Releases: protegeproject/protege-distribution
Releases · protegeproject/protege-distribution
Protégé 5.0.0 RC1
This release candidate provides mainly bug fixes and some minor functionality enhancements.
New functionality
- Changed the OS X distribution so that it is a Mac OS X Application Bundle. This allows Protege to be placed in the dock on OS X and allows .owl ontology files to doubled clicked in the Finder in order to open them (protegeproject/protege#388)
- Added a table to the plugin preferences pane that shows installed plugins and their versions (protegeproject/protege#389)
- Added functionality to display error messages for mis-spelt property and individual names in the object property assertion editor (protegeproject/protege#382)
- Changed the behaviour of the ontology annotations view so that ontology annotations are sorted (protegeproject/protege#402). Certain well known annotations receive a higher priority than others in the sorting, in particular dc:title, dc:creator and dc:contributor (protegeproject/protege#405), dc:rights and dc:terms (protegeproject/protege#406) and dc:published (protegeproject/protege#407).
- Updated the default bookmarked ontology URLs (protegeproject/protege#409)
Bug Fixes
- Altered the column sizes in the About window to make it more readable (protegeproject/protege#390)
- Fixed a problem with drag and drop where direct subclasses of owl:Thing that did not have explicit subclass axioms could not be dragged from under owl:Thing (protegeproject/protege#387)
- Updated the OWL API to 4.2.3 (protegeproject/protege#393). This fixes a bug where axiom annotations on rule would be deleted if the signature of the rule was changed during a rename operation in Protege. and protegeproject/protege#371. It also fixes a bug where a runtime exception could be thrown during ontology parsing if the ontology contains punned properties (protegeproject/protege#376)
- Changed the preferences dialog so that it resizes itself to completely fit on smaller displays (protegeproject/protege#397)
- Fixed a problem where Protege would crash if annotation values were IRIs that were equal to the ontology IRI and had an empty string rendering. This problem was most notably present with the prov ontology (protegeproject/protege#400)
- Fixed a problem with the Rules view that threw exceptions when trying to edit rules (protegeproject/protege#398)
- Fixed a problem where Protege would sometimes display empty error messages (protegeproject/protege#396)
- Fixed a problem where individuals that were created as direct instances of owl:Thing would not receive the focus after creation (protegeproject/protege#374)
- Fixed a problem where the right hand side of the entities tab would be greyed out (due to the selection history being cleared) after adding an instance of owl:Thing (protegeproject/protege#379)
- Fixed a problem where the right hand side of the entities tab would be greyed out (due to the selection history being cleared) after synchronising the reasoner if owl:Thing was the selected class (protegeproject/protege#380)
- Fixed a problem where the inferred class hierarchy could cause Protege to crash with certain reasoners under certain conditions (protegeproject/protege#403)
- Changed the behaviour when creating individuals so axioms stating that an individual is an instance of owl:Thing are not added to the ontology (in order to parallel the behaviour of the class hierarchy) (protegeproject/protege#401)
Bundled Plugin Updates
Protégé 5.0.0 Beta 24
Summary
This release provides new functionality, enhancements to existing functionality and also fixes various bugs.
Enhancements and Fixes
- Annotation literal values that are Image URLs will now be displayed as images if this option is selected (protegeproject/protege#315).
- Auto-update would install new plugins with the same file name as previous versions of the plugins, which could be confusing if the file name included version information. This behaviour has been changed. (protegeproject/protege#363)
- The plugin update dialog has been simplified by removing the tabbed display. (protegeproject/protege#361)
- Tidied the info text in the plugin update dialog. (protegeproject/protege#359)
- In some cases, an error message would be displayed after plugin installation even if there plugin had been installed without problems. Fixed. (protegeproject/protege#356)
- Fixed a problem where the datatype selection panel would not remove listeners after being closed. (protegeproject/protege#326)
- The new annotation property button on the annotation hierarchy view is always enabled now. If no property is selected then the new property will be added as a top level property. (protegeproject/protege#340)
- Fixed a bug where drag and drop would not work in the presence of axiom annotations. (protegeproject/protege#358)
- Fixed a bug where the selection could change in an unprompted fashion after classification (protegeproject/protege#354).
