public StaticProtocolItem ReplaceVariablesWithValues(StaticProtocolItem ToRun)
{
//This method will take a protocol item that has variables, and replace it with actual values,
//It should be called before the method is run
StaticProtocolItem NewProtocolItem = ToRun.Clone();
NewProtocolItem.ContainingProtocol = this;
for (int i = 0; i < NewProtocolItem.Parameters.Length; i++)
{
object o = ToRun.Parameters[i];
//check if it is a string
if (o is string)
{
string VariableName;
//now have to go through and remove all of the variables, replacing them with other strings
String myval = (String)o;
while (true)
{
bool variableInString = ProtocolManager.GetVariableNameFromText(myval, out VariableName);
if (variableInString)
{
string ToReplace = Variables[VariableName].Value.ToString();
myval = myval.Replace(VariableName, ToReplace);//swap out the value and searchagain
}
else
{ break; }
}
ToRun.Parameters[i] = myval;
}
else if (o is ReferenceToProtocolVariable)
{
ReferenceToProtocolVariable RefToVariable = (ReferenceToProtocolVariable)o;
ToRun.Parameters[i] = Variables[RefToVariable.ToString()].Value;
}
}
return NewProtocolItem;
}
public ListBoxProtocolItem()
{
Instruction = new StaticProtocolItem();
}
public StaticProtocolItem Clone()
{
StaticProtocolItem SP = new StaticProtocolItem();
SP.MethodName = this.MethodName;
SP.Parameters = this.Parameters;
SP.InstrumentName = this.InstrumentName;
SP.ContainingProtocol = this.ContainingProtocol;
return SP;
}
private void CreateProtocolItems(string ExpName,int Slot)
{
ExpSlot = Slot;
toVictorInstruction = new StaticProtocolItem();
toVictorInstruction.InstrumentName = "Macros";
toVictorInstruction.Parameters = new object[1] { Slot };
toVictorInstruction.MethodName = "MovePlateFromIncubatorToVictor";
OD_OutDirec=ExpName + "_" + Slot.ToString();
ODReadInstruction = new StaticProtocolItem();
ODReadInstruction.MethodName = "ReadPlate2";
ODReadInstruction.InstrumentName = "PlateReader";
ODReadInstruction.Parameters = new object[2] {OD_OutDirec, OD600ProtocolID };
VenusReadInstruction = ODReadInstruction.Clone();
//VenusReadInstruction = new StaticProtocolItem();
//VenusReadInstruction.MethodName = "ReadPlate2";
//VenusReadInstruction.InstrumentName = "Plate_Reader";
//VenusReadInstruction.Parameters = new object[2] { "Ve_" + OD_OutDirec, VenusProtocolID };
VenusReadInstruction.Parameters[1] = VenusProtocolID;
awayFromVictorInstruction = toVictorInstruction.Clone();
awayFromVictorInstruction.MethodName = "MovePlateFromVictorToIncubatorWithLidOnTransferStation";
DT = new DelayTime();
DT.minutes = MinBetweenReads;
ReturnInstruction = new StaticProtocolItem();
ReturnInstruction.MethodName = "ModifyGrowthProtocol";
ReturnInstruction.InstrumentName = this.Name;
//Last item is passed in by the parser
ReturnInstruction.Parameters = new object[2] { ExpName, Slot };
}
/// <summary>
/// This method creates a protocol to run a certain type of
/// experiment for the user, in this case an experiment that moves plates
/// from an incubator to a plate reader periodically.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void btnStartGrowthRate_Click(object sender, EventArgs e)
{
try
{
//this will create and start a protocol, first to check for errors
int minuteDelay = 0;
int cycles = 0;
if (txtGrowthRateEmail.Text == "" | txtGrowthRateExperimentName.Text == "" | txtGrowthRateMinutes.Text == "" | txtGrowthRateTimesToMeasure.Text == "")
{
ShowError("You did not fill out all of the required fields");
}
else if (lstGrowthRatesProtocol.SelectedIndex == -1)
{
ShowError("You did not select any slots");
}
// For SkypeAlarm
else if (ClarityEngine.UseAlarm && ClarityEngine.Clarity_Alarm!=null && ClarityEngine.Clarity_Alarm.Connected && !ClarityEngine.Clarity_Alarm.ValidNumbers(textbox_number.Text))
{
ShowError("Your number is not valid!");
}
else
{
try { minuteDelay = Convert.ToInt32(txtGrowthRateMinutes.Text); cycles = Convert.ToInt32(txtGrowthRateTimesToMeasure.Text); }
catch { ShowError("Could not convert your delay or measurement into an integer, please enter an appropriate value"); return; }
if (minuteDelay < 9 | minuteDelay > 25 * 60)
{
ShowError("Your delay time is weird, please make it greater then 9 minutes or less than 25 hours");
return;
}
if (cycles < 0 | cycles > 200)
{
ShowError("You seem to have selected less than 0 or more than 200 readings, please pick an alternative");
return;
}
Protocol NewProt = new Protocol();
NewProt.ProtocolName = txtGrowthRateExperimentName.Text;
