Document searchResultsAsRDF.rdf and submissionIsland.html endpoints

[Copilot]

Two endpoints were undocumented in user-story-06-technical.md: /search/searchResultsAsRDF.rdf (PhyloWS RSS 1.0 feed) and /json/submissionIsland.html (submission JSON for dynamic UI).

Changes to user-story-06-technical.md

• RSS/Atom Feed Endpoints: Added /search/searchResultsAsRDF.rdf alongside existing /rss.xml and /feed.xml
• Data Standards: Updated RSS 1.0 row to reference the endpoint
• Pages to Account For: Added both endpoints to relevant tables
• PhyloWS Search Results as RDF Feed: New section documenting request flow when format=rss1 is specified
• JSON Endpoints for Dynamic UI: New section documenting SubmissionToJsonController, authentication requirements, and response structure

Changes to user-story-03-submission.md

• Step 7: Review and Submit: Integrated submissionIsland.html into Submission Summary section explaining the AJAX-based dynamic UI update flow
• Pages to Account For: Added endpoint to table
• Error handling: Documented graceful degradation when JSON endpoint fails

Example: PhyloWS RSS 1.0 flow

GET /phylows/study/find?query=dcterms.contributor=Smith&format=rss1
    → StudySearchController.handleQueryRequest()
    → SearchController.searchResultsAsRDF()
    → searchResultsAsRDF.jsp (RSS 1.0 output)

Original prompt

The https://github.com/TreeBASE/treebase/blob/v3-ui-ux/doc/v3/user-story-06-technical.md neglects to document two additional pages/endpoints:

• /search/searchResultsAsRDF.rdf - this is related to the phylows functionality: when a phylows query is performed, the result set is presented as an RDF/XML (RSS) feed through this endpoint. Study very carefully how this works and integrate it in the right locations in user story 6. Do not make new sections but do fit it in where it needs to go, including in the section on pages that are accounted for.

• /json/submissionIsland.html - this is related to the dynamic UI: it serializes a submission as JSON so that it can be traversed on the client side to check for the status of the different parts of a submission and update the UI accordingly. Within the technical documentation it should be discussed as a JSON endpoint. Here, too, study carefully what it does, what the flow is, and integrate it in the existing document where appropriate. If it additionally can be integrated cleanly into https://github.com/TreeBASE/treebase/blob/v3-ui-ux/doc/v3/user-story-03-submission.md, then do so as well. Again, do not make new sections. Weave it in the existing narrative and make sure that the page/endpoint is accounted for.

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