PowerShell For Fun

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###########################################
# File Name: su.msh
# Launch a new msh.exe with someone else's identity
# from tony http://mshforfun.blogspot.com/
###########################################
$SuAccount = get-credential
$StartInfo = new-object System.Diagnostics.ProcessStartInfo
$StartInfo.FileName = "msh.exe"
$StartInfo.UserName = $SuAccount.UserName
$StartInfo.Password = $SuAccount.Password
$StartInfo.LoadUserProfile = $true
$StartInfo.UseShellExecute = $false
$StartInfo.WorkingDirectory = (get-location).Path
[System.Diagnostics.Process]::Start($StartInfo)

$StartInfo.Arguments="-noexit -command `$Host.UI.RawUI.WindowTitle=\`"Microsoft Command Shell ($($SuAccount.UserName)) \`""

new-property HKLM:\SOFTWARE\Microsoft\MSH\1\ShellIds `
-property ConsolePrompting -value "True" -force

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/27/2006 01:16:00 AM  3 comments

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##############################################
# File Name: id.msh
# Return User and Group information of current logon user
# By Tony http://mshforfun.blogspot.com
##############################################
$me=[System.Security.Principal.WindowsIdentity]::GetCurrent()
"UserSID= " + $me.User + " (" + $me.Name + ")"
"AuthenticationType= " + $me.AuthenticationType
"ImpersonationLevel= " + $me.ImpersonationLevel
"Token= " + $me.Token
"Groups= "
foreach($Group in $me.Groups)
{
"`tGroupSID= " + $Group + " (" + $Group.Translate([System.Security.Principal.NTAccount]) + ")"
}

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/24/2006 11:41:00 PM  0 comments

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[system.enum]::getnames([System.Security.AccessControl.FileSystemRights])

[int]([System.Security.AccessControl.FileSystemRights]::Read)

[System.Security.AccessControl.FileSystemRights]::ReadData `
-bor [System.Security.AccessControl.FileSystemRights]::ReadExtendedAttributes `
-bor [System.Security.AccessControl.FileSystemRights]::ReadAttributes `
-bor [System.Security.AccessControl.FileSystemRights]::ReadPermissions

[System.Security.AccessControl.FileSystemRights] "ReadData, ReadExtendedAttributes, ReadAttributes, ReadPermissions"

$Rights= [System.Security.AccessControl.FileSystemRights]::Read `
-bor [System.Security.AccessControl.FileSystemRights]::Write

$Inherit=[System.Security.AccessControl.InheritanceFlags]::ContainerInherit `
        -bor [System.Security.AccessControl.InheritanceFlags]::ObjectInherit
$Prop=[System.Security.AccessControl.PropagationFlags]::InheritOnly

# set AccessControlType : Allow / Deny
$Access=[System.Security.AccessControl.AccessControlType]::Allow
# create new access rule
$AccessRule = new-object System.Security.AccessControl.FileSystemAccessRule `
("testac",$Rights,$Inherit,$Prop,$Access)
# validate access rule
$Sid = $AccessRule.IdentityReference.Translate`
([System.Security.Principal.securityidentifier])
$ACL=get-acl D:\msh\tmp
$ACL.AddAccessRule($AccessRule)
set-acl -AclObject $ACL -Path D:\msh\tmp

$ACL=get-acl D:\msh\tmp
$ACL.SetAccessRuleProtection(
           # changes from parent won't propagate
           $true,
           # do not keep current inheritance settings
           $false );
set-acl -AclObject $ACL -Path D:\msh\tmp

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/16/2006 10:44:00 AM  3 comments

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Tags: msh    monad

# posted by Anonymous : 1/13/2006 04:51:00 PM  0 comments

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• EInfo:  Provides field index term counts, last update, and available links for each database.
• ESearch:  Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user's environment.
• EPost:  Posts a file containing a list of primary IDs for future use in the user's environment to use with subsequent search strategies.
• ESummary: Retrieves document summaries from a list of primary IDs or from the user's environment.
• EFetch:  Retrieves records in the requested format from a list of one or more primary IDs or from the user's environment.
• ELink:  Checks for the existence of an external or Related Articles link from a list of one or more primary IDs.  Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles;  creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.
• EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
• ESpell: Retrieves spelling suggestions.