- Added an option to disable drag and drop in the various hierarchies (protegeproject/protege#347)
- Added support for pluggable context (popup) menus. (protegeproject/protege#348)
- Added some out of the box context menu items to the class hierarchy (protegeproject/protege#350)
- Made the instances view show the type (Class) that is used to filter the list (protegeproject/protege#349)
- Altered the default view arrangement on the Individuals by Type tab (protegeproject/protege#351)
- Fixed a bug that prevented auto-completion from working in the property chain dialog (protegeproject/protege#352)
- Fixed a problem that could cause spurious entity selections (protegeproject/protege#338 and protegeproject/protege#346)
- Added the declaration axioms count to the metrics panel (protegeproject/protege#342)
- The search window now selects the previous search text when it opens. (protegeproject/protege#344)
- The view log button on the error dialog does not work (protegeproject/protege#329)
Bundled Plugin Updates
- Updated the Cellfie plugin to 1.0.0-beta-7
- Updated the SWRL plugin to 1.0.0-beta-19
Protégé 5.0.0 Beta 23
Summary
This release provides new functionality, enhancements to existing functionality and also fixes various bugs.
New Functionality
- Added a preference panel for specifying the logged in user. This can be used by plugins and is also used when auto-creation of metadata is enabled.
- It is now possible to automatically attach meta-data to freshly created classes (#283). Thanks go to @cmungall for suggesting this and for input from the OBO community for contribution of ideas (in particular @tberardini, @mellybelly,
@mcourtot, @dosumis).
- Images that are pointed to by annotation values are now displayed inline as thumbnails (#315)�
New Plugins
SWRL Plugin
The SWRL Plugin is a port of the the SWRL tab functionality from Protégé 3. Read more at https://github.com/protegeproject/swrltab-plugin/releases
DL Query Plugin
Updated the DL Query plugin to version 3.0.1. For details please see: https://github.com/protegeproject/dlquery/releases/tag/org.coode.dlquery-3.0.1
Enhancements and Fixes
- Asserted and inferred hierarchies are now combined into single views. They can be switched using the drop down box, or by pressing "a" for asserted or "i" for inferred when the associated view has the focus. (#145)
- Cleaned up the metrics view by removing unnecessary clutter
- Copying errors from the log view to the clipboard now includes stack traces (#297)
- Added a button for clearing the log in the log view (#296)
- The error icon is now cleared after the log view is closed (#305)
- Cleaned up and refined the user interface and reduced clutter where possible
- Moved the log file location to the user home directory (#299)
- Fixed a problem where Protege did not detect when loaded source files had changed externally and offer to reload them (#300)
- Fixed a problem with syntax checking in the general class axioms view (#302)
- The object property hierarchy now displays sub-properties correctly (#306)
- Added a log message to describe when plugin update files cannot be parsed
- Removed formatting markers that showed up in console logs on Windows (#303)
- Added a missing flag to the Windows run.bat file that ensures array index out of bound exceptions do not occur (#307 and #226)
- Fixed a problem with adding data ranges to properties (#308)
- Fixed a problem that caused icons on tabs to be painted incorrectly (#309)
- Well known IRIs that have well known prefixes are now rendered as prefix names regardless of the selected renderer (#310)
- The auto-complete would not match annotation properties (#311)
- Fixed a problem where "Optional" would appear in ontology IRIs rendered in the user interface (#313)
- Fixed a problem where imported ontologies were loaded using the incorrect OWL API method. This could cause import loading to raise errors when adding imports (#314)
- Changed the accelerator key for copying tab indented text from hierarchies because it clashed with the copy accelerator key (#316)
- Made it possible to copy class names from the class hierarchy (#222)
- Adjusted run scripts so that they work better with symbolic links (#318) (thanks go to @ShahimEssaid for the contribution)
- Fixed a problem where the explanation dialog would raise an error if there were no explanation plugins installed (#319)
- Fixed a problem with drag being enabled when it was disabled in the UI preferences (#322)
- Fixed a problem where an inconsistent ontology exception would leak out from the inferred object property hierarchy (#328)
- Fixed a problem where "Render by Prefixed Annotation property would display two prefixes (#327)
Protégé 5.0.0 Beta 21
Summary
This release provides new functionality, enhancements to existing functionality and also fixes various bugs.
