merge sparql endpoints

[recalcitrantsupplant]

update sparql functions
update tests
add otherAnnotationProps to annotations
remove startup graph posting

[recalcitrantsupplant]

Could I please get a fairly comprehensive review of this as the changes are significant and breaking. In particular testing with the frontend. I have tested visually with the FE.

[recalcitrantsupplant]

I've just noticed /object is not working - will fix later today. This shouldn't block others reviewing the changes.

[recalcitrantsupplant]

Resolves #115 .
Resolves #115 .
Resolves #124 NB addition of /tbox-cache endpoint which shows the tbox cache; also fix of /purge-tbox-cache endpoint. Persistence/reading of cache on shutdown/startup removed.

[nicholascar]

This was great fun to review: I was worried about the shear number of files but I got through them quickly since it's mostly code removal and simplification! Also, I'm thrilled to see your really neat functions and bonus documentation @recalcitrantsupplant! Great PR.

[edmondchuc]

Phew, finished! Looks good, just left some minor comments in there. I'll run it with prez-ui and test it tomorrow. Should be good to go shortly after that.

[edmondchuc]

Requested change in https://github.com/RDFLib/prez/pull/127/files/2fcd93ab6a7daf90e9bf32f4b02386c0a10750b9#r1236251610 will fix #127.

[edmondchuc]

This line needs to be removed.

prez/prez/routers/profiles.py

Line 81 in 2fcd93a

"GenericPrez",

[edmondchuc]

I think the last thing is to remove prez_type=GenericPrez on line 70 and GenericPrez on line 80 in

prez/prez/routers/profiles.py

Lines 70 to 80 in f90b743

	prez_type="GenericPrez",
	prof_and_mt_info=prof_and_mt_info,
	)
	profile_query = generate_item_construct(profiles_item, prof_and_mt_info.profile)
	profile_graph = profiles_graph_cache.query(profile_query).graph
	return await return_from_graph(
	profile_graph,
	prof_and_mt_info.mediatype,
	prof_and_mt_info.profile,
	prof_and_mt_info.profile_headers,
	"GenericPrez",

.

[edmondchuc]

Once you've made that change in the last comment, I'll do one last test and distill the changes into dot points here so we can paste it into the release notes.

[recalcitrantsupplant]

Thanks - removed now

[edmondchuc]

Fixes

• Merge multiple SPARQL endpoints into one #115
• Some caching issues related to labels #124
• SPARQL query request incorrectly adds trailing slash to endpoint URL #95
• The tbox_cache.nt is problematic in dev and testing environments #121
• Example compose file with frontend #55

Changes

• Prez is now read-only for a given SPARQL endpoint
  • Prez no longer loads vocabularies to the SPARQL store on startup and instead loads it into an in-memory graph object
• Simplified docker-compose local setup
• Prez no longer persists the in-memory graph cache to disk. Each Prez restart now starts in a deterministic state with a clean cache
• No longer uses base URL in HTTP client and as a result, no longer adds a trailing / to the URL of the requests made using the HTTP client
• For search, invalid search_methods values now returns a HTTP status code of 400
• SPARQL proxy endpoint filters out the Host header and sets it to the base URL of the target SPARQL endpoint

Added

• Extends annotation functionality to SPARQL queries. SPARQL queries sent to prez's SPARQL endpoint with +anot in their mediatypes (e.g. text/anot+turtle) will include annotations in the results. Currently only applied to CONSTRUCT queries. Annotations are not included/counted towards LIMIT clauses.
• HTTP endpoint to clear in-memory graph cache
• HTTP endpoint to view in-memory graph cache
• Documentation for Prez annotation properties
• Documentation for common Prez environment variables

Breaking

• SPARQL endpoints for each subsystems have been consolidated into one
• SPARQL Update and SPARQL HTTP Store support dropped
• Environment variables for SPARQL related config removed and simplified
  • SPARQL_ENDPOINT
  • SPARQL_USERNAME
  • SPARQL_PASSWORD

@recalcitrantsupplant do you agree with this list?

[edmondchuc]

One last thing, can you fix the formatting for the documentation section on annotation properties please? See https://github.com/RDFLib/prez/blob/798be47cdf185cc10d2078db1de40f7fb2e1831f/README-Dev.md#annotation-properties.

[recalcitrantsupplant]

Cheers, I've edited your comment to include info on "annotated SPARQL queries" under Added, and fixed the markdown table.

[edmondchuc]

Looking good now. Thanks @recalcitrantsupplant for addressing my comments.