set-alias installutil $env:windir\Microsoft.NET\Framework\v2.0.50727\installutil
installutil EntrezSnapin.dll

get-mshsnapin -reg
add-mshsnapin EntrezSnapin

using System;
using System.ComponentModel;
using System.Management.Automation;
using System.Collections;
namespace Entrez
{
    /// <summary> This class defines the properties of a snapin</summary>
    [RunInstaller(true)]
    public class EntrezSnapin : MshSnapIn
    {
        /// <summary>Creates an instance of DemonSnapin class.</summary>
        public EntrezSnapin() : base()
        {
        }
        ///<summary>The snapin name which is used for registration</summary>
        public override string Name
        { get
            { return "EntrezSnapin";
            }
        }
        /// <summary>Gets vendor of the snapin.</summary>
        public override string Vendor
        { get
            { return "http://mshforfun.blogspot.com";
            }
        }
        /// <summary>Gets description of the snapin. </summary>
        public override string Description
        { get
            { return "Cmdlets to build your own NCBI Entrez Data pipeline";
            }
        }       
    }
    /// <summary>
    /// Submit search to entrez database and return results IDs
    /// </summary>
    [Cmdlet("search", "entrez", SupportsShouldProcess = true)]
    public class SearchEntrezCmd : Cmdlet
    {
        #region Parameters
        private string db="pubmed";
        /// <summary>Entrez Database</summary>
        [Parameter(Mandatory=true, Position=0)]
        public string Database
        {
            get { return db; }
            set { db = value; }
        }
        private string term;
        /// <summary>search terms or phrases with or without Boolean operators</summary>
        [Parameter(Mandatory = true, Position = 1)]
        public string Keywords
        {
            get { return term; }
            set { term = value; }
        }
        private string retmax = "50";
        /// <summary>Maximum number of records to return</summary>
        [Parameter(Position = 2)]
        public string MaxRecord
        {
            get { return retmax; }
            set { retmax = value; }
        }
        private string email = "";
        /// <summary>To identify your search results history on server</summary>
        [Parameter(Position = 3)]
        public string Email
        {
            get { return email; }
            set { email = value; }
        }
        private string field = "";
        /// <summary>specific search field for pubmed database</summary>
        [Parameter(Position = 4)]
        public string Field
        {
            get { return field; }
            set { field = value; }
        }
        private string reldate = "";
        /// <summary>Limit items a number of days immediately preceding today's date</summary>
        [Parameter(Position = 5)]
        public string RelativeDate
        {
            get { return reldate; }
            set { reldate = value; }
        }
        private string mindate = "";
        /// <summary>Lower bounded of two specific dates</summary>
        [Parameter(Position = 6)]
        public string MinimumDate
        {
            get { return mindate; }
            set { mindate = value; }
        }
        private string maxdate = "";
        /// <summary>Lower bounded of two specific dates</summary>
        [Parameter(Position = 7)]
        public string MaximumDate
        {
            get { return maxdate; }
            set { maxdate = value; }
        }
        private string datetype = "";
        /// <summary>Limit dates to a specific date field based on database</summary>
        [Parameter(Position = 8)]
        public string DateType
        {
            get { return datetype; }
            set { datetype = value; }
        }
        #endregion

