Releases | Open Source Science

widoco - WiDOCO 1.4.25: Documentation fixes and new provenance flag

This version of WIDOCO fixes documentation broken links, clarifies how to download Docker images and includes a new option for excluding the provenance page from documentation (thanks to @MikiDi)

What's Changed

Bump docker/build-push-action from 5.3.0 to 5.4.0 by @dependabot in https://github.com/dgarijo/Widoco/pull/709
CLI option to exclude provenance link by @MikiDi in https://github.com/dgarijo/Widoco/pull/710
Improved documentation (broken links)

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.24...v1.4.25

- JavaScript
Published by dgarijo almost 2 years ago

widoco - WiDOCO 1.4.23: Hotfix for SWRL rules

This release introduces a hotfix for ontologies with SWRL rules and empty labels.

What's Changed

External Property Parser: Fix comparison to optional variable by @vChavezB in https://github.com/dgarijo/Widoco/pull/693
Develop by @dgarijo in https://github.com/dgarijo/Widoco/pull/701

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.23...v1.4.24

- JavaScript
Published by dgarijo about 2 years ago

widoco - WiDOCO 1.4.23: Bugfixes

Quick release for three minor bugs detected by @SirkoS:

Error in dark mode table
Markdown support when using the uniteSections flag
Content override when HTML sections were set up by hand.

What's Changed

bugfixes by @SirkoS in https://github.com/dgarijo/Widoco/pull/690
Merging latest master/develop by @dgarijo in https://github.com/dgarijo/Widoco/pull/691

New Contributors

@SirkoS made their first contribution in https://github.com/dgarijo/Widoco/pull/690

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.22...v1.4.23

- JavaScript
Published by dgarijo about 2 years ago

widoco - WiDOCO 1.4.22: Dark mode and flexibility for loading references

This version of Widoco adds a great dark mode by @vChavezB and some fixes to allow pointing to the code repo where a vocabulary is maintained, removing obsolete html annotations and allowing to load your own reference section from a config file.

What's Changed

Run widoco with unprivileged user in container by @janvlug in https://github.com/dgarijo/Widoco/pull/669
Fixed SWRL Toc by @vChavezB in https://github.com/dgarijo/Widoco/pull/670
Bump docker/metadata-action from 5.4.0 to 5.5.0 by @dependabot in https://github.com/dgarijo/Widoco/pull/673
Added darkmode by @vChavezB in https://github.com/dgarijo/Widoco/pull/672
Parsing external owl entities (direct/indirect imports) + individual facts with external owl entites by @vChavezB in https://github.com/dgarijo/Widoco/pull/668
Bump docker/metadata-action from 5.5.0 to 5.5.1 by @dependabot in https://github.com/dgarijo/Widoco/pull/678
feat: Considering owl:unionOf for rdfs:domain and rdfs:range by @Murloc6 in https://github.com/dgarijo/Widoco/pull/679
Allow loading local ontologies for imports by @vChavezB in https://github.com/dgarijo/Widoco/pull/674
Fix #618 by @dgarijo in https://github.com/dgarijo/Widoco/pull/685
fix(extraction): Do not force lower-case if URI do not have label by @Murloc6 in https://github.com/dgarijo/Widoco/pull/686
Develop by @dgarijo in https://github.com/dgarijo/Widoco/pull/687
version update by @dgarijo in https://github.com/dgarijo/Widoco/pull/689

New Contributors

@Murloc6 made their first contribution in https://github.com/dgarijo/Widoco/pull/679

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.21...v1.4.22

- JavaScript
Published by dgarijo about 2 years ago

widoco - WiDOCO 1.4.21: Better support for rules and minor fixes

This release introduces the following changes: * Better support for SWRL rules thanks to @vChavezB * Fix #658 problems displaying custom introduction sections * Improved documentation and README * Now the affiliation parenthesis and commas are more consistent for authors (#572) * Fixed a problem when using the flag -confFile making disappear the namespace declaration section

