SoftwareUnderstanding · Anas-Elhounsri · Dec 11, 2025 · Dec 11, 2025
diff --git a/src/metacheck/data/pitfalls_outputs/output_1000_pitfalls.jsonld b/src/metacheck/data/pitfalls_outputs/output_1000_pitfalls.jsonld
@@ -0,0 +1,99 @@
+{
+  "@context": "https://w3id.org/example/metacheck/0.1.0/",
+  "@type": "SoftwareQualityAssessment",
+  "name": "Quality Assessment for tamasgal/km3pipe",
+  "description": "Extemporary analysis framework for KM3NeT",
+  "creator": {
+    "@type": "schema:Person",
+    "name": "Anonymous",
+    "email": "example@email.com"
+  },
+  "dateCreated": "2025-11-18T09:39:43Z",
+  "license": [
+    "@id: https://opensource.org/license/mit"
+  ],
+  "assessedSoftware": {
+    "@type": "schema:SoftwareApplication",
+    "name": "tamasgal/km3pipe",
+    "softwareVersion": "v6.8.1",
+    "url": "https://github.com/tamasgal/km3pipe"
+  },
+  "checks": [
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "The metadata file (codemeta or other) has a version which does not correspond to the version used in the latest release",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P001",
+      "evidence": "P001 detected: codemeta.json version '9.5.0' does not match release version '6.8.1'",
+      "suggestion": "Ensure the version in your metadata matches the latest official release. Keeping these synchronized avoids confusion for users and improves reproducibility."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "The metadata file (codemeta or other) codeRepository does not point to the same repository",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P016",
+      "evidence": "P016 detected: Issue detected in output_1000.json",
+      "suggestion": "Make sure that the codeRepository URL in your metadata exactly matches the repository hosting your source code."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "codemeta.json dateModified is outdated compared to the actual repository last update date",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W002",
+      "evidence": "W002 detected: Issue detected in output_1000.json",
+      "suggestion": "You need to align the version in your metadata file with your latest release tag. Automating this synchronization as part of your release process is highly recommended."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/codemeta"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "Programming languages in codemeta.json do not have versions",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W004",
+      "evidence": "W004 detected: dateModified in codemeta.json is outdated compared to actual repository last update",
+      "suggestion": "Include version numbers for each programming language used. Defining these helps ensure reproducibility and compatibility across systems."
+    }
+  ]
+}
diff --git a/src/metacheck/data/pitfalls_outputs/output_1002_pitfalls.jsonld b/src/metacheck/data/pitfalls_outputs/output_1002_pitfalls.jsonld
@@ -0,0 +1,118 @@
+{
+  "@context": "https://w3id.org/example/metacheck/0.1.0/",
+  "@type": "SoftwareQualityAssessment",
+  "name": "Quality Assessment for IndrajeetPatil/statsExpressions",
+  "description": "Tidy data frames and expressions with statistical summaries 📜",
+  "creator": {
+    "@type": "schema:Person",
+    "name": "Anonymous",
+    "email": "example@email.com"
+  },
+  "dateCreated": "2025-11-18T09:39:45Z",
+  "license": [
+    "@id: https://opensource.org/license/mit"
+  ],
+  "assessedSoftware": {
+    "@type": "schema:SoftwareApplication",
+    "name": "IndrajeetPatil/statsExpressions",
+    "softwareVersion": "1.7.1",
+    "url": "https://github.com/IndrajeetPatil/statsExpressions"
+  },
+  "checks": [
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "The metadata file (codemeta or other) has a version which does not correspond to the version used in the latest release",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P001",
+      "evidence": "P001 detected: DESCRIPTION version '1.7.1.9000' does not match release version '1.7.1'",
+      "suggestion": "Ensure the version in your metadata matches the latest official release. Keeping these synchronized avoids confusion for users and improves reproducibility."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "In codemeta.json contIntegration link returns 404",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P015",
+      "evidence": "P015 detected: Issue detected in output_1002.json",
+      "suggestion": "You need to update the outdated URLs to point to the current CI platform, or remove the property if no active CI is in place. A good pratcie would be to periodically test all external links, especially those related to CI or build status."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/codemeta"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "Programming languages in codemeta.json do not have versions",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W004",
+      "evidence": "W004 detected: dateModified in codemeta.json is outdated compared to actual repository last update",
+      "suggestion": "Include version numbers for each programming language used. Defining these helps ensure reproducibility and compatibility across systems."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "codemeta.json Identifier is a name instead of a valid unique identifier, but an identifier exist",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W006",
+      "evidence": "W006 detected: Issue detected in output_1002.json",
+      "suggestion": "You should replace plain name in your identifier field with persistent identifiers, such as DOIs or SWHIDs, to improve discoverability and interoperability."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "codemeta.json developmentStatus is a URL instead of a string",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W009",
+      "evidence": "W009 detected: Issue detected in output_1002.json",
+      "suggestion": "You need to replace URLs in the developmentStatus field with descriptive text values, such as 'active', 'beta', or 'stable'. This maintains schema compliance and clarity."
