oru2xds 2.0.25

Description:

oru2xds 2.0.25

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. They are automatically installed by pip when satisfying the dependencies for oru2xds.
Installing
$ pip install oru2xds

If you plan to use it right now, without first testing it using xdstoolkit, proceed to the Configuration section
If you want to install and run oru2xds in a docker container, execute
$ docker pull antocm/oru2xds

Install and execute XDS toolkit for testing purposes (optional)
If you do not have a tested IHE XDS repository, or if you want to try oru2xds first against a reference implementation like xdstoolkit, here is how to do it. We will run xdstoolkit as a docker container (from https://hub.docker.com/r/antocm/xdstools)
$ docker pull antocm/xdstools:7.11.0
$ docker image ls

Now you have XDS toolkit installed as a docker image running in http://localhost:8080/xdstools7/
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/xdstools:7.11.0
And stop it with:
$ docker stop $(docker ps -q --filter ancestor=antocm/xdstools:7.11.0)
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/xdstools7/
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/xdstools7/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 oru2xds:
$ python3 oru2xds.py
Open another terminal window, and send an HL7 test message to the configured HL7 listening port
$ mllp_send -p 2575 -f examples/sample3-ORU-R01.hl7 --loose localhost
Look at the HL7 ACK response message. If it is a positive acknowledgement, everything went OK. If not, you should look into the log files for more details.
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.
Configuration
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 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

Running
When oru2xds is executed, it will run forever as a daemon service.
$ python3 /usr/local/lib/python3.10/site-packages/oru2xds/oru2xds.py
If you want to send an HL7 example report message, issue
$ mllp_send -p 2575 -f examples/sample3-ORU-R01.hl7 --loose localhost
As a docker image
If you installed the docker image, you can now execute it.
$ docker run -it --rm -p 2575:2575 antocm/oru2xds
This command will automatically execute oru2xds and waits for HL7 messages in port 2575.
If you want to send an HL7 example report message from the same container, issue:
$ docker ps
$ docker exec -it <container_id> bash
# mllp_send -p 2575 -f examples/sample3-ORU-R01.hl7 --loose localhost

In case you also want to run xdstoolkit as a docker image to provide the XDS repository, proceed as in section [Install and execute XDS toolkit for testing purposes (optional)](#Install and execute XDS toolkit for testing purposes (optional)). Then, obtain the IP address of this container using docker ps, take note of the container id, then issue docker inspect <container_id> | grep IPAddress. Take this address, then configure it in the antocm/oru2xds container dropping a shell into the container docker run -it --rm -p 2575:2575 antocm/oru2xds bash, editing the file config.py and setting the IP addres of the xdstoolkit container as the repository address in the variable SERVICE_URL. Finally, run python3 oru2xds.py. Get the container id of the antocm/oru2xds using docker ps and execute a second shell to the antocm/oru2xds container with docker exec -it <container_id> bash and finally execute the issue of an HL7 example message using mllp_send -p 2575 -f examples/sample3-ORU-R01.hl7 --loose localhost.
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

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