New Contributors

@MikiDi made their first contribution in https://github.com/dgarijo/Widoco/pull/644
@vChavezB made their first contribution in https://github.com/dgarijo/Widoco/pull/653

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.20...v1.4.21

- JavaScript
Published by dgarijo over 2 years ago

widoco - WiDOCO 1.4.20: Increased Metadata support and many fixes

This new release addresses the issues listed below, and it updates the metadata guides:

Name is expanded and documented in table and guides (614).
DateRelease and dateModified overlap (fixed) (614)
Support for http and https in schema.org properties (before only https). This flexibility is to address potential mismatch properties.
Fixed Licensius integration issues (607)
Placed JSON-LD before than HTML in htaccess so we can import ontologies in the JSON-LD playground (i.e., from browser)
Support for extended ontologies added from the ontology metadata (with voaf:extends) (614)
Separated abstract from description. Used ontology description for the description section (544)
Imported ontologies have been added to the documentation table (614)
skos:editorialNote (592)
editorialNote is not added in guide (now added)
Added preferred metadata terms in checklist, and added examples for each (242)
Added dce and dct as elements and terms for dublin core.
Added support for:
- pav:version (http://purl.org/pav/version) (versionInfo)
- http://purl.org/dc/terms/hasVersion (versionInfo)
- http://purl.org/pav/lastUpdatedOn (modified)
- http://www.w3.org/2007/05/powder-s#describedBy (source)
Added support for logos (and guidelines to add them #497).
Fixed error: when saving properties, there are some nulls in publisher.
Added support for mod:status.
Added support for describedby (source)
Add editorialNote in metadata guide.
Add source in Widoco (ontology level). And load/save in properties. And form. And HTML.
Add seeAlso in Widoco (ontology level). And load/save in properties. And form. And HTML.
Explain how to run from code (#574)
add support for schema:creativeWorkStatus.
Sort NS table (#610)
Checked equivalentClass works correctly.
JFileChooser in GUI (602) (except a minor one for browsing folders)
Fix #605 about the main gui when saving withot the --rewriteAll option.
If multiple labels (skos:prefLabel, rdfs:label) are provided, just pick just one. #556
Added funding and funder information
Intro section (new property) (#544, #612)
Intro: load it from properties file if available.
Supported serializations (new prop)
Fixed problem with funders.
Added tests.
Separate namespace declaration in a different html (#609)
isDefinedBy in data properties does not work well (#588)
Bug: properties extending annotation properties do not work (530)
Rules: add a new section + doc (#591)

- JavaScript
Published by dgarijo almost 3 years ago

widoco - WiDOCO 1.4.19: Small fixes on redirections and version

This new release of WIDOCO: - Addresses a problem with the name of the files for the rdf/xml serialization (at times .owl, at time .rdf). Now it's always .owl. - Adds a small icon (RDF) to the documentation pages - Adds the version of the WIDOCO JAR explicitly with the command --version - OOPS! tests are now static, not requiring the service to work for the build to pass.

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.18...v1.4.19

- JavaScript
Published by dgarijo about 3 years ago

widoco - WIDOCO 1.4.18: Fix javascript issues

This version fixes: - Minor problems in the generated HTML. - Minor problems with mixed content in the javascript - Clarifies documentation on which fields Widoco adopts.

New Contributors

Thanks to: * @telecsur made their first contribution in https://github.com/dgarijo/Widoco/pull/517 * @janvlug made their first contribution in https://github.com/dgarijo/Widoco/pull/538 * @HanKruiger made their first contribution in https://github.com/dgarijo/Widoco/pull/540 * @JohannesLipp made their first contribution in https://github.com/dgarijo/Widoco/pull/547 * @ioggstream made their first contribution in https://github.com/dgarijo/Widoco/pull/561

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.17...v1.4.18

- JavaScript
Published by dgarijo about 3 years ago

widoco - WIDOCO 1.4.17: Update OOPS! Web service. GitHub actions

This version fixes OOPS! (newest URL) and sets up GitHub actions so users with different versions of Java can use Widoco.

