Several Features & Improvements about web-gocam HOT 7 OPEN

@lpalbou what is this item? gorest: scheduled to be available as npm package, including with types (TypeScript)

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We'll also want to work with others (@tmushayahama @suzialeksander etc.) to choose the look-and-feel toolkits that we'll be using. As well as keeping an eye on making things a little more ADA-compliant.

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@kltm some answers:

• gorest: I was referring to the client-side code retrieving data from the gorest api. I plan to create that as a separate module, so that @tmushayahama can directly use it from Noctua Form & Review... as for the moment, he decided not to use my API but instead to duplicate the SPARQL queries behind my API, even though I warned him those queries will evolve over time (...)

• Look-And-Feel: let's coordinate on that. I know Tremayne is using Angular Material, I am too. I just have additional scss files to further configure the styling. But yes, it should be harmonized across all apps.

• ADA-compliant: sure, let me know what you have in mind. For the moment, gocam site scores 79% with LightHouse audit on accessibility but we could improve a few things (e.g. the link for evidence per gocam are only green icons so I could try to put a alt="" somewhere to describe them)

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• gorest, while an good exercise and experiment, I'm not particularly comfortable having this as an API leaking into production software--we need to work on uniformity, common APIs, and libraries. The underlying SPARQL should be available as templates, so there should be little duplication or worry about drift there. As well, given our large es5 base at this point, common libraries should be written in a way so that they can easily be included elsewhere (such as having a standard babel workflow that we work out).

• For look-and feel, we've already made a lot of use of Bootstrap, so my druthers would be to continue to evolve along those lines. If Material, was there a particular toolkit (a la bootstrap) that we could use more generally, for both standard static pages, Vue components, legacy components, etc.?

• ADA-compliant, honestly, I was thinking more about a different site; I'll take a bit more of a look around.

• I noticed that you have https://app.swaggerhub.com/apis/geneontology/gosparql/2.2 , this is the API you are referring to above?

• You seem to be using your own URL scheme for wiki links; these should be standardized across our presence.

• We should check back in with @dougli1sqrd about our progress along the lines of the GOOSE replacement (re: https://geneontology.cloud/query/sparql-examples)

• Links for the Noctua editor should generally be: http://noctua.geneontology.org/ (although note my barista whoops here geneontology/noctua#568).

• Align on feedback form (apologies, that's on my plate right now)

• GO logo links should generally go back to the main site.

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Answers by Topic:

• GOREST: the integration of my API inside BioLink is nearly finished, so this is not really an issue. However please remember BioLink can not be used at the moment for any data access on any secured site since BioLink is unsecured (http) and unfortunately so is the RDF endpoint too. We must deploy both BioLink and RDF endpoints to secured https if we want them to be used from https sites such as the next GO site or the Alliance.

  • Yes, https://app.swaggerhub.com/apis/geneontology/gosparql/2.2 is the updated swagger documentation of GORESTI that was available before the NYC meeting in May.
  • SPARQL templates: already discussed many time and we agree. Most of my queries have been in the sparqlr repo for some time (even though I have to update them since they still change quite often): https://github.com/geneontology/sparqlr/tree/master/templates/website. The next step would be to deploy those templates on some shared CDN or repository service or better to include them in OntoBio/BioLink.
  • es5: that's what I did with curie-util-es5 but if we want more "common" libraries, we need to discuss 1) on what 2) for what concrete case, 3) which language and why 4) who will develop it and 5) its priority.

• ADA-compliant: I already follow a certain number of recommendations and the gocam site scores 79% on accessibility while amigo has 71% and noctua.berkeleybop has 72% (LightHouse Audit). If you have some suggestions to improve our accessibility, please let me know. However, this may not be a priority compared to other developments (general data access, validation checks, go site and documentations, interactive notebooks asked by the SAB, visualization of gocams, gocams matching, etc).

• GOOSE replacement: since the discussion we had where @dougli1sqrd seems to be in charge of this, I stopped any related development. In the meantime, I have updated the SPARQL endpoint link to switch back to the http://rdf.geneontology.org/#query so /query/sparql-examples should not be used anymore. Btw, I had some security warnings recently on the gocam site due to the yasgui library that uses an old jquery library (< v3.0) with security issues.

• Feedback Form: I will be waiting for your instructions, but I would have appreciated to be part of that discussion since my feedback button was here before the NYC meeting in May. Also depending of the functionalities you want, the GitHub API (https://developer.github.com/v3/issues/) already allows to post issues with title, body, labels and even assignees.

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Any way this ticket can be split to make it more readable?

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Hi Suzy, this is a summary of items to complete the gocam site, so it will stay like that to keep track of the progression, however I have created and referenced other tickets for specific topics of that list:

• Documentation: #8
• SIF Archive: #7
• Feedback Form: #9

If there is another topic you would want separate for further discussions, either create or let me know.

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