        private string usehistory = "y";
        private string tool = "Monad_Entrez_Client";
        private string retstart = "0";
        private string rettype = "uilist";
        private string sort = "";
        /// <summary>
        /// Communicating purpose only
        /// </summary>
        protected override void BeginProcessing()
        {
            WriteVerbose("Searching Entrez database...\r\nDatabase: " + db + "\r\nKeywords: " + term);
        }
        /// <summary>
        /// Get Entrez search results
        /// </summary>
        protected override void ProcessRecord()
        {
            if (ShouldProcess("Searching Entrez database...\r\nDatabase: " + db + "\r\nKeywords: " + term))
            {
                try
                {
                    WriteVerbose("Creating Entrez WebService...");
                    eUtils.eUtilsService serv = new eUtils.eUtilsService();
                    WriteDebug("WebService:" + serv.ToString());
                    WriteVerbose("Submit search...");
                    // call NCBI ESearch utility
                    // NOTE: search term should be URL encoded
                    eUtils.eSearchResultType Search_Results = serv.run_eSearch_MS(db, term, "", "", usehistory, tool, email, field, reldate, mindate, maxdate, datetype, retstart, retmax, rettype, sort );
                    WriteDebug("Search Results:" + Search_Results.ToString());
                    if (Search_Results.ERROR != null)
                    {
                        ThrowTerminatingError(new ErrorRecord(new Exception("web service method error"), "eUtils.run_eSearch_MS", ErrorCategory.InvalidResult, Search_Results));
                    }
                    WriteVerbose("Number of results item found:" + Search_Results.Count);
                    WriteVerbose("Getting results summary...");
                    // call NCBI ESummary utility
                    // NOTE: search term should be URL encoded
                    eUtils.eSummaryResultType Summary_Results = serv.run_eSummary_MS( db, "", Search_Results.WebEnv, Search_Results.QueryKey, Search_Results.RetStart, Search_Results.RetMax,  tool, email );
                    WriteDebug("Results summary:" + Summary_Results.ToString());
                    if (Summary_Results.ERROR != null)
                    {
                        ThrowTerminatingError(new ErrorRecord(new Exception("web service method error"), "eUtils.run_eSummary_MS", ErrorCategory.InvalidResult, Summary_Results));
                    }
                    WriteVerbose("Number of item retrieved:" + Summary_Results.DocSum.Length);
                    WriteVerbose("Write results to pipline...");
                    // results output
                    WriteObject(Summary_Results);
                }
                catch (Exception e)
                {
                    ThrowTerminatingError(new ErrorRecord(e, "eUtils", ErrorCategory.ResourceUnavailable, db+term));
                }
            }
        }
    }
}

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/12/2006 10:35:00 PM  0 comments

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Quote from /\/\o\/\/ blog entry Hosting Iron python in MSH: "Nice thing about Monad that it's easy to host other Languages inline." Well, since /\/\o\/\/ did VB.net, Monad team blog did C# and those japanese guy did python. I would like to something a biologist should do: Hosting R Environment in MSH.

R is an integrated suite of software facilities for data manipulation, calculation and graphical display. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. R language is an interpreted computer language derived from S language. Scientist use R mostly as a statistical analysis tool. You can download a copy of R from R-project home page (under GNU license).

My last project involve R is a gene expression profile analysis from microarray experiment two years ago. If you were a computer geek, it will take you less than 30min to learn to use R environment because it is object-oriented and synax similar to C.

Monad can can interact with other program using COM-based technologies. For example:
1. From /\/\o\/\/ blog: Monad Really Does Rock
2. From Monad team blog: Check spelling script

In order to use R language interpreter in MSH, we need another R addon: R-DCOM, which works with Rproxy.dll (in the R distribution) and R.dll to support transfer of data to and from R and remote execution of R commands, as well as embedding of an R graphics window.