What's Changed

update readme and pom with proper versions by @dgarijo in https://github.com/dgarijo/Widoco/pull/502
switch import fonts to always use https scheme by @renefritze in https://github.com/dgarijo/Widoco/pull/509
[ci] setup gh actions + dependabot by @renefritze in https://github.com/dgarijo/Widoco/pull/507
Github actions set up by @renefritze by @dgarijo in https://github.com/dgarijo/Widoco/pull/512

New Contributors

@renefritze made their first contribution in https://github.com/dgarijo/Widoco/pull/509

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.16...v1.4.17

- JavaScript
Published by dgarijo about 4 years ago

widoco - WIDOCO 1.4.16: Support for German and Dutch

This version of WIDOCO includes support for German and Dutch (thanks to Flores Bakker), extraction of metadata from local authors and organizations URIs (if you describe authors and their organizations in your ontology, WIDOCO will automatically detect it) and additional support for adding images in your documentation.

What's Changed

Fix/duplicate namespace declarations by @pmcb55 in https://github.com/dgarijo/Widoco/pull/471
Only show legend entries if relevant by @pmcb55 in https://github.com/dgarijo/Widoco/pull/472
Dockerize project by @ccamel in https://github.com/dgarijo/Widoco/pull/479
Support for adding images with GUI by @dgarijo in https://github.com/dgarijo/Widoco/pull/492
Fix #262 by @dgarijo in https://github.com/dgarijo/Widoco/pull/493
German translation by @JohnnyMoonlight in https://github.com/dgarijo/Widoco/pull/494
Support for it and de by @dgarijo in https://github.com/dgarijo/Widoco/pull/495
Fix #498 by @engapa in https://github.com/dgarijo/Widoco/pull/500

New Contributors

@ccamel made their first contribution in https://github.com/dgarijo/Widoco/pull/479
@JohnnyMoonlight made their first contribution in https://github.com/dgarijo/Widoco/pull/494
@engapa made their first contribution in https://github.com/dgarijo/Widoco/pull/500

Full Changelog: https://github.com/dgarijo/Widoco/compare/v1.4.15...v1.4.16

- JavaScript
Published by dgarijo over 4 years ago

widoco - WIDOCO 1.4.15: Major bug fixes

This release addresses the following problems: - fixed return types for jsonld and rdf (#454) - fixed small caps issue for case sensitivity files in Unix (#455) - fix wrong metadata in prefix (#453) - Incorporated previous prereleases fixes.

All bugs fixed in this release can be found here

- JavaScript
Published by dgarijo almost 5 years ago

widoco - WIDOCO 1.4.15_1 (pre-release): Namespace prefixes fixes and WebVowl update

This pre-release fixes issues regarding namespace prefixes (now they will be rad directly from the ontology instead of using LODE); it updates WebVOWL to the latest version (which let's you change the settings in your visualization)

More information on the addressed issues can be seen in: https://github.com/dgarijo/Widoco/milestone/2?closed=1

- JavaScript
Published by dgarijo over 5 years ago

widoco - WIDOCO 1.4.15 (pre-release): Bug fixes and FAQ

(This is a pre-relase. For more information about the next release see https://github.com/dgarijo/Widoco/milestone/2) This pre-release of WIDOCO fixes some bugs and adds a FAQ for common questions posted as issues. In particular, this solves: - External links will now open in another window instead of appearing dotted. - Fixed issue that made the index not be generated when including all the sections in a single html. - Added a FAQ explaining why by default the documentation cannot be seen locally. - Added a FAQ regarding how to use markdown on class definitions. - Error with a missing path when the CLI was run, which resulted in the /sections folder not being generated. - Fixed a typo in acknowledgments - Fixed typo in schema.org snippet. - Fixed a few URLs from http -> https

- JavaScript
Published by dgarijo almost 6 years ago

widoco - WIDOCO 1.4.14: Multiple updates and bug fixes

This version of WIDOCO updates some of the web services used: * Updated a comprehensive --help command. * Reviewed metadata properties (added incompatibleWith) * Removed JENA dependencies (now only OWLAPI is used) * Unified logging (now only SLF4J is used). * Fixed pointers in WIDOCO guidelines. * Updated OOPS! webservice call. * Fixed invalid ttl file when generating the provenance of a documentation.

