event handlers) so they can be called by remote control TcpListener thread (TBD).

LMSF_Gen5: On NewExp ButtonClick, check if experiment file exists and ask ok to overwrite-

LMSF_Gen5: Check that Read Starts Sucessfully before calling WaitForFinishThenExportAndClose();

LMSF_Gen5: Set output textbox to autoscroll to end of messages

LMSF_Gen5: Add generic error handling try-catch wrapper to all calls to LMSF_Gen5_Reader.dll

LMSF_Gen5: Add IsExperimentQueuedOrRunning property, and move controls enabled state setting to OnPropertyChanged() method (via call to UpdateControlEnabledStatus())

LMSF_Gen5: Add IsConnected property and button to switch between remote and local control

LMSF_Gen5: Add initial TCP Server code with event handlers

Switch SimpleTCP to local source instead of NuGet (might need to mofiy some of it)

LMSF Scheduler: Add ComboBox to select reader for TCP configuration setting, also add variables for use with TCP communication

LMSF Scheduler: Change ConfigureReader() so it could be called by other code: move user interaction (MessageBox) to combo box event handler

LMSF_Gen5_Reader: Add code back to display reader name at top of window

SimpleTCP: Add IsConnected() method

Move WrapTcpMessage() to SimpleTCP.Message class as static method

SimpleTCP: Add CheckMessageHash() method

LMSF_Gen5: Change name of Property IsReadRunning -> IsReaderBusy; also set this property appropriately during CarrierIn(); and CarrierOut();

SimpleTCP: Add UnwrapTcpMessage() method

LMSF_Gen5: Add enum status {Idle, Busy}

LMSF_Gen5: Add message unwrapping and reply to MessageReceived()

LMSF Scheduler: Add SendTcpMessage() method

LMSF_Gen5: change Remote/Local button lables to "Switch to..."

LMSF Scheduler: Add GetConnectedReadersList() method for validation checks

LMSF Scheduler: Add ValidateExpId() method and use it in parsing experiment IDs

LMSF_Utilities: Add IsDirectoryWritable() method

LMSF_Gen5_Reader: combine code for automatic generation of .xpt and export file names into a single method (GetExperimentFilePath()) to keep them consistent

LMSF Scheduler: Add "Gen5/" and "WaitFor/ <reader>/" commands

LMSF_Gen5: Add validation check to experimentID textbox

LMSF_Gen5: Add code to de-queue and run commands that get recieved

LMSF Scheduler: Set ReaderName property correctly - based on computer hostname

LMSF Scheduler: Set IPs for different readers

LMSF_Gen5: Add code run CarrierOut and CarrierIn commands in ParseAndRunCommand()

LMSF_Gen5.Gen5Window: Change readerStatus to property (ReaderStatus) and stop setting it in the IsReaderBusy property setter;
    But do set the IsReaderBusy property in the RemoteControl_DoWork() method so that it will appropriately signal to the Scheduler "WaitFor/ <reader>" command.
	Also, rename the enum ReaderStatus -> ReaderStatusStates

LMSF Scheduler: Inrease Sleep time in WaitForGen5()

LMSF Scheduler: Add AddOutputText(string txt) method and use it in place of "OutputText +=" - so that everything gets captured to log file

LMSF_Gen5: Change messageQueue type to string so that messageQueue.Contains() works as expected to avoid duplicate commands getting queued

LMSF Scheduler: Add Exception handling in SendTcpMessage(), client.WriteLineAndGetReply() - with excpetion written to log file; any excpetion results in a re-try.

LMSF Scheduler: Add autoscroll to bottom

LMSF Scheduler: Add datetime stamps to each line sent to log file

LMSF Scheduler: Add wrapped message to output text after, "sending message to reader..."

LMSF Scheduler: Add output text after "Running Gen5 Command:"

LMSF Scheduler Gen5/: In validation, when not connected add text about turning on connection on the Scheduler end. Also add label for the relevant control on the GUI

LMSF Scheduler: Change message on connection comboBox - depending on whether or not the reader is currently connected
    also, don't change indicator to green if connection isn't made

LMSF_Gen5.Gen5Window: Change property name TextOut -> OutputText, and tempOutTextBox -> outputTextBox, for consistency with Scheduler

LMSF_Gen5.Gen5Window: Add output to log file (and add AddOutputText() method similar to LMSF Scheduler)

add tab to log file lines after timestamp

change log file name endings to "-gen5.trc" and "-lmsf.trc"

Change output message for non-queued/duplicate messages, to make it more clear

Change message hash timestamp format to "fff"

LMSF Scheduler Gen5/<reader>/ RunExp: Add status check to make sure reader actually starts the read before moving on - to avoid having WaitFor/ <reader> return with "Idle" because read had not yet started.

