uc-cdis / peregrine

GraphQL search API service
Apache License 2.0
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bump sqlalchemy, pyyaml, bunch of other stuff #130

Closed vpsx closed 5 years ago

vpsx commented 5 years ago

PyYAML: Happily, Peregrine was already using PyYAML's safe_load() instead of load(). So we were good to just bump.

gdcdictionary: Now that gdcdictionary is a PyPI package its location in the Docker container changed. So the cd in the RUN part of the Dockerfile broke. The cd along with the lines after it served to write version information about gdcdictionary to version_data.py. This PR changes the Peregrine /_version endpoint to just get the gdcdictionary version programmatically, so that we can remove the broken lines in the Dockerfile. The dictionary commit hash is removed entirely now that we are getting gdcdictionary via PyPI.

flask: import CORS from flask_cors not flask.ext.cors

Improvements

change the Peregrine /_version endpoint to just get the gdcdictionary version programmatically, so that we can remove recently-broken lines in the Dockerfile

Dependency updates

bump sqlalchemy 0.9.9 to 1.3.5 bump psqlgraph bump gen3datamodel bump datamodelutils bump dictionaryutils bump gdcdictionary bump authutils bump pyyaml to 5.1 remove flask-postgres-session (was unused) bump sheepdog