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OTH Exporter

Development notes

The exporter is Go application. A Makefile is supplied. The Makefile is the main way to interact with the project.

The Makefile has the following targets:

================================================================================
Standard OTH targets:
================================================================================
cleanall             Cleans everything
clean                Cleans source and dependencies
compile              Compile project
dockerize            Dockerize component
format               Runs formatter
help                 This help
release              Release component
setup                Runs setup - if any
start                Starts in development mode
tag                  Set version
test                 Runs test for component

================================================================================
Extra targets:
================================================================================
buildcontainer       Builds docker container
ci-test              Run tests for cmponent
clean-build          Removes croos compilation files
clean-cover          Removes coverage files
clean-dist           Removes distribution files
cover                Runs coverage
docker-enter         Enter container
docker-logs          Tails logs from container
docker-run           buildcontainer application in container
docker-stop          Stop running container
documentation        Compiles the README.md from README.org
ecr-login            Performs ECR login
integrationtest      Runs integration tests
list                 List packages
mysql                connnect to dev db
push-to-ecr          Push container to ecr
resetdb              Drop current database and re-apply migrations
serve                Just starts API
tag-container        tags docker image
tags                 Displays tags
testall              Test all then things

While in development the target `start` will start the reflex utility, which will reload the application if any relevant files are altered.

Modifying database structure

The database migrations are managed by the golang-migrate project. There is a subcommand for doing database upgrades which is exporter migrate. This command is run at every container start.

Running a local environment to test on

Setting up a docker based development environment can by done by running:

make start-dev-env

This will all dependent systems and databases in a docker network.

Setting up a local development environment requires 3 parts:

  1. XDS Repository
  2. Running XDS generator
  3. Running this exporter

Local XDS repository

Start XDS repository til test, følgende docker-compose.yml anvendes

version: "3.9"  # optional since v1.27.0

services:
  openxds-server:
    image: registry.nspop.dk/components/dds/openxds:snapshot
    # networks:
    #   - dds_net
    depends_on:
      - openxds-db
      - openxds-logs-db
    environment:
      - XDS_REGISTRY_HOST=localhost
      - XDS_REGISTRY_PORT=8010
      - XDS_REGISTRY_URL=/axis2/services/xdsregistryb
      - XDS_REPOSITORY_UNIQUE_ID=1.3.6.1.4.1.21367.2010.1.2.1125
      - XDS_HOME_COMMUNITY_ID=urn:oid:1.3.6.1.4.1.21367.2010.1.2.2045
      - XDS_DB_DIALECT=org.hibernate.dialect.MySQLDialect
      - XDS_DB_DRIVER=com.mysql.jdbc.Driver
      - XDS_DB_OPENXDS_URL=jdbc:mysql://openxds-db:3306/openxds
      - XDS_DB_OPENXDS_USERNAME=openxds
      - XDS_DB_OPENXDS_PASSWORD=open123
      - XDS_DB_LOGS_URL=jdbc:mysql://openxds-logs-db:3306/openxdslogs
      - XDS_DB_LOGS_USERNAME=logs
      - XDS_DB_LOGS_PASSWORD=logs123
      - XARGS=-Xmx128m
      - XDS_LOG_LEVEL=DEBUG
    ports:
      - "8010:8010"
      - "8020:8020"

  openxds-db:
    image: mariadb:10.1
    # networks:
    #   - dds_net
    environment:
      - MYSQL_ROOT_PASSWORD=root
      - MYSQL_DATABASE=openxds
      - MYSQL_USER=openxds
      - MYSQL_PASSWORD=open123
    volumes:
      - ./database/openxds/openxds.sql:/docker-entrypoint-initdb.d/01_db.sql
      - ./database/openxds/sds_2504_testdata.sql:/docker-entrypoint-initdb.d/50_sds2504test.sql
      - ./database/my.cnf:/etc/mysql/my.cnf

  openxds-logs-db:
    image: mariadb:10.1
    # networks:
    #   - dds_net
    environment:
      - MYSQL_ROOT_PASSWORD=root
      - MYSQL_DATABASE=openxdslogs
      - MYSQL_USER=logs
      - MYSQL_PASSWORD=logs123
    volumes:
      - ./database/openxds/openxdslogs.sql:/docker-entrypoint-initdb.d/db.sql
      - ./database/my.cnf:/etc/mysql/my.cnf

