Merge pull request #42 from sanctuuary/best_practices

Adhere to the best coding practices

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+v.kasalica[at]esciencecenter.nl.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTION.md

@@ -0,0 +1,64 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Types of Contributions
+
+### Report Bugs
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+You can never have enough documentation! Please feel free to contribute to any
+part of the documentation, such as the official docs, docstrings, or even
+on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `RESTful APE` for local development.
+
+1. Download a copy of `RESTful APE` locally.
+2. **Fork** the `RESTful APE` repo on GitHub
+3. **Clone** the project to your own machine
+4. Make changes to the code. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+5. Commit and push your changes.
+6. Open a pull request.
+
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include additional tests if appropriate.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all currently supported operating systems and versions of Python.
+
+## Code of Conduct
+
+Please note that the `RESTful APE` project is released with a
+Code of Conduct. By contributing to this project you agree to abide by its terms.

README.md

@@ -5,8 +5,8 @@
 | Badges | |
 |:----:|----|
 | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8082/badge)](https://www.bestpractices.dev/projects/8082) |
-| **Packages and Releases** |  [![Latest release](https://img.shields.io/github/release/sanctuuary/RESTAPE.svg)](https://github.com/sanctuuary/APE/releases/latest) [![Static Badge](https://img.shields.io/badge/RSD-RESTfulAPE-ape)](https://research-software-directory.org/software/restape)
-| **Build Status** | ![build](https://github.com/sanctuuary/RestAPE/actions/workflows/maven.yml/badge.svg)
+| **Packages and Releases** |  [![Latest release](https://img.shields.io/github/release/sanctuuary/RESTAPE.svg)](https://github.com/sanctuuary/APE/releases/latest) [![Static Badge](https://img.shields.io/badge/RSD-RESTfulAPE-ape)](https://research-software-directory.org/software/restape) |
+| **Build Status** | ![build](https://github.com/sanctuuary/RestAPE/actions/workflows/maven.yml/badge.svg) [![CodeQL](https://github.com/sanctuuary/restape/actions/workflows/codeql.yml/badge.svg)](https://github.com/sanctuuary/restape/actions/workflows/codeql.yml) |
 | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10048236.svg)](https://doi.org/10.5281/zenodo.10048236) |
 | **License** |  [![GitHub license](https://img.shields.io/github/license/sanctuuary/RESTAPE)](https://github.com/sanctuuary/RESTAPE/blob/master/LICENSE) |
 
@@ -55,4 +55,4 @@ This adds the specified APE file to your local Maven repository.
 You can now build the back-end using:
 ````shell
 $ mvn package -DskipTests=true
-````
+````

SECURITY.md

@@ -0,0 +1,32 @@
+# Security Policy
+
+## Supported Versions
+
+Use this section to inform users about which versions of RESTful APE are currently supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 0.2.x   | :white_check_mark: |
+| 0.1.x   | :white_check_mark: |
+
+## Reporting a Vulnerability
+
+If you discover a security vulnerability in RESTful APE, please report it by sending an email to v.kasalica[at]esciencecenter.nl. We ask that you do not publicly disclose the issue until it has been addressed.
+
+In your report, please provide the following information:
+
+- A brief description of the vulnerability.
+- Steps to reproduce the vulnerability.
+- Versions of RESTful APE affected.
+
+We are committed to responding promptly to security reports. We will acknowledge your email within a week and will strive to provide a timeline for resolution as soon as possible.
+
+## Security Response Team
+
+Our security response team consists of the following individuals:
+
+- Vedran Kasalica (v.kasalica[at]esciencecenter.nl)
+
+Please contact the team directly for security-related matters.
+
+Thank you for helping to keep RESTful APE secure!

pom.xml

@@ -42,7 +42,7 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-web</artifactId>
-			<version>3.1.4</version>
+			<version>3.2.1</version>
 		</dependency>
 
 		<dependency>
@@ -61,28 +61,28 @@
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-actuator</artifactId>
-			<version>3.1.4</version>
+			<version>3.2.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-data-jpa -->
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-data-jpa</artifactId>
-			<version>3.1.4</version>
+			<version>3.2.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-validation -->
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-validation</artifactId>
-			<version>3.1.4</version>
+			<version>3.2.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-devtools -->
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-devtools</artifactId>
-			<version>3.1.4</version>
+			<version>3.2.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
@@ -92,23 +92,25 @@
 			<version>2.2.224</version>
 			<scope>runtime</scope>
 		</dependency>
+		<!-- https://mvnrepository.com/artifact/io.github.sanctuuary/APE -->
 		<dependency>
 			<groupId>io.github.sanctuuary</groupId>
 			<artifactId>APE</artifactId>
 			<version>2.2.6</version>
 		</dependency>
 
+		<!-- https://mvnrepository.com/artifact/org.springdoc/springdoc-openapi-starter-webmvc-ui -->
 		<dependency>
 			<groupId>org.springdoc</groupId>
 			<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
-			<version>2.1.0</version>
+			<version>2.3.0</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.graalvm.js/js -->
 		<dependency>
 			<groupId>org.graalvm.js</groupId>
 			<artifactId>js</artifactId>
-			<version>22.3.2</version>
+			<version>23.0.2</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.projectlombok/lombok -->