Create basic Feature module endpoints

GMOD / Apollo3

JBrowse 2 plugin for editing annotations on an Apollo server

Apache License 2.0

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Create basic Feature module endpoints #52

Closed garrettjstevens closed 2 years ago

garrettjstevens commented 2 years ago

This will have:

~~the MongoDB schema for features~~
A feature controller that does
- ~~GET: /features/getFeatures?seq_id=chr1&start=1000&end=2000~~
- GET: /features/:featureId
- GET: /features (this returns all features)

~~When retrieving features by range, top-level features with all their children are returned.~~

When retrieving features by id, the features and any of its children are returned, but not any of its parent or sibling features.

garrettjstevens commented 2 years ago

@kyostiebi The feature schema (and other schemas) are now in place on the main branch and ready for the modules.

kyostiebi commented 2 years ago

New repo (Issue52) has been created and it contains:

new modules: assemblies, features and refuses
new folder 'schemas' that contains first schemas for Assemblies, RefSeqs and Features -collections
GET: features/getFeatures and GET: /features/:featureId -end points

kyostiebi commented 2 years ago

Should we also pass assemblyId as GET parameter because the db may contain several assemblies?

garrettjstevens commented 2 years ago

@kyostiebi yes, we should. Also, I rebased that branch so that it didn't conflict with the changes on main and opened a PR so I could add some review comments: https://github.com/GMOD/jbrowse-plugin-apollo/pull/54

kyostiebi commented 2 years ago

Start and End position changes are now handled in Apollo-shared -package. Also initial changeLog -schema has been created in ../apollo-shared/src/schemas/changeLog.schema.ts.

garrettjstevens commented 2 years ago

This is now updated so that it will come after #59, and does not include the features/getFeatures range request.

kyostiebi commented 2 years ago

This is now implemented in branch Issue52B.