oru2xds 2.0.0

Receive HL7 messages and send them to an XDS.b repository

ORU2XDS

oru2xds allows you to receive an HL7 v2.x message in ER7 format, with MLLP transport, into an IHE XDS.b Provide and Register Document Set-b [ITI-41] transaction, as actor Document Source, which is sent to an XDS repository as a properly formatted SOAP message over HTTP. The result of the operation is then used to build an HL7 v2.x ACK^R01 acknowledge message back to the source.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

You should have some modules available to python3, in order to run oru2xds. Required Python modules are hl7, striprtf, lxml, uuid, requests and requests-toolbelt.

Installing

$ sudo apt install python3-pip
$ pip3 install lxml
$ pip3 install aiorun
$ pip3 install -U hl7
$ pip3 install striprtf
$ pip3 install requests
$ pip3 install requests-toolbelt

Download oru2xds converter files

TODO: ...

Install XDS toolkit for testing purposes (optional)

Run XDS Toolkit in a docker container Folow https://hub.docker.com/r/antocm/xdstools

$ docker pull antocm/xdstools774
$ docker image ls

Now you have XDS toolkit installed as a docker image running in http://localhost>:8080/xdstools4/

XDS Toolkit config password: easy Tomcat UI username/password: admin/admin

You can now run the XDS toolkit with:

$ docker run -it -p 8080:8080 -p 8888:8888 -p 8443:8443 -v $PWD/cache:/tmp/xdstoolkit-cache antocm/xdstools774

And stop it with:

$ docker stop $(docker ps -q --filter ancestor=antocm/xdstools774)

If you want to restart it, you can just docker start docker ps -q -l # restart it in the background docker attach docker ps -q -l # reattach the terminal & stdin

To list images use $ docker image ls To list running containers use $docker ps

Preparations for a test conversion

• a XDS toolkit should be available. Open a browser in http://localhost:8080/xdstools4/
• Go to "Toolkit configuration" on the left toolbar.
• Type the admin password "easy".
• Check the "External cache" to be /tmp/xdstoolkit-cache which should be now mapped to the directory "cache" of your current directory.
• Check the Toolkit Port to be 8080, as defined above.
• Close the "ToolkitConf" tab.
• Go to "Simulators" on the left toolbar.
• Select actor type and select "Document Repository/Registry", Simulator ID "1" and press "Create Actor Simulator".
• Select the row with ID "Default__1" and press the "Edit" button below.
• Confirm that PnR endpoint is http://localhost:8080/xdstools4/sim/default__1/rep/prb
• Close the "SimConfig default__1" tab.
• Close the "SimCntl" tab.
• Go to "Manage Patient IDs" on the left toolbar.
• In the "Favorite Patient IDs" list, select the patient "IHEBLUE-2709^^^&1.3.6.1.4.1.21367.13.20.3000&ISO"
• From the "Generate V2 Patient Identity Feed", make sure that "Patient ID to send" is "Selection in Favorites"
• From the SAML dropdown list, select "SAML OFF"
• From the "Send to"Document Registry:", select "default__1"
• Press "Run" to issue a patient identity feed
• You are ready to perform an initial test.

Running a test conversion

From the working directory where you have downloaded the oru2xds converter:

$ ./oru2xds.py

Open another terminal window, and send an HL7 test message to the configured HL7 listening port

$ ~/.local/bin/mllp_send -p 2575 -f tests/sample1-ORU-R01.hl7 --loose localhost

Look at the HL7 ACK response message,

Examine the resulting logs

Log files are placed in the log directory. oru2xds-<DATE>.log - general logs cda/ - folder with the generated HL7 CDA document xds_requests/ - folder with the generated XDS Provide and Register Document Set-b requests soap/ - folder with the generated SOAP requests and responses

Depending on the configuration set on config.py, for the variables

    LOG_XDS_REQUEST_TOFILE = True/False
    LOG_SOAP_ENVELOPE_TOFILE = True/False
    LOG_SOAP_RESPONSE_TOFILE = True/False

you may define if those files are generated or not.

Configurations

oru2xds general configurations

General configuration for the oru2xds is located in the file config.py. You may edit the file to suit your needs. Mapping between HL7 v2.x ORU message

• CDA metadata is placed in the file hl7_cda.py
• XDS metadata is placed in the file ihe_xds.py.

All metadata configuration must be done in the section below the marker.

HL7 CDA Metadata configurations

Metadata should be according to the Implementation Guide for CDA Release 2: Implementation Guide for CDA Release 2: Imaging Integration Levels 1, 2, and 3 Basic Imaging Reports in CDA and DICOM Diagnostic Imaging Reports (DIR) – Universal Realm CDAR2_II_BIMGRPTS_R1_INF_2009MAR.pdf

Configuring the mapping of the fields is tricky. It should be done inside the Python scripts, setting the values of the properties of the class .

