I haven't tested this, but this is what I'm suggesting. New part is colored blue.

XData BPL [ XMLNamespace = "http://www.intersystems.com/bpl" ]
{
<process language='objectscript' request='CUH.Mess.DCIQ.JsonIn' response='CUH.Mess.DCIQ.JsonOut' height='3400' width='2000' >
<context>
<property name='JsonObjectIn' type='CUH.Mess.DCIQ.JsonInObj' instantiate='1' />
<property name='HL7QRY' type='EnsLib.HL7.Message' instantiate='0' />
<property name='HL7ADR' type='EnsLib.HL7.Message' instantiate='0' />
<property name='JsonObjectOut' type='CUH.Mess.DCIQ.JsonOutObj' instantiate='1' />
<property name='RequestNumber' type='%String' initialexpression='""' instantiate='0' >
<parameters>
<parameter name='MAXLEN'  value='50' />
</parameters>
</property>
<property name='IsInteger' type='%Boolean' instantiate='0' />
<property name='ProcError' type='%String' initialexpression='""' instantiate='0' >
<annotation><![CDATA[Error message to be sent back in the Response.]]></annotation>
<parameters>
<parameter name='MAXLEN'  value='50' />
</parameters>
</property>
<property name='ValidOriginUrl' type='%String' instantiate='0' >
<parameters>
<parameter name='MAXLEN'  value='100' />
</parameters>
</property>
<property name='ValidContactType' type='%String' instantiate='0' >
<parameters>
<parameter name='MAXLEN'  value='50' />
</parameters>
</property>
<property name='ValidIDNumberType' type='%String' initialexpression='""' instantiate='0' >
<parameters>
<parameter name='MAXLEN'  value='50' />
</parameters>
</property>
<property name='ValidNHSCodeType' type='%String' initialexpression='""' instantiate='0' >
<parameters>
<parameter name='MAXLEN'  value='50' />
</parameters>
</property>
</context>
<sequence xend='200' yend='3500' >
<scope xpos='200' ypos='250' xend='200' yend='2850' >
<annotation><![CDATA[Handles all errors]]></annotation>
<code name='Initialize JSON request' xpos='200' ypos='350' >
<![CDATA[ set context.JsonObjectIn = ##class(CUH.Mess.DCIQ.JsonInObj).%New()
 do context.JsonObjectIn.%JSONImport(request.bodyJson)]]>
</code>
<if name='Is "data" an array?' condition='context.JsonObjectIn.data.%IsA("%DynamicArray")' xpos='200' ypos='450' xend='200' yend='700' >
<true>
<assign name="Make &quot;data&quot; a %DynamicObject" property="context.JsonObjectIn.data" value="context.JsonObjectIn.data.%Pop()" action="set" xpos='335' ypos='600' />
</true>
</if>
<assign name="Valid URL" property="context.ValidOriginUrl" value="##class(Ens.Util.FunctionSet).Lookup(&quot;CUH.DCIQToEpic.OriginUrl&quot;,$NAMESPACE,&quot;&quot;,3)" action="set" languageOverride="" xpos='200' ypos='800' >
<annotation><![CDATA[Environment specific]]></annotation>
</assign>
<assign name="Valid ContactType" property="context.ValidContactType" value="##class(Ens.Util.FunctionSet).Lookup(&quot;CUH.DCIQToEpic.ContactType&quot;,$NAMESPACE,&quot;&quot;,3)" action="set" languageOverride="" xpos='200' ypos='900' >
<annotation><![CDATA[Environment specific]]></annotation>
</assign>
<assign name="Valid IDNumberType" property="context.ValidIDNumberType" value="##class(Ens.Util.FunctionSet).Lookup(&quot;CUH.DCIQToEpic.IDNumberType&quot;,$NAMESPACE,&quot;&quot;,3)" action="set" languageOverride="" xpos='200' ypos='1000' >
<annotation><![CDATA[Environment specific]]></annotation>
</assign>
<assign name="Valid NHSCodeType" property="context.ValidNHSCodeType" value="##class(Ens.Util.FunctionSet).Lookup(&quot;CUH.DCIQToEpic.NHSCodeType&quot;,$NAMESPACE,&quot;&quot;,3)" action="set" languageOverride="" xpos='200' ypos='1100' >
<annotation><![CDATA[Environment specific]]></annotation>
</assign>
<if name='Check OriginUrl' condition='context.JsonObjectIn.meta."origin_url"=context.ValidOriginUrl' xpos='200' ypos='1200' xend='200' yend='2600' >
<true>
<if name='Check Contact Type' condition='(context.JsonObjectIn.data."0"."con_type"=context.ValidContactType)||(context.JsonObjectIn.data."con_type"=context.ValidContactType)' xpos='470' ypos='1350' xend='470' yend='2500' >
<true>
<if name='Check idNumber Type' condition='(context.JsonObjectIn.data.idNumbers.GetAt(1).type)=context.ValidIDNumberType' xpos='740' ypos='1500' xend='740' yend='2400' >
<true>
<assign name="Get Request Number" property="context.RequestNumber" value="context.JsonObjectIn.data.idNumbers.GetAt(1).number" action="set" languageOverride="" xpos='1010' ypos='1650' />
<code name='Integer pattern' xpos='1010' ypos='1750' >
<![CDATA[ set context.IsInteger = ((context.RequestNumber)?.N)]]>
</code>
<if name='Integer?' condition='context.IsInteger' xpos='1010' ypos='1850' xend='1010' yend='2300' >
<annotation><![CDATA[Checks if Requested Number sent is an Integer]]></annotation>
<true>
<transform name='Create HL7 query' class='CUH.Tran.GetDCIQJsonPatientToEpicQRYQ011' source='context.JsonObjectIn' target='context.HL7QRY' xpos='1280' ypos='2000' />
<call name='Send to MPIQueryHandler' target='MPI Query Handler' async='0' xpos='1280' ypos='2100' >
<request type='EnsLib.HL7.Message' >
<assign property="callrequest" value="context.HL7QRY" action="set" languageOverride="" />
</request>
<response type='EnsLib.HL7.Message' >
<assign property="context.HL7ADR" value="callresponse" action="set" languageOverride="" />
</response>
</call>
<transform name='Converts HL7 to JSON' class='CUH.Tran.EpicADRA19ToDCIQJsonPatient' source='context.HL7ADR' target='context.JsonObjectOut' xpos='1280' ypos='2200' />
</true>
<false>
<assign name="Error No Number" property="context.ProcError" value="&quot;MRN needs to be a positive numeric value&quot;" action="set" languageOverride="" xpos='1010' ypos='2000' />
</false>
</if>
</true>
<false>
<assign name="Error idNumber Type" property="context.ProcError" value="&quot;Invalid idNumber Type&quot;" action="set" languageOverride="" xpos='740' ypos='1650' />
</false>
</if>
</true>
<false>
<assign name="Error Contact Type" property="context.ProcError" value="&quot;Invalid Patient Contact Type&quot;" action="set" languageOverride="" xpos='470' ypos='1500' />
</false>
</if>
</true>
<false>
<assign name="Error Origin Url" property="context.ProcError" value="&quot;Origin URL not authorized!&quot;" action="set" languageOverride="" xpos='200' ypos='1350' />
</false>
</if>
<faulthandlers>
<catchall xpos='200' ypos='2700' xend='200' yend='350' >
<assign property="context.ProcError" value="&quot;Error in the Json/HL7 conversion/transformation block&quot;" action="set" languageOverride="" xpos='200' ypos='250' />
</catchall>
</faulthandlers>
</scope>
<assign name="Assign Error to Response" property="context.JsonObjectOut.errors" value="context.ProcError" action="set" languageOverride="" xpos='200' ypos='2950' />
<if condition='context.JsonObjectOut.errors&apos;=""' xpos='200' ypos='3050' xend='200' yend='3400' >
<annotation><![CDATA[Check if any errors]]></annotation>
<true>
<trace name='Log the Error' value='context.JsonObjectOut.errors' xpos='470' ypos='3200' />
<assign name="Returns {}" property="response.bodyJson" value="&quot;{}&quot;" action="set" languageOverride="" xpos='470' ypos='3300' />
</true>
<false>
<code name='Returns Valid Response' xpos='200' ypos='3200' >
<![CDATA[ set temp = ##class(CUH.Mess.DCIQ.JsonOut).%New()
 do context.JsonObjectOut.%JSONExportToString(.temp)
 set response.bodyJson = temp]]>
</code>
</false>
</if>
</sequence>
</process>
}

