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adding gunicorn instead of uwsgi and modifying the base image. #362

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EliseCastle23 wants to merge 57 commits into master from feat/GPE-788

+370 −325

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EliseCastle23 commented Jul 17, 2023

I am removing uwsgi to be replaced by gunicorn and making modifications to use the new python3.9 base image. I had to make some modifications for indexd to be compatible with the AL2 base image.


          adding gunicorn instead of uwsgi and modifying the base image to use …

21eac2b

…the new python 3.9

github-actions bot added the @requires-indexd label

github-actions bot commented Jul 17, 2023

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

EliseCastle23 added 17 commits

July 17, 2023 09:03


          resetting the lock and toml files as I changed to try an resolve a po…

a306bbe

…etry error


          changing workers to 1 and adding the Docker cmd

d436084


          changed the format of the CMD in the Dockerfile, changed the port fro…

e76088f

…m 8000 to 80, and changed the base image to point to the "quay" repo


          removing comment and re-building image

a441e9a


          Changing the user to "nobody" so the container doesn't run as root. A…

c121d94

…lways set gunicorn to run as user "nobody"


          changing the Dockerfile to use user "appuser" instead of "nobody" as …

ffc63f8

…it was causing issue. Also, changing the base image.


          did a mutli-stage Dockerbuild to reduce image size

03ecf41


          changing to port 8000 for testing

f2d7006


          changing back to port 80 for Jenkins testing

03223c2


          changing back to port 8000 and will modify the indexd service

3751d38


          made changes to the Dockerfile to fix error with indexd being install…

56fdfba

…ed by changing where the "git" command runs. I also had to install postgresql-devel in the runtime image so "local_settings" can be imported.


          removing the dockerrun from the indexd_setup script

e8eff00


          increasing timeouts for testing

8deb1bc


          adding a worker class for better concurrency

72e163e


          testing gevent

d97fe2b


          removing gevent as it is no longer needed.

453c861


          changing the base image for indexd as I moved the python3.9 image to …

d3f403e

…the "base-repo"

EliseCastle23 marked this pull request as ready for review

September 22, 2023 16:16

EliseCastle23 and others added 9 commits

September 26, 2023 15:58


          changing the image indexd is based on

cfe4742


          updating the image that the runtime iamge is based on

86ff8dd


          feat: update to new base image

7092eec


          Merge pull request #369 from uc-cdis/feat/base-image

79fb97e

Feat/base image


          Add gunicorn

f58c38b


          Change Dockerfile to use gen3 user

45efbe2


          adding nginx to indexd

7fd7b7e


          dummy commit

64e536e


          fixing case issue

54ff527

EliseCastle23 and others added 8 commits

November 1, 2024 10:30


          adding "poetry run" to "gunicorn" command

b255010


          updating pyproject dependencies

d12ad68


          updating poetry install command

7a86165


          update poetry install cmd

6f93e8d


          removing source command

aa0502d


          updating base image

78634f6


          updating "AS"

69e82d7


          Update Dockerfile

c537faa

github-actions bot commented Nov 4, 2024

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          fixing variable syntax

2be1a74

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          updating workflow to include arm images

d5e4578

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$$\textcolor{#ffa500}{\tt{TOTAL}}$$	$$\textcolor{#23d18b}{\tt{44}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#ffa500}{\tt{46}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

Avantol13 reviewed

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          removing unneeded file

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github-actions bot commented Nov 15, 2024

filepath	$$\textcolor{#23d18b}{\tt{passed}}$$	$$\textcolor{#f14c4c}{\tt{failed}}$$	$$\textcolor{#ffa500}{\tt{skipped}}$$	SUBTOTAL
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$$\textcolor{#ffa500}{\tt{tests/test\_data\_upload.py}}$$	$$\textcolor{#23d18b}{\tt{8}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{9}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_graph\_submit\_and\_query.py}}$$	$$\textcolor{#23d18b}{\tt{7}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{7}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_dbgap.py}}$$	$$\textcolor{#23d18b}{\tt{4}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{5}}$$
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$$\textcolor{#23d18b}{\tt{tests/test\_audit\_service.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_gen3client.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{TOTAL}}$$	$$\textcolor{#23d18b}{\tt{43}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#f14c4c}{\tt{46}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

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@requires-indexd