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Merge pull request #969 from KnowledgeCaptureAndDiscovery/dev
Fixing citation reconciliation and documentation
2 parents 72615b8 + 6b4d7d6 commit 5719ace

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‎README.md‎

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@@ -27,6 +27,7 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
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- **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
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- **Citation**: Preferred citation(s) as the authors have stated in their readme file. SOMEF recognizes Bibtex, Citation File Format files and other means by which authors cite their papers (e.g., by in-text citation).
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For CITATION.cff files, SOMEF now generates two separate entries: one for the software tool and another for the preferred citation (if available). This ensures metadata like DOI or version is correctly assigned to each entity.
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SOMEF now performs citation reconciliation: scholarly publications (articles) are assigned in codemeta to `referencePublication`, while the software itself is credited in `creditText`. (See https://somef.readthedocs.io/en/latest/output/#codemeta-format).
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We recognize the following properties:
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- Title: Title of the publication
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- Author: list of author names in the publication
@@ -41,7 +42,7 @@ We recognize the following properties:
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- **Contact**: Contact person responsible for maintaining a software component
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- **Continuous integration**: Link to continuous integration service(s)
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- **Contribution guidelines**: Text indicating how to contribute to this code repository
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- **Contributors**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
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- **Contributor**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
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- **Creation date**: Date when the repository was created
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- **Copyright holder**: Entity or individual owning the rights to the software. The year is also extracted, if available.
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- **Date updated**: Date of last release.

‎docs/author.md‎

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@@ -3,11 +3,11 @@ These fields are defined in the [Authors file specification](https://opensource.
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| Software metadata category | SOMEF metadata JSON path | AUTHORS metadata file field |
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|-------------------------------|---------------------------------------------|------------------------------|
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| authors - value | authors[i].result.value | *(1)* value |
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| authors - name | authors[i].result.name | *(2)* name |
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| authors - email | authors[i].result.email | *(3)* email |
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| authors - given name | authors[i].result.given_name | *(4)* if type person |
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| authors - last name | authors[i].result.last_name | *(5)* if type person |
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| author - value | author[i].result.value | *(1)* value |
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| author - name | author[i].result.name | *(2)* name |
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| author - email | author[i].result.email | *(3)* email |
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| author - given name | author[i].result.given_name | *(4)* if type person |
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| author - last name | author[i].result.last_name | *(5)* if type person |
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---
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‎docs/bower.md‎

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@@ -3,7 +3,7 @@ These fields are defined in the [Bower specification](https://github.com/bower/s
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| Software metadata category | SOMEF metadata JSON path | BOWER.JSON metadata file field |
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|-----------------------------|---------------------------------------|---------------------|
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| authors | authors[i].result.value | authors[] |
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| author | author[i].result.value | authors[] |
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| description | description[i].result.value | description |
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| has_package_file | has_package_file[i].result.value | URL of the bower.json file |
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| homepage | homepage[i].result.value | homepage |

‎docs/cargo.md‎

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@@ -3,9 +3,9 @@ These fields are defined in the [Cargo.toml specification](https://doc.rust-lang
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| Software metadata category | SOMEF metadata JSON path | CARGO.TOML metadata file field |
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|-------------------------------|--------------------------------------------|------------------------------|
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| authors - value | authors[i].result.value | package.authors |
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| authors - name | authors[i].result.name | package.authors *(1)* |
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| authors - email | authors[i].result.email | package.authors *(2)* |
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| author - value | author[i].result.value | package.authors |
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| author - name | author[i].result.name | package.authors *(1)* |
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| author - email | author[i].result.email | package.authors *(2)* |
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| code_repository | code_repository[i].result.value | package.repository |
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| description | description[i].result.value | package.description |
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| has_package_file | has_package_file[i].result.value | URL of the cargo.toml file |

‎docs/citationcff.md‎

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@@ -3,10 +3,10 @@ These fields are defined in the [CITATION.cff specification](https://citation-fi
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| Software metadata category | SOMEF metadata JSON path | CITATION.cff metadata file field |
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|----------------------------|---------------------------------------|---------------------|
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| citation - authors - name | citation[i].result.authors[j].name | authors / preferred-citation.authors |
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| citation - authors - family_name | citation[i].result.authors[j].family_name | authors.family-names |
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| citation - authors - given_name | citation[i].result.authors[j].given_name | authors.given-names |
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| citation - authors - url | citation[i].result.authors[j].url | authors.orcid |
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| citation - author - name | citation[i].result.author[j].name | authors / preferred-citation.authors |
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| citation - author - family_name | citation[i].result.author[j].family_name | authors.family-names |
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| citation - author - given_name | citation[i].result.author[j].given_name | authors.given-names |
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| citation - author - url | citation[i].result.author[j].url | authors.orcid |
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| citation - doi | citation[i].result.doi | doi / preferred-citation.doi |
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| citation - datePublished | citation[i].result.datePublished | date-released |
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| citation - is_preferred_citation | citation[i].result.is_preferred_citation | "True" if from preferred-citation. Omitted otherwise|

