Automated Metadata Quality Report from CodeMetaSoft

[SergioZSZ]

This issue was created automatically after running metadata quality checks. Several warnings or pitfalls were detected and may be worth reviewing.

This automated issue includes:

• Detected metadata pitfalls and warnings
• A suggested codemeta.json when no codemeta.json was detected
• Suggestions for fixing each issue

Context

This analysis is performed by the CodeMetaSoft project to help improve research software metadata quality.

This is a first initiative aimed at identifying and reporting metadata quality issues across research software repositories.
At this stage, we only provide diagnostics and recommendations.
In future iterations, we plan to propose automated fixes for the detected issues to further simplify the improvement process and reduce manual effort.

Each pitfall and warning is identified by a unique code (e.g. P001 for pitfalls, W004 for warnings) that corresponds to specific metadata quality issues.
You can find more details about these checks and how to address them in the RSMetacheck catalog.

Metadata Quality Report

Repository: https://github.com/oeg-upm/FAIR-Research-Object
Analysis Date: 2026-06-22
sw-metadata-bot version: 0.5.0
RSMetacheck version: 0.3.1

📄 Missing codemeta.json

No root codemeta.json file was detected in the repository. A generated suggestion is provided below.

{
  "@context": "https://w3id.org/codemeta/3.0",
  "@type": [
    "SoftwareSourceCode",
    "SoftwareApplication"
  ],
  "license": {
    "name": "Apache License 2.0",
    "url": "https://spdx.org/licenses/Apache-2.0",
    "identifier": "https://spdx.org/licenses/Apache-2.0"
  },
  "codeRepository": "https://github.com/oeg-upm/FAIR-Research-Object",
  "issueTracker": "https://api.github.com/repos/oeg-upm/FAIR-Research-Object/issues",
  "dateCreated": "2021-11-23",
  "dateModified": "2025-11-19",
  "downloadUrl": "https://github.com/oeg-upm/FAIR-Research-Object/releases",
  "name": "FAIR-Research-Object",
  "logo": "https://raw.githubusercontent.com/oeg-upm/FAIR-Research-Object/main/docs/fairos_logo.png",
  "programmingLanguage": [
    "HTML",
    "Python"
  ],
  "softwareRequirements": [
    {
      "name": "rocrate",
      "@type": "SoftwareApplication",
      "version": "==0.6.1"
    },
    {
      "name": "validators",
      "@type": "SoftwareApplication",
      "version": "==0.18.2"
    },
    {
      "name": "graphviz",
      "@type": "SoftwareApplication",
      "version": "==0.20"
    },
    {
      "name": "somef",
      "@type": "SoftwareApplication",
      "version": "==0.8.0"
    },
    {
      "name": "conda-forge::python",
      "@type": "SoftwareApplication",
      "version": "3.7.6"
    },
    {
      "name": "conda-forge::markdown",
      "@type": "SoftwareApplication",
      "version": "3.2.2"
    },
    {
      "name": "conda-forge::pymdown-extensions",
      "@type": "SoftwareApplication",
      "version": "7.1"
    },
    {
      "name": "conda-forge::pygments",
      "@type": "SoftwareApplication",
      "version": "2.6.1"
    },
    {
      "name": "conda-forge::r-base",
      "@type": "SoftwareApplication",
      "version": "3.6.2"
    },
    {
      "name": "conda-forge::r-optparse",
      "@type": "SoftwareApplication",
      "version": "1.6.6"
    },
    {
      "name": "conda-forge::r-rcolorbrewer",
      "@type": "SoftwareApplication",
      "version": "1.1_2"
    },
    {
      "name": "conda-forge::r-reshape2",
      "@type": "SoftwareApplication",
      "version": "1.4.4"
    },
    {
      "name": "conda-forge::r-ggplot2",
      "@type": "SoftwareApplication",
      "version": "3.3.2"
    },
    {
      "name": "conda-forge::r-tidyr",
      "@type": "SoftwareApplication",
      "version": "1.1.0"
    },
    {
      "name": "conda-forge::r-scales",
      "@type": "SoftwareApplication",
      "version": "1.1.1"
    },
    {
      "name": "conda-forge::r-pheatmap",
      "@type": "SoftwareApplication",
      "version": "1.0.12"
    },
    {
      "name": "conda-forge::r-lattice",
      "@type": "SoftwareApplication",
      "version": "0.20_41"
    },
    {
      "name": "conda-forge::r-upsetr",
      "@type": "SoftwareApplication",
      "version": "1.4.0"
    },
    {
      "name": "conda-forge::r-xfun",
      "@type": "SoftwareApplication",
      "version": "0.15"
    },
    {
      "name": "conda-forge::gawk",
      "@type": "SoftwareApplication",
      "version": "5.1.0"
    },
    {
      "name": "conda-forge::pigz",
      "@type": "SoftwareApplication",
      "version": "2.3.4"
    },
    {
      "name": "bioconda::fastqc",
      "@type": "SoftwareApplication",
      "version": "0.11.9"
    },
    {
      "name": "bioconda::trim-galore",
      "@type": "SoftwareApplication",
      "version": "0.6.5"
    },
    {
      "name": "bioconda::bwa",