After insatll R and r-DCOM, we can enjoy the power of R under MSH prompt:

# Create a new com object for R

$RCom = new-object -com StatConnectorSrv.StatConnector

# Call Init method to load R environment

$RCom.Init("R")

# Check out available methods

$Rcom |gm

TypeName: System.__ComObject#{18c8b660-81a2-11d3-9254-00e09812f727}

Name MemberType Definition
---- ---------- ----------
AddGraphicsDevice Method void AddGraphicsDevice (string, ISGFX)
Close Method void Close ()
Evaluate Method Variant Evaluate (string)
EvaluateNoReturn Method void EvaluateNoReturn (string)
GetConnectorInformation Method string GetConnectorInformation (Informa...
GetErrorId Method int GetErrorId ()
GetErrorText Method string GetErrorText ()
GetInterpreterInformation Method string GetInterpreterInformation (Infor...
GetServerInformation Method string GetServerInformation (Informatio...
GetSupportedTypes Method void GetSupportedTypes (int)
GetSymbol Method Variant GetSymbol (string)
Init Method void Init (string)
RemoveGraphicsDevice Method void RemoveGraphicsDevice (string)
SetCharacterOutputDevice Method void SetCharacterOutputDevice (IStatCon...
SetErrorDevice Method void SetErrorDevice (IStatConnectorChar...
SetSymbol Method void SetSymbol (string, Variant)
SetTracingDevice Method void SetTracingDevice (IStatConnectorCh...
SetUserInterfaceAgent Method void SetUserInterfaceAgent (IStatConnec...

# Send expression to R interpreter
# where c() is a function to assign a "vector" Variant to x
# remember R language is case senitive

$Rcom.EvaluateNoReturn ("x <- c(79.98, 80.04, 80.02, 80.04, 80.03, 80.03, 80.04, 79.97, 80.05, 80.03, 80.02, 80.00, 80.02)")
$Rcom.EvaluateNoReturn ("y <-c(80.02, 79.94, 79.98, 79.97, 79.97, 80.03, 79.95, 79.97)")

# use R graphic device to make boxplot

$Rcom.EvaluateNoReturn ("boxplot(x, y)")

# Student t test: two variant; two sided; unpaired

$Rcom.Evaluate("t.test(x, y, alternative = c(`"two.sided`"))")

3.24986738055522 #t
12.0271084945182 #delta-f
0.00693932661444795 #P-value (if less than 0.05, means statitical significant)
0.0138552637266242 #lower 95 percent confidence interval
80.0207692307692 #average of x
0 #alternative hypothesis: true difference in means is not equal to 0
two.sided
Welch Two Sample t-test
x and y
# Dispose R Environment

$Rcom.Close()

Have fun!

[Edit: Monad has now been renamed to Windows PowerShell. This script or discussion may require slight adjustments before it applies directly to newer builds.]

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/09/2006 12:39:00 AM  1 comments

Sunday, January 08, 2006

GUI version of NCBI Blastn(nr) MSH script

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An NCBI Blastn (using nr database) client MSH script with winform GUI. See NCBI Blastn under MSH command line for a introduction of NCBI Blastn program.

Although personally I like command line interface, there are always some users prefer GUI. Well, since monad can use System.Windows.Forms.form, it can create comman winform GUI which is similar to what tk/tcl can do.

One of the big advantage of monad is that script block can be used a event handler.

Another thing need to mention is that monad use grave-accent(`) but not "\" for escape sequences. To get more help on escape character using command:
help about_escape_character
Because NCBI Blast server running unix like OS, so the returning results using \n but not \r\n for a new line. We have to replace those \n with \r\n to get a proper view in textbox control.

# Blastn-GUI.msh
# ===========================================================================
#
# This code is for test purposes only. Use it at your own risk.
#
# Please do not submit or retrieve more than one request every two seconds.
#
# Results will be kept at NCBI for 24 hours. For best batch performance,
# It is recommend that you submit requests after 2000 EST (0100 GMT) and
# retrieve results before 0500 EST (1000 GMT).
#
# by tony 2006 http://mshforfun.blogspot.com/
# ===========================================================================
[void] [Reflection.Assembly]::Load( `
"System.Windows.Forms, Version=2.0.0.0, Culture=neutral, `
PublicKeyToken=b77a5c561934e089")
$script:form = new-object System.Windows.Forms.form
$Panel = new-object System.Windows.Forms.Panel
$Label = new-object System.Windows.Forms.Label
$Query = new-object System.Windows.Forms.TextBox
$Submit = new-object System.Windows.Forms.Button
$script:Results = new-object System.Windows.Forms.TextBox
$script:Status = new-object System.Windows.Forms.TextBox