Start by:

docker-compose up

XDS generator service

Go to repository

make start
Configuration

For running against xds-test repository as mentioned above, the following settings can be used:

spring:
  output:
    ansi:
      enabled: detect

logging:
  level:
    root: warn
    org:
      apache:
        cxf: info
    io:
      oth:
        xdsgenerator:
            handlers:
            KihDataController: info
  pattern:
    dateformat: yyyy-MM-dd HH:mm:ss.SSS
    console: "%d %-5p %-30.30logger{29}: %m %n %ex{2}"

management:
  endpoint:
    health:
      probes:
        enabled: true
      show-details: always

server:
  error:
    include-stacktrace: never
  port: 9010
  tomcat:
    accesslog:
      enabled: true
      pattern: "%t sip=%h r=\"%r\" htsc=%s B=%b tt=%D tid=%I ua=\"%{User-Agent}i\""
    basedir: tomcat

# XDS Settings
xds:
  repositoryuniqueid: 1.2.208.176.43210.8.1.29
  generate:
    # Set this to true for using xds-test
    documentid: true
  iti41:
    endpoint: http://localhost:8020/axis2/services/xdsrepositoryb
# SOR mapping for all measurements
sor:
  code: 6071000016008
  name: TeleCare Nord


# DGWS Setup for vaults and what note
dgws:
  # true if should be signed
  enabled: false
  sts:
    url: https://test2.ekstern-test.nspop.dk:8443/sts/services/SecurityTokenService
  keystore:
    type: production
    alias: nets danid a/s - tu voces gyldig
    filename: classpath:VOCES_gyldig_2022.p12
    password: Test1234
  certificate:
    itsystem: TRUST2408 Systemtest XIX CA
    orgname: NETS DANID A/S
    cvr: 30808460

for using against medcom test

spring:
  output:
    ansi:
      enabled: detect

logging:
  level:
    root: warn
    org:
      apache:
        cxf: info
    io:
      oth:
        xdsgenerator:
            handlers:
            KihDataController: info
  pattern:
    dateformat: yyyy-MM-dd HH:mm:ss.SSS
    console: "%d %-5p %-30.30logger{29}: %m %n %ex{2}"

management:
  endpoint:
    health:
      probes:
        enabled: true
      show-details: always

server:
  error:
    include-stacktrace: never
  port: 9010
  tomcat:
    accesslog:
      enabled: true
      pattern: "%t sip=%h r=\"%r\" htsc=%s B=%b tt=%D tid=%I ua=\"%{User-Agent}i\""
    basedir: tomcat

# XDS Settings
xds:
  repositoryuniqueid: 1.2.208.176.43210.8.1.29
  generate:
    # Set this to true for using xds-test
    documentid: false
  iti41:
    endpoint: http://kih.test.xdsrepositoryb.medcom.dk:8031/kih-iti41/iti41
# SOR mapping for all measurements
sor:
  code: 6071000016008
  name: TeleCare Nord


# DGWS Setup for vaults and what note
dgws:
  # true if should be signed
  enabled: true
  sts:
    url: https://test2.ekstern-test.nspop.dk:8443/sts/services/SecurityTokenService
  keystore:
    type: production
    alias: nets danid a/s - tu voces gyldig
    filename: classpath:VOCES_gyldig_2022.p12
    password: Test1234
  certificate:
    itsystem: TRUST2408 Systemtest XIX CA
    orgname: NETS DANID A/S
    cvr: 30808460

Export

The exporter requires a local database. (included in the docker based developent environment)

Bootstrap and restart the service

make resetdb start

Data can be exported in two ways:

  1. Batch mode a. Intended for re-exporting all measurements from an OTH installation
  2. Normally operations, using cron/scheduled job/curl

To trigger the batch export, using the exportall subcommand:

go run main.go exportall

Or setup for normal operations by:

go run main.go serve

Then in another shell, trigger the export like so:

curl http://localhost:8360/export

Backends

The following describes how to setup a backend to export to.

