Upgrade mongo from 4.4. to 5.0

[imnasnainaec]

Resolves #1703
Includes: Replace mongo calls with mongosh

The mongo shell is depricated (https://www.mongodb.com/docs/manual/release-notes/5.0-compatibility/#deprecations); replacing with mongosh.

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This change is 

[codecov-commenter]

Codecov Report

Merging #1704 (4d1ab4e) into master (a8f8ffc) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1704   +/-   ##
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  Coverage   52.21%   52.21%           
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  Files         275      275           
  Lines        8498     8498           
  Branches      616      616           
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  Hits         4437     4437           
  Misses       3568     3568           
  Partials      493      493           

Flag	Coverage Δ
backend	80.22% <ø> (ø)
frontend	32.68% <ø> (ø)

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[jmgrady]

Reviewable status: 0 of 3 files reviewed, 1 unresolved discussion (waiting on @imnasnainaec)

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maintenance/scripts/combine_app.py line 117 at r1 (raw file):

        db_results = self.exec(
            self.get_pod_id(CombineApp.Component.Database),
            ["/usr/bin/mongosh", "--quiet", "CombineDatabase", "--eval", cmd],

This is a breaking change. The Combine is running MongoDB 4.4 which does not have mongosh, it only has mongo. This change needs to wait until we have analyzed and tested The Combine with Mongo 5.0. I don't think that has been done yet.

Unfortunately, the README.md is not specific - it just instructs the reader to install Mongo. The link provided gives instructions for installing MongoDB 6.0 which we cannot run in a production environment yet (at least with official Docker images). The README.md should be updated to direct readers to install Mongo 4.4.

Code quote:

  ["/usr/bin/mongosh", "--quiet", "CombineDatabase", "--eval", cmd],

[jmgrady]

Reviewable status: 0 of 6 files reviewed, all discussions resolved (waiting on @imnasnainaec)

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maintenance/scripts/combine_app.py line 117 at r1 (raw file):

Previously, jmgrady (Jim Grady) wrote…

This is a breaking change. The Combine is running MongoDB 4.4 which does not have mongosh, it only has mongo. This change needs to wait until we have analyzed and tested The Combine with Mongo 5.0. I don't think that has been done yet.

Unfortunately, the README.md is not specific - it just instructs the reader to install Mongo. The link provided gives instructions for installing MongoDB 6.0 which we cannot run in a production environment yet (at least with official Docker images). The README.md should be updated to direct readers to install Mongo 4.4.

I have pushed a change to this PR that sets the MongoDB to version 5.0. I have also verified that the maintenance scripts work using mongosh and MongoDB 5.0.

[jmgrady]

Reviewed 3 of 3 files at r1, all commit messages.
Reviewable status: 3 of 6 files reviewed, all discussions resolved (waiting on @imnasnainaec)

[jmgrady]

Reviewed 3 of 3 files at r2.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @imnasnainaec)