Update data explorer indexer to run on Python 3

DataBiosphere / data-explorer-indexers

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Update data explorer indexer to run on Python 3 #152

Closed wnojopra closed 4 years ago

wnojopra commented 5 years ago

Tested by indexing amp_pd, 1000_genomes, and e2e tests.

TODO: Test that this works on GCP, in your test project(s).

1000 Genomes Framingham The new AMP PD data NHS baseline_second_data_release Leave the clusters around so Melissa can double-check.

wnojopra commented 4 years ago

Hi @melissachang , I'm going to be making pull requests for my forked changes, but wanted to start with the Python3 changes.

For this particular PR, I've added you as an editor on my GCP project aaa-willyn-test. I have a cluster named elasticsearch-cluster-20200611-110711 that has 1000 genomes and Framingham indexed. I'll index the others in this cluster but you should be free to start your review.

wnojopra commented 4 years ago

Thanks. 1000 genomes, framingham, and AMP PD look good.

@melissachang , it looks like the circleci step is still "waiting for status to be reported", even though the tests have all completed successfully. Is there any thing you can check on your end? Perhaps there are some settings in branch protections to check (see https://support.circleci.com/hc/en-us/articles/360004346254-Workflow-status-checks-never-completes-because-of-ci-circleci-Waiting-for-status-to-be-reported)