Open the hl7_cda.py and look for the placeholder '################################################################### '## Main configuration '###################################################################

All the configuration should be done before the placeholder shows up:

'################################################################### '## End of Main configuration '###################################################################

they must be inserted programatically under each metadata field structure, as sampled there.

self.m_author = {
			"time": hl7message['OBR.F22'],
			"id_extension": hl7message['OBR.F32.R1.C1.S1'],
			"id_root": "1.3.6.1.4.1.55196.1.3.2.4",
			"assignedAuthorAssignedPersonName": hl7message['OBR.F32.R1.C1.S2'],
			"assignedAuthorRepresentedOrganizationIdRoot": "1.3.6.1.4.1.55196.1.3",
			"assignedAuthorRepresentedOrganizationName": "Example hospital - Radiology department"
		}

XDS Metadata configurations

Configuring the mapping of the fields is tricky. It should be done inside the Python scripts, setting the values of the properties of the class .

Open the ihe_xds.py and look for the placeholder '################################################################### '## Main configuration '###################################################################

All the configuration should be done before the placeholder shows up:

'################################################################### '## End of Main configuration '###################################################################

they must be inserted programatically under each metadata field structure, as sampled there.

For example, the m_DocumentEntry_author is built as:

	m_DocumentEntry_author = [[
		{
			"authorvalue": [hl7message['OBR.F32.R1.C1.S2']],
			"authorrole": "authorPerson",
		},
		{
			"authorvalue": ["Example hospital - Radiology department"],
			"authorrole": "authorInstitution"
		}
	]]

The authorPerson is taken from the HL7 message as hl7message['OBR.F32.R1.C1.S2'] meaning OBR segment, field 32, component 1, sub-component 2. The authorRole is hard coded with a fixed value.

Here are the fields that are required or optional in an XDS DocumentEntry and SubmissionSet. Folder is not supported.

These are the following fields that should go into an XDS document submission request

• Metadata Element Metadata Attribute XDS DS

• DocumentEntry author R2

• DocumentEntry availabilityStatus O

• DocumentEntry classCode R

• DocumentEntry comments O

• DocumentEntry confidentialityCode R

• DocumentEntry creationTime R

• DocumentEntry entryUUID R

• DocumentEntry eventCodeList O

• DocumentEntry formatCode R

• DocumentEntry hash O

• DocumentEntry healthcareFacilityTypeCode R

• DocumentEntry homeCommunityId O

• DocumentEntry languageCode R

• DocumentEntry legalAuthenticator O

• DocumentEntry limitedMetadata X

• DocumentEntry mimeType R

• DocumentEntry objectType R

• DocumentEntry patientId R

• DocumentEntry practiceSettingCode R

• DocumentEntry referenceIdList O

• DocumentEntry repositoryUniqueId O

• DocumentEntry serviceStartTime R2

• DocumentEntry serviceStopTime R2

• DocumentEntry size O

• DocumentEntry sourcePatientId R

• DocumentEntry sourcePatientInfo O

• DocumentEntry title O

• DocumentEntry typeCode R

• DocumentEntry uniqueId R

• DocumentEntry URI O

• SubmissionSet author R2

• SubmissionSet availabilityStatus O

• SubmissionSet comments O

• SubmissionSet contentTypeCode R

• SubmissionSet entryUUID R

• SubmissionSet homeCommunityId O

• SubmissionSet intendedRecipient O

• SubmissionSet limitedMetadata X

• SubmissionSet patientId R

• SubmissionSet sourceId R

• SubmissionSet submissionTime R

• SubmissionSet title O

• SubmissionSet uniqueId R

Note: Folder is not implemented

• Folder availabilityStatus O
• Folder codeList R
• Folder comments O
• Folder entryUUID R
• Folder homeCommunityId O
• Folder lastUpdateTime O
• Folder limitedMetadata X
• Folder patientId R
• Folder title R
• Folder uniqueId R

Built With

• lxml - All XML processing
• aiorun - creates the HL7 server service
• python-hl7 - MLLP server and HL7 message parser
• striprtf - Convert RTF file to strings
• requests - HTTP send and receive
• requests-toolbelt - Multipart encoding and decoding

Contributing

Please read CONTRIBUTING.md for details on the code of conduct, and the process for submitting pull requests.

Author

• Antonio Martins - Initial work - (https://github.com/antocm)

License

This project is licensed under the GPLv3 License - see the LICENSE.md file for details

Acknowledgments

• IHE XDS.b profile and all the available documentation
• HL7 CDA Implementation Guide for CDA Release 2: Imaging Integration Levels 1, 2, and 3 Basic Imaging Reports in CDA and DICOM Diagnostic Imaging Reports (DIR) – Universal Realm CDAR2_II_BIMGRPTS_R1_INF_2009MAR.pdf