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Upgrade to python3 #160

Merged
merged 13 commits into from
Jul 2, 2019
Merged

Upgrade to python3 #160

merged 13 commits into from
Jul 2, 2019

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johnbradley
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@johnbradley johnbradley commented Jun 27, 2019 •
edited

Changes

  • Upgrades to python3
  • Upgrades pyyaml and uses safe methods
  • Updates flag for mocha test command that has changed
  • Updates production/Dockerfile and production/imads.conf to use python 3
  • Upgrades SQLAlchemy, Flask, and Jinja2 to fix vulnerabilities
  • Updated third party bigBedToBed to fix a bug 1210409

Fixes #158
Fixes #157

Created #159 to look into simplifying deployment with a http proxy.

This is currently deployed/tested on http://imads-dev.gcb.duke.edu.

@johnbradley
upgrade pyyaml
a050f13
@johnbradley
upgrade to python3 and pyyaml 5.1
30fc312
@johnbradley
update circleci to python 3
7be34dc
@johnbradley
upgrade Jinja2 for CVE-2019-10906 and CVE-2016-10745
abd71c0 
https://nvd.nist.gov/vuln/detail/CVE-2019-10906
https://nvd.nist.gov/vuln/detail/CVE-2016-10745
@johnbradley
fix mocha test command
578b84a 
Fix for error:
```
✖ ERROR: --compilers is DEPRECATED and no longer supported.
          See https://git.io/vdcSr for migration information.
```
https://github.com/mochajs/mocha/wiki/compilers-deprecation
@johnbradley
Upgrade SQLAlchemy and Flask
32925b8 
https://nvd.nist.gov/vuln/detail/CVE-2018-1000656
https://nvd.nist.gov/vuln/detail/CVE-2019-7548
https://nvd.nist.gov/vuln/detail/CVE-2019-7164
@johnbradley
update to latest version of bigBedToBed
1210409 
This is to fix an issue where it failed to link to libpng 12.
@johnbradley
switch to libapache2-mod-wsgi-py3
9ad9160
@johnbradley
install mod_wsgi via pip
8c76ba6 
Apache kept running the /usr/bin/python which is python3.5
and not python3.6 which we installed packages for.
https://stackoverflow.com/questions/44914961/install-mod-wsgi-on-ubuntu-with-python-3-6-apache-2-4-and-django-1-11
@johnbradley
add apache2-dev requirement for pip mod_wsgi
671bcca
@johnbradley
python3 wsgi setup from bespin-api
56ac741 
Uses apache wsgi python3 setup from bespin-web
@johnbradley
fix yaml load in config reading
36c3557
@johnbradley
base64 encoding fixes for python3
835ba8d
@johnbradley johnbradley requested a review from dleehr June 27, 2019 16:58
dleehr
dleehr approved these changes Jul 1, 2019
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LGTM

@johnbradley johnbradley merged commit b0c11fd into master Jul 2, 2019
@johnbradley johnbradley deleted the 158-python3 branch July 2, 2019 13:13
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@dleehr dleehr dleehr approved these changes

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Upgrade to python3 pyyaml vulnerability
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@johnbradley @dleehr