new properties (license, version) from citation.cff. Fixes #935

README.md

@@ -23,13 +23,20 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
   - Family name: Last name of an author
   - Email: email of author
   - URL: website or ORCID associated with the author
+- **Application type**: type of software (command line application, notebook, ontology, scientific workflow, etc.)
 - **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
-- **Citation**: Preferred citation 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). We aim to recognize the following properties:
+- **Citation**: Preferred citation 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). 
+For CITATION.cff files, SOMEF now generates two separate entries: one for the software and another for the preferred citation (is_preferred_citation: True). This ensures metadata like DOI or version is correctly assigned to each entity.
+We aim to recognize the following properties:
   - Title: Title of the publication
   - Author: list of author names in the publication
   - URL: URL of the publication 
   - DOI: Digital object identifier of the publication
   - Date published
+  - Version: Software version (if applicable)
+  - Journal: Journal name where the paper was published
+  - Year: Year of publication
+  - Pages: Page range in the journal
 - **Code of conduct**: Link to the code of conduct of the project
 - **Code repository**: Link to the GitHub/GitLab repository used for the extraction
 - **Contact**: Contact person responsible for maintaining a software component
@@ -48,13 +55,14 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
 - **Forks url**: Links to forks made of the project
 - **Full name**: Name + owner (owner/name)
 - **Full title**: If the repository is a short name, we will attempt to extract the longer version of the repository name
+- **Funding**: Funding information associated with the project. **Note**: Currently, this information is only extracted from existing `codemeta.json` files within the repository.
 - **Identifier**: Identifier associated with the software (if any), such as Digital Object Identifiers and Software Heritage identifiers (SWH). DOIs associated with publications will also be detected. 
 - **Images**: Images used to illustrate the software component
 - **Installation instructions**: A set of instructions that indicate how to install a target repository
 - **Invocation**: Execution command(s) needed to run a scientific software component
 - **Issue tracker**: Link where to open issues for the target repository
 - **Keywords**: set of terms used to commonly identify a software component
-- **License**: License and usage terms of a software component
+- **License**: License and usage terms of a software component. Now we also extract license from citation.cff.
 - **Logo**: Main logo used to represent the target software component
 - **Maintainer**: Individuals or teams responsible for maintaining the software component, extracted from the CODEOWNERS file
 - **Name**: Name identifying a software component
@@ -77,12 +85,11 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
 - **Repository status**: Repository status as it is described in [repostatus.org](https://www.repostatus.org/).
 - **Requirements**: Pre-requisites and dependencies needed to execute a software component
 - **Run**: Running instructions of a software component. It may be wider than the `invocation` category, as it may include several steps and explanations.
-- **Runtime platform**: specifies runtime platform or script interpreter dependencies required to run the project..
+- **Runtime platform**: specifies the runtime environment or script interpreter dependencies (e.g., Python, Java).
 - **Script files**: Bash script files contained in the repository
 - **Stargazers count**: Total number of stargazers of the project
 - **Support**: Guidelines and links of where to obtain support for a software component
 - **Support channels**: Help channels one can use to get support about the target software component
-- **Type**: type of software (command line application, notebook, ontology, scientific workflow, etc.)
 - **Usage examples**: Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it
 - **Workflows**: URL and path to the computational workflow files present in the repository
 

docs/bibtext.md

@@ -0,0 +1,11 @@
+The following metadata fields can be extracted from a BibTeX *.bib file. 
+These fields are defined in the [BibTeX specification](https://www.bibtex.org/Format/), and are mapped according to the [CodeMeta crosswalk for BibTeX](https://github.com/codemeta/codemeta/blob/master/crosswalks/BibTeX.csv).
+
+| Software metadata category | SOMEF metadata JSON path | BibTeX metadata file field |
+|----------------------------|---------------------------------------|---------------------|
+| citation - value | citation[i].result.value | Full BibTeX entry (reconstructed) |
+| citation - author | citation[i].result.author | author |
+| citation - doi | citation[i].result.doi | doi |
+| citation - title | citation[i].result.title | title |
+| citation - url | citation[i].result.url | url |
+| citation - format | citation[i].result.format | Fixed to "bibtex" |