- JavaScript
Published by dgarijo about 6 years ago

widoco - WIDOCO 1.4.13: Linking evaluation in documentation

This version of WIDOCO removes a few of unused dependencies and, if desired, shows a link to the OOPS! evaluation generated in the documentation. Before, this link had to be added manually.

Thanks to @HaydarAk for the suggestions on how to show it in the main page.

- JavaScript
Published by dgarijo over 6 years ago

widoco - WIDOCO 1.4.12: Big fixes and new configurations

This version of WIDOCO addresses the following issues (thanks to @pmcb55 for his contributions!!) * #354: The page would display centered in the visualization instead of the element loaded. * #362: Upgraded to latest version of OWL API * #361: Allowed adding a "-uniteAllSections" flag that will print all sections on the same document. Hence, dynamic loading will be removed. * Tidying up PROV rendering. * Small typo fixes in the default html

- JavaScript
Published by dgarijo over 6 years ago

widoco - WIDOCO 1.4.11: Better logging and bug fixes

This version of WIDOCO integrates the pull requests from @seralf to improve logging and simplify dependencies. In addition, it addresses the following issues: * #344: Now double "#" errors have been removed from changelog. * #350: Fixed an issue in which the references would overwrite the main section

- JavaScript
Published by dgarijo about 7 years ago

widoco - WIDOCO 1.4.10: Pull requests, updates and bug fixes

This version of WIDOCO incorporates pull requests from @seralf and @jgeluk (updating to the latest version of WebVowl) and fixes the following issues: * #333 Now if there is an error in one of the imports the application will continue running instead of failing. * #217 Now the changelog can be expanded and collapsed, which makes it easier to navigate * #313 A link will be added in the index page if provided in the config file (using contextURI="YOUR URL") * #339 Now WIDOCO will generate the folders four your htaccess file as well.

In addition, now the base encoding is UTF-8.

- JavaScript
Published by dgarijo about 7 years ago

widoco - WIDOCO 1.4.9: Supporting schema.org

This version of WIDOCO addresses the following: * #274: Now WIDOCO will include the domain and range if you use schema:domainIncludes and schema:rangeIncludes to declare it in your object properties or data properties with . Note that WIDOCO still does not support plain rdf:Property. * Reduced the level of logging

- JavaScript
Published by dgarijo over 7 years ago

widoco - WIDOCO 1.4.8: Logging and automated citation

This release of WIDOCO includes: * Fixes from @jgeluk to do proper logging. * Fix #264: now an automated citation will be produced for your ontology by default (if the appropriate metadata is there: creators, revision, and URL (this version) * JenaCatalogIRIMapper now supports Jena's ont-policy.rdf file to resolve imports with local files * Fixed #321, now WIDOCO uses a more recent version of OWL API

- JavaScript
Published by dgarijo over 7 years ago

widoco - WIDOCO 1.4.7: Dependency and bug fixes

This release of WIDOCO fixes the following issues: * #305: Now when you launch WIDOCO without parameters, the console will also show a description of the tool and will explain how to run it. * #309 Removed the absolute layout dependency that prevented WIDOCO JAR from being run. * #311 Now the publisher will show on the GUI correctly (before it would only if it had a URL) * #314: Added an html tag around the external sections so the browser won't complain * #316 Fixed the generation of the table of contents so "back to TOC" wouldn't appear * #317 Fixed the GUI so the "Imported ontologies" label appears as imported and not "extended" It also removes the restlet dependency, which had a vulnerability and was not used anymore.

