cBioPortal / cbioportal-core

Externalized cBioPortal Core
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Change Assert() into Warning for db.user/db.password/... #26

Closed sheridancbio closed 7 months ago

sheridancbio commented 7 months ago

This change is needed because the msk importer currently requires the deprecated parameters: db.user, db.password, db.connection_string, db.portal_db_name, db.host, db.driver

The change of the Assert() statement into a logged warning in JdbcDataSource.java was approved and merged into the cbioportal codebase previously with https://github.com/cBioPortal/cbioportal/pull/10424

This PR also cleans up the code, providing functions for:

According to the final section notes of https://docs.oracle.com/javase/specs/jls/se7/html/jls-14.html#jls-14.10 it is bad practice to handle invalid argument problems through assert() because assert processing is disabled by default but validity of arguments should be checked regardless of whether assertions are enabled or not. Also, an appropriate exception is not thrown by assert(), which causes an AssertionError to be thrown instead. For these reasons, assert() was replaced by throw new RuntimeException(), which causes the construction of the datasource bean to fail during the bean construction stage of context creation, exiting the application.

sheridancbio commented 7 months ago

Closing this PR because automated tests were failing for a PR between forks (updating dependencies / maven.yml). The replacement PR is here: #27