+    }
+  ]
+}
diff --git a/src/metacheck/data/pitfalls_outputs/output_1003_pitfalls.jsonld b/src/metacheck/data/pitfalls_outputs/output_1003_pitfalls.jsonld
@@ -0,0 +1,102 @@
+{
+  "@context": "https://w3id.org/example/metacheck/0.1.0/",
+  "@type": "SoftwareQualityAssessment",
+  "name": "Quality Assessment for RECeSS-EU-Project/benchscofi",
+  "description": "Package which contains implementations of published collaborative filtering-based algorithms for drug repurposing.",
+  "creator": {
+    "@type": "schema:Person",
+    "name": "Anonymous",
+    "email": "example@email.com"
+  },
+  "dateCreated": "2025-11-18T09:39:46Z",
+  "license": [
+    "@id: https://opensource.org/license/mit"
+  ],
+  "assessedSoftware": {
+    "@type": "schema:SoftwareApplication",
+    "name": "RECeSS-EU-Project/benchscofi",
+    "softwareVersion": "v2.0.1",
+    "url": "https://github.com/RECeSS-EU-Project/benchscofi",
+    "schema:identifier": {
+      "@id": "https://doi.org/10.5281/zenodo.8241505"
+    }
+  },
+  "checks": [
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "The metadata file (codemeta or other) has a version which does not correspond to the version used in the latest release",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P001",
+      "evidence": "P001 detected: codemeta.json version '1.0.0' does not match release version '2.0.1'",
+      "suggestion": "Ensure the version in your metadata matches the latest official release. Keeping these synchronized avoids confusion for users and improves reproducibility."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "codemeta.json uses bare DOIs in the identifier field instead of full https://doi.org/ URL",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "P014",
+      "evidence": "P014 detected: Issue detected in output_1003.json",
+      "suggestion": "You should include the full DOI URL form in your metadata (e.g., https://doi.org/XX.XXXX/zenodo.XXXX)"
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/metadatafile"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "codemeta.json dateModified is outdated compared to the actual repository last update date",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W002",
+      "evidence": "W002 detected: Issue detected in output_1003.json",
+      "suggestion": "You need to align the version in your metadata file with your latest release tag. Automating this synchronization as part of your release process is highly recommended."
+    },
+    {
+      "@type": "CheckResult",
+      "assessesIndicator": {
+        "@id": "https://w3id.org/example/metacheck/i/indicators/codemeta"
+      },
+      "checkingSoftware": {
+        "@type": "schema:SoftwareApplication",
+        "name": "metacheck",
+        "@id": "https://w3id.org/example/metacheck/tools/",
+        "softwareVersion": "0.1.0"
+      },
+      "process": "Programming languages in codemeta.json do not have versions",
+      "status": {
+        "@id": "schema:CompletedActionStatus"
+      },
+      "checkId": "W004",
+      "evidence": "W004 detected: dateModified in codemeta.json is outdated compared to actual repository last update",
+      "suggestion": "Include version numbers for each programming language used. Defining these helps ensure reproducibility and compatibility across systems."
+    }
+  ]
+}