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* Some changes to cset_upload.py to allow site observation short codes (#527) * stashing * fix: cset_upload.py updated to allow new-style site observation codes NB! this probably still won't work! I suspect the file I was given is broken and I cannot test it further * stashing * stashing * Short code prefix and tooltip to backend Target loader now reads short code prefix and tooltip from meta_aligner.yaml. Tooltip is saved to Experiment model. TODO: make tooltip available via API * Prefix tooltip now serverd by api/site_observation * stashing * Site observation groups for shortcodes now by experiment * feat: download structure fixed TODO: add all the yamls * All yaml files added to download * New format to download zip (issue 1326) (#530) * stashing * stashing * feat: download structure fixed TODO: add all the yamls * All yaml files added to download * cset_upload.py: lhs_pdb renamed to ref_pdb * Renamed canon- and conf site tags * Adds support for key-based SSH connections