PowerShell Remoting Project Home

Thursday, January 12, 2006

Author a Monad Cmdlet as Web Service Client

Steps to author a cmdlet, Search-Entrez, which works as NCBI eUtils web service client to build your own Entrez data pipeline.

For those who don't use Entrez:  Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. If you were a biologist, you probably use Entrez everyday. The graphic below for a breif view of Entrez integration.

Usually general user will access Entrez by its web form interface. For data mining NCBI made a utility called: eUtils, which provide a URL tool as well as a SOAP interface. The URL tool requires to construct a customized search URL and returns results as XML. To save some time,  I decided to use  SOAP  interface (version 1.3a). More help on eUtils utility can be found here.  Information about SOAP interface can be  find here.

eUtils have contain several tools :  We will use ESearch and ESummary this time. Now let's start:
1. Create a "Class Libaray" in Visual C# Express.
2. Project -> Add Reference -> System.Management.Automation
3. Project -> Add Web Reference ->
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils_lite.wsdl (without EFech tool) -> Go -> Change Web Refernece name to "eUtils"
4. Create new class derived from MshSnapin object.
5. Create new class derived from Cmdlet object.
6. Build project to EntrezSnapin.dll.
7. Install mshsnapin using .NET SDK installutils.exe tool.
set-alias installutil $env:windir\Microsoft.NET\Framework\v2.0.50727\installutil
installutil EntrezSnapin.dll
8. Load mshsnapin using add-mshsnapin cmdlet
get-mshsnapin -reg
add-mshsnapin EntrezSnapin
9. Now you can enjoy powerful Entrez search tool under msh prompt.
C# Code:
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));
                }
            }
        }
    }
}


[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:       


Comments:
Oes Tsetnoc one of the ways in which we can learn seo besides Mengembalikan Jati Diri Bangsa. By participating in the Oes Tsetnoc or Mengembalikan Jati Diri Bangsa we can improve our seo skills. To find more information about Oest Tsetnoc please visit my Oes Tsetnoc pages. And to find more information about Mengembalikan Jati Diri Bangsa please visit my Mengembalikan Jati Diri Bangsa pages. Thank you So much.
Oes Tsetnoc | Semangat Mengembalikan Jati Diri Bangsa
 

Post a Comment



Links to this post:

Create a Link



<< Home