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Enhancements to Galaxy profiles and workflow testing. #773

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merged 1 commit into from Feb 23, 2018

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jmchilton commented Feb 23, 2018

Add a new profile database type option "postgres_docker". The existing "postgres" type option expects a local database to be accessible via the "psql" command on Planemo's PATH - probably few people have postgres running directly on their development machine and fewer still have it configured to allow passwordless entry. This newer variant is a much simpler interface - it starts a named container for the official Docker postgres image and uses that to manage the profile. This should make using profiles easier for most developers.

This new modality does have some shortcomings - it should probably be redone to persist the database somewhere -or- start and stop the same container (currently when the container is stopped the data is gone).

This also updates the workflow test that encounters Galaxy locks to pickup the environment variable PLANEMO_TEST_WORKFLOW_RUN_PROFILE and PLANEMO_TEST_WORKFLOW_RUN_PROFILE_DATABASE_TYPE and use these to create and use a profile during testing if set as well as setting that variable in Travis to leverage the postgres service already configured for other tests. This more or less fixes what I had in mind with #772 but it would be nice to leverage galaxyproject/galaxy#4887 for greater test isolation.

Enhancements to Galaxy profiles and workflow testing.
Add a new profile database type option "postgres_docker". The existing "postgres" type option expects a local database to be accessible via the "psql" command on Planemo's PATH - probably few people have postgres running directly on their development machine and fewer still have it configured to allow passwordless entry. This newer variant is a much simpler interface - it starts a named container for the official Docker postgres image and uses that to manage the profile. This should make using profiles easier for most developers.

This new modality does have some shortcomings - it should probably be redone to persist the database somewhere -or- start and stop the same container (currently when the container is stopped the data is gone).

This also updates the workflow test that encounters Galaxy locks to pickup the environment variable PLANEMO_TEST_WORKFLOW_RUN_PROFILE and PLANEMO_TEST_WORKFLOW_RUN_PROFILE_DATABASE_TYPE and use these to create and use a profile during testing if set as well as setting that variable in Travis to leverage the postgres service already configured for other tests. This more less fixes what I had in mind with #772 but it would be nice to leverage galaxyproject/galaxy#4887 for greater test isolation.

@jmchilton jmchilton force-pushed the jmchilton:profiles_revisited branch from ee2d9de to e594f5f Feb 23, 2018

@jmchilton jmchilton merged commit 63770ac into galaxyproject:master Feb 23, 2018

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