- JavaScript
Published by dgarijo over 7 years ago

widoco - WIDOCO 1.4.6: Tutorial and bug fixes

This version of WIDOCO includes the following updates: * Updated the OWL2Vowl library to the latest version (old library was producing errors in some ontologies) * Included a tutorial (http://dgarijo.github.io/Widoco/doc/tutorial/) describing the GUI step by step and all its functionality * Added support for selecting ontologies in JSON * Added contributing guidelines into readme.md * Fixed namespaces when selecting documentation in several languages * Now it's possible to edit the rewrite base path in the .htaccess file. * Fixed a typo in the .htaccess for serving json * Fixed an encoding problem when showing french labels. * @kartgk fixed an error with the import closure of ontologies (in case not all imports of imported ontologies wanted to be displayed) * Added the correct version numbers to pom file. * Fixed an issue in lang cs that made the table of namespaces not to show correctly

- JavaScript
Published by dgarijo over 7 years ago

widoco - WIDOCO 1.4.5: Updated WebVowl and support for Czech

This version of WIDOCO includes the following updates: * Updated webVowl to version 1.1.2 (latest) * Allowed disabling showing ontology serializations (-doNotDisplaySerializations flag). Both in the console and GUI * Added support for Czech localization (also in GUI)

Thanks to Petr Kremen for contributing with the Czech localization

- JavaScript
Published by dgarijo almost 8 years ago

widoco - WIDOCO 1.4.4: Added support for Google Analytics

This version of WIDOCO allows to add a Google Analytics code to track the traffic received in one of the pages. WIDOCO assumes you have a UA code. You can use it on the GUI, through a config file or in the command line by adding -analytics yourcode

- JavaScript
Published by dgarijo about 8 years ago

widoco - WIDOCO 1.4.3: Bug Fixes and support for french

This release fixes the following issues: * Added support for french (thanks to Maxime Lefrancois) * When imported ontologies had characters like "<" they were not showing. * Added JSON-LD serialization for ontologies automatically * When annotation properties have blank nodes, they will now be ignored instead of failing * Updated contributor list * Blank nodes are now absent from the provenance page. * Fixed default language when restarting WIDOCO. * Fixed the language form (now french can be selected, and it has the proper icons)

- JavaScript
Published by dgarijo about 8 years ago

widoco - WIDOCO 1.4.2: Small fixes and merged contributions

This release includes the latest contributions to the project: * Fixes in HTML * Fixes in how OOPS! is called Also, now the license name is the URI if no name is provided (and URI is) instead of "license name goes here", and the java encoding has been included in the pom file to prevent UTF-8 errors in compilation.

- JavaScript
Published by dgarijo over 8 years ago

widoco - WIDOCO 1.4.1: Metadata support and major bug fixes

WIDOCO now will comply with most of the terms listed in https://w3id.org/widoco/bestPractices. A few of them are still unsopported (e.g., rdfs:seeAlso) and will be added in next releases.

In this version, I have added support for all the deprecation terms in LODE, as well as support for skos:prefLabel and better recognition of some of the terms when the range can be a String or a resource.

Changes: * Now the examples have a "pre" label, so if they include rdf text or json text they show properly. * A pointer to the guidelines has been added in the interface * When invoking the program using command line, the default behavior is to load the properties from the ontology. Only if a config file is provided, the properties won't be loaded. There is still a flag, which I have preferred to leave for possible legacy issues. * Markup is now recognized in all sections * The diagram is now optional (by default it was always produced in older versions) * This release also includes a doc folder with guidelines on the metadata properties to use, a benchmark of ontologies used for testing, a gallery with what WIDOCO can accomplish and a summary of projects that have adopted WIDOCO.

Bug fixes: * Changed the pom file with another plugin for creating the JAR, because some of the RIO parsers were not creating the appropriate serializations of the ontology. * Added robustness when the changelog was created. If a wrong URI is provided, then the changelog will not be created. * Changed how the ontology is chosen so there won't be errors in MAC systems. * Fixed some of the language tags. * Polished some errors related to the interface.

