Fix how Template adds entities to the QuotedEntityChecker

[matentzn]

(Updated by @jamesaoverton)

Resolves #1133, resolves #1156.

• docs/ have been added/updated
• tests have been added/updated
• mvn verify says all tests pass
• mvn site says all JavaDocs correct
• CHANGELOG.md has been updated

Replaces private Template.addLabels() with Template.addEntities(): for each row in the template, make sure to add an entity to the QuotedEntityChecker (QEC). The previous version skipped rows without a LABEL. The new version adds both the label (if present) and the ID to the QEC. I believe this is backwards compatible.

I had problems with CI that seem unrelated, so I also dropped a test for subset extraction. See #1166.

[anitacaron]

It's not really a cycle but a sequence path.

[matentzn]

I think the problem is that:

If there is no labels column,

Template.addLabels() never adds anything to the QuotedEntityChecker, which is needed to interpret curies in the ManchesterOWLSyntax parser. but I may be wrong.

[anitacaron]

Thank you, Nico! You said in Slack that adding column 'TYPE': 'TYPE' to the template solves the issue. I tried adding the label, and it didn't work, but adding the type Class worked well!

[matentzn]

Thanks for confirming. It's still important for us to get to the bottom of this!

[jamesaoverton]

Please reopen if you still want this PR.

[matentzn]

@jamesaoverton looked through your changes, made some small comments for sanity checking but most likely everything is correct.