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diff --git a/issues/edit-rif-metadata.gmi b/issues/edit-rif-metadata.gmi new file mode 100644 index 0000000..546dc80 --- /dev/null +++ b/issues/edit-rif-metadata.gmi @@ -0,0 +1,121 @@ +# Edit RIF Metadata in GN2 + +## Tags + +* assigned: bonfacem, jnduli +* priority: high +* status: closed + +## Tasks + +### Viewing +* [X] API: Get WIKI/RIF by symbol from rdf. + +> GET /wiki/<symbol> + +``` +[{ + "symbol": "XXXX", + "reason": "XXXX", + "species": "XXXX", + "pubmed_ids": ["XXXX", "XXXX"], // empty array when non-existent + "web_url": "XXXX" // Optional + "comment": "XXXX", + "email": "XXXX", + "categories": ["XXXX", "XXXX"], // Enumeration + "version": "XXXX", + "initial": "XXXX", // Optional user or project code or your initials. +}] +``` + +* [X] UI: Modify traits page to have "GN2 (GeneWiki)" +* [X] UI: Integrate with API + +### Editing + +* [X] API: Edit comment by id in mysql/rdf: modifies GeneRIF and GeneRIFXRef tables. +* [X] API: Modify edit comments by id to include RDF changes. + +> POST /wiki/<comment-id>/edit + +``` +{ + "symbol": "XXXX", + "reason": "XXXX", + "species": "XXXX", + "pubmed_ids": ["XXXX", "XXXX"], // Optional + "web_url": "XXXX" // Optional + "comment": "XXXX", + "email": "XXXX", + "categories": ["XXXX", "XXXX"], // Enumeration + "initial": "XXXX", // Optional user or project code or your initials. +} +``` +* [X] UI: Add buttons that edit various relevant sections. +* [X] UI: Edit page needs to fetch categories from GeneCategory table. When comment write fails, alert with error. When comment write success, update the comment on the page, and alert with success. +* [X] API: Modify edit comments by id to include RDF changes. +* [X] GN auth integration + +### History + +* [X] API: End-point to fetch all the historical data +* [X] UI: Page that contains history for how comments changes. + +> GET /wiki/<comment-id>/history + +``` +[{ + "symbol": "XXXX", + "reason": "XXXX", + "species": "XXXX", + "pubmed_ids": ["XXXX", "XXXX"], // Optional + "web_url": "XXXX" // Optional + "comment": "XXXX", + "email": "XXXX", + "categories": ["XXXX", "XXXX"], // Enumeration + "version": "XXXX", + "initial": "XXXX", // Optional user or project code or your initials. +}] +``` + +### Misc ToDos: + +* [X] Review performance of query used in 72d9a24e8e65 [Genenetwork3] + +### Ops + +* [X] RDF synchronization with SQL (gn-machines). +* [X] Update RDF in tux02. +* [X] UI: Add "edit" button after testing. + +### Resolution + +Genenetwork2: +=> https://github.com/genenetwork/genenetwork2/pull/858 UI/fetch rif using recent apis #858 +=> https://github.com/genenetwork/genenetwork2/pull/864 Add comment history page. #864 +=> https://github.com/genenetwork/genenetwork2/pull/865 Add support for auth in Rif Edit #865 +=> https://github.com/genenetwork/genenetwork2/pull/866 Add a page for searching GeneWiki by symbol. #866 +=> https://github.com/genenetwork/genenetwork2/pull/881 Add display page for NCBI RIF metadata. #881 +=> https://github.com/genenetwork/genenetwork2/pull/881 Add display page for NCBI RIF metadata. #881 +=> https://github.com/genenetwork/genenetwork2/pull/882 GN editting UI improvements #882 + + +GeneNetwork3: +=> https://github.com/genenetwork/genenetwork3/pull/180 Update script that updates Generif_BASIC table #180 +=> https://github.com/genenetwork/genenetwork3/pull/181 Add case insensitive prefixes for rif wiki #181 +=> https://github.com/genenetwork/genenetwork3/pull/184 Api/get wiki from rdf #184 +=> https://github.com/genenetwork/genenetwork3/pull/185 feat: add api calls to get categories and last comment #185 +=> https://github.com/genenetwork/genenetwork3/pull/186 Api/fetch the latest wiki by versionid #186 +=> https://github.com/genenetwork/genenetwork3/pull/187 Api/get end point to fetch all historical data #187 +=> https://github.com/genenetwork/genenetwork3/pull/189 Add auth to edit RIF api call #189 +=> https://github.com/genenetwork/genenetwork3/pull/190 Api/update rif queries #190 +=> https://github.com/genenetwork/genenetwork3/pull/193 Api/edit rif endpoint #193 +=> https://github.com/genenetwork/genenetwork3/pull/194 Fix C0411/C0412 pylint errors in gn3.api.metadata.api.wiki. #194 +=> https://github.com/genenetwork/genenetwork3/pull/195 Add rif tests #195 +=> https://github.com/genenetwork/genenetwork3/pull/196 Handle missing GN3_SECRETS for CI testing. #196 +=> https://github.com/genenetwork/genenetwork3/pull/197 Rif edit atomicity #197 +=> https://github.com/genenetwork/genenetwork3/pull/198 Run tests against Virtuoso that is spun locally. #198 +=> https://github.com/genenetwork/genenetwork3/pull/199 Add rdf-tests after the check phase. #199 +=> https://github.com/genenetwork/genenetwork3/pull/200 Api/ncbi metadata #200 + +* closed |