      "@type": "SoftwareApplication",
      "version": "0.7.17"
    },
    {
      "name": "bioconda::samtools",
      "@type": "SoftwareApplication",
      "version": "1.10"
    },
    {
      "name": "bioconda::picard",
      "@type": "SoftwareApplication",
      "version": "2.23.1"
    },
    {
      "name": "bioconda::bamtools",
      "@type": "SoftwareApplication",
      "version": "2.5.1"
    },
    {
      "name": "bioconda::pysam",
      "@type": "SoftwareApplication",
      "version": "0.15.3"
    },
    {
      "name": "bioconda::bedtools",
      "@type": "SoftwareApplication",
      "version": "2.29.2"
    },
    {
      "name": "bioconda::ucsc-bedgraphtobigwig",
      "@type": "SoftwareApplication",
      "version": "357"
    },
    {
      "name": "bioconda::deeptools",
      "@type": "SoftwareApplication",
      "version": "3.4.3"
    },
    {
      "name": "bioconda::macs2",
      "@type": "SoftwareApplication",
      "version": "2.2.7.1"
    },
    {
      "name": "bioconda::homer",
      "@type": "SoftwareApplication",
      "version": "4.11"
    },
    {
      "name": "bioconda::subread",
      "@type": "SoftwareApplication",
      "version": "2.0.1"
    },
    {
      "name": "bioconda::phantompeakqualtools",
      "@type": "SoftwareApplication",
      "version": "1.2.2"
    },
    {
      "name": "bioconda::preseq",
      "@type": "SoftwareApplication",
      "version": "2.0.3"
    },
    {
      "name": "bioconda::multiqc",
      "@type": "SoftwareApplication",
      "version": "1.9"
    },
    {
      "name": "bioconda::bioconductor-biocparallel",
      "@type": "SoftwareApplication",
      "version": "1.20.0"
    },
    {
      "name": "bioconda::bioconductor-deseq2",
      "@type": "SoftwareApplication",
      "version": "1.26.0"
    },
    {
      "name": "bioconda::bioconductor-vsn",
      "@type": "SoftwareApplication",
      "version": "3.54.0"
    }
  ],
  "releaseNotes": "This is a new release of the FAIR Research Object assessment tool. The main features included are:\r\n\r\n**Compliance with FTR Specification (v1.3.0)**\r\nThis release aligns the repository with the FAIR Test Results (FTR) specification v1.3.0, enabling standardized, machine-actionable representations of FAIR assessment results.\r\n\r\n**Structured representation of FAIR evaluation components**\r\nIntroduction and integration of core concepts such as tests, metrics, benchmarks, and test results, with explicit relationships between them.\r\nRefactored Research Object structure\r\n\r\n**Enhanced semantic metadata and interoperability**\r\nAdoption of updated metadata models (e.g., JSON-LD contexts and vocabularies) to ensure alignment with FTR and improve interoperability across FAIR tools and platforms.\r\n\r\n**Integration with the OSTrails ecosystem**\r\nImproved compatibility with FAIR assessment tools, registries, and workflows within the OSTrails initiative.\r\n\r\n**General refactoring and cleanup**\r\nRenaming of fields, removal of legacy structures, and overall consistency improvements across the repository.\r\n\r\nRepository: https://github.com/oeg-upm/FAIR-Research-Object\r\nFTR Specification: https://github.com/OSTrails/FAIR_testing_resource_vocabulary",
  "softwareVersion": "v0.0.3",
  "datePublished": "2022-05-31",
  "buildInstructions": [
    "https://github.com/oeg-upm/FAIR-Research-Object/tree/main/docs",
    "https://raw.githubusercontent.com/oeg-upm/FAIR-Research-Object/main/README.md",
    "https://fairos.readthedocs.io/en/latest/?badge=latest"
  ],
  "author": [
    {
      "@type": "Organization",
      "identifier": "oeg-upm",
      "@id": "https://github.com/oeg-upm"
    }
  ],
  "referencePublication": [
    {
      "@type": "ScholarlyArticle",
      "identifier": "https://doi.org/10.1007/978-3-031-16802-4_6",
      "name": "FAIROs: Towards FAIR Assessment in Research Objects",
      "author": [
        {
          "@type": "Organization",
          "name": "Esteban Gonz'alez"
        },
        {
          "@type": "Organization",
          "name": "Alejandro Ben'itez"
        },
        {
          "@type": "Organization",
          "name": "Daniel Garijo"
        }
      ]
    }
  ],
  "identifier": [
    "https://zenodo.org/badge/latestdoi/431199041"
  ],
  "readme": "https://raw.githubusercontent.com/oeg-upm/FAIR-Research-Object/main/README.md",
  "description": [
    "Repository for the work on evaluating FAIRnes of Research Objects"
  ]
}

---

This report was generated automatically by sw-metadata-bot on your main default branch.

If you're not interested in participating, please comment "unsubscribe" and we will remove your repository from our list.
If you would like the pitfalls and warnings to be fixed automatically, please comment "auto-fix" and we will prioritize adding this feature in future iterations.