EMBL-EBI Web Services

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====== C# ======

===== Introduction =====

C# is the primary programming language of the .NET framework. See our [[..:dot_net|.NET tutorial]] for an overview of the features of the .NET platform and the development environments.

In this tutorial we look at how to use the [[:|EBI Web Services]] with C# in the [[..:dot_net#microsoft_.net_sdk|Microsoft .NET SDK]] and [[..:dot_net#mono|Mono]] development environments.

===== Microsoft .NET SDK and Mono =====

==== Create Service Stubs ====

From the service WSDL (e.g. http://www.ebi.ac.uk/ws/services/WSDbfetch?wsdl) generate stub classes using the ''wsdl'' tool:
<code>wsdl "http://www.ebi.ac.uk/ws/services/WSDbfetch?wsdl"</code>

==== Use Service ====

Then in the program create an instance of the service object:
<code csharp>WSDBFetchServerService Dbfetch = new WSDBFetchServerService();</code>

This object provides methods corresponding to those defined in the WSDL so to call the ''fetchData'' method of the [[services:dbfetch|WSDbfetch]] service we can use:
<code csharp>string result = Dbfetch.fetchData("UNIPROT:ADH1A_HUMAN", "default", "raw");</code>

The ''fetchData'' method returns a string containing the requested database entry, which can be output with:
<code csharp>Console.Write(result);</code>

==== Compile Program ====

Once the program has been completed, it need to be compiled. This is slightly different depending on the chosen environment. Assuming the program is in a file called ''wsdbfetch.cs'':

=== Microsoft .NET SDK ===

<code>csc wsdbfetch.cs WSDBFetchServerService.cs</code>

=== Mono ===

<code csh>mcs wsdbfetch.cs WSDBFetchServerService.cs -r:System.Web.Services</code>

==== Run the Program ====

The resulting ''.exe.'' file can be run as follows:

MS Windows, assuming the .NET runtime is installed:
<code>wsdbfetch.exe</code>

Non-Windows Mono environments:
<code csh>mono wsdbfetch.exe</code>

Note: some non-Windows environments (e.g. Linux) can be configured to support direct execution of .NET programs, allowing the use of the Windows style method.

==== Using Data Structures ====

The methods in the [[:services:dbfetch|WSDbfetch service]] all use simple string parameters. Many of the other EBI services use more complex input structures. For example [[:services:archive:pfa:WSInterProScan]] requires a structure containing the various parameters and the input sequence to be passed to the ''runInterProScan'' method:

<code csharp>
// The input parameters
inputParams input = new inputParams();
// Set the required parameters
input.email = "your@email"; // User e-mail address
input.async = true; // Async submission
input.seqtype = "p"; // Protein input sequence
input.crc = true; // Use IprMatches lookup
// The input data
data[] content = new data[1];
content[0] = new data();
// Input type
content[0].type = "seqeunce";
// Input data
content[0].content = @">Q8E5Q5_STRA3
MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI
VAQIVQIVFPVIPGGVTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLF
MDQKTFDKYESKLETSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPI
SIIGYSYLWIYGGDILKNFLN";
// Submit the job
WSInterProScanService InterProScan = new WSInterProScanService(); 
string jobId = InterProScan.runInterProScan(input, content);
Console.WriteLine(jobId);
</code>

The ''runInterProScan'' method returns a job identifier which can be used with the ''checkStatus'' method to get the status of the job (e.g. ''RUNNING'', ''DONE'' or ''ERROR'') and the ''poll'' method to get the results of the job.

<code csharp>
string status = "PENDING";
// Check status and wait if not finished
while(status == "RUNNING" || status == "PENDING") {
  status = InterProScan.getStatus(jobId);
  Console.WriteLine(status);
  if(status == "RUNNING" || status == "PENDING") {
    // Wait before polling again.
    System.Threading.Thread.Sleep(15000);
  }
}
// Get results
Byte[] res = InterProScan.poll(jobId, "toolraw");
// Convert result into a string for output
System.Text.ASCIIEncoding enc = new System.Text.ASCIIEncoding();
string tempStr = enc.GetString(res);


// Output the result
Console.Write(tempStr);
</code>

===== Sample Clients =====

Most SOAP Web Services at [[http://www.ebi.ac.uk/|EMBL-EBI]] have sample clients which provide command-line access to the service and example code. For .NET most of the clients are implemented in C#, for example:

==== Document/literal SOAP ====

^ Service ^ Sample client ^
| [[:services:EB-eye]] | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/bin/EBeyeCliClient.exe|EBeyeCliClient.exe]]'';\\ Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/EBeyeClient.cs|EBeyeClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EBeyeCliClient/EBeyeCliClient.cs|EBeyeCliClient.cs]]'' |
| [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/bin/IPRScanCliClient.exe|IPRScanCliClient.exe]]'';\\ Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/AbstractWsClient.cs|AbstractWsClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/IPRScanClient.cs|IPRScanClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/IPRScanCliClient/IPRScanCliClient.cs|IPRScanCliClient.cs]]'' |
| [[:services:sss:NCBI BLAST (SOAP)]] | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/bin/NcbiBlastCliClient.exe|NcbiBlastCliClient.exe]]'';\\ Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/AbstractWsClient.cs|AbstractWsClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/NcbiBlastClient.cs|NcbiBlastClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/NcbiBlastCliClient/NcbiBlastCliClient.cs|NcbiBlastCliClient.cs]]'' |
| [[:services:dbfetch|WSDbfetch (SOAP)]] | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/bin/WSDbfetchCliClient.exe|WSDbfetchCliClient.exe]]'';\\ Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/WSDbfetchClient.cs|WSDbfetchClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/WSDbfetchCliClient/WSDbfetchCliClient.cs|WSDbfetchCliClient.cs]]'' |

==== RPC/encoded SOAP ====

^ Service ^ Sample client ^
| [[:services:dbfetch|WSDbfetch (SOAP)]] | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/bin/wsdbfetch.exe|wsdbfetch.exe]]'';\\ Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/src/wsdbfetch.cs|wsdbfetch.cs]]'' |
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