Adjustments to allow use with TopBraid 6.3

cBioPortal / oncotree

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Adjustments to allow use with TopBraid 6.3 #216

Closed sheridancbio closed 4 years ago

sheridancbio commented 4 years ago

updated topbraid queries for oncotree_version
update web request to TopBraid to include login parameter
workaround broken MSK crosswalk API link : load current links from resource file when crosswalk.disable_cvs_querying is set
resource file staticCrosswalkOncotreeMappings.txt added with current definitions (from production cache)
specify key and value types for Ehcache Cache references
switch away from deprecated ApiInfo constructor and CORS filter specification
add additional details to logging
drop crosswalk server interaction logic and configuration options

averyniceday commented 4 years ago

Integration tests didn't pass - oncotree didn't startup after 10 minutes. Did the added changes increase start time?

sheridancbio commented 4 years ago

Integration tests didn't pass - oncotree didn't startup after 10 minutes. Did the added changes increase start time?

I'm working on this ... I think tests are close to passing. There were a couple of problems -- one bugfix had to do with the classpath for the static resource file. Another had to do with setting the port in the integration test script. Another had to do with the short-ish wait time between probes -- when the cache is empty, each probe cause the resetCache to be restarted and it was not having enough time to ever complete successfully. Another issue is that if you cancel the tests the caches are left in an unstable state and then followup tests don't run. Hopefully I can get a successful run soon.

sheridancbio commented 4 years ago

@averyniceday I have removed the configuration option for interacting with the (defunct) crosswalk server and the relevant web request logic and exception handling. I left in place (as comments) the logic for falling back on the backup cache if the service is unavailable and the primary cache is corrupted. Currently this cannot happen, because all crosswalk queries are serviced via the static resource file.

Integration tests are now running successfully (thank you @ao508). I put some code into the integration script to locate the cache and backup cache directories in a temporary space (rather than relying on the settings in the production properties file)