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javadatapipeline

JAVA Implementation of the FAIR Data Pipeline API

https://github.com/fairdatapipeline/javadatapipeline

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

JAVA Implementation of the FAIR Data Pipeline API

Basic Info
  • Host: GitHub
  • Owner: FAIRDataPipeline
  • License: lgpl-3.0
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 55.5 MB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 5
Created almost 5 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Zenodo

README.md

javaDataPipeline

test with reg partial test License: LGPL v3 DOI

Java implementation of the FAIR Data Pipeline API

Documentation can be found on https://www.fairdatapipeline.org/docs/API/Java/

JavaDocs are automatically published on https://www.fairdatapipeline.org/javaDataPipeline/

To use a release version (latest: 1.0.0-rc3) include the following dependency (available from mavenCentral):

gradle group: 'org.fairdatapipeline', name: 'api', version: '1.0.0-rc3'

javaSimpleModel

Please have a look at https://github.com/FAIRDataPipeline/javaSimpleModel for a simple example on how to use the javaDataPipeline, including an example of the user written config.yaml, and how to integrate it with the FAIR CLI command line interface.

What does it implement?

  • It reads the config.yaml that is re-written by FAIR CLI (not to be confused with the user written config.yaml)
  • It registers a model Coderun session in the FAIR Data Registry, including all the data inputs and/or outputs, from the model, and its code repository, its config.yaml, and its submission (startup) script.
  • It allows the Coderun session to raise Issues with Object_components, codeRepo, config file, and submission script, and these Issues are registered in the Data Registry.
  • It allows reading and writing of Dataproducts whose Object contains either 1 wholeobject unnamed Object_component (for reading and writing 'external' whole-file file formats).
  • It allows reading and writing of Data_products containing a FAIR Data Pipeline (TOML) Parameter File.
  • It does not yet support HDF5 files.

Owner

  • Name: FAIR Data Pipeline
  • Login: FAIRDataPipeline
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 120
  • Total Committers: 3
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.092
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Bram Boskamp b****m@b****p 109
Ryan J Field 5****d 10
bobturneruk 3****k 1
Committer Domains (Top 20 + Academic)
boska.mp: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 2
  • Total pull requests: 10
  • Average time to close issues: 9 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.8
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • richardreeve (1)
  • bobturneruk (1)
Pull Request Authors
  • B0SKAMP (5)
  • RyanJField (4)
  • bobturneruk (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 6
repo1.maven.org: org.fairdatapipeline:dataregistry

The library used by javaDataPipeline API to access the FAIR DataPipeline Registry

  • Versions: 3
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 32.0%
Dependent packages count: 32.0%
Last synced: 8 months ago
repo1.maven.org: org.fairdatapipeline:api

javaDataPipeline API

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.8%
Average: 46.6%
Dependent packages count: 50.1%
Forks count: 52.5%
Stargazers count: 62.8%
Last synced: 8 months ago

Dependencies

api/build.gradle maven
  • com.fasterxml.jackson.core:jackson-annotations 2.13.2 implementation
  • com.fasterxml.jackson.dataformat:jackson-dataformat-yaml 2.13.2 implementation
  • com.fasterxml.jackson.datatype:jackson-datatype-guava 2.13.2 implementation
  • com.fasterxml.jackson.datatype:jackson-datatype-jdk8 2.13.2 implementation
  • com.fasterxml.jackson.datatype:jackson-datatype-jsr310 2.13.2 implementation
  • com.fasterxml.jackson.module:jackson-module-parameter-names 2.13.2 implementation
  • com.google.guava:guava 31.1-jre implementation
  • com.moandjiezana.toml:toml4j 0.7.2 implementation
  • commons-codec:commons-codec 1.15 implementation
  • commons-io:commons-io 2.11.0 implementation
  • jakarta.ws.rs:jakarta.ws.rs-api 3.0.0 implementation
  • org.apache.commons:commons-math3 3.6.1 implementation
  • org.apache.maven:maven-artifact 3.8.4 implementation
  • org.glassfish.jersey.core:jersey-client 3.0.4 implementation
  • org.glassfish.jersey.inject:jersey-hk2 3.0.4 implementation
  • org.glassfish.jersey:jersey-bom 3.0.4 implementation
  • org.immutables:value-annotations 2.9.0 implementation
  • org.slf4j:slf4j-api 1.7.36 implementation
  • org.slf4j:slf4j-simple 1.7.36 implementation
  • org.assertj:assertj-core 3.22.0 testImplementation
  • org.javatuples:javatuples 1.2 testImplementation
  • org.junit.jupiter:junit-jupiter 5.8.2 testImplementation
  • org.mockito:mockito-core 4.3.1 testImplementation
  • org.skyscreamer:jsonassert 1.5.0 testImplementation
dataregistry/build.gradle maven
  • com.fasterxml.jackson.core:jackson-annotations 2.13.2 implementation
  • com.fasterxml.jackson.core:jackson-databind 2.13.2.2 implementation
  • com.fasterxml.jackson.datatype:jackson-datatype-jsr310 2.13.2 implementation
  • com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider 2.13.2 implementation
  • commons-io:commons-io 2.11.0 implementation
  • jakarta.activation:jakarta.activation-api 2.1.0 implementation
  • jakarta.ws.rs:jakarta.ws.rs-api 3.0.0 implementation
  • org.apache.commons:commons-lang3 3.12.0 implementation
  • org.glassfish.jersey.core:jersey-client 3.0.4 implementation
  • org.glassfish.jersey.inject:jersey-hk2 3.0.4 implementation
  • org.glassfish.jersey:jersey-bom 3.0.4 implementation
  • org.slf4j:slf4j-api 1.7.36 implementation
  • org.slf4j:slf4j-simple 1.7.36 implementation
  • org.hamcrest:hamcrest 2.2 testImplementation
  • org.junit.jupiter:junit-jupiter 5.8.2 testImplementation
  • org.mockito:mockito-core 4.3.1 testImplementation
.github/workflows/build-test-with-registry.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
  • codecov/codecov-action v2 composite
.github/workflows/build-test.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
.github/workflows/gradle-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
.github/workflows/javadoc.yml actions
  • JamesIves/github-pages-deploy-action 4.1.5 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
build.gradle maven