sormas-rest

REST interface for SORMAS

This is a one-stop-shop for all systems that need access to the SORMAS data:

• Synchronization of data with the SORMAS Android app
• Data access for the SORMAS Angular web app
• Exchanging data with other SORMAS instances
• External services like symptom diaries or citizen applications
• Synchronization of data with other surveillance or to data analysis systems

Authentication

Access to the API is by default restricted by HTTP Basic authentication. Using OIDC/OAUTH2/Bearer authentication is also possible depending on how keycloak is set up. See Authentication & Authorization.

For basic auth use the username and password as credentials for your HTTP requests. The user needs to have a user role having the SORMAS_REST user right.

API Documentation

The SORMAS REST API is documented automatically. The OpenAPI specification files are generated during the build process and can be found at ${Project Root}/sormas-rest/target/swagger.{json,yaml}.

You can render the OpenAPI specification with tools like editor.swagger.io. This allows you to inspect endpoints and example payloads, generate a matching API client for many languages, and to easily interact with the API of a live instance.

OpenAPI / Swagger

The OpenAPI files are generated with the swagger-maven-plugin and the Swagger Annotation Framework^[1].

If you are only interested in the OpenAPI specification files, you may either download a recent SORMAS release where the files reside in the openapi directory, take a look at the files in sormas-rest, or execute the following command inside the sormas-base module's directory to build them for yourself:

# Requires Maven to be installed!
mvn package --projects ../sormas-rest --also-make -Dmaven.test.skip=true

The specification files are created at the path specified above.

---

[1] Swagger Annotations Guide on GitHub: https://github.com/swagger-api/swagger-core/wiki/Swagger-2.X---Annotations

External Visit API

The purpose of this API is to enable communication between SORMAS and other symptom journals. Only users with the role REST_EXTERNAL_VISITS_USER are authorized to use the endpoints. Authentication is done using basic auth, with the user and password. For technical details please contact the dev team on GitHub Discussions.

Workflow Description

About external follow up

Follow up in SORMAS is done via visits. Visits hold information about symptoms at a specific time point. Visits can be created for cases and contacts, either via the SORMAS-UI or the external visits journal API.

About persons, cases and contacts

This is a very basic concept that one needs to understand when working with visits. In SORMAS, a person entity represents a physically existing person. Cases and contacts represent epidemiological occurrences. When a person was in contact with an infectious environment, the person has a contact in SORMAS. When the person was in contact with such environments twice, it gets two contacts. When a person falls ill, it gets a case with the according disease. This means: In SORMAS, each contact and case relates to exactly one person. One person can have several contacts and cases, though. Follow up is done for a contact (or a case, which can be enabled in the SORMAS feature configuration). Contacts (or cases) initiate follow up. A person, though, either shows symptoms or not. It can not show symptoms for just one contact and not for the other. Thus, visits are related to all active contacts (and cases) of a person. Also, the communication with external symptom journals is PERSON BASED. Only the person uuid is used, visits are uploaded to each active case and contact of a person.

Person status variables

It is important to understand the meaning of two variables: the follow-up status and the symptom journal status.

The follow-up status describes the follow-up for a contact or a case. Possible values are defined in the FollowUpStatus enum

Follow up can be done with, or without an external journal, the follow-up status makes no distinction there. Because the follow-up status is contact and case specific,but the communication with external journals is person based, SORMAS determines the most important follow-up status of all contacts and cases related to the person in question when communicating with external journals. Whenever there is follow-up ongoing for any of the persons contacts (and cases if the case follow-up feature is enabled in SORMAS), SORMAS will state the FollowUpStatus.FOLLOW_UP for that person towards external journals.

The SymptomJournalStatus describes the state of a person related to external symptom journals. It is not contact or case specific.

Configuration in SORMAS

In the domain folder, there is a sormas.properties. it holds the following values relevant for an external journal:

• interface.patientdiary.authurl: used to fetch an authentication token (see 1. below).

• interface.patientdiary.frontendAuthurl: URL used to retrieve tokens for frontend requests. If not specified, no tokens will be fetched for such.

• interface.patientdiary.tokenLifetime: Lifetime of tokens fetched via the authurl or the frontendAuthurl. To be specified in seconds. Can be set to 0 for no token caching. Defaults to 21600 (6 hrs.).

• interface.patientdiary.probandsurl: used to register new persons in the external journal (see 2. below).

