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Align production with staging#555

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alanbchristie merged 66 commits intoproductionxchem/fragalysis-backend:productionfrom stagingxchem/fragalysis-backend:stagingCopy head branch name to clipboardMar 12, 2024

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Commits on Feb 12, 2024

• Some changes to cset_upload.py to allow site observation short codes (#527)

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• stashing

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Commits on Feb 13, 2024

• stashing

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• Short code prefix and tooltip to backend

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Commits on Feb 14, 2024

• Prefix tooltip now serverd by api/site_observation

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• stashing

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• Site observation groups for shortcodes now by experiment

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• Merge pull request #528 from xchem/m2ms-1334-short-code-prefix

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Commits on Feb 15, 2024

• feat: download structure fixed

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• All yaml files added to download

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• New format to download zip (issue 1326) (#530)

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Commits on Feb 16, 2024

• cset_upload.py: lhs_pdb renamed to ref_pdb

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• Merge pull request #531 from xchem/m2ms-1327-ref-mols

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• Renamed canon- and conf site tags

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• Merge pull request #532 from xchem/m2ms-1277-canon-conf-tags

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Commits on Feb 19, 2024

• Adds support for key-based SSH connections (#534)

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• build(deps): bump cryptography from 42.0.0 to 42.0.2 (#533)

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• docs: Updates documentation (#536)

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• build(deps): bump django from 3.2.20 to 3.2.24 (#535)

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Commits on Feb 20, 2024

• fix: reverting wrong changes

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• fix: reverting wrong changes (#538)

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• Merge branch 'staging' into m2ms-1327-rhs-upload

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Commits on Feb 22, 2024

• stashing

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• Merge branch 'staging' into m2ms-1326-download-zip

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• add site observation's ligand sdf to aligned_files

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• Merge pull request #540 from xchem/m2ms-1326-download-zip

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Commits on Feb 23, 2024

• fix: custom pdb now downloadable

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• Merge pull request #541 from xchem/m2ms-1327-rhs-upload

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Commits on Feb 27, 2024

• fix: increased loglevel to error on unexpected exceptions block

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• Merge pull request #542 from xchem/target_loader_loglevel_fix

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Commits on Feb 29, 2024

• Merge branch 'production' into staging

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• fix: Discourse service check now checks API key before creating a service (#544)

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• build(deps): bump cryptography from 42.0.2 to 42.0.4 (#539)

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• metadata.csv populated

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Commits on Mar 1, 2024

• upload_name automatically pouplated when creating tags in UI

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• Merge branch 'staging' into m2ms-1343-metadata

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• Merge pull request #546 from xchem/m2ms-1343-metadata

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• changes to api/download_structures

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• don't download neighbourhoods.yaml unless trans_matrix_info is checked

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• fixed error handling (errors.csv) and not returning combined sdf

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• Merge pull request #547 from xchem/m2ms-1326-download-zip-api

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Commits on Mar 4, 2024

• fix: Added parsing directives to DownloadStructuresserializer

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• Merge pull request #548 from xchem/m2ms-1326-download-zip-api

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• Consecutive numbering of observations under canon site

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• Merge pull request #549 from xchem/m2ms-1361-site-numbering

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Commits on Mar 5, 2024

• SiteObservatdion.tag split to tag and tag_prefix (1361)

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• fix: crystallographic_files folders in download now sans suffix (#550)

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• Merge pull request #551 from xchem/m2ms-1361-site-numbering

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• Merge branch 'production' into staging

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• fix: tag names underdand prefix in download's metadata.csv

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• Merge pull request #552 from xchem/m2ms-1343-tags-missing

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Commits on Mar 7, 2024

• fix: return all proteins listed in api/download_structures

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• Merge pull request #553 from xchem/m2ms-1375-missing-proteins

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• fix: fixed 'All structures' option not working in download dialog

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• Merge pull request #554 from xchem/m2ms-1375-missing-proteins

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• Migrations for new file fields

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• Issue 1326 - mol and smiles added to download bundle

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Commits on Mar 8, 2024

• Target loader should handle empty code_prefix and tooltip

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• Column 'Downloaded' to metadata.csv in downloads

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• fix: restore 'upload_name' in site obvs tags to prefix-tag format

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• Merge pull request #556 from xchem/restore_tag_upload_name

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Commits on Mar 11, 2024

• Removed ligand_smiles workaround

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• Merge pull request #557 from xchem/m2ms-1326-more-files-to-zip

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• Merge pull request #558 from xchem/m2ms-1368-empty-shortcode

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• fix: Add force_error_display to connection functions (default False) (#559)

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Commits on Mar 12, 2024

• Merge branch 'production' into staging

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