Right before this statement:

<assign name="Valid URL" property="context.ValidOriginUrl" value="##class(Ens.Util.FunctionSet).Lookup(&quot;CUH.DCIQToEpic.OriginUrl&quot;,$NAMESPACE,&quot;&quot;,3)" action="set" xpos='200' ypos='450' >

One thing you could do:
At the top of your BPL, add an <if> checking if "data" is an array or an object:

if context.JsonObjectIn.data.%IsA("%DynamicArray")

If it is, then use an assign to set context.JsonObjectIn.data to the last element of the array (%Pop() returns the last element of an array):

set context.JsonObjectIn.data = context.JsonObjectIn.data.%Pop()

After doing this, the rest of the actions should work the same for either input.

Note that this assumes that when "data" is an array that the array only has one item in it. If it can have multiple items then you'll need to add logic to choose the correct item.

Can you give some more information about what's happening? Is it returning an error? Does the JSON string look right in the trace log?

In the message trace for the whole process, what is the value of DocType in the Body tab?

Check the settings on your inbound HL7 service and make sure that Message Schema Category is set to your custom schema (ADT_ALL).

And in the Developer Tools "Network" tab, do any of the requests return HTTP codes other than 200?

In Developer Tools, can you try the "Disable Cache" option and then reload the page?

This screenshot is from Firefox, but Chrome also has this option in the Network tab.

Are you doing this in ObjectScript or in a DTL?

You can use GetColumnCount, use a for loop to iterate through the column numbers, and request the data for each column using GetData, or get the column name using GetColumnName.

This is just how the message viewer displays it. But is the message complete when the business operation writes it to the file?

Try changing Batch Handling to "Whole Batch".

Good question. In OAuth the response will include the expiration time, so that's what I was expecting here.

If the response doesn't include an expiration time does the vendor's documentation say anything about if tokens can be used for more than 1 request and if so how long it's valid for? If you know it's supposed to be valid for 60 minutes then you could just log the time when you requested the token and use that to track it.

It doesn't look like OAuth. If it were, the payload should include a grant_type and username is called "username" rather than "email":

https://www.oauth.com/oauth2-servers/access-tokens/password-grant/
https://www.oauth.com/oauth2-servers/access-tokens/client-credentials/

There could be non-OAuth token-based authentication methods. I expect the %SYS.OAuth stuff won't work for something non-OAuth.

What does the payload look like that you have to send in order to get a token? We can see if it looks like OAuth or not.

OnInit() only gets called when starting the operation.

If your tokens have an expiration time then you need to check if the token is expired on each call and fetch a new one if needed. You can just store the token and expiration time in properties and check them on each call.

I would start by checking if some other process is already using port 5000 (or whatever port JavaGateway is trying to run on). It would also be good to check the JavaGateway

Since you're on Linux you can check this with netstat:

netstat --listening --numeric-ports