schema-salad LockFailed when running under Docker

[dleehr]

When running in Docker under openshift, the following error appears at the start of a calrissian run:

Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: ('https://schema.org/docs/schema_org_rdfa.html', LockFailed('failed to create /.cache/salad/b/2/8/9/0/calrissian-gatk4-preprocessing-pkg-7rxg9-55dae700.13435938927651500254',))
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: ('https://schema.org/docs/schema_org_rdfa.html', LockFailed('failed to create /.cache/salad/b/2/8/9/0/calrissian-gatk4-preprocessing-pkg-7rxg9-55dae700.13435938927651500254',))

I suspect that schema-salad's home-dir lookup for caching is involved, and setting an environment variable on the pod would fix it.

[dleehr]

Probably just a matter of setting an env var in the Dockerfile for HOME or TMPDIR

[dleehr]

The relevant code in schema_salad attempts to create a FileCache in $HOME if that variable exists.

At runtime, $HOME is set to / and the container user is a random UID (e.g. 1000320000)

$ whoami
whoami: cannot find name for user ID 1000320000
$ touch /file
touch: cannot touch '/file': Permission denied

[dleehr]

This is a regression introduced in #42. The messages didn't appear with the S2I-built image. When using the centos/python-36-centos7 python image, $HOME is set to /opt/app-root/src/, and an arbitrary user has permissions to write there.

Remedy is to create a HOME directory in the Dockerfile, as the s2i image does:

1. https://github.com/sclorg/s2i-base-container/blob/master/core/Dockerfile#L27 (Dockerfile entry to set ENV HOME)
2. https://github.com/sclorg/s2i-base-container/blob/3c2b4d2e896a3fdea29f19580af1fe3d50c3db84/core/Dockerfile#L69-L72 (Dockerfile entry to make directory and change ownership)