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Release latest staging code #591

Merged
merged 57 commits into from
May 21, 2024
Merged

Release latest staging code #591

merged 57 commits into from
May 21, 2024

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alanbchristie
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dependabot bot and others added 30 commits March 18, 2024 21:49
Bumps [django](https://github.com/django/django) from 3.2.24 to 3.2.25.
- [Commits](django/django@3.2.24...3.2.25)

---
updated-dependencies:
- dependency-name: django
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Graceful handling of files from RCSB PDB (issue 1282)
Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.2.0 to 10.3.0.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.2.0...10.3.0)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
* fix: Attempt to debug timeout errors

* fix: More logging on service_query

* fix: Varioustimeout adjustments

* fix: Removed exception during timeout

* fix: Explit log on SSH connection error

* fix: Retry attempts for MySQL connections

* fix: Service timeout now 28 (was 17)

* fix: Add pymysql read and write timeouts

* fix: Quiter (expected) connection failure handling

* fix: TIMEOUT now DEGRADED

* fix: Fix while loop exit conditions

* fix: Better loop logic

* style: services logging reduced and back to debug

* fix: SSHTunnel logging now ERROR (was DEBUG)

* fix: Quieter securty

* fix: More failures permitted (and debug tweaks)

* fix: Leaner logging

* fix: Leaner logging (only report when we're having topruble)

* fix: Better constant name

* fix: Reduced service logging

* docs: Doc tweak

* fix: Minor log tweak

* fix: Fixed duplicate log content

---------

Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
Changes so far:
- removed endpoint FirstAssemblyview
- moved the functionality to template_protein field in
TargetSerializer
- removed TargetMoleculesserializer
- removed sequences field from TargetSerializer

This is a result of Boris' comment in
github (m2ms/fragalysis-frontend#1373 (comment))
where he said the field isn't used and template_protein field is not
used. Looking at the code where this may be used, revealed that
Targetmoleculesserializer can be removed as well

NB! they're not removed-removed right now, only commented in. This
commit can be used to restore the code.
First reference PDB from assemblies.yaml available in API
TODO: add and test PATCH method on PoseSerializer
Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7.
- [Release notes](https://github.com/kjd/idna/releases)
- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst)
- [Commits](kjd/idna@v3.6...v3.7)

---
updated-dependencies:
- dependency-name: idna
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Also, added exclude directives to .pre-commit-config.yaml to not touch
django migration files
Added 'hidden' property to viewer.Tag model
* refactor: Quieter ISPyB cache

* refactor: Security cache log now quieter

* fix: Better cache logic - and reduced log

---------

Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
Nested serializer for pose, but I don't think I can use them
Data loads successfully but actual v2 upload has not been tested
Fix static ressources not being loaded
Revert "Fix static ressources not being loaded"
Added sorting keys for versioned key. V1 data loading, waiting for
fixes in conf site presentation to continue with v2
Allows sending incomplete requests (no idea why seralizer isn't
populating fields).
Also fixed a bug where field updates on poses with multiple
observations where blocked.
kaliif and others added 26 commits May 2, 2024 09:32
Reads and processes upload_2+ data where version numbers are given in suffix
Allow uploading fully versioned data (issue 1311)
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](tqdm/tqdm@v4.66.1...v4.66.3)

---
updated-dependencies:
- dependency-name: tqdm
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Only non-superseded sites available from the api (issue 1311)
build(deps): bump django from 3.2.24 to 3.2.25
Bumps [black](https://github.com/psf/black) from 23.12.0 to 24.3.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.12.0...24.3.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
build(deps): bump pillow from 10.2.0 to 10.3.0
build(deps): bump idna from 3.6 to 3.7
Better check for already uploaded data
build(deps-dev): bump black from 23.12.0 to 24.3.0
build(deps): bump tqdm from 4.66.1 to 4.66.3
Backend part of poses feature (issue 1392)
Not sure why the previous merge didn't work
* feat: Experiment with django prometheus

* feat: Fix build

* fix: Fix build (locking drf)

* feat: Fix lock file

* feat: Update to non-slim Python 3.11.9

* feat: Back to slim image

* fix: Some basic internal metrics

* fix: Removed rogue line

* fix: Fix lint issues

* fix: Removed custom metrics

---------

Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
@alanbchristie alanbchristie requested a review from kaliif May 21, 2024 13:04
@alanbchristie alanbchristie merged commit d4681de into production May 21, 2024
1 check failed
@alanbchristie alanbchristie deleted the staging-conflict-fix branch May 21, 2024 13:14
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3 participants