Configuration Options#
This is a non-exhaustive list of available configuration options for the recruIT deployment.
When deploying using Helm, many of these options are automatically configured or exposed via values.yaml.
You can find a complete description of all available chart configuration options here:
https://github.com/miracum/charts/blob/master/charts/recruit/README.md#configuration. If anything is missing, you
can use the extraEnv option to supply additional environment variables to the modules.
"Staging Default Value" refers to the default value for that option when deploying via Docker Compose
using the .staging.env file.
Used by multiple modules#
| Variable | Description | Staging Default Value |
|---|---|---|
| FHIR_URL | URL of a FHIR server used to store the screening lists and retrieve patient data (if available). Used by all modules. | http://fhir:8080/fhir |
Screening List#
| Variable | Description | Staging Default Value |
|---|---|---|
| KEYCLOAK_DISABLED | Disable Keycloak authentication for the screening list. | false |
| KEYCLOAK_CLIENT_ID | Keycloak client id for the screening list component. | uc1-screeninglist |
| KEYCLOAK_REALM | The Keycloak realm. | MIRACUM |
| KEYCLOAK_AUTH_URL | URL of the Keycloak server (should end with /auth). |
http://host.docker.internal:38086/auth |
| DE_PSEUDONYMIZATION_ENABLED | Whether or not the resources from the FHIR server should be de-pseudonymized before being displayed in the screening list. See De-Pseudonymization for details | false |
| DE_PSEUDONYMIZATION_SERVICE_URL | The URL to the FHIR Pseudonymizer service used for de-pseudonymization. | "" |
| DE_PSEUDONYMIZATION_API_KEY | The API key used to authenticate against the FHIR Pseudonymizer | "" |
| HIDE_DEMOGRAPHICS | Don't show age and gender of the persons | false |
| HIDE_LAST_VISIT | Don't show the last visit information | false |
| HIDE_EHR_BUTTON | Don't show the button to show EHR information of the person | false |
| PROXY_IS_SECURE_BACKEND | If FHIR_URL points to a server using HTTPS, then you should set this to 1 or true |
false |
Query Module#
| Variable | Description | Staging Default Value |
|---|---|---|
| ATLAS_URL | URL of the ATLAS WebAPI endpoint. Usually ends in /WebAPI. Used by the query module.¹ |
http://ohdsi-webapi:8080/WebAPI |
| ATLAS_DATASOURCE | Name of the ATLAS datasource used to generate the cohorts from. | OHDSI-CDMV5 |
| OMOP_JDBCURL | JDBC URL of the OMOP database. | jdbc:postgresql://omopdb:5432/OHDSI |
| OMOP_USERNAME | Username to access the OMOP database. | postgres |
| OMOP_PASSWORD | Password to access the OMOP database. | postgres |
| OMOP_RESULTSSCHEMA | Name of the database schema containing the results of the cohort generation. | synpuf_results |
| OMOP_CDMSCHEMA | Name of the database schema containing the actual clinical data. | synpuf_cdm |
| QUERY_SCHEDULE_UNIXCRON | A UNIX-compliant CRON expression to configure the execution schedule of the query module (see https://crontab.guru/). | */5 * * * * (Run every 5 minutes) |
| QUERY_SELECTOR_MATCHLABELS | Comma-separated list of labels which must be present in either the cohort's name or description enclosed in [] in order to be processed by the query module.² |
UC1,Test |
| QUERY_WEBAPI_AUTH_ENABLED | Set to true if the OHDSI WebAPI requires authentication. | false |
| QUERY_WEBAPI_AUTH_LOGIN_PATH | The login method to use. See https://github.com/OHDSI/Atlas/blob/master/js/config/app.js#L20 for a list of possible paths. | /user/login/db |
| QUERY_WEBAPI_AUTH_USERNAME | The username to login as. Note that this user needs permissions to query and generate cohorts. | "" |
| QUERY_WEBAPI_AUTH_PASSWORD | The password used to login. | "" |
| QUERY_APPEND_RECOMMENDATIONS_TO_EXISTING_LIST | if true, instead of overwriting the contents of the List for each cohort based on what the last generation run returned, append to this list | false |
| QUERY_FORCE_UPDATE_SCREENING_LIST | if true, always send a List resource as part of the transaction even if nothing changed | false |
| QUERY_ONLY_CREATE_PATIENTS_IF_NOT_EXIST | if true, send Patient resources as "conditional-creates" on their first identifier instead of using "conditional-update". Useful if the server is already filled with Patient resources from a different system | false |
| QUERY_COHORTSIZETHRESHOLD | Maximum number of patients to be included in the generated screening list. A warning will appear on the screening list view if a list exceeded this count. | 100 |
| QUERY_WEBAPI_COHORT_CACHE_SCHEMA | The name of the schema which contains the cohort definitions cache. | ohdsi |
| QUERY_RUN_ONCE_AND_EXIT | If set to true, run the query module only once against all discovered cohort definitions and exit. Useful when running the module as part of a larger workflow. See here for an example using Argo Workflows. |
false |
¹: This is usually the same URL you configured in the config-local.js file when setting up the ATLAS server.
²: For example, the default values of UC1,Test require the cohort definitions name or description in Atlas to contain either
the string [UC1] or [Test] in order to be processed by the query module.
Notification Module#
| Variable | Description | Staging Default Value |
|---|---|---|
| NOTIFY_WEBHOOK_ENDPOINT | External URL for the notification module's webhook endpoint. Should end in /on-list-change.³ |
http://notify:8080/on-list-change |
| NOTIFY_RULES_CONFIG_PATH | Path to the notification rule configuration file. The file is mounted inside the notification module. | ./staging/notify-rules.yml |
| NOTIFY_MAIL_HOST | Host of the SMTP server used to send notification emails. | maildev |
| NOTIFY_MAIL_SMTP_PORT | SMTP port on the host. | 1025 |
| NOTIFY_MAIL_USERNAME | SMTP username. | user |
| NOTIFY_MAIL_PASSWORD | SMTP password. | pass |
| NOTIFY_MAILER_LINKTEMPLATE | Template used to generate a clickable link in the notification emails. [list_id] is mandatory and is replaced with the lists internal id.⁴ |
http://recruit-list.127.0.0.1.nip.io/recommendations/[list_id] |
| NOTIFY_MAILER_FROM | The sender email address for the created notification mails. | rekrutierung@miracum.org |
³: If your FHIR server is running on fhir.example.com and your notification module runs on notify.example.com:8080,
then this value should be set to http://notify.example.com:8080/on-list-change. The default exposed port of the notification module is 38087. This external port is used when the FHIR server can't access the notification module using the Docker-network internal host and port notify:8080.
⁴: If your screening list is running on https://list.example.com:38080/, then this value should be set to
https://list.example.com:38080/recommendations/[list_id].