• interface.patientdiary.url: used to open a person in the external journal (see 6. below).

• interface.patientdiary.email: used to authenticate at the external journal (see 1. below).

• interface.patientdiary.password: used to authenticate at the external journal.

• interface.patientdiary.defaultuser.username: This user will be created in SORMAS and can be used by the external journal to authenticate.

• interface.patientdiary.defaultuser.password: The above user's password.

• interface.patientdiary.acceptPhoneContact: used to configure whether the phone number is considered relevant for registering a person in the external journal. It affects the validation of persons in SORMAS (see 2. below). Defaults to true

Workflows

SORMAS fetching an authentication token from the external journal

POST to the interface.patientdiary.authurl.

Request body:

{
    "email" : [patientdiary.email],
    "password" : [patientdiary.password]
}

where [patientdiary.email] is replaced with interface.patientdiary.email and [patientdiary.password] with interface.patientdiary.password specified in the sormas.properties.

Expected response body:

{
    "success" : true,
    "userId" : [some-user-id],
    "token" : [token]
}

The token returned will be used to authenticate in other requests. Its lifetime can be configured via the interface.patientdiary.tokenLifetime property.

One special scenario is fetching a token for frontend calls (see 6.): When the interface.patientdiary.frontendAuthurl is configured, it is used instead of the interface.patientdiary.authurl here. If it is not configured, no token will be used.

Registration of a new person in the external journal

This process involves several steps that are triggered via the REGISTER button a privileged user can see in the top right corner when having opened a case or a contact.

To be able to see this button, the user must have at least one of the following user roles: national user, contact supervisor, contact officer, community officer, surveillance officer, surveillance supervisor, or admin supervisor.

First comes a SORMAS-internal validation of contact details. The person to be registered needs to have at least an email address (or a phone number if that is accepted for registration, see interface.patientdiary.acceptPhoneContact) to pass this validation.Also, when there are several email addresses or phone numbers, one of them has to be marked primary contact detail, so that it is clear which contact detail shall be used.

Then comes an external validation of the contact details. For this, SORMAS fetches an authentication token as in 1. Then it sends a GET request to the following URL for each contact detail to be used in the external journal:

GET [interface.patientdiary.probandsurl]/probands?q=[URL-encoded-query-parameter-and-value], with a header like x-access-token: [token].

The [URL-encoded-query-parameter-and-value] consists of a parameter-value-pair. The parameter is either Email or Mobile phone. The value holds the contact detail to be validated.

An unencoded example for this is "Email" = "[email protected]", the URL-encoded version is %22Email%22%20%3D%20%22example%40example.de%22.

[token] is replaced with the token fetched for authorization.

The CURL equivalent for an exemplary call is
curl --request GET 'https://probands-URL.com//probands?q=%22Email%22%20%3D%20%22example%40example.de%22' --header 'x-access-token: my-access-token'.

Expected result is a PatientDiaryQueryResponse which information about any person already registered in the external journal and using the same contact detail.

It needs to be structured as follows:

PatientDiaryQueryResponse {
    total: integer,
    count: integer,
    results: List<PatientDiaryPersonData>
}

• total should state how many persons are registered in the external journal (this information is currently never used in SORMAS).

• count should state how many registered persons using the same contact detail were found.

• results need to contain a PatientDiaryPersonData for each match:

PatientDiaryPersonData {
    _id: string,
    idatId: PatientDiaryIdatId
}

• _id should be a unique identifier for the person this data is about (this information is currently never used in SORMAS)

The PatientDiaryIdatId needs to be structured as follows:

PatientDiaryIdatId{
    idat: PatientDiaryPersonDto
}

The PatientDiaryPersonDto holds the actual person data:

PatientDiaryPersonDto{
    personUUID: string,
    firstName: string,
    lastName: string,
    gender: string,
    birthday: string,
    contactInformation: PatientDiaryContactInformation,
    endDate: string
}

• personUUID should be the UUID of the person in SORMAS. This UUID is used to sync with external journals (this information is currently never used in SORMAS).
• firstName and lastName need to hold the first and last name of the person.
• gender should hold the persons gender (this information is currently never used in SORMAS).
• birthday should hold the person's birthday (this information is currently never used in SORMAS).
• contactInformation should hold the contact information of that person, which should for logical reasons always contain (at least) the contact detail provided by SORMAS in the query.
• endDate should hold the date after which follow up is supposed to be stopped by the external journal.