LMSF Scheduler : Make bottom task button area a bit bigger

LMSF_Gen5: Add CarrierIn() step before RunExp() in ParseAndRunCommand() for RunExp command - becasue the Gen5Reader.CarrierIn() has the code to re-try 3 times if there is a bump error

LMSF_Gen5: Add AbortRead button and command

SimpleTCP: Replace DataReceived with DelimiterDataReceived() in WriteLineAndGetReply() so that both message and reply are handled as lines (delimieted by Delimiter = 0x13)

LMSF_Gen5: Add oldMessageQueue - to take messages that have been run - to avoid running duplicates that arrive slowly (after the original has run and been dequeued)

Test and merge into main branch

In GetExpId(), create matching saveDirectory on all connected server computers

For all user dialog boxes in LMSF_Utilities, set IsDefault = false for all buttons

LMSF_Utilities: Don't let get concentration dialog close with empty units field

LMSF_Utilities: Add method GetMetaTypeList(), and change IsValidMetaType()

LMSF Scheduler: With Get/ validation, add list of valid types if "Not a valid metadata type"

LMSF Scheduler: Add numeric comparisons to If/ command, ">, >=, <, <="

LMSF Scheduler: In RunRemoteHamilton(), make sure metaDicitonary is sucessfully exported before sending command to Hamilton

LMSF Scheduler: Add parsing for RemoteHam/ <Hamilton name>/ ReadCounters command

LMSF Scheduler: In RunRemoteHamilton() with ReadCounters command, add wait for method completion then read tip status into dictionary

Hamilton Remote: Add handling of ReadCounters command

Re-write script parsing to use "Command(...)" format instead of "Command/" format

LMSF Scheduler: Enable commas in Set() by re-concatenating arguments

LMSF Scheduler: Change action on SelectComboBox_DropDownClosed() to match new command format

Change Enabled state of input text box to true during run, but set editable state to false

Add "next step" text box to show the next line that will be run

Change status indicator colors in remotes (Hamilton and Gen5): Busy=yellow, Idle=green

In remotes, StatusCheck messages get queued directly to oldMessageQueue

Add parameter to set ping interval on WaitFor()

Add CopyRemoteFiles command to copy files from remote data directories to local data directory

Update help document

Fix validation error with Remote Hamilton(rem, ReadCounters) - validation expects a 3rd parameter
	Also, if methodPath ends with "Edit Tip Counters.hsl", also read tip counter file (and change the validation check accordingly)
	
Add RunScript() command
	Read in script file in InitSteps(), just after inputSteps = InputText.Split(new[] { "\r\n", "\r", "\n" }, StringSplitOptions.RemoveEmptyEntries);

fix bug: if script file not found, protocol aborts but input window is not editable

Make sure user prompts are always on top

In RemoteHam(S-Cell-STAR, ReadCounters), attach method file path to XML node

In send-TCP-message loop, if AbortCalled=true, then exit loop
	Also, automatically recconect if send message fails N times.

fix startup status colors on remotes
	
Add "Are you sure you want to abort?" dialog to make sure protocol does not get accidentally aborted.

ovp variables that are set by Overlord() call, should get appended to the XML\

Test this: In send-TCP-message loop, if AbortCalled=true, then exit loop
	Also, automatically reconnect if send message fails N times.
	
make inputSteps into a list (instead of an array)

Keep comment lines in inputSteps list, but ignore them in ParseStep()

Save XML file every time it the XML is added to; Don't add to xml if abortCalled

Add code to validate and insert manually entered step during pause

Add ExportDictionary and ImportDictionary() commands mechanism for stop/pause, re-write, continue
	ExportDictionary() - exports dictionary either to dataDirectory or user specified directory
	ImportDictionary() - imports dictionary from user specified file

Add options to handle runtime key-not-found error: user can manually enter key/value into dictionary - and re-run step-


LoadXML() command to go with ImportDictionary() for restarting an experiment

Change so that manually entered step runs when InsertStep button is clicked (if it validates)

Add Math() Command
	Enable simple math (+, -, *, /, %) with numeric quantities
	
Add Error status to ServerStatusStates

Add error reporting (by checking log file at completion of run) to Remote Hamilton

Remote Hamilton run-time error reporting:
	When method finishes, Remote Hamilton checks log file for lines that contain "error"
	On error, adds lines from log file to errorList
	if errorList is not empty, status is set to Error.
	
	The Main Window gets status back as "Error"
		Pause, alert user

Add Basic error handling (pause and alert user) in WaitForRemote() method 
	
Take out "Validate with User input..."