OIO XDS

This requires the xds-generator backend.

OTH Exporter

The OTH Exporter (exporter) is a component, which handles:

  • Exporting measurements from OTH to external system
  • The following external systems are supported:
    • OIO XDS
  • Keeping track of, which types should be exported
  • Handling of soft and hard failures:
    • Soft failures is the backend export failing, can be retries
    • Hard failures, when retry of exports keep failing mark measurement as permanently failed

For more information about the exporter please visit the documentation.

The exporter has the following endpoints:

GET http://localhost:8360
{
  "apiVersion": "1.1_build1",
  "environment": "dev",
  "links": {
    "measurement": "http://localhost:8360/measurement",
    "export": "http://localhost:8360/export",
    "failed": "http://localhost:8360/failed",
    "health": "http://localhost:8360/health",
    "status": "http://localhost:8360/status",
    "self": "http://localhost:8360/"
  }
}

The following methods/endpoints are supported by the exporter.

The /health endpoint

The /health endpoint is used to access basic health information about the service. It only supports HTTP GET

The output is as follows:

GET http://localhost:8360/health
{
  "apiVersion": "1.0.6_build1",
  "environment": "dev"
}

The health checks queries:

  • database
  • if kih export is selected:
    • Sosiserver for idcard signing
    • KIHDB for export

The /export endpoint

The /export endpoint is used trigger the export. It only supports HTTP GET

When the export is started it does as follows:

  1. Find time of last run
  2. Get measurements from opentele from 30 minutes before time of lastrun
  3. For each measurement:
    1. Check if measurement is already known and exported?
    2. Convert measurements to output format
    3. Export measurements
    4. Mark measurement as exported
  4. Check if results was paginiation, if yes fetch next batch and perform steps in step 3
  5. Mark run as completed

The output is as follows:

GET http://localhost:8360/export

#+BEGIN_SRC js
[
  {
    "Success": true,
    "Measurement": {
      "id": "d99394ab-2c51-440f-9aa1-4b97e62c8696",
      "measurement": "https://docker-demo.oth.io/clinician/api/patients/14/measurements/397",
      "patient": "https://docker-demo.oth.io/clinician/api/patients/14",
      "status": "COMPLETED",
      "created_at": "2020-02-25T15:58:40+01:00",
      "updated_at": "2020-02-25T15:58:41.361090851+01:00"
    }
  },
  {
    "Success": true,
    "Measurement": {
      "id": "883e39d0-ca2c-4995-9897-53c7b05528eb",
      "measurement": "https://docker-demo.oth.io/clinician/api/patients/13/measurements/396",
      "patient": "https://docker-demo.oth.io/clinician/api/patients/13",
      "status": "COMPLETED",
      "created_at": "2020-02-25T15:58:41+01:00",
      "updated_at": "2020-02-25T15:58:41.729067684+01:00"
    }
  },
]
// GET http://localhost:8360/export
// HTTP/1.1 200 OK
// Content-Type: application/json; charset=utf-8
#+END_SRC

The /status endpoint

The /statuss endpoint is used to access basic metrics from the underlying service. It only supports HTTP GET

The output is as follows:

GET http://localhost:8360/status
{
  "Measurements": {
    "TotalMeasurements": 397,
    "TempFailedMeasurements": 0,
    "RejectedMeasurements": 5,
    "FailedMeasurements": 0
  },
  "LastRun": {
    "TimeStamp": "2020-02-25T16:14:18+01:00",
    "Status": "COMPLETED"
  },
  "Runs": {
    "Total": 2,
    "Failed": 0,
    "Successfull": 2
  },
  "Source": {
    "Endpoint": "https://docker-demo.oth.io/clinician/api"
  },
  "Destination": {
    "Endpoint": "https://kihdb-devel.oth.io/services/monitoringDataset"
  }
}

The /failed endpoint

The /failed endpoint is used to trigger, failed measurements

The /measurement endpoint

The =/measurement/ endpoint is used to retrieve a measurement using the ID for the measurement. The operations fetches both the exporters internal state, as well as the actual measurement and patient from OTH.