docs/citationcff.md

@@ -0,0 +1,26 @@
+The following metadata fields can be extracted from a CITATION.cff file. 
+These fields are defined in the [CITATION.cff specification](https://citation-file-format.github.io/), currently at version [1.2.0](https://github.com/citation-file-format/citation-file-format/releases/tag/1.2.0), and are mapped according to the [CodeMeta crosswalk](https://github.com/codemeta/codemeta/tree/master/crosswalks).
+
+| Software metadata category | SOMEF metadata JSON path | CITATION.cff metadata file field |
+|----------------------------|---------------------------------------|---------------------|
+| citation - authors - name | citation[i].result.authors[j].name | authors / preferred-citation.authors |
+| citation - authors - family_name | citation[i].result.authors[j].family_name | authors.family-names |
+| citation - authors - given_name | citation[i].result.authors[j].given_name | authors.given-names |
+| citation - authors - url | citation[i].result.authors[j].url | authors.orcid |
+| citation - doi | citation[i].result.doi | doi / preferred-citation.doi |
+| citation - datePublished | citation[i].result.datePublished | date-released |
+| citation - is_preferred_citation | citation[i].result.is_preferred_citation | "True" if from preferred-citation. Omitted otherwise|
+| citation - journal | citation[i].result.journal | preferred-citation.journal |
+| citation - year | citation[i].result.year | preferred-citation.year |
+| citation - pages | citation[i].result.pages | preferred-citation.pages |
+| citation - title | citation[i].result.title | title / preferred-citation.title |
+| citation - type | citation[i].result.type | type / preferred-citation.type *(1)* |
+| license - value | license[i].result.value | license |
+| license - spdx_id | license[i].result.spdx_id | license |
+| license - name | license[i].result.name | license  |
+
+---
+
+*(1)* 
+For the CFF main block, the type is mapped to SoftwareApplication. For the preferred-citation block, it is mapped to ScholarlyArticle.
+

docs/codemetajson.md

@@ -28,8 +28,9 @@ These fields are defined in the [Codemeta specification](https://github.com/code
 | development_status       |   development_status[i].result.value  |     developmentStatus  |
 | download_url              |   download_url[i].result.value          |     downloadUrl              |
 | has_package_file         |   has_package_file[i].result.value         |   URL of the codemeta.json file |
-| funding - funder                   |   funding[i].result.funder       |     funding.funder or funding.funder.name  |    
-| funding - funding                   |   funding[i].result.funding     |     String.fundingIdentifier | 
+| funding - funder          |   funding[i].result.funder       |     funder.@id or funder.name  *(1)*|    
+| funding - funding         |   funding[i].result.funding     |     funding *(1)*| 
+| funding - value	        |   funding[i].result.value	|   funding string or funder.name *(1)*|
 | identifier               |   identifier[i].result.value       |     identifier                     |
 | issue_tracker             |   issue_tracker[i].result.value           |     issueTracker             |
 | keywords                  |   keywords[i].result.value          |     keywords                 |
@@ -49,4 +50,41 @@ These fields are defined in the [Codemeta specification](https://github.com/code
 | version                   |   version[i].result.value   |     softwareVersion  or version        |
 
 
-
+---
+
+*(1)* 
+
+- SOMEF json result: 
+
+```
+"funding": [
+  {
+    "result": {
+      "value": "1549758; Codemeta: A Rosetta Stone for Metadata in Scientific Software",
+      "type": "String",
+      "funder": {
+        "@id": "https://doi.org/10.13039/100000001",
+        "@type": "Organization",
+        "name": "National Science Foundation"
+      },
+      "funding": "1549758; Codemeta: A Rosetta Stone for Metadata in Scientific Software"
+    },
+    "confidence": 1,
+    "technique": "code_parser",
+    "source": "https://raw.githubusercontent.com/.../codemeta.json"
+  }
+]
+```
+
+- CODEMETA output: 
+```
+"funder": {
+    "@id": "https://doi.org/10.13039/100000001",
+    "@type": "Organization",
+    "name": "National Science Foundation"
+  },
+"funding": "1549758; Codemeta: A Rosetta Stone for Metadata in Scientific Software",
+```
+
+
+

docs/condaenvironment.md

@@ -35,15 +35,15 @@ dependencies:
         "value": "python=3.8.5",
         "name": "python",
         "version": "3.8.5",
-        "type": "Software_application",
+        "type": "SoftwareDependency",
         "dependency_type": "runtime",
         "dependency_resolver": "conda"
     },
     "result": {
         "value": "albumentations==0.4.3",
         "name": "albumentations",
         "version": "0.4.3",
-        "type": "Software_application",
+        "type": "SoftwareDependency",
         "dependency_type": "runtime",
         "dependency_resolver": "pip"
     },

