https://github.com/databiosphere/java-pfb
https://github.com/databiosphere/java-pfb
Last synced: about 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/databiosphere/java-pfb
- Owner: DataBiosphere
- License: bsd-3-clause
- Created: 2023-06-20T13:47:04.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2026-01-12T17:03:19.000Z (2 months ago)
- Last Synced: 2026-01-12T22:23:01.644Z (2 months ago)
- Language: Java
- Size: 1.17 MB
- Stars: 1
- Watchers: 14
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
# Java-PFB
A Java implementation of the [pyPFB](https://github.com/uc-cdis/pypfb) library that includes a CLI and a Java library.
As discussed in the docs provided by [pyPFB](https://github.com/uc-cdis/pypfb/blob/master/docs/index.md#introduction), PFB files are Avro files with a particular required schema. Given the specific [PFB schema](library/src/main/avro/pfbSchema.avdl), the [gradle avro plugin](https://github.com/davidmc24/gradle-avro-plugin) automatically generates class files on project build. Together with the [Avro Java library](https://avro.apache.org/docs/1.11.1/getting-started-java/), we are able to deserialize the PFB files and get the relevant peices of data: The schema, metadata, nodes, and table row data.
To learn more about PFBs, see [pfb.md](docs/pfb.md).
## Getting Started
See the [library README](library/README.md) for more details on how to reference the library in your project.
The CLI is a wrapper around the library. See the [CLI README](cli/README.md) for more information.
## Developer Information
### Publishing
See [library](library/README.md) and [cli](cli/README.md) readmes for more details.
### Running SourceClear locally
[SourceClear](https://srcclr.github.io) is a static analysis tool that scans a project's Java
dependencies for known vulnerabilities. If you get a build failure due a SourceClear error and want
to debug the problem locally, you need to get the API token from vault before running the gradle
task.
```shell
export SRCCLR_API_TOKEN=$(vault read -field=api_token secret/secops/ci/srcclr/gradle-agent)
./gradlew srcclr
```
Results of the scan are uploaded to [Veracode](https://sca.analysiscenter.veracode.com/workspaces/jppForw/projects/768265/issues). You can request an account to view results from #dsp-infosec-champions.
### Running SonarQube locally
[SonarQube](https://www.sonarqube.org) is a static analysis code that scans code for a wide
range of issues, including maintainability and possible bugs. If you get a build failure due to
SonarQube and want to debug the problem locally, you need to get the the sonar token from vault
before runing the gradle task.
```shell
export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/java-pfb)
./gradlew sonar
```
Unlike SourceClear, running this task produces no output unless your project has errors. To always
generate a report, run using `--info`:
```shell
./gradlew sonar --info
```
We run the scans for two projects: [java-pfb](https://sonarcloud.io/project/overview?id=DataBiosphere_java-pfb) and [java-pfb-cli](https://sonarcloud.io/project/overview?id=DataBiosphere_java-pfb-cli). The results are uploaded to the sonarcloud dashboard.
### Benchmarking
[Java Microbenchmark Harness (JMH)](https://github.com/openjdk/jmh/tree/master) is a high-performance
benchmarking tool for individual Java methods. It is integrated into this project via the
[JMH Gradle plugin](https://plugins.gradle.org/plugin/me.champeau.jmh).
To run the benchmarks manually:
```shell
./gradlew jmh
```
After benchmarks run, you can view the results at library/build/reports/jmh/human.txt.
Benchmarks automatically run via GitHub Actions for all PRs and for all pushes to the `main` branch.
You can view `main` branch benchmarks at https://databiosphere.github.io/java-pfb/dev/bench/.
For PRs, navigate to your most recent commit and look for a comment on that commit.
Note that benchmarks run via GitHub Actions are variable, since the runner machines are variable.
Developers are encouraged to run benchmarks locally while developing to best assess the impact
of their changes.