FDNS Reporting Microservice

This is the project with the Reporting microservice for generating reports from the data lake in XML, JSON, CSV or XLSX.

Running locally

Carefully read the following instructions for information on how to build, run, and test this microservice in your local environment.

Before you start

You will need to have the following software installed to run this microservice in your local environment:

• Docker, Installation guides
• Docker Compose, Installation guides
• Windows Users: This project uses Make. Please use Cygwin or the Windows Subsystem for Linux for running the commands in this README

Build

First, you'll need to build the image. You can build the image by running the following command:

make docker-build

Run

Once the image has been built, you can run it with the following command:

make docker-run

Test

To check if the microservice is running, open the following URL in your browser:

http://127.0.0.1:8091/

Documentation

To access the Swagger documentation, open the following URL in your browser:

http://127.0.0.1:8091/swagger-ui.html

Docker Compose

This microservice is designed to be used with other microservices. Please look at the docker-compose file for more information.

OAuth 2 Configuration

This microservice is configurable so that it can be secured via an OAuth 2 provider.

Scopes: This application uses the following scope: fdns.reporting

Please see the following environment variables for configuring with your OAuth 2 provider:

• OAUTH2_ACCESS_TOKEN_URI: This is the introspection URL of your provider, ex: https://hydra:4444/oauth2/introspect
• OAUTH2_PROTECTED_URIS: This is a path for which routes are to be restricted, ex: /api/1.0/**
• OAUTH2_CLIENT_ID: This is your OAuth 2 client id with the provider
• OAUTH2_CLIENT_SECRET: This is your OAuth 2 client secret with the provider
• SSL_VERIFYING_DISABLE: This is an option to disable SSL verification, you can disable this when testing locally but this should be set to false for all production systems

Minio

Be sure that your local configuration is correct by editing ~/.mc/config.json:

"local": {
    "url": "http://localhost:9000",
    "accessKey": "minio",
    "secretKey": "minio123",
    "api": "S3v4"
}

Create the required minio bucket where we'll store the HL7 and CDA messages:

mc mb local/reporting

Then, you'll need to run the two Kafka jobs. You can find more information in the project fdns-ms-reporting-kafka.

Additional Configuration

To be sure that it runs properly, just open the following URL in your browser:

http://127.0.0.1:8091/

You can submit a new request to get a ZIP file containing all items in JSON or XML by POSTing this query:

{
  "query": "",
  "format": "json",
  "index": "ngmvps.message"
}

Or

{
  "query": "",
  "format": "xml",
  "index": "ngmvps.message"
}

If you want to get a CSV or an XLSX file, the Kafka jobs will need to use a configuration provided to fdns-ms-combiner. If you know that a configuration is already store in this micro service, you can use the following query:

{
  "query": "",
  "format": "csv",
  "index": "ngmvps.message",
  "config": "ngmvps-message"
}

Or

{
  "query": "",
  "format": "xlsx",
  "index": "ngmvps.message",
  "config": "ngmvps-message"
}

If you prefer to provide a custom mapping, the Reporting micro service will create the Combiner configuration for you on the fly. Here is the syntax:

{
  "query": "",
  "format": "xlsx",
  "index": "message",
  "mapping": [{
    "path": "$.extractor.version",
    "label": "Message Version"
  }, {
    "path": "$.extractor.hash",
    "label": "Message Hash"
  }, {
    "path": "$.extractor.UCID.hash",
    "label": "Case ID"
  }, {
    "path": "$.extractor.timestamp.$numberLong",
    "label": "Timestamp"
  }, {
    "path": "$.sourceType",
    "label": "Type"
  }, {
    "path": "$.patient.name",
    "label": "Patient Name"
  }, {
    "path": "$.patient.dob",
    "label": "Patient DOB"
  }, {
    "path": "$.patient.sex",
    "label": "Patient Sex"
  }, {
    "path": "$.observation.name",
    "label": "Condition"
  }, {
    "path": "$.observation.code",
    "label": "Condition Code"
  }, {
    "path": "$.jurisdiction.name",
    "label": "Reporting Facility"
  }, {
    "path": "$.jurisdiction.id",
    "label": "Jurisdiction Code"
  }, {
    "path": "$.ingestion.payloadName",
    "label": "Message Payload"
  }, {
    "path": "$.ingestion.fromPartyId",
    "label": "Message From"
  }, {
    "path": "$.ingestion.localFileName",
    "label": "Message File Name"
  }, {
    "path": "$.ingestion.receivedTime",
    "label": "Message Received"
  }, {
    "path": "$.ingestion.messageRecipient",
    "label": "Message Recipient"
  }]
}

It's possible as well to specify the drawer name where you want to export the final reports as shown below (if you don't specify it, it will be exported to the reporting drawer):

{
  ...,
  "export": {
    "drawerName": "ngmvps"
  }
}

How to access the documentation

To access the Swagger documentation, just open the following URL in your browser:

http://127.0.0.1:8091/swagger-ui.html

Public Domain

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

The source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

The source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see https://www.apache.org/licenses/LICENSE-2.0.html.

The source code forked from other open source projects will inherit its license.

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Contributing

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Notices

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