Add output script file saved during SaveXML() (usually at the end of the run)

Add parameters to ReadScript to set dictionary values needed by the script
	#InsertVariables to indicate where in the script file to insert Set() commands if script file is run via a ReadScript() command

Long identifiers, take out RegEx validation/restriction

Fix bug during CopyRemoteFiles(): don't try to copy files from "local host"

Add GetTimeNow() command to get the current date-time, using DateTime.Now.ToString("HH:mm:ss");

Add date-time handling to Math command - for "+" and "-" operations.

When adding protocol node to XML, add lmsf script file name/path
Also add Input script file-path as comment on first line of output script file

Add "NoUser" optional parameter to AppendXML() so that it can run without user intervention

Fix slow validation with remote connections


TODO:

Check Timer code; the "Time remining" display is not accurate

Add "Hamilton Only/Simulation Mode" - with check box, for running only the Hamilton and RemoteHam steps
	Add 2nd checkbox for "Convert RemoteHam to local Hamilton"

Add Gen5 command to get mean OD from the last read?


Add Get(dateTime, timeKey) to get date-time from user

Do not output comments with #?

Add IfKeyExists() or IfNoKey() command


	
	
Add new command for Remote Hamilton, GetError(int errorIndex)
	This is not a command that needs to be run from the script. It is part of the automated error recovery. So will only be called within the c# code.
	sends errorList[errorIndex] back as a message
	Need to remove all commas detected in error lines (replace with semi-colons), to avoid issues with TCP message wrapping and unwrapping (which uses commas as separators)
	
Walk-away error handling:
	have a script (.lmsf) file for each error handling situation
	new command OnError(<error code>, <error script>)
			


Combine metadata list/database from multiple computers

Change Overlord variable setting format from "[varibale] value" to "variable = value" (wait for SDK)

error log



Add additional optional parameters to Hamilton() and RemoteHam() that set dictionary keys and write values to XML

Command to read/write from/to the carousel inventory file
Or Carousel inventory that works like Hamilton Tip Counter.

Run-time error handling
	Pause and Notify
	Retry
	Manually change dictionary entry, then retry
	Edit command line then retry
	Ignore/Continue
	
	Walk-away error handling:
		have a script (.lmsf) file for each error handling situation
		new command OnError(<error code>, <error script>)
		



Nested keys

Not necesary: Add else to If(...
	
Change step list (inputSteps) to Queue or Stack?

Add automatic generation of database with run times for Hamilton and Gen5 methods?

Not necesary: Nested If()

Change arguments passed to BackgroundWorkers to dictionaries, instead of lists.

send email alerts



Test what happens if SaveXML/ is run twice



Make everything thread safe:
	First For each class with multiple threads, list all the threads other than the main/GUI thread, and then all the variables/properties accessed by each thread:
		LMSF Scheduler.MainWindow
			Thread runStepsThread
				StepsThreadProc()
					IsRunning, get
					IsPaused, get
					IsOneStep, get
					InitSteps()
						metaDictionary, set
						concDictionary, set
						isCollectingXml, set
						inputSteps, get, set
						InputText, get
						stepNum, set
						totalSteps, get, set
						stepsRunning, set			can delete this variable
						isValidating, get
						OutputText, get, set		intentionally not locking this variable
						ExperimentFileName, get
						logFilePath, get
						metaDataFilePath, set
						NewLogFile()
							logFilePath, set
							NewLogFileName()
					Step()
						AbortCalled, get
						IsRunning, set
						stepNum, get, set
						totalSteps, get
						inputSteps, get
						isValidating, get
						logFilePath, get
						IsRunning, set
						IsOneStep, set
						AddOutputText()
						ParseStep()
							metaDictionary, set
							concDictionary, set
							GetConnectedReadersList()
								ReaderList, get
								readerClients, get
							RunOverlord()
								WaitingForStepCompletion, set
								ovProcess, get, set
								isCollectingXml, get
								protocolNode, get
							RunHamilton()
								WaitingForStepCompletion, set
								hamProcess, get, set
								isCollectingXml, get
								protocolNode, get
							RunRemoteHamilton()
								isCollectingXml, get
								protocolNode, get
								SendTcpMessage()
									readerClients, get
									AbortCalled, set
							RunGen5()
								isCollectingXml, get
								protocolNode, get
								SendTcpMessage()
									readerClients, get
									AbortCalled, set
									
							RunTimer()
								WaitingForStepCompletion, set
								stepTimerDialog, get, set
							WaitForOverlord()
								WaitingForStepCompletion, get, set
								ovProcess, get
								isCollectingXml, get
							WaitForHamilton()
								WaitingForStepCompletion, get, set
								hamProcess, get
								isCollectingXml, get
							WaitForTimer()
								WaitingForStepCompletion, get, set
							WaitForRemoteProcess()
								WaitingForStepCompletion, get, set
								isCollectingXml, get
							RunNewXml()
							RunAppendXml()
							RunSaveXml()
							RunUserPrompt()
							RunUserYesNo()
							RunAddXml()
							RunSet()
							RunGet()
							RunGetExpId()
							RunGetFile()
							RunStartDialog()
					