NewProt.ErrorEmailAddress = txtGrowthRateEmail.Text;
NewProt.ErrorPhoneNumber = textbox_number.Text;
NewProt.Instructions = new List<ProtocolInstruction>();
for (int i = 0; i < cycles; i++)
{
foreach (int plateslot in lstGrowthRatesProtocol.SelectedItems)
{
//move from incubator to platereader
StaticProtocolItem SP = new StaticProtocolItem();
SP.InstrumentName = "Macros";
SP.Parameters = new object[1] { plateslot };
SP.MethodName = "MovePlateFromIncubatorToVictor";
NewProt.Instructions.Add(SP);
//read plate
StaticProtocolItem SP2;
if (chk48WellPlate.Checked)
{
SP2 = new StaticProtocolItem();
SP2.MethodName = "ReadPlate2";
SP2.InstrumentName = "PlateReader";
SP2.Parameters = new object[2] { NewProt.ProtocolName + INSTRUMENT_NAME_DELIMITER + plateslot.ToString(), WELL48_PLATE_PROTOCOL_ID };
NewProt.Instructions.Add(SP2);
}
else if (chkGBO.Checked)
{
SP2 = new StaticProtocolItem();
SP2.MethodName = "ReadPlate2";
SP2.InstrumentName = "PlateReader";
SP2.Parameters = new object[2] { NewProt.ProtocolName + INSTRUMENT_NAME_DELIMITER + plateslot.ToString(), GBO_PLATE_PROTOCOL_ID };
NewProt.Instructions.Add(SP2);
}
else
{
SP2 = new StaticProtocolItem();
SP2.MethodName = "ReadPlate";
SP2.InstrumentName = "PlateReader";
SP2.Parameters = new object[1] { NewProt.ProtocolName + INSTRUMENT_NAME_DELIMITER + plateslot.ToString() };
NewProt.Instructions.Add(SP2);
}
//now to move the old plate back
SP2 = SP.Clone();
SP2.MethodName = "MovePlateFromVictorToIncubatorWithLidOnTransferStation";
NewProt.Instructions.Add(SP2);
}
DelayTime DT = new DelayTime();
DT.minutes = minuteDelay;
NewProt.Instructions.Add(DT);
}
DialogResult DR = MessageBox.Show("Are you sure you have entered the right values and are ready to load this protocol?", "Final Check", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (DR == DialogResult.Yes)
{
ClarityEngine.AddProtocol(NewProt);
UpdateLoadedProtocols();
if (ClarityEngine.CurrentRunningState == RunningStates.Idle)//this timer is running while a protocol is waiting to go
{
DialogResult DR2 = MessageBox.Show("Would you like to start your protocol immediately?", "Begin Protocol", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (DR2 == DialogResult.Yes)
{
ClarityEngine.StartProtocolExecution();
}
}
}
}
}
catch { ShowError("Weird error occurred"); }
}
private void btnGenerateNSFData_Click(object sender, EventArgs e)
{
try
{
int tranNum;
List<Protocol> ProtsToAdd = new List<Protocol>();
//this will create and start a protocol, first to check for errors
if (txtNSFTransferNumber.Text == "" | txtNSFName.Text == "")
{
ShowError("You did not fill out all of the required fields");
}
else if (lstNSFPlates.SelectedIndex == -1)
{
ShowError("You did not select any slots");
}
else
{
try { tranNum = Convert.ToInt32(txtNSFTransferNumber.Text); }
catch { ShowError("Could not convert your transfer number into an integer, please enter an appropriate value"); return; }
//NSFExperiment tmp = new NSFExperiment();
foreach (int plateslot in lstNSFPlates.SelectedItems)
{
Protocol NewProt = new Protocol();
NewProt.ErrorEmailAddress = "";
string baseName = "NSF-" + txtNSFName.Text + "-" + txtNSFTransferNumber.Text.ToString();
NewProt.ProtocolName = baseName + "_" + plateslot.ToString();
StaticProtocolItem SP = new StaticProtocolItem();
SP.MethodName = "CreateProtocol";
//SP.InstrumentName = tmp.Name;
SP.Parameters = new object[2] { baseName, plateslot };
NewProt.Instructions.Add(SP);
ProtsToAdd.Add(NewProt);
}
Protocol Watcher = new Protocol();
Watcher.ProtocolName = "NSF-Error-" + txtNSFTransferNumber.Text.ToString();
Watcher.ErrorPhoneNumber = "4158234767";
Watcher.MaxIdleTimeBeforeAlarm = 50;
Watcher.ErrorEmailAddress = this.NSFErrorEmails;
DelayTime DT = new DelayTime();
DT.minutes = 60 * 70;
Watcher.Instructions.Add(DT);
ProtsToAdd.Add(Watcher);
}
DialogResult DR = MessageBox.Show("Are you sure you have entered the right values and are ready to load this protocol?", "Final Check", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (DR == DialogResult.Yes)
{
foreach (Protocol p in ProtsToAdd)
{
ClarityEngine.AddProtocol(p);
}
UpdateLoadedProtocols();
if (ClarityEngine.CurrentRunningState==RunningStates.Idle)//this timer is running while a protocol is waiting to go
{
DialogResult DR2 = MessageBox.Show("Would you like to start your protocols immediately?", "Begin Protocol", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (DR2 == DialogResult.Yes)
{
ClarityEngine.StartProtocolExecution();
}
}
}
}
catch { ShowError("Weird error occurred"); }
}