function SubmitQuery([String]$Sequence)
{
 if ($Sequence -match "[^ATGCatgcNn]")
 {
    $Status.Text += "Error 1: Invalid charactors in query sequence! Only A/T/G/C/N can be used!`r`n`r`n"
    $Status.Refresh()
    $Status.ScrollToCaret()
    return
 }
 
 $Status.Text += "`r`n==================================================`r`n"
 $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Submiting sequence...`r`n"
 $Status.Refresh()
 $Status.ScrollToCaret()

 $uri="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=blastn&DATABASE=nr&QUERY=" + $Sequence
 $BlastClient = new-object System.Net.WebClient
 $pagecontent = $BlastClient.DownloadString($uri);
 if ($pagecontent -match "   RID = (.*)")
 {
   $RID=$Matches[1]
   $Status.Text += "RID =" + $RID + "`r`n"
   $Status.Refresh()
   $Status.ScrollToCaret()
  }

 if ($pagecontent -match "   RTOE = (.*)")
 {
  $TimeToComplete= $Matches[1]
  $Status.Text += "Estimated Time to finish searching: " + $TimeToComplete + " seconds`r`nWaiting...`r`n`r`n"
  $Status.Refresh()
  $Status.ScrollToCaret()
 }

 Start-sleep $TimeToComplete

 While ($true)
 {
  
   $uri= "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=" + $RID   
   $pagecontent = $BlastClient.DownloadString($uri);
   if ($pagecontent -match "Status=WAITING")
   {
    $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Search not finished yet, waiting... `r`n"
    $Status.Refresh()
    $Status.ScrollToCaret()
    Start-sleep 5
    continue
   }
   if ($pagecontent -match "Status=FAILED")
   {
     $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 2 -- Search failed!`r`n`r`n"
     $Status.Refresh()
     return
   }
   if ($pagecontent -match "Status=UNKNOWN")
   {
     $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 3-- Search expired!`r`n`r`n"
     $Status.Refresh()
     return
   }
   if ($pagecontent -match "Status=READY")
   { 
      if ($pagecontent -match "ThereAreHits=yes")
      {
         $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Search complete, retrieving results...`r`n`r`n"
     $Status.Refresh()
     $Status.ScrollToCaret()
     break
      }
      else
      {
        $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 4-- No hits found!`r`n`r`n"
    $Status.Refresh()
        return
      }
   }
   $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 5-- Unknown error! `r`n`r`n"
   $Status.Refresh()
   return
}
$uri= "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=" + $RID + "&ALIGNMENTS=500&ALIGNMENT_VIEW=QueryAnchored&FORMATOBJECT=Alignment&FORMAT_TYPE=TEXT"
$Results.Text = $BlastClient.DownloadString($uri).Replace("`n","`r`n");
return
}

$form.text = "NCBI Blastn(nr) GUI"
$form.Size =  "800,600"

$Panel.Size = "794, 32"
$Panel.Location = "0, 0"

$Label.Text = "Query:"
$Label.Location = "10, 8"
$Label.Size = "80, 32"
$Panel.Controls.Add($Label)

$Query.Location = "100, 8"
$Query.Size = "500, 20"
$Panel.Controls.Add($Query)

$Submit.Location = "710, 8"
$Submit.Text = "Submit"
$Submit.Add_Click({SubmitQuery($Query.Text)})
$Panel.Controls.Add($Submit)

$form.Controls.Add($Panel)

$Results.Location = "0, 40"
$Results.Multiline = $True
$Results.Size = "790, 400"
$Results.ScrollBars = "Vertical"
$Results.ReadOnly = $true
$form.Controls.Add($Results)

$Status.Location = "0, 440"
$Status.Multiline = $True
$Status.Size = "790, 100"
$Status.ScrollBars = "Vertical"
$Status.ReadOnly = $true
$form.Controls.Add($Status)

$form.showdialog() 

[Edit: Monad has now been renamed to Windows PowerShell. This script or discussion may require slight adjustments before it applies directly to newer builds.]