New Functionality
- Added the ability to copy sub-hierarchies as tab indented text. This applies to class and property hierarchies. Select a class or property and choose "Copy sub-hierarchy as tab indented text" from the Edit menu. (#233)
- Moved to the OWL API 4.1.3. This is a major upgrade and it is possible that some plugins will need updating so that they will be compatible with this version of Protege.
- Improved logging. Logs are now visible via the "Show log" item on the "Window" menu. Note: to enjoy the colorful logs also on Windows, you will need to install ANSICON (see https://goo.gl/dcDhwA).
- Added an option to hide deprecated classes in the class tree. See the "Display deprecated (obsolete) entities" on the View menu. (#270)
- Moved to Java 8.
New Plugins
Cellfie
Cellfie supports the creation of OWL ontologies from spreadsheets through a flexible mapping mechanism. To import data from a spreadsheet, go to Tools menu > Create axioms from Excel workbook. Cellfie is bundeled with the Protege distribution. Read more: https://github.com/protegeproject/cellfie-plugin, https://github.com/protegeproject/cellfie-plugin/wiki.
User Interface Enhancements and Fixes
- ArrayIndexOutOfBounds exception could be thrown (in a seemly random fashion) when rendering things, which caused the user interface to become scrambled. This was due to a bug in the JVM and we have applied a recommended work around. (#226)
- Updated the labels on the Entity Preferences panel so that it no longer refers to URIs (#176)
- Search results are now shown in a popup dialog rather than a popup list. This means that the search results can be kept open and moved around instead of being fixed and overlapping the editing window. (#189)
- Pressing return when a search result is selected in the search window now closes the search window (#188)
- Double clicking a search result in the search window now closes the search window in addition to selecting the search result (#192)
- Sized the entity search box so that it is the correct size on non-OSX look and feels (#146)
- The keyboard shortcut for find (search) is now CTRL+F. Find in specific view is now CTRL+SHIFT+F (#193)
- Components in dialogs are now focused consistently over different operating systems. Thanks to @fourcube. (#228)
- The various hierarchies (class, property etc.) can be auto-expanded. However, the mouse/keyboard combination (CTRL+Click) was not working properly on windows. This has been fixed. (#231)
- The "Create new" (entity) key combination was the same as the key combination for "New Ontology". This has been changed to CTRL+E. (#232)
- Fixed a problem where spurious axiom annotations were displayed when changing entity selection. (#223)
- The reasoner status message did not display correctly on Windows. Fixed. (#224)
- The Protege icon was missing from the OS X distribution. (#211)
- The Protege icon was missing from the Linux distribution. (#225)
- Plugin update problems are now logged as "info" so that users can see the problems in the log (#172)
- Fixed the "Zero length error" that could sometimes arise when search for an entity (#134)
- Pressing "Escape" on the plugin update dialog throws an exception. Fixed (#273)
- Added help text to the save as dialog. (#271)
- Removed the dashed border on inferred axiom rows in order to reduce clutter (#277)
- Fixed a problem that caused an error after ticking and un-ticking the Regular Expression box on the search panel if an invalid regular expression was present (#275)
- Tidied up the look and feel of some preference panels. Some preference options have been consolidated.
- Fixed a problem where boolean values for data property assertions would not parse as expected and cause the value to always be set to false. (#285)
- Improved the error message for view plugins that could not be loaded (#291)
Reasoning Enhancements
- Improved the algorithm for detecting and filtering ontology changes that should trigger reasoning (#170 - thanks to @ykazakov)
Development Enhancements and Fixes
- Build products that include JREs are now only built when preparing a release, otherwise the platform independent build product is the only one that is built (#173)
- Removed spurious import of internal apache package (Thanks to @sesuncedu)
- Fixed a naming problem with OWLDescriptionChecker and OWLDescriptionSetChecker. This fix stops maven recompiling everything when not necessary. (Thanks to @sesuncedu)
- The plugin.xml is now contained in the resources folder rather than the top level folder.
- Removed the defunct IDE folder from the repository (#261)
- Switched to SLF4J and Logback for logging.
- Clear preferences does not always work - list and array preferences are not cleared. Thanks to @ykazakov (#186)
- Updated the maven co-ordinates for various artefacts. Developers - please ensure you use the correct co-ordinates (the new co-ordinated have short, non-qualified names, for the artefact ids)
- Updated developer documentation for building in Eclipse.