Example:

GET localhost:8360/measurement/7ee1c80c-d687-4c02-9ac4-8a9bc8586111
{
  "patient": {
    "createdDate": "2021-06-25T07:06:37.000Z",
    "uniqueId": "2512688916",
    "username": "Lisa",
    "firstName": "Lisa",
    "lastName": "Jensen",
    "dateOfBirth": null,
    "sex": "female",
    "status": "active",
    "address": "21 Carter Building Washington",
    "postalCode": "DC 20510",
    "city": "Washington DC",
    "place": null,
    "phone": null,
    "mobilePhone": "",
    "email": "",
    "comment": null,
    "patientGroups": [
      {
        "name": "Obstructive Lung Disease Clinic",
        "links": {
          "patientGroup": "https://docker-demo.oth.io/clinician/api/patientgroups/4"
        }
      }
    ],
    "relatives": [],
    "links": {
      "self": "https://docker-demo.oth.io/clinician/api/patients/14",
      "questionnaireSchedules": "https://docker-demo.oth.io/clinician/api/patients/14/questionnaire_schedules",
      "measurements": "https://docker-demo.oth.io/clinician/api/patients/14/measurement-types",
      "questionnaireResults": "https://docker-demo.oth.io/clinician/api/patients/14/questionnaire-results",
      "patientThresholds": ""
    }
  },
  "measurement": {
    "timestamp": "2021-06-02T09:00:00+02:00",
    "type": "bloodsugar",
    "measurement": {
      "unit": "mmol/L",
      "value": 6.900000095367432,
      "ignored": {
        "by": {
          "firstName": "",
          "lastName": "",
          "email": "",
          "links": {}
        }
      }
    },
    "origin": {
      "manualMeasurement": {
        "enteredBy": ""
      },
      "deviceMeasurement": {
        "connectionType": "bluetooth_spp",
        "manufacturer": "MyGlycoHealth",
        "model": "MyGlycoHealth",
        "primaryDeviceIdentifier": {
          "macAddress": "AA:BB:CC:DD:EE:FF"
        },
        "hardwareVersion": "A2",
        "firmwareVersion": "Z3",
        "softwareVersion": "B1",
        "additionalDeviceIdentifiers": [
          {
            "systemId": "123456",
            "other": {
              "description": "",
              "value": ""
            }
          },
          {
            "other": {
              "description": "manufacturer_id",
              "value": "ACF123G155"
            }
          }
        ]
      }
    },
    "links": {
      "patient": "https://docker-demo.oth.io/clinician/api/patients/14"
    }
  },
  "storedMeasurement": {
    "id": "7ee1c80c-d687-4c02-9ac4-8a9bc8586111",
    "measurement": "https://docker-demo.oth.io/clinician/api/patients/14/measurements/279",
    "patient": "https://docker-demo.oth.io/clinician/api/patients/14",
    "status": "COMPLETED",
    "created_at": "2021-05-21T13:58:15+02:00",
    "updated_at": "2021-05-21T13:58:16+02:00"
  }
}

Configuration

The exporter is configured using exporter.yaml file.