PatientDiaryIdatId {
    email: string,
    phone: PatientDiaryPhone
}

• email should hold the email address for the person
• phone should hold the phone number of that person:

PatientDiaryPhone {
    number: string,
    internationalNumber: string,
    nationalNumber: string,
    countryCode: string,
    dialCode: string,
}

To put this all together, here is an example PatientDiaryQueryResponse with one person using the same contact detail:

{
    "total" : 100,
    "count" : 1,
    "results" : [{
        "_id" : "60586691d4c30700119515c8",
        "idatId" : {
            "idat" : {
            "contactInformation" : {
                "phone" : null,
                "email" : "[email protected]"
            },
            "personUUID" : "RMTEF2-UZXCXE-7YBJK6-KUMSSEME",
              "firstName" : "Maria",
              "lastName" : "Muster",
              "gender" : "female",
              "birthday" : null
            }
        }
    }]
}

SORMAS allows to continue with the registration of a new person only when the person has a unique first name, so when all persons of the response have a different one (or if the response does not contain any matches, which needs to show in PatientDiaryQueryResponse.count == 0). This validation is necessary to avoid confusion of person related data in some external journals.

When there are no validation errors in the process described above, SORMAS fetches an authentication token as described in 1. and then uses it to request the external journal to register the person:

POST [interface.patientdiary.probandsurl]/external-data/[personUUID].

The [personUUID] is replaced with the UUID of the person, which is later used to sync data between the external journal and SORMAS.

Expected response body:

{
    "success" : [boolean],
    "message" : [messageString]
}

[boolean] is expected to be true in case of successful registration. SORMAS then sets the symptom journal status to REGISTERED and displays the message to the user.

When [boolean] is false, the message is shown as an error to the user.

To fetch data relevant for the registration, the external journal can use the /visits-external/person/{personUuid} API endpoint described below.

Synchronization of person data changed in SORMAS

It may happen that person data (like a contact detail) gets changed after a person is registered in an external journal. SORMAS notifies external journals about such a change with first fetching an authentication token as descriced in 1., and the using this token for this request:

PUT [interface.patientdiary.probandsurl]/external-data/[personUUID]

The external journal is expected to refetch the person data via the /visits-external/person/{personUuid} API endpoint described below and save the changes.

After re-fetching the person data, the symptom journal does its own internal validation and responds to SORMAS with the synchronization result, containing eventual validation errors.

The expected response body:

{
    "success" : [boolean],
    "message" : [messageString],
    "errors" : [{
        "errorKey": [errorString]
      }]
}

If the changes were done manually by a user from the person edit form, the synchronization result is shown to the user in a popup window, so that the user can fix eventual errors and resynchronize the person data.

Upload of symptom journal data to SORMAS

For this, the /visits-external API endpoint has to be used. This is described below.

Upload of a symptom journal status to SORMAS

For this, the /visits-external/person/{personUuid}/status API endpoint is to be used. This is described below.

Opening a person in the external journal from within SORMAS

Once the symptom journal status of a person is set to REGISTERED or ACCEPTED, the external journal button in the SORMAS-UI changes. It does not provide a registration anymore, but the options to open the person in the external journal and to cancel external follow up. This button can be found when having opened a contact (or a case if the case follow-up feature is enabled in SORMAS) in the top right corner. If the user chooses to open the person in the external journal, SORMAS opens a new browser tab with the following URL:

[interface.patientdiary.url]/data?q=[personUuid]&queryKey=sicFieldIdentifier

SORMAS expects the external journal to present a view of the person there.

If the interface.patientdiary.frontendAuthurl is configured, SORMAS fetches an authentication token as described in 1, and appends it to the URL:

[interface.patientdiary.url]/data?q=[personUuid]&queryKey=sicFieldIdentifier&token=[token]

Deletion of a person from an external journal

As described above, the journal button can offer the option to cancel external follow up. If a user choses this option, SORMAS fetches an authentication token as described in 1., and uses it to request:

DELETE [interface.patientdiary.probandsurl]/external-data/[personUUID]

Expected response body:

{
    "success" : [boolean],
    "message" : [messageString]
}

[boolean] is expected to be true in case of successful deletion. SORMAS then sets the symptom journal status to DELETED and displays the message to the user.

When [boolean] is false, the message is shown as an error to the user.

Please note that this does not affect any follow-up status. Cancelling follow up of a contact or case is independent of cancelling external follow up of a person.