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/08/2006 01:07:00 AM  0 comments

Tuesday, January 03, 2006

Play with ACL in MSH (continued)

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/\/\o\/\/ kindly replied my blog entry “Play with ACL in MSH”. In his blog entry “Adding a Simple AccesRule to a file ACL in MSH”, he found a shortcut to create an instance of “System.Security.AccessControl.FileSystemAccessRule”. Great job! But things can get even better!

1. You want to change a accessrule but not overwrite it, so AddAccessRule() method is better than SetAccessRule() method. If you want to grant a FullControl privilege to exact same user, they are the same. What if you want to apply a more complex privilege? For example: Read + Write nut not Delete.

2. get-acl cmdlet return different object:
For a file, it will return “System.Security.AccessControl.FileSecurity”;
For a directory, it will return “System.Security.AccessControl.DirectorySecurity”.
Luckily enough, both object have AddAccessRule() and RemoveAccessRule() methods. And Even better, both methods take a “System.Security.AccessControl.FileSystemAccessRule” as parameter. So we can set Access control of a file or directory in one simple script.

# AddRemove-AccessRule.MSH
# Add or remove simple access rule to a file/directory
# using text parameters
#
# original writen by /\/\o\/\/ 2006
# http://mow001.blogspot.com
#
# modified by tony 2006
# http://mshforfun.blogspot.com
#
#Usage AddRemove-Acl FileOrDirectory (Action) user Rights (Access)
# Action: Add / Remove
# Rights: ListDirectory / ReadData / WriteData / CreateFiles /
# CreateDirectories / AppendData / ReadExtendedAttributes /
# WriteExtendedAttributes / Traverse / ExecuteFile /
# DeleteSubdirectoriesAndFiles / ReadAttributes / WriteAttributes/ Write /
# Delete / ReadPermissions / Read / ReadAndExecute / Modify /
# ChangePermissions / TakeOwnership / Synchronize / FullControl
# Access: Allow / Deny

Param (
$FileDir,
$User,
$Action = "Add",
[System.Security.AccessControl.FileSystemRights] $Rights,
[System.Security.AccessControl.AccessControlType] $Access = "Allow"
)


trap{Break}

$AccessControl = get-acl $FileDir

$AccessRule = new-object System.Security.AccessControl.FileSystemAccessRule($User,$Rights,$Access)

# check if given user is Valid, this will break function if not so.
$Sid = $AccessRule.IdentityReference.Translate([System.Security.Principal.securityidentifier])

resolve-path $FileDir

"=============================================================="
"Before changes"
$AccessControl.AccessToString

if ($Action.ToUpper() -eq "ADD") {$AccessControl.AddAccessRule($AccessRule)}
elseif ($Action.ToUpper() -eq "REMOVE") {$AccessControl.RemoveAccessRule($AccessRule)}

set-acl -aclobject $AccessControl -path $FileDir

"=============================================================="
"After " + $Action + " access rule: " + "User-"+ $User + " Rights-" + $Rights + " Access-" + $Access
(get-acl $FileDir).AccessToString

[Edit: Monad has now been renamed to Windows PowerShell. This script or discussion may require slight adjustments before it applies directly to newer builds.]

Tags: msh    monad   PowerShell

# posted by Anonymous : 1/03/2006 04:10:00 PM  0 comments

Working with SQL server in monad using pre-compiled .NET Class Library (3)

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Now the usual routine operation:

Add a plasmid
Edit a plasmid

Why there is no “Delete plasmid” operation?

