identify the shapes for which to develop ShEX

wikipathways / GPML2RDF

GPML2RDF converter

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identify the shapes for which to develop ShEX #67

Open egonw opened 5 years ago

egonw commented 5 years ago

The list (growing):

[ ] Pathway
[ ] DataNode
[ ] GeneProduct
[ ] Protein
[ ] Metabolite
[ ] Interaction
[ ] DirectedInteraction
[ ] TypedDirectedInteraction
[ ] ...

egonw commented 5 years ago

Okay, done:

looked at a pretty good draft from January: https://github.com/shexSpec/schemas/blob/master/biology/pathways/Wikipathways/wp_rdf.shex (made minor fixes)
added the complementary manifest: https://github.com/shexSpec/schemas/blob/master/biology/pathways/Wikipathways/wp_rdf.json
split out a separate ShEx for DataNode: https://github.com/wikipathways/GPML2RDF/tree/master/WP2RDF/src/test/resources/shex

But now I'm stuck (cc @andrawaag @nunogit):

I think we first need HTTPS support on http://sparql.wikipathways.org/ first.

ericprud commented 5 years ago

Yeah, the HTTPS miltia has seized control of the browsers. You're basically stuck setting up HTTPS everywhere in order to work in today's Web.

egonw commented 4 years ago

HTTP is working now.

ericprud commented 4 years ago

Meaning the browser is is no longer refusing to load HTTP resources? Is it because the rawgit image you loaded was from HTTP instead of HTTPS?

egonw commented 4 years ago

Interesting questions. Not sure. I always thought it was the HTTP/-S difference between the currently loaded HTML and the additional remote resources that mattered, not just between the additional remote resources.

Anyway, the one thing that changed is that the WikiPathways SPARQL endpoint now supports HTTPS too.

I also note the typo in my comment of two days ago, which should have said: "HTTPS is working now" :)

ericprud commented 4 years ago

I also note the typo in my comment of two days ago, which should have said: "HTTPS is working now" :)

Ahh yes, that implies a different subject.

Re HTTP/S. This is a continuously-shifting battle-ground. As last I understood it, most browsers would refuse to fetch HTTPS from a page loaded with HTTP. At some point after that change, I believe rawgit changed to only serve HTTPS, which had the effect of requiring that all required resources be available by HTTPS. Then the squirrels arrived and chewed off my fingers and I swore off web development forever.

egonw commented 3 years ago

Some initial info here: https://github.com/egonw/shexWorkingBio/blob/master/index.md