Code cleanup and cache refreshing

cBioPortal / oncotree

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Code cleanup and cache refreshing #102

Closed mandawilson closed 6 years ago

mandawilson commented 6 years ago

Removed meta information from JSON responses
Removed unused code (methods, classes)
Cleaned up code
Cache
- Fully initialize cache on startup
- Refresh the cache daily at 11am
- Added refresh endpoint
- Expire cache if it has not been refreshed for more than 3 days
- refreshCache endpoint hidden in Swagger

NOTE: web/src/main/java/org/mskcc/oncotree/api/TumorTypesApi.java has two TODO items we should do something about.

mandawilson commented 6 years ago

I will create a separate PR to fix the memory leak, and then will rebase this on that one.

mandawilson commented 6 years ago

The caching code needs unit tests.

mandawilson commented 6 years ago

@zhx828 We have made major changes here to the API, but haven't committed to them yet. We also don't have a deployment plan yet.

mandawilson commented 6 years ago

I will rebase once this is merged: https://github.com/cBioPortal/oncotree/pull/103

zhx828 commented 6 years ago

@mandawilson thanks for letting me know. I think it would be better to have a testing instance for all the changes, I can also do some testing with OncoKB instance connected.

mandawilson commented 6 years ago

Bump the maven version number too.

mandawilson commented 6 years ago

Remove queryid from search endpoint?

mandawilson commented 6 years ago

Are errors returned as HTML or JSON?

sheridancbio commented 6 years ago

I think that since we are going to deploy this code as ROOT.war in the oncotree-tomcat and then migrate to it, we can deploy now without breaking existing clients. I am removing the do-not-merge tag.