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cBioPortal / oncotree

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Fixing integration tests #175

Closed mandawilson closed 5 years ago

mandawilson commented 5 years ago 
Fixing integration tests
- was not correctly testing if oncotree was running
    * JOB_RUNNING was empty, even when job was actually running
    * if JOB_RUNNING was empty, then attempted to query oncotree
    * was timing out too soon, oncotree takes a long time to startup
    * check for job running needed a sleep before it or no job was found
    * break and exit with error if ONCOTREE is inaccessible (timeout)
- oncotree_to_oncotree.py
    * cross_version_oncotree_translator.py renamed oncotree_to_oncotree.py
    * variable TEST_ONCOTREE_VERSION_MAPPER_FILENAME didn't exist
    * ONCOTREE_VERSION_MAPPER_TEST_SUCCESS was not tested at end
    * expected output default_oncotree_file_converted.txt needed updating for UNKNOWN oncotree code
- added some comments