The following options are available to configure exporter:

version: '1.1_build1'
environment: 'dev'

logfile: '/var/log/exporter'
loglevel: 'warn'
logging:
  repository: debug
  measurement: debug

export:
  start: 2020-06-01 # must be a date
  retrydays: 15
  created_by: OTH Test Exporter
  nodevicewhitelist: true
  backend: oioxds
  oioxds:
    xdsgenerator:
      url: http://localhost:9010/api/createphmr
      healthcheck: http://localhost:9010/actuator/health

clinician:
  batchsize: 1000
  url: "https://oth-demo.oth.io/clinician/api"

authentication:
  key: <insert key>
  secret: <insert secret>

database:
  hostname: localhost
  username: root
  password: opentele
  type: 'mysql'
  port: 3306
  database: 'exporter'

The application specific settings are under the exporter space. The settings mean the following:

  • clinician: Settings for clinician
    • url Where the measurements API is located
    • batchsize control how many measurements are retrieved
  • export The exporter backends
    • backend Denotes which type is to be deployed. Choices are kih or oioxds
    • start The start date for using when to export measurements
    • retrydays How many days must temporary failed measurements be marked as temporary failed before moving to permanently failed
    • nodevicewhitelist Use the by MedCom defined device whitelist, or use the origin data from a measurement.

Setting up the local IdP

The keys for OTH IdP must be manually created. This can be done with the following steps:

  1. Create client using the IdPs keys
  2. Grant permission to client.

IdP keys can be retrieved using salt on the minion like this:

The persmissions can then be created using:

The above will return a response, which key and secret. The response will look something like this:

{
  "permissions": [
    {
      "service": "Clinician",
      "name": "ROLE_MEASUREMENT_READ",
      "links": {
        "permission": "https://oth-demo.oth.io/idp2/permissions/111"
      },
      "displayName": "Read: Measurements",
      "description": "Read measurements"
    },
    {
      "service": "Clinician",
      "name": "ROLE_PATIENT_READ",
      "links": {
        "permission": "https://oth-demo.oth.io/idp2/permissions/9"
      },
      "displayName": "Read: Patients",
      "description": "Read patients"
    }
],
  "name": "exporter client",
  "links": {
    "self": "https://oth-demo.oth.io/idp2/clients/17"
  },
  "clientSecret": "MGm1bDqVgle74C_UxiEx4J4IJdXOcnvPHHBsZ-OB_Zazqw2sqpdrImswbH",
  "clientKey": "1A8ByV0-hm6-doZ8bCFiaPI6O",
  "auditId": "fb60b1eb-8f37-11ea-9f02-0242ac110006"
}
+END_EXAMPLE

* Using exporter as injector to OIOXDS
The binary can be used to inject measurements into KIHDB or OIOXDS

This can be achieved by using the =exporter testinject= subcommand. The short hand =exporter ti= can also be use.

The =testinject= commands takes the following arguments:
exporter ti -h

#+RESULTS:
Reads measurements and patients from file and exports based on config

Usage:
  exporter testinject [flags]

Aliases:
  testinject, ti

Flags:
  -b, --backend string         -b indicates with exporter backend to use. Supported backends: kih (default "kih")
  -f, --file string            -f is a path to JSON file measurent data to be sent
  -h, --help                   help for testinject
      --kihcreatedby string    Sets created by in OIO request
      --kihsosiserver string   Sets URL for SOSI Server
      --kihurl string          Sets URL for KIHDB endpoint (https://kihdb-devel.oth.io/services/monitoringDataset) (default "https://kihdb-devel.oth.io/services/monitoringDataset")
  -p, --patient string         -p is a path to JSON file with patient information
      --setnow                 Set timestamp on measurement to now?
  -s, --source string          -s is a path to directory with JSON files with measurent data to be sent
      --usesosi                Use SOSI?

Global Flags:
      --exporter string   config file (default is exporter.yaml)

For instance to inject a single test file, this can be accomplished like this:
exporter testinject -b oioxds --date 2019-01-01T10:10:10 --kihcreatedby "OTH Test" -f ./backend/kih/testdata/pulse.json \
    -p ./backend/testdata/person_m33.json --xdsgen http://docker-demo.oth.io:9010/api/createphmr

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