From Electronic Health Records to Electronic Data Capture systems
This application facilitates user-assisted automated pre-filling of eCRFs in an EDC system with clinical patient data originating from an EHR system or clinical data warehouse, thus avoiding manual error-prone re-entry. Patient records can either be read from an i2b2 data warehouse schema or via the FHIR interface of an EHR. You are welcome to write your own connectors to read from (or write to) other data sources. The EHR2EDC app requires a PostgreSQL database (for storing users, their roles and credentials) and a mongoDB database (for storing studies). The PostgreSQL database is versioned using Flyway (TM). The EHR2EDC module has connectors for and has been tested with the Medidata Rave (TM) and OpenClinica (TM) Electronic Data Capture (EDC) systems.
A large part of this code base was developed to support the pilot activities of the EIT Health EHR2EDC project. More information can be found here.
Another large part of this code base was developed for the InSite platform.
See license.txt
The relevant clinical observations made before, during or after a subject visit or the relevant clinical observations for an unscheduled event are to be recorded in a structured way (not free-text) in one or more of the EHR data sources that are integrated in your data warehouse or accessed through FHIR. The time between making a relevant clinical observation and the availability of the corresponding structured clinical observation record in the EHR data sources must be less than the expected EDC data entry timeline as communicated by the sponsor of the study for which you use these capabilities. There must be no technical constraints that prohibit the EHR data sources update daily (full or incremental). The software must be allowed to connect to the EDC system that is used by the sponsor for data entry for a given study for which you use this software. This may require adapting local firewall rules.
This application can be considered a modular monolith adopting many concepts of the Clean Architecture and relying on some DDD concepts like domain vocabulary and domain events. The EHR2EDC capabilities were implemented as new modules on an existing application (the InSite Clinical Workbench, referred to in this code base as local workbench).
The application contains the following maven modules:
- ehr2edc: core of the ehr2edc application
- infrastructure: cross-cutting application concerns
- local-workbench: generic application concerns, e.g. login, user management
- local-workbench-ehr2edc: api between ehr2edc module and local workbench module: for listing users and for retrieving the current user
- local-workbench-main: Spring boot application for running local workbench on tomcat
- local-workbench-war: packaging as a war (web archive)
- local-workbench-web: web application resources
- local-workbench-zip: deployment artifacts
You'll need Maven. Run mvn package to produce a deployable war.
This application relies on PostgreSQL for managing users and their credentials. You can point the web application to your postgres database using the following VM properties:
| VM property | Example |
|---|---|
| database.url | jdbc:postgresql://localhost/lwb |
| database.username | lwb_user |
| database.password | password |
If you start with an empty database, you can enable flyway migrations to have the tables and their initial content generated:
| VM property | Value |
|---|---|
| spring.flyway.enabled | true |
Make sure you have a mongoDB running. You can configure the connection with the following VM properties:
| VM property | Example |
|---|---|
| ehr2edc.db.mongodbquery.host | localhost |
| ehr2edc.db.mongodbquery.port | 27017 |
| ehr2edc.db.mongodbquery.database | insite |
| ehr2edc.db.mongodbquery.username | insite |
| ehr2edc.db.mongodbquery.password | password |
| ehr2edc.db.mongodbquery.authentication-database | admin |
To authenticate as a user, you must provide a username, password, and the authentication database associated with that user.
Enable mongo transactions by setting the following vm property:
| VM property | Value |
|---|---|
| ehr2edc.mongo.transactions | true |
EHR2EDC uses Spring Data MongoDB, and is configured to connect to a local Mongo in a Docker container when running locally.
Local configuration can be found at ehr2edc-infra-mongo-query.properties.
Following commands help you setup the local container, and accessing the database through the Mongo Shell. The insite database is populated by the mongo-migrator project.
- Start a local mongo container
docker run -d -p 27017-27019:27017-27019 \
-e MONGO_INITDB_ROOT_USERNAME=insite \
-e MONGO_INITDB_ROOT_PASSWORD=password \
--name ehr2edc-mongo \
mongo:3.6.12
- Open local mongo shell
docker exec -it ehr2edc-mongo \
mongo -u insite -p password --authenticationDatabase admin
Use the following command to start a mongo shell and create a replicaset on your local mongo instance:
docker exec ehr2edc-mongo mongo -u insite -p password --authenticationDatabase admin --eval "rs.initiate({_id : \"insite-mongo-set\", members: [{_id : 0, host : \"localhost:27017\"}]})"
It should print something like this: { "ok" : 1 }
Deploy the war on Apache Tomcat.
Your environment should be runnable immediately if you start tomcat with these options:
-Dspring.profiles.active=FLYWAY_MIGRATE -Dlogging.level.org.hibernate=error -Dsynchronize.studies=false -Ddatabase.url=jdbc:postgresql://localhost/lwb -D -Dspring.flyway.enabled=true -Ddatabase.username=lwb_user -Ddatabase.password=lwb_user -Ddatabase.url=jdbc:postgresql://localhost:5432/lwb -Dspring.jmx.enabled=false -Dehr2edc.mongo.transactions=true -Dehr2edc.api.admin.credentials.username=test -Dehr2edc.api.admin.credentials.password=test -Ddatawarehouse.datasource.url=jdbc:postgresql://localhost:5432/i2b2demodata -Ddatawarehouse.datasource.username=user -Ddatawarehouse.datasource.password=pass
You create a study by importing a valid ODM v1.3.2 file.
