Show deprecated concepts without replacement in change list

[osma]

Reasons for creating this PR

It was reported in #1513 that

concepts that have the owl:depracted true element/value only, BUT do not have the (optional) dct:replacedBy element seem to be missed completely/altogether and do not show up in the 'New and Deprecated' lists at all.

This PR fixes the problem by making sure that deprecated concepts which do not have an isReplacedBy relationship are shown. For example "elevated tracks" in this screenshot is a deprecated concept which doesn't have a replacement (I removed it manually from the YSO version I used for testing):

I verified that the performance of the "New and Deprecated" page is unchanged; possibly it is actually slightly better (1.4 seconds instead of 1.5 for the test case I used).

Link to relevant issue(s), if any

• Closes Tab 'New and Deprecated' lists of concepts #1513 (NB the issue mentions another problem about deprecated concepts shown in the hierarchy, but we need more clarification on that and a separate issue would be good)

Description of the changes in this PR

• reformat the SPARQL query snippet in GenericSparql.generateChangeListQuery to make it more readable and easily editable
• change the querying and handling of deprecated concepts for the change list so that also concepts without isReplacedBy are included in the list; the deprecation status must be tracked separately from the possible replacement
• adjust the changes test vocabulary adding a deprecated concept without isReplacedBy and add tests to check that it is included as well (I had to adjust other unit tests that broke due to the changes in the test vocabulary)

Known problems or uncertainties in this PR

The same or similar changes need to be repeated for Skosmos 3 as well.

Checklist

• phpUnit tests pass locally with my changes
• I have added tests that show that the new code works, or tests are not relevant for this PR (e.g. only HTML/CSS changes)
• The PR doesn't reduce accessibility of the front-end code (e.g. tab focus, scaling to different resolutions, use of .sr-only class, color contrast)
• The PR doesn't introduce unintended code changes (e.g. empty lines or useless reindentation)

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
3 Code Smells

No Coverage information
0.0% Duplication

[codecov]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (99448fc) 70.08% compared to head (caf4c18) 70.08%.

Additional details and impacted files

@@            Coverage Diff            @@
##             master    #1529   +/-   ##
=========================================
  Coverage     70.08%   70.08%           
- Complexity     1658     1659    +1     
=========================================
  Files            32       32           
  Lines          4272     4272           
=========================================
  Hits           2994     2994           
  Misses         1278     1278           

Files	Coverage Δ
model/sparql/GenericSparql.php	92.52% <100.00%> (ø)

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[jeanninebeeken]

Hi Osma,

Thank you for fixing the issue. May I ask whether the fix will be part of/visble in version 2.17 or only from version 3.0 onwards, thanks.

Best wishes,
Jeannine

[joelit]

Looks good (even though switching to Skosmos 2 for testing was a bit twiddly)

[osma]

@jeanninebeeken

Thank you for fixing the issue. May I ask whether the fix will be part of/visble in version 2.17 or only from version 3.0 onwards, thanks.

This will first be fixed on the development branch (master) and on the Skosmos 2.x maintenance branch v2.16-maintenance which you can start using immediately; if you followed the recommended installation instructions, upgrading will be a simple git pull command. Later we may release either a 2.16.x point release or 2.17 containing the fix - not sure about these, since we're focusing on Skosmos 3 development, so 2.x releases are not a priority.

The same fix has to be done for Skosmos 3 as well so we don't lose the improved functionality. For now this means only porting the back-end parts, because the change list is not yet implemented in the new Skosmos 3 front-end.