Restore pose column in metadata.csv #664
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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] <[email protected]>
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] <[email protected]>
* 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 <[email protected]>
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] <[email protected]>
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 <[email protected]>
Data loads successfully but actual v2 upload has not been tested
Fixes bare html API pages
Fix static ressources not being loaded
Revert "Fix static ressources not being loaded"
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.
fix: log compound names when alignment is not found (issue 1495)
Removed target name from canon site and conformer site tags (issue 1496)
Sort canon sites by number of site observations (issue1498)
Shorter versions of crystalform sites-, conformer sites- and canon sites tags (issue 1496)
Shortcode dropped the 'x' character, longcode was made shorter with 'v' as an version indicator
Introduced by canon site sorting, issue 1498
Updated both short- and longcode (issue 1499)
Ribbon was missing because the 'template_protein' attribute was missing, because the path was compiled incorrectly and file was not found. Template protein file is not explicitly given in metadata, so trial-error method is used.
Second upload working (issue 1492)
catch block was wrongly positioned and may have been masking error messages
Fixes a bug in target loader's create_objects func
/ instead of + and _
Updated tag name format (issue 1508)
kaliif
approved these changes
Sep 13, 2024
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