This is done by POSTing it as a multipart file to the /ehr2edc/studies endpoint, like so:
curl -X POST $HOST/ehr2edc/studies -F file=/path/to/my/odm.xml
Next, you'll want to add mappings to the study to enable prefilling the study's eCRFs with ehr data. Adding a mapping for a given item (identified by odm ItemDef OID) is done with the following REST call:
curl -X POST "$HOST"/ehr2edc/studies/"$STUDY_ID"/item-query-mappings -H "Content-Type: application/json" -d "/path/to/my/mapping.json"
For example, the json to map a patient's birth date to the I_DEMOG_AGE item in an eCRF containing the subject's current age, could look as follows:
{
"itemId": "I_DEMOG_AGE",
"query": {
"type": "demographic",
"criteria": {
"criteria": [
{
"type": "demographicType",
"demographicType": "BIRTH_DATE"
}
]
}
},
"projectors": [
{
"type": "dateOfBirth"
},
{
"type": "dateOfBirthToAge",
"unit": "YEARS"
},
{
"type": "ageToNumerical"
}
]
}
You can connect to an EHR data source by executing the following mongo update:
document=$(cat /path/to/link-ehr.json)
mongo -u $MONGO_USER -p $MONGO_PASSWORD --authenticationDatabase "${AUTH_SOURCE}" --eval "db.getCollection(\"EHRConnection\").remove({ \"studyId\": \"${EFFECTIVE_STUDY_ID}\"});" $DATABASE
mongo -u $MONGO_USER -p $MONGO_PASSWORD --authenticationDatabase "${AUTH_SOURCE}" --eval "db.getCollection(\"EHRConnection\").insert($document);" $DATABASE
where link-ehr.json looks something like:
{
"_id": "___EFFECTIVE_STUDY_ID___",
"uri": "http://hapi.fhir.org/baseDstu2",
"system": "FHIR"
}
The system property value is either MONGO (legacy mongo model as populated from i2b2 by the mongo-migrator module) or FHIR (FHIR SDTU2-compliant EHR)
If you are using a MONGO EHR connection, you can populate it from an i2b2 data warehouse by running the following command against your running application:
curl -u test:test -X POST http://localhost:8080/ehr2edc/datawarehouse
In the above command you have to pass the api administrative username and password to authorize the operation.
These correspond to the values of the ehr2edc.api.admin.credentials.username and ehr2edc.api.admin.credentials.password configuration properties.
This will start the export of patientIds in the i2b2 database to the mongo db.
The following configuration properties can be used to customize your i2b2 database connection settings:
| Configuration property | Example |
|---|---|
| datawarehouse.datasource.url | jdbc:postgresql://localhost:5432/i2b2demodata |
| datawarehouse.datasource.username | user |
| datawarehouse.datasource.password | password |
| datawarehouse.datasource.driver-class-name | org.postgresql.Driver |
You can connect to an EDC system for reading subjects, writing eCRFs or for creating subjects by executing the following REST API call:
curl -X POST $HOST/ehr2edc/edc/connection -d /path/to/my/link-edc.json -H "Content-Type: application/json"
For connecting to Medidata Rave (TM) set the edcSystem json property to RAVE. For OpenClinica (TM) set it to OPEN_CLINICA.
The connection type values for reading, writing or creating are READ_SUBJECTS, SUBMIT_EVENT, WRITE_SUBJECT respectively.
For example, the json file for connecting to a study on Rave for reading subjects could look as follows:
{
"studyId": "RAVE_STUDY_ID",
"type": "READ_SUBJECTS",
"edcSystem": "RAVE",
"externalSiteId": "MY_RAVE_SITE_ID",
"clinicalDataURI": "https://innovate.mdsol.com/RaveWebServices/studies/Mediflex(Dev)/Subjects",
"username": "me",
"password": "$3cReT",
"enabled": true
}
After you have started the web application, when you point your browser to it, you will get redirected to the login page.
Click the request account link to create a new account.
After completing this form, when you log in as an administrator and head for the user listing screen,
you should see the newly requested account.
Clicking the pending state next to the new account, and then clicking the accept button, will activate the account.
After activating the account, the user will be listed as active. The administrator can also assign roles to the account. To list and access all defined studies, you'll need the Data Relationship Manager (DRM) role.
As an administrator, you can also create the account yourself by clicking the invite a new user button. The user will receive an email to choose a password and activate their account.
When accessing the application as a DRM (or as a user assigned to a given study), you will see all defined studies listed on the main page (or only the studies to which you have been assigned if you are not a DRM).
Click a study name to select it.
The left menu allows going to the list of members assigned to the study team (investigators).
The left menu allows going to the list of subjects (patients) enrolled in the study
Clicking a subject takes you to the overview of study events. Events represent a collection of forms to be collected at scheduled or unscheduled points in time during the subject's participation in the study:
From this view you can select an event for which forms are to be prefilled with EHR data:
The result looks like this:
Prefilled forms are accessible from a subject overview by clicking the name of the event of interest.
You can then review the form data that was prefilled based on the selected time point:
You can access the complete history of prefilled forms
Similarly you can access the complete history of prefilled form submissions to the EDC
If you have questions, please reach us at info@custodix.com.