Loop over HL7 OBX fields and add the results to a database

I needed to loop over OBX segments in an HL7 message, then extract the values and write them to a database.

There are several ways of doing this, such as calling a sub-workflow, but I wanted a single-step process, so instead I just created the c# code in a Code Activity.  It's pretty straightforward.  HL7 Soup has a great API for working with HL7, and I use both Looping over segments as well as the simple to use GetValueAtPath.  API details can be found here.

Note that you can also turn this into a reusable activity following these steps.

//Bring in the assemblies that we need that are not included by default.
#r "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.7.1\System.Data.dll"

string connectionString = @"Server=xps17\sqlexpress;Database=HL7 Soup;User Id=HL7 Soup;Password=xxx;";
//Get the message template
IHL7Message message = (IHL7Message)activityInstance.Message; //Use IHL7Message for HL7 Messages and IMessage for other message types

using (System.Data.SqlClient.SqlConnection connection = new System.Data.SqlClient.SqlConnection(connectionString))
{
    //get other values not in the loop
    string patientName = message.GetValueAtPath("PID-5.2");
    
    connection.Open();
    
    //Get all OBX segments and loop over them
    IHL7Segments allSegments = message.GetSegments("OBX");
    foreach (IHL7Segment segment in allSegments)
    {
        //update your database
        using (System.Data.SqlClient.SqlCommand command = connection.CreateCommand())
        {
            string obxvalue2 = segment.GetField(2).Text; 
            string obxvalue5 = segment.GetField(5).GetComponent(1).Text;
            
            command.CommandText =$"Insert into MyTable (fieldname, fieldname2,fieldname3) values ('{patientName}','{obxvalue2}','{obxvalue5}')";
            command.ExecuteNonQuery();
       
        }
    }
    connection.Close();
}

HL7 Soup Licensing Proxy error

I was attempting to license HL7 Soup and Integration Host on a hospital network, but I was getting an error preventing the license number from activating.

The problem was that the calls went through a proxy server.

The solution was to open the .config file for each app and uncomment the section that tells the proxy server to use the default credentials.

 <system.net>

    <defaultProxy useDefaultCredentials="true">

    </defaultProxy>

  </system.net>

This isn't credentials for calling the server, just the proxy server.

Integration Host HTTP sender as code

 The HTTP Sender in HL7 Soup's Integration Host is simple to use, but doesn't expose every possible feature of HTTP messaging.  I had to retrieve response headers, and these are not provided back in the UI.

Fortunately it uses c# in the code activity, so I was able to add the following code to save the day.

 //The following code is just a indication for getting started for an Activity. Edit or delete as you wish. Use the variable workflowInstance and activityInstance to access the running states of the workflow.

using System.Net;
using System.IO;

Encoding encoding = Encoding.UTF8;
               
using (WebClient client = new WebClient())
{
    client.UseDefaultCredentials = true;
    
    client.Headers.Add("Content-Type","text/plain"); 
    
    //Add all the headers that you want.
    // client.Headers.Add("yourHeaderName", workflowInstance.GetVariable("yourVariableName"));
    
    
    byte[] data = null;
       
    //Payload for posts if you need it.
    //var payload = "";
    //if (posting the message)
    //{
    //   payload =activityInstance.Message.Text;
    //    if (payload != null)
    //     {
    //        data = encoding.GetBytes(payload);
    //    }
    //     else
    //     {
    //         data = new byte[] { };
    //     }
    // }
    
    //credentials
    client.Credentials = new NetworkCredential("","");
    
    
    
    //Get the method as a string.
    string method = "GET";
    
    string url = HTTP://url.com";
    
    //Call HTTP Service
    string result = "";
    if (method == "GET")
    {
        //Get cannot pass a payload
        using (Stream stream = client.OpenRead(url))
        {
                 using (var streamReader = new StreamReader(stream))
                {
                    result = streamReader.ReadToEnd();
                }
         }
    }
    else
    {
        //Post, Put and Delete pass a payload.
        var bytes = client.UploadData(url, method, data);
        result = encoding.GetString(bytes);
    }
    
    if ( client.ResponseHeaders!=null)
    {
        foreach (var responseHeader in client.ResponseHeaders)
        {
            //process your response headers
            //e.g.
            workflowInstance.SetVariable("MyVariable", responseHeader.ToString());
        }
    }
    
}

Processing HL7 in the Cloud

While Integration Host has long been my preferred program for processing HL7 messages I've only really used it in local settings. Being able to handle workflows in the cloud was something I've wanted to do for a while now so you can imagine my delight when I saw the announcement on their website that their program was now available as a Docker container and that they'd already published a tutorial on getting it up and running on Azure as a container instance. 

 It's stupidly easy to get going and the Azure container instance pulls directly from their Dockerhub repo so there's no mucking around with downloading and uploading files. All in all, I can see this being a popular way to use Integration Host going forward.

Change HL7 Soup Senders or Receivers to a text Encoding that is not listed

 Not all text Encodings are listed in the HL7 Soup UI.  It makes it too noisy for most users, so only the common ones are there. However, you can change it to any installed encoding via the following steps.

1. Create your sender. Set the Encoding to 8859-1 and save it.
2. Close HL7 Soup
3. Load the file in notepad C:\ProgramData\Popokey\HL7Soup\Settings\1\FunctionSettings.json
4. Search in the file for the name of your sender.
5. Change the Encoding property to your Encoding. Google "C# encodings" if you want to find the official encoding name.
6. Save the file
7. Reopen HL7 Soup.

Now, if you send with that sender, it will use your Encoding.