			BackgroundWorker remoteMonitorWorker
				RemoteProcessMonitor_DoWork()
					GetRemoteServerStatus()
						SendTcpMessage()
							readerClients, get
							AbortCalled, set
				RemoteProcessMonitor_RunWorkerCompleted()
					WaitingForStepCompletion, set
					
			BackgroundWorker ovMonitorWorker
				OutsideProcessMonitor_DoWork()
					outside_Process, get
				OutsideProcessMonitor_RunWorkerCompleted()
					WaitingForStepCompletion, set
			
			BackgroundWorker hamMonitorWorker
				OutsideProcessMonitor_DoWork()
					outside_Process, get
				OutsideProcessMonitor_RunWorkerCompleted()
					WaitingForStepCompletion, set
			
			BackgroundWorker timerMonitorWorker
				TimerMonitor_DoWork()
					stepTimerDialog, get
				TimerMonitor_RunWorkerCompleted()
					WaitingForStepCompletion, set
			
		LMSF Scheduler.MainWindow
			fields/properties to lock:
				WaitingForStepCompletion
					At first, it might not seem like this is necessary because there is no place in the code where WaitingForStepCompletion needs to remain locked for more than one line;
						but based on this: http://jonskeet.uk/csharp/threads/volatility.shtml, I'm going to put locks on all the flow control booleans.
					lock is inside property getter and setter
				IsRunning, IsPaused



Message from server (reader/STAR) when finished instead of repeated inquiry from Scheduler

TestReaderCommunication



Add sleep time as optional parameter to WaitFor/








test for graceful closing and/or exit of Scheduler and Gen5Window - with respect to TCP connections







Reader initialization.


Add quick connection test in SimpleTCP.IsConnected()
LMSF Scheduler: on sending command, check if connected first, then reconnect if necessary
	
Set up maxRetries in Scheduler.SendTcpMessage()

For remote readers, automatically change protocol path?





TCP client/listener
	send connection requests from Main LMSF (clients)
		LMSF Scheduler - clients
		LMSF_Gen5 - server
		
	best bet: "TCP Socket Off-the-shelf" from Code Project
	TCP port numbers: 41798-42507 are Unassigned, but Unauthorized Use Known on port 42000
	
		So, use 42222, 42223, 42224..., 42999
		
		


Add real-time plotting

Test RunReaderControlCommand()








LMSF Scheduler: Add copy file - to allow user to copy files into experiment data directory


Boolean combinations in If/


control-s shortcut to save


Add cells now/later dialog, w/ 'now', 'later', and 'abort' buttons








Attune front end? 4 buttons: Startup, perf test, run experiment, shutdown
	Uses LMSF Scheduler and Utilities code





Open timer dialog near top of screen?


Open Overlord to edit procedure button

control which screen Overlord opens on (screen one preferred)

Comnbine MetaList.csv files from multiple sources (STAR and Overlord Main)








one-line constructors for custom dialogs



Copy functionality from Venus LMSF Utilities library

User input steps: need C# metadata -> xml?


(Probably) Hard-to-do stuff:

Highlight lines in output that have errors (or change text to red)
    would require changing to a RichTextBox and more complicated text entry
	Still need to figure out Binding - since the idea I had to bind to the Document Property of the Control doesn't work
	
	    First, switch the Binding Property from OutPutText to OutPutDocument (Document class)
	
	    Then, change return type of the ParseStep() method to Paragraph
		
	    Then, in the Step() method, replace  the line,
		    OutputText += ParseStep(stepNum, inputSteps[stepNum]); 
	    with:
		    OutPutDocument.Blocks.Add(ParseStep(stepNum, inputSteps[stepNum]));
			
		And in the ParseStep() method, at the end, 
			Paragraph newOutText = new Paragraph();
			newOutText.Inlines.Add(outString);
			newOutText.FontWeight = FontWeights.Bold; - if validation error
			newOutText.Foreground = Brushes.Red; - or Black if passed validation
			
			return newOutText;



Add code to make sure Overlord is started before leaving RunOverlord() - since it is a bit slow to start up
    Couldn't figure out how to do that- tabling it for now.














"C:\Program Files (x86)\PAA\Overlord3\Procedures\Common\Peel Plate.ovp" -r -c -v [Plates] 10 [Barcode] "12345678" [Gen5.Protocol.Path] "C:\Gen5 Path..."