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https://github.com/mskcc/smile-message-publisher
Spring Boot LIMS SampleMetadata publisher framework
https://github.com/mskcc/smile-message-publisher
Last synced: about 2 months ago
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Spring Boot LIMS SampleMetadata publisher framework
- Host: GitHub
- URL: https://github.com/mskcc/smile-message-publisher
- Owner: mskcc
- License: agpl-3.0
- Created: 2020-11-17T16:02:24.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2022-06-01T15:49:17.000Z (over 2 years ago)
- Last Synced: 2023-08-06T05:35:24.346Z (over 1 year ago)
- Language: Java
- Size: 112 KB
- Stars: 0
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# SMILE Message Publisher
Spring Boot LIMS SampleMetadata publisher framework
# SMILE Publisher 📘
The SMILE Publisher is one of several components that comprise the SMILE distributed microservices system. It runs as a standalone tool that may publish directly to specific SMILE topics given the appropriate consumer permissions are provided.
### The SMILE Publisher runs in 2 modes:
**1. LIMS Request IDs mode**
- Option 1: Provide comma-separated list of request ids directly
- Option 2: Provide a start date and (optionally) an end date to fetch LIMS requests delivered within the specified date range
**2. File reading (or message recovery) mode**
This mode can be run to publish messages to a stream directly from a file with tab-separated values. The file must follow the same structure that the publishing logger file uses.
File structure:
- Column 1: Date message was received (YYYY/MM/DD)
- Column 2: Message topic
- Column 2: Message contents
## Run
### Custom properties
Make an `application.properties` based on [application.properties.EXAMPLE](src/main/resources/application.properties.EXAMPLE).
All properties are required with the exception of some NATS connection-specific properties. The following are only required if `nats.tls_channel` is set to `true`:
- `nats.keystore_path` : path to client keystore
- `nats.truststore_path` : path to client truststore
- `nats.key_password` : keystore password
- `nats.store_password` : truststore password
Configure your `log4j.properties` based on [log4j.properties.EXAMPLE](src/main/resources/log4j.properties.EXAMPLE). The default configuration writes to std.out which is standard for container environments.
### Locally
**Requirements:**
- maven 3.6.1
- java 8
Add `application.properties` and `log4j.properties` to the local application resources: `src/main/resources`
Build with
```
mvn clean install
```
Run with
```
java -jar target/smile_publisher.jar
```
### With Docker
**Requirements**
- docker
Build image with Docker
```
docker build -t /: .
```
Push image to DockerHub
```
docker push /:
```
If the Docker image is built with the properties baked in then simply run with:
```
docker run --name sample-publisher /: -jar /publisher/smile_publisher.jar
```
Otherwise use a bind mount to make the local files available to the Docker image and add `--spring.config.location` to the java arg
```
docker run --mount type=bind,source=,target=/publisher/src/main/resources --name sample-publisher /: -jar /publisher/smile_publisher.jar --spring.config.location=/publisher/src/main/resources/application.properties
```