docs/gemspec.md

@@ -79,7 +79,7 @@ spec.requirements = [
 
 Result: add_depency -> type runtime; add_development_dependencyd -> type dev 
 ```
-    [{'result': {'value': 'railties: >= 3.0', 'name': 'railties', 'version': '>= 3.0', 'type': 'Software_application', 'dependency_type': 'runtime', 'dependency_resolver': 'bundler'}, 'confidence': 1, 'technique': 'code_parser', 'source': 'https://example.org/bootstrap-datepicker-rails.gemspec'}, {'result': {'value': 'bundler: >= 1.0', 'name': 'bundler', 'version': '>= 1.0', 'type': 'Software_application', 'dependency_type': 'dev','dependency_resolver': 'bundler'}, 'confidence': 1, 'technique': 'code_parser', 'source': 'https://example.org/bootstrap-datepicker-rails.gemspec'}]
+    [{'result': {'value': 'railties: >= 3.0', 'name': 'railties', 'version': '>= 3.0', 'type': 'SoftwareDependency', 'dependency_type': 'runtime', 'dependency_resolver': 'bundler'}, 'confidence': 1, 'technique': 'code_parser', 'source': 'https://example.org/bootstrap-datepicker-rails.gemspec'}, {'result': {'value': 'bundler: >= 1.0', 'name': 'bundler', 'version': '>= 1.0', 'type': 'SoftwareDependency', 'dependency_type': 'dev','dependency_resolver': 'bundler'}, 'confidence': 1, 'technique': 'code_parser', 'source': 'https://example.org/bootstrap-datepicker-rails.gemspec'}]
 ```
 
 

docs/index.md

@@ -15,6 +15,7 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
 
 - **Acknowledgement**: Text acknowledging funding sources or contributors
 - **Application domain**: The application domain of the repository. This may be related to the research area of a software component (e.g., Astrophysics) or the general domain/functionality of the tool (i.e., machine learning projects)<sup>[1](#myfootnote1)</sup> 
+- **Application type**: type of software (command line application, notebook, ontology, scientific workflow, etc.)
 - **Assets**: files attached to the release
   - url: URL of the publication of the file
   - name: name of the file
@@ -31,12 +32,18 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
   - URL: website or ORCID associated with the author
   - Affiliation: name of organization or affiliation
 - **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
-- **Citation**: Preferred citation 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). We aim to recognize the following properties:
+- **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). 
+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.
+We aim to recognize the following properties:
   - Title: Title of the publication
   - Author: list of author names in the publication
   - URL: URL of the publication 
   - DOI: Digital object identifier of the publication
-  - Date published:
+  - Date published
+  - Version: Software version (if applicable, i.e., the main citation is a software deposit)
+  - Journal: Journal name where the paper was published
+  - Year: Year of publication
+  - Pages: Page range in the journal
 - **Code of conduct**: Link to the code of conduct of the project
 - **Code repository**: Link to the GitHub/GitLab repository used for the extraction
 - **Contact**: Contact person responsible for maintaining a software component
@@ -55,14 +62,15 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
 - **Forks url**: Links to forks made of the project
 - **Full name**: Name + owner (owner/name)
 - **Full title**: If the repository is a short name, we will attempt to extract the longer version of the repository name
+- **Funding**: Funding information associated with the project. **Note**: Currently, this information is only extracted from existing `codemeta.json` files within the repository.
 - **Homepage**: URL of the item.
 - **Identifier**: Identifier associated with the software (if any), such as Digital Object Identifiers and Software Heritage identifiers (SWH). DOIs associated with publications will also be detected. 
 - **Images**: Images used to illustrate the software component
 - **Installation instructions**: A set of instructions that indicate how to install a target repository
 - **Invocation**: Execution command(s) needed to run a scientific software component
 - **Issue tracker**: Link where to open issues for the target repository
 - **Keywords**: set of terms used to commonly identify a software component
-- **License**: License and usage terms of a software component
+- **License**: License and usage terms of a software component 
 - **Logo**: Main logo used to represent the target software component
 - **Name**: Name identifying a software component
 - **Ontologies**: URL and path to the ontology files present in the repository
@@ -85,12 +93,11 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
 - **Repository status**: Repository status as it is described in [repostatus.org](https://www.repostatus.org/).
 - **Requirements**: Pre-requisites and dependencies needed to execute a software component
 - **Run**: Running instructions of a software component. It may be wider than the `invocation` category, as it may include several steps and explanations.
-- **Runtime platform**: specifies runtime platform or script interpreter dependencies required to run the project.
+- **Runtime platform**: specifies the runtime environment or script interpreter dependencies (e.g., Python, Java)
 - **Script files**: Bash script files contained in the repository
 - **Stargazers count**: Total number of stargazers of the project
 - **Support**: Guidelines and links of where to obtain support for a software component
 - **Support channels**: Help channels one can use to get support about the target software component
-- **Type**: type of software (command line application, notebook, ontology, scientific workflow, etc.)
 - **Usage examples**: Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it
 - **Workflows**: URL and path to the computational workflow files present in the repository