Because Biologists Never, Never, Ever lose their plasmids!


1. Add following code to our PlasmidView.DLL:

namespace PlasmidView

public class SQLProvider
{
public static PlasmidFull PlasmidFull_ByPlasmidID (int plasmidid)
{… }

public static void Plasmid_Add (PlasmidFull PlasmidToAdd)
{… }
public static void Plasmid_Edit (PlasmidFull PlasmidToEdit)
{…}

public static string Enzyme_ByEnzymeID (int enzymeID)
{…}
public static string BacResistanceType_ByTypeID (int TypeID)
{…}
public static string MamResistanceType_ByTypeID (int TypeID)
{…}
public static string InsertType_ByInsertTypeID (int insertTypeID)
{…}
}
public class PlasmidFull : PlasmidCore
{…}
}

2. Get a Plasmid by PlasmidID

[void][System.Reflection.Assembly]::LoadFile("D:\MSH\PlasmidView.dll")
$Plasmid= [PlasmidView.SQLProvider]::PlasmidFull_ByPlasmidID (10)
$Plasmid

BacResistance : 1
MamResistance : 2
HasGlycerolStock : False
InsertDescription : IL-17R full length receptor
InsertLength : 2451
InsertTypeID : 1
InsertType : Human
LeftEnzymeID : 14
LeftEnzyme : BamHI
RightEnzymeID : 62
RigthEnzyme : NcoI
IsBluntLigation : False
IsSequenced : True
Comments :
FullSeq :
InsertSeq :
PlasmidID : 10
BoxID : B
BoxPosition : 1
PlasmidName : IL-17R-FL-HA
DateCreated : 10/30/2005 9:18:18 PM
UserID : 1
UserCreated : me
PlasmidType : Cytokine Receptor
PlasmidTypeID : 3
ParentPlasmidID : 9
ParentPlasmid : pCMV4 HA Neo

3. Edit this plasmid entry

$Plasmid.PlasmidName = “mouse IL-17R-FL-HA”
$Plasmid.InsertTypeID = 2
[PlasmidView.SQLProvider]::Plasmid_Edit($Plasmid)
$Plasmid= [PlasmidView.SQLProvider]::PlasmidFull_ByPlasmidID (10)
$Plasmid

BacResistance : 1
MamResistance : 2
HasGlycerolStock : False
InsertDescription : IL-17R full length receptor
InsertLength : 2451
InsertTypeID : 2
InsertType : Mouse
LeftEnzymeID : 14
LeftEnzyme : BamHI
RightEnzymeID : 62
RigthEnzyme : NcoI
IsBluntLigation : False
IsSequenced : True
Comments :
FullSeq :
InsertSeq :
PlasmidID : 10
BoxID : B
BoxPosition : 1
PlasmidName : mouse IL-17R-FL-HA
DateCreated : 10/30/2005 9:18:18 PM
UserID : 1
UserCreated : me
PlasmidType : Cytokine Receptor
PlasmidTypeID : 3
ParentPlasmidID : 9
ParentPlasmid : pCMV4 HA Neo
4. Add a plasmid entry

$Plasmid= new-object PlasmidView.PlasmidFull
$Plasmid.BacResistance = 1
$Plasmid.MamResistance = 2
$Plasmid.HasGlycerolStock = $False
$Plasmid.InsertDescription = "truncated IL-17R receptor"
$Plasmid.InsertLength = 1851
$Plasmid.InsertTypeID = 2
$Plasmid.LeftEnzymeID = 14
$Plasmid.RightEnzymeID = 62
$Plasmid.IsBluntLigation = $False
$Plasmid.IsSequenced = $True
$Plasmid.BoxID = "B"
$Plasmid.BoxPosition = 90
$Plasmid.PlasmidName = "truncated mouse IL-17R-FL-HA"
$Plasmid.DateCreated = get-date
$Plasmid.UserID = 1
$Plasmid.PlasmidTypeID = 3
$Plasmid.ParentPlasmidID = 9

