public bool AttemptToReseatLid(Protocol toModify, AdditionalMethodArguments eargs)
{
IncubatorServ Incubator = eargs.InstrumentCollection.ReturnInstrumentType<IncubatorServ>();
TransferStation TransStation = eargs.InstrumentCollection.ReturnInstrumentType<TransferStation>();
Twister Robot = eargs.InstrumentCollection.ReturnInstrumentType<Twister>();
TransStation.TurnOnVacuumAndLiftLid();
TransStation.MoveStationOut();
Robot.MovePlateFromTransferStationToPlateReader(eargs);
TransStation.MoveStationIn();
TransStation.TurnOffVacuumAndReturnLid();
TransStation.TurnOnVacuumAndLiftLid();
TransStation.MoveStationOut();
Robot.MovePlateFromPlateReaderToIncubator();
TransStation.MoveStationIn();
TransStation.TurnOffVacuumAndReturnLid();
return true;
}
//TODO: Convert so that htis uses XML serialization instead
//http://support.microsoft.com/kb/815813
public static void ProtocolToXMLFile(Protocol curProtocol, string Filename)
{
XmlTextWriter XWriter = new XmlTextWriter(Filename, Encoding.ASCII);
XWriter.Formatting = Formatting.Indented;
XWriter.WriteStartDocument();
XWriter.WriteStartElement("Protocol");
//first to write the name
XWriter.WriteStartElement("ProtocolName");
XWriter.WriteString(curProtocol.ProtocolName);
XWriter.WriteEndElement();
//now the error emails
XWriter.WriteStartElement("ErrorEmailAddress");
XWriter.WriteValue(curProtocol.ErrorEmailAddress);
XWriter.WriteEndElement();
//now the phone number
XWriter.WriteStartElement("ErrorPhoneNumber");
XWriter.WriteValue(curProtocol.ErrorPhoneNumber);
XWriter.WriteEndElement();
//Here we have code to loop through and drop the variables in
XWriter.WriteStartElement("Variables");
foreach (string varName in curProtocol.Variables.Keys)
{
ProtocolVariable PV = curProtocol.Variables[varName];
XWriter.WriteStartElement("Variable");
XWriter.WriteStartElement("Name");
XWriter.WriteString(PV.Name);
XWriter.WriteEndElement();
XWriter.WriteStartElement("Value");
XWriter.WriteStartAttribute("Type");
XWriter.WriteValue(PV.DataType.ToString());
XWriter.WriteEndAttribute();
XWriter.WriteValue(PV.Value.ToString());
XWriter.WriteEndElement();
XWriter.WriteEndElement();
}
XWriter.WriteEndElement();//end variables
XWriter.WriteStartElement("Instructions");
//now to loop through all the instructions and make it happen
foreach (object o in curProtocol.Instructions)
{
XWriter.WriteStartElement("Instruction");
XWriter.WriteStartAttribute("InstType");
XWriter.WriteValue(o.GetType().ToString());
XWriter.WriteEndAttribute();
//now to unload the properties here
//System.Windows.Forms.MessageBox.Show(o.GetType().GetProperties().Length.ToString());
var toTest = Type.GetType("System.Object[]");
foreach (FieldInfo PI in o.GetType().GetFields())
{
if (PI.FieldType.ToString() == "System.Object[]") //the parameters are always passed as an object array, this is kind of silly now since all my methods only take one argument, but in the future who knows.
{
object[] Params = (object[])PI.GetValue(o);
XWriter.WriteStartElement("Parameters");
foreach (object Param in Params)
{
XWriter.WriteStartElement("Parameter");
XWriter.WriteStartAttribute("Type");
XWriter.WriteValue(Param.GetType().ToString());
XWriter.WriteEndAttribute();
//XWriter.WriteValue(Param);
//switched to accomodate new types
XWriter.WriteString(Param.ToString());
XWriter.WriteEndElement();
}
XWriter.WriteEndElement();
}
else if (PI.FieldType == typeof(Protocol)) continue;//Ignore the containing protocol bit
else
{
XWriter.WriteStartElement(PI.Name);
XWriter.WriteStartAttribute("Type");
XWriter.WriteValue(PI.FieldType.ToString());
XWriter.WriteEndAttribute();
XWriter.WriteValue(PI.GetValue(o));//should throw an error if not a valid type
XWriter.WriteEndElement();
}
}
XWriter.WriteEndElement();
}
XWriter.WriteEndElement();
XWriter.WriteEndElement();
XWriter.WriteEndDocument();
XWriter.Close();
}
public static Protocol XMLFileToProtocol(string Filename)
{
//Starting to approach the point where I need to break this up....
//7-27-2012 now trying to select nodes.