‎docs/codemetajson.md‎

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@@ -4,23 +4,23 @@ These fields are defined in the [Codemeta specification](https://github.com/code
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| Software metadata category | SOMEF metadata JSON path | CODEMETA.JSON metadata file field |
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|-------------------------------|------------------------------|--------------------------------------------|
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| application_domain | application_domain[i].result.value | applicationCategory |
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| authors - value | authors[i].result.value | author.name or author.givenName + author.familyName |
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| authors - email | authors[i].result.email | author.email |
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| authors - affiliation | authors[i].result.affiliation | author.affiliation |
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| authors - identifier | authors[i].result.identifier | author.identifier or author.@id |
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| author - value | author[i].result.value | author.name or author.givenName + author.familyName |
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| author - email | author[i].result.email | author.email |
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| author - affiliation | author[i].result.affiliation | author.affiliation |
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| author - identifier | author[i].result.identifier | author.identifier or author.@id |
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| citation - value | citation[i].result.value | referencePublication.name or referencePublication.title |
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| citation - title | citation[i].result.title | referencePublication.name or referencePublication.title |
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| citation - url | citation[i].result.url | referencePublication.url |
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| citation - date published | citation[i].result.date_published | referencePublication.datePublished
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| citation - doi | citation[i].result.doi | referencePublication.identifier |
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| code_repository | code_repository[i].result.value | codeRepository |
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| continuous_integration | continuous_integration[i].result.value | contIntegration |
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| contributors - value | contributors[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
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| contributors - name | contributors[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
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| contributors - last_name | contributors[i].result.value | contributor.familyName |
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| contributors - given_name | contributors[i].result.value | contributor.givenName |
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| contributors - identifier | contributors[i].result.value | contributor.@id |
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| contributors - email | contributors[i].result.value | contributor.email |
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| contributor - value | contributor[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
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| contributor - name | contributor[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
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| contributor - last_name | contributor[i].result.value | contributor.familyName |
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| contributor - given_name | contributor[i].result.value | contributor.givenName |
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| contributor - identifier | contributor[i].result.value | contributor.@id |
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| contributor - email | contributor[i].result.value | contributor.email |
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| date_created | date_created[i].result.value | dateCreated |
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| date_updated | date_updated[i].result.value | dateModified |
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| date_published | date_published[i].result .value | datePublished |

‎docs/composer.md‎

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| Software metadata category | SOMEF metadata JSON path | COMPOSER.JSON metadata file field |
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|-------------------------------|-----------------------------------|-----------------------------------|
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| authors - value | authors[i].result.value | authors.name |
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| authors - name | authors[i].result.name | authors.name |
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| authors - name | authors[i].result email | authors.email |
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| authors - url | authors[i].result.url | authors.homepage |
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| authors - role | authors[i].result.role | authors.role |
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| author - value | author[i].result.value | authors.name |
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| author - name | author[i].result.name | authors.name |
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| author - name | author[i].result email | authors.email |
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| author - url | author[i].result.url | authors.homepage |
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| author - role | author[i].result.role | authors.role |
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| code_repository | code_repository[i].result.value | repository or repository.url |
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| description | description[i].result.value | description |
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| has_package_file | has_package_file[i].result.value | URL of the composer.json file |

‎docs/description.md‎

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@@ -3,8 +3,8 @@ These fields are defined in the [DESCRIPTON specification](https://r-pkgs.org/de
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| Software metadata category | SOMEF metadata JSON path | DESCRIPTION metadata file field |
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|-------------------------------|---------------------------------|---------------------|
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| authors | authors[i].result.value | Authors *(1)* |
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| authors | authors[i].result.email | Authors *(2)* |
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| author | authors[i].result.value | Authors *(1)* |
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| author | authors[i].result.email | Authors *(2)* |
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| code_repository | code_repository[i].result.value | URL *(3)* |
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| description | description[i].result.value | Description *(4)* |
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| has_package_file | has_package_file[i].result.value | URL of the DESCRIPTION file |

docs/dockerfiledoc.md renamed to docs/docker_file_doc.md

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| Software metadata category | SOMEF metadata JSON path | DOCKERFILE metadata file field |
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|-----------------------------|-----------------------------------------|------------------------------------|
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| authors | authors[i].result.value | org.opencontainers.image.authors *(1)* |
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| authors | authors[i].result.value | LABEL maintainer *(1)* |
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| author | author[i].result.value | org.opencontainers.image.authors *(1)* |
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| author | author[i].result.value | LABEL maintainer *(1)* |
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| code_repository | code_repository[i].result.value | org.opencontainers.image.url |
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| description | description[i].result.value | org.opencontainers.image.description |
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| documentation | documentation[i].result.value | org.opencontainers.image.documentation |

‎docs/gemspec.md‎

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| Software metadata category | SOMEF metadata JSON path | .gemspec metadata file field |
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|-------------------------------|--------------------------------|--------------------------------------|
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| authors | authors[i].result.value | gem.authors *(1)* |
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| author | authors[i].result.value | gem.authors *(1)* |
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| description | description[i].resultvalue | description *(2)* |
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| has_package_file | has_package_file[i].result.value | URL of the filename.gemspec file |
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| homepage | homepage[i].result.value | homepage *(3)* |

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