Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found 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 -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Repository
RESTful API for the APE library
Basic Info
- Host: GitHub
- Owner: sanctuuary
- License: apache-2.0
- Language: Java
- Default Branch: main
- Homepage: https://ape-framework.readthedocs.io/en/latest/docs/restful-ape/introduction.html
- Size: 339 KB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 18
- Releases: 4
Metadata Files
README.md
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| DOI |
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| License | 
The RESTful API for the APE library (RESTful APE) allows users to interact with APE's automated pipeline exploration features through HTTP requests. APE automates the exploration of computational pipelines from large collections of computational tools.
Users can submit pipeline exploration requests to the APE server and receive results in JSON format. This interface allows interaction with APE via web browsers or any HTTP client and can be integrated into other applications.
In addition to APE's core feature of automated workflow composition, the API performs design-time benchmarking of workflows by aggregating tool-specific information such as licenses and citations for better workflow comparison.
RESTful APE is packaged in a Docker image.
Overall, the RESTful API for APE provides a flexible way to leverage APE's capabilities in scientific workflows.
Development
RESTful API for the APE library, based on Spring Boot.
To run the Spring Boot directly, you can run the following cmd:
mvn spring-boot:run
Alternatively, you can build the jar package
mvn clean package
and then run the jar package
java -jar target/restape-[version].jar
OpenAPI documentation is available at
````
````
Configure .env file
To configure the application, you can create a .env file in the root directory of the project. See the following content as an example:
REST_APE_PORT = 4444
PUBMETRIC_ENDPOINT= localhost
PUBMETRIC_PORT = 8000
We use REST_APE_PORT to specify the port on which the application will run. When run locally under REST_APE_PORT=4444 the service would be available on localhost:4444.
The PUBMETRIC_ENDPOINT and PUBMETRIC_PORT are used to specify the endpoint and port of the Pubmetric service that is used to retrieve tool metrics.
Use local APE version
If the APE version you wish to use is not available on the Mvn repository you can install APE in your local repository and use it to build the back-end. To do so, download or compile the APE version you wish to use. In the location where you have the resulting APE.jar file, run the following command:
shell
mvn install:install-file -Dfile=APE-<version>.jar
This adds the specified APE file to your local Maven repository. You can now build the back-end using:
shell
mvn package -DskipTests=true
Owner
- Name: Sanctuuary
- Login: sanctuuary
- Kind: organization
- Email: v.kasalica@esciencecenter.nl
- Location: Netherlands
- Website: https://ape.science.uu.nl/
- Repositories: 6
- Profile: https://github.com/sanctuuary
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'RESTful APE'
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Vedran
family-names: Kasalica
email: v.kasalica@esciencecenter.nl
affiliation: Netherlands eScience Center
orcid: 'https://orcid.org/0000-0002-0097-1056'
- family-names: Peter
given-names: Kok
email: p.kok@esciencecenter.nl
affiliation: Netherlands eScience Center
orcid: 'https://orcid.org/0000-0002-6630-7326'
- family-names: Nauman
given-names: Ahmed
email: n.ahmed@esciencecenter.nl
affiliation: Netherlands eScience Center
orcid: 'https://orcid.org/0000-0003-3559-9941'
- family-names: Anna-Lena
given-names: Lamprecht
email: anna-lena.lamprecht@uni-potsdam.de
affiliation: University of Potsdam
orcid: 'https://orcid.org/0000-0003-1953-5606'
- family-names: Magnus
given-names: Palmblad
email: n.m.palmblad@lumc.nl
affiliation: Leiden University Medical Center
orcid: 'https://orcid.org/0000-0002-5865-8994'
identifiers:
- type: doi
value: 10.5281/zenodo.10048235
repository-code: 'https://github.com/sanctuuary/restape'
url: 'https://github.com/sanctuuary/restape#readme'
abstract: >-
A RESTful API for the APE library (RESTful APE) provides a
way for users to interact with APE's automated pipeline
exploration capabilities through HTTP requests. APE is a
command line tool and Java API that automates the
exploration of possible computational pipelines from large
collections of computational tools.
The RESTful API allows users to submit requests to the APE
server for pipeline exploration, which returns results in
a standard format such as JSON or XML. Users can interact
with APE through a web browser or any other HTTP client,
and the API can be integrated into other applications for
seamless pipeline exploration.
Overall, the RESTful API for APE provides a powerful and
flexible way for users to leverage APE's capabilities in
their scientific workflows.
keywords:
- automated workflow composition
- RESTful API
license: Apache-2.0
GitHub Events
Total
- Create event: 5
- Release event: 1
- Issues event: 1
- Delete event: 4
- Push event: 14
- Pull request review event: 12
- Pull request review comment event: 5
- Pull request event: 9
Last Year
- Create event: 5
- Release event: 1
- Issues event: 1
- Delete event: 4
- Push event: 14
- Pull request review event: 12
- Pull request review comment event: 5
- Pull request event: 9
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- vedran-kasalica (3)
Pull Request Authors
- vedran-kasalica (24)
- dependabot[bot] (8)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v3 composite
- actions/setup-java v3 composite
- advanced-security/maven-dependency-submission-action 571e99aab1055c2e71a1e2309b9691de18d6b7d6 composite
- eclipse-temurin 17-jdk-jammy build
- org.projectlombok:lombok 1.18.26 provided
- com.h2database:h2
- io.github.sanctuuary:APE 2.1.3
- org.graalvm.js:js 22.3.2
- org.springdoc:springdoc-openapi-starter-webmvc-ui 2.1.0
- org.springframework.boot:spring-boot-devtools
- org.springframework.boot:spring-boot-starter-actuator
- org.springframework.boot:spring-boot-starter-data-jpa 3.1.0
- org.springframework.boot:spring-boot-starter-validation
- org.springframework.boot:spring-boot-starter-web
- org.springframework.boot:spring-boot-starter-test test