Protocol NewProtocol = new Protocol();
XmlDocument XmlDoc = new XmlDocument();
XmlTextReader XReader = new XmlTextReader(Filename);//http://dn.codegear.com/article/32384
XmlDoc.Load(XReader);
//first node is xml, second is the protocol, this is assumed and should be the case
//XmlNode ProtocolXML = XmlDoc.ChildNodes[1];
XmlNode ProtocolXML = XmlDoc.SelectSingleNode("/Protocol");
XmlNode name=ProtocolXML.SelectSingleNode("/ProtocolName");
NewProtocol.ProtocolName = ProtocolXML.SelectSingleNode("ProtocolName").InnerText;
NewProtocol.ErrorPhoneNumber = ProtocolXML.SelectSingleNode("ErrorPhoneNumber").InnerText;
NewProtocol.ErrorEmailAddress = ProtocolXML.SelectSingleNode("ErrorEmailAddress").InnerText;
Assembly assembly = Assembly.GetExecutingAssembly();
XmlNode VariablesNode = ProtocolXML.SelectSingleNode("Variables");
if (VariablesNode != null)
{
foreach (XmlNode variable in VariablesNode.ChildNodes)
{
string Name = variable.ChildNodes[0].InnerText;
string variableTypeString = variable.ChildNodes[1].Attributes[0].Value;
Type VariableType = System.Type.GetType(variableTypeString);
object valueAsString = variable.ChildNodes[1].InnerText;
var Value = Convert.ChangeType(valueAsString, VariableType);
ProtocolVariable PV = new ProtocolVariable(Name, VariableType, Value);
NewProtocol.Variables.Add(PV.ToString(), PV);
}
}
XmlNode instructionsNode = ProtocolXML.SelectSingleNode("Instructions");
foreach (XmlNode instruct in instructionsNode.ChildNodes)
{
string DataType = instruct.Attributes[0].Value;
Type InstructionType = assembly.GetType(DataType);
object ProtocolInstruction = Activator.CreateInstance(InstructionType);
string ValueType, Value;
foreach (XmlNode Property in instruct.ChildNodes)
{
if (Property.Name == "Parameters")//this means I have a static protocol item
{
ArrayList AL = new ArrayList();
object[] ParameterArray;
if (Property.ChildNodes.Count == 0) { ParameterArray = new object[0]; }
else
{
ParameterArray = new object[Property.ChildNodes.Count];
int ParameterIndex = 0;
foreach (XmlNode Parameter in Property.ChildNodes)
{
ValueType = Parameter.Attributes[0].Value;
Value = Parameter.InnerText;
ParameterArray[ParameterIndex] = ReturnValue(ValueType, Value);
ParameterIndex++;
}
}
StaticProtocolItem ProtocolItem = (StaticProtocolItem)ProtocolInstruction;
ProtocolItem.Parameters = ParameterArray;
ProtocolItem.ContainingProtocol = NewProtocol;
}
else
{
FieldInfo FI = ProtocolInstruction.GetType().GetField(Property.Name);
ValueType = Property.Attributes[0].Value;
Value = Property.InnerText;
object ValuetoSet = ReturnValue(ValueType, Value);
FI.SetValue(ProtocolInstruction, ValuetoSet);
}
}
NewProtocol.Instructions.Add(ProtocolInstruction as ProtocolInstruction);
}
XReader.Close();
return NewProtocol;
}
/// <summary>
/// Sets the current protocol to the next one to run.
/// </summary>
public void UpdateCurrentProtocol()
{
if (Protocols.Count > 0)
{
Protocols.Sort((x, y) => x.NextExecutionTimePoint.CompareTo(y.NextExecutionTimePoint));
CurrentProtocolInUse = Protocols[0];
}
}
public void RemoveProtocol(Protocol ProtocolToRemove)
{
if (Protocols.Count == 1)
{//empty out the current protocol in use
CurrentProtocolInUse = null;
Protocols.Remove(ProtocolToRemove);
}
else
{
if (CurrentProtocolInUse == ProtocolToRemove)
{
CurrentProtocolInUse = null;
Protocols.Remove(ProtocolToRemove);
FindMilliSecondsUntilNextRunAndChangeCurrentProtocol();
}
else
{
Protocols.Remove(ProtocolToRemove);
}
}
UpdateAlarmProtocols();
}
public void AddProtocol(Protocol ProtocolToAdd)
{
ProtocolToAdd.NextExecutionTimePoint = DateTime.Now;
if (Protocols.Count == 0)//check if this is the most current protocol
{
CurrentProtocolInUse = ProtocolToAdd;
}
Protocols.Add(ProtocolToAdd);
UpdateAlarmProtocols();
}
public static bool VerifyProtocolVariablesReferences(Protocol ProtocolToRun)
{
//This is a method that will ensure that all of the references to variables in a protocol work out,
//it will go through the instructions and check that the variables that are referenced exist
foreach (object o in ProtocolToRun.Instructions)
{
if (o is StaticProtocolItem)
{
StaticProtocolItem SP = (StaticProtocolItem)o;
//now to move through and check all
foreach (object Param in SP.Parameters)
{
if (Param is string)
{
//check all variable names in a string
List<string> VariableNames = GetAllVaraibleNamesFromText((string)Param);
foreach (string vName in VariableNames) { if (!ProtocolToRun.Variables.ContainsKey(vName)) { return false; } }
}
else if (Param is ReferenceToProtocolVariable)
{
ReferenceToProtocolVariable CurRef = (ReferenceToProtocolVariable)Param;
if (!ProtocolToRun.Variables.ContainsKey(CurRef.ToString())) { return false; }
}
}
}
}
return true;
}
private Protocol CreateProtocolFromForm()
{
Protocol newProtocol = new Protocol();
if (txtProtocolName.Text == "" | txtEmails.Text == "")
{
throw new Exception("You must name your protocol and provide an email address");
}
if (lstProtocol.Items.Count == 0)
{
throw new Exception("There are no instructions in your protocol, please add them.");
}
newProtocol.ErrorEmailAddress = txtEmails.Text;
newProtocol.ErrorPhoneNumber = txtNumbers.Text;
newProtocol.ProtocolName = txtProtocolName.Text;
newProtocol.Instructions = ProtocolListBoxToProtocolInstructionList(lstProtocol);
foreach (object o in lstCurrentVariables.Items)
{
ProtocolVariable PV = (ProtocolVariable)o;
newProtocol.Variables.Add(PV.ToString(), PV);
}
//newProtocol.Instructions = ProtocolConverter.ProtocolWithRepeatsToProtocolWithout(newProtocol.Instructions);
return newProtocol;
}
/// <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"); }
}