- JavaScript
Published by dgarijo about 9 years ago

widoco - WIDOCO 1.4.0: Inline visualization diagrams

This release removes the external dependency to WebVowl, and creates a visualization that can be seen in the ontology document itself (overview section). In addition, the following changes have been made: * Migrated the framework to use a recent version of OWL API (hence the size of the JAR) * Bug fixes in meta data (more to come in future releases) * Made WIDOCO more robust to errors * Published a benchmark of ontologies used to test WIDOCO. If you want us to try a new one, just open an issue! * Published a draft of the best practices for ontology annotation (currently under work). These are meant * Published a showcase gallery with examples of WIDOCO's features * Published a report on the known usages by WIDOCO.

webvowl

- JavaScript
Published by dgarijo about 9 years ago

widoco - Widoco 1.3.1: Bug fixes and metadata enrichment

This release fixes several issues and extends LODE to accept more metadata options for defining terms and adding examples. * Fixed an issue with the changelog that produced an empty bullet when the domain or range of a property was an union or intersection. * Added tests with different ontologies that help inspecting whether a new change leads to errors or not. * Extended LODE to accept: prov:definition, vann:example, obo:definition (with the appropriate class name), obo:usageExample, vaem:rationale, skos:definition and terms:source. * Extended Widoco to accept terms:bibliographicCitation, bibo:status, bibo:doi and owl:backwardsCompatibleWith * If an error is produced while generating the changelog or the evaluation reports, the section is not generated. Before, an empty section would remain. * Fixed table of contents not being translated. * When generating the documentation of an ontology, if it imports another ontology that cannot be imported for any reason, Widoco will ignore the import instead of failing. * Added the possibility to ignore namedIndividuals when generating the documentation through console.

- JavaScript
Published by dgarijo about 9 years ago

widoco - Widoco 1.3.0: Automated changelog section

This version of Widoco creates an automated changelog section of your ontology. For all classes, properties and data properties, Widoco will calculate the new changes, additions and deletions and present them in a human-readable manner. In order to benefit from this feature, you just have to annotate your ontology with the URI of the previous version. You can use owl:priorVersion, dc:replaces or prov:wasRevisionOf to annotate your ontology (Widoco will only consider one file to compare against).

Additional improvements: * RDF-a annotations are replaced with JSON-LD snippets. The page is just annotated with schema.org. The rdf-a annotations made it difficult to maintain, and the structured extraction tool provided by Google did not work. With the JSON-LD snippet everything is clearer. The provenance of the page itself is published separately. * Now it is possible to generate ONLY the cross reference section of an ontology. * Bug fix that led to errors when opening some ontologies like OBI

Overview sample of the changelog:

- JavaScript
Published by dgarijo over 9 years ago

widoco - Widoco 1.2.3: [Bug fix] Licensius is optional

The Licensius web service has been unstable lately. This led to long waits from the server, even with a timer on the request. Therefore retrieving the license using this service is now optional and loading metadata properties from the ontology is faster.

- JavaScript
Published by dgarijo over 9 years ago

widoco - Widoco 1.2.2: Major bug fixes and improvements

This version fixes the following issues/improvements: - 188: lang separator doesn't work on unix systems. Changed ";" to "-" as separator - 189: return a non-zero value if there are problems generating the doc - 151: text area in the table should be bigger - 177: Ability to provide authors institution URI in the config - 155: allow possibility of adding Zenodo URI (DOI) - 132: could improve placeholder text - 174: Dynamic sections - 170: Check why isDefinedBy is not recognized sometimes - 171: Separate configuration from vocabulary metadata

In addition, I have fixed the custom style CSS, saving the publisher in the config file, producing an alt in images to avoid broken images when no connection is available and issues with the consistency in sections and back to toc titles.

Finally, the toc will be now dynamic, so it will get updated if new headers with class "list" are added to the document.