$Plasmid
$Plasmid= [PlasmidView.SQLProvider]::Plasmid_Add($Plasmid)
[PlasmidView.SQLProvider]::Plasmid_All() where-object {$_.PlasmidName
-like "*truncated mouse IL-17R-FL-HA*"}

PlasmidID : 22
BoxID : B
BoxPosition : 90
PlasmidName : truncated mouse IL-17R-FL-HA
DateCreated : 1/3/2006 12:09:52 AM
UserID : 1
UserCreated : me
PlasmidType : Cytokine Receptor
PlasmidTypeID : 3
ParentPlasmidID : 9
ParentPlasmid : pCMV4 HA Neo

Conclusion:
1. One of the advantages of using monad is that it is fully integrated with .Net frameworks. Although MSH does not have class definition machinery right now, we can easily construct a customized class in C# and use it in monad.

2. Pre-compiled class library will greatly simplify monad script. Even a new user can be trained to work with fairly complex administration jobs.

3. Security should always be in mind! Expose crucial objects or methods to unauthorized user may cause disastrous effect to system.

Tags: msh    monad

# posted by Anonymous : 1/03/2006 12:23:00 AM  0 comments

Sunday, January 01, 2006

Working with SQL server in monad using pre-compiled .NET Class Library (2)

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Now we can do something fun.

1. Add following code to our PlasmidView.DLL

using System.Collections;
namespace PlasmidView
{
     public class SQLProvider
     {

// return ArrayList of “PlasmidCore” objects of all plasmid information
public static ArrayList Plasmid_All ()
{...}

// return a PlasmidCore object
public static PlasmidCore PlasmidCore_ByPlasmidID (int plasmidid)
{...}

// return User objects
public static User User_ByUserID (int userid)
{...}

// return Plasmid Type (String)
public static string PlasmidType_ByPlasmidTypeID (int plasmidTypeID)
{...}

public class PlasmidCore
{... }

public class User
{... }
}

I omit most of C# code here

2. Try to get all plasmid informtion

[void][System.Reflection.Assembly]::LoadFile("D:\MSH\PlasmidView.dll")
[PlasmidView.SQLProvider]::Plasmid_All()

PlasmidID       : 1
BoxID           : A
BoxPosition     : 1
PlasmidName     : pCMV4 Hygro
DateCreated     : 10/30/2005 8:58:24 PM
UserID          : 1
UserCreated     : me
PlasmidType     : Backbone Vector
PlasmidTypeID   : 1
ParentPlasmidID : 0
ParentPlasmid   : None

PlasmidID       : 2
BoxID           : A
BoxPosition     : 2
PlasmidName     : pCMV4 Neo
DateCreated     : 10/30/2005 9:07:16 PM
UserID          : 1
UserCreated     : me
PlasmidType     : Backbone Vector
PlasmidTypeID   : 1
ParentPlasmidID : 0
ParentPlasmid   : None
…

3. Try to search plasmid with “hygro” in their names:

[PlasmidView.SQLProvider]::Plasmid_All()  where-object {$_.PlasmidName -like “*hygro*”} foreach-object {“============”; “ID:”+ $_.PlasmidID; “Name:” + $_.PlasmidName}

============
ID:1
Name:pCMV4 Hygro
============
ID:20
Name:TAg Hygro
…

Conclusion:
1. We can easily return a group of objects to monad using ArrayList. Unlike strong typed language (for example, C#) monad detects the base object of each Item in ArrayList. You do NOT have to cast each ArrayList Item to its original base object (PlasmidView.PlasmidCore) when quoting them in a pipline.

2. When database is small, using where-object cmdlet to do search is a good idea. Actually I even forgot I had a Plasmid_Search( ) method in my original C# code. But when database grew bigger, better use a Search function to return limited number of objects only from search results.

Tags: msh    monad

# posted by Anonymous : 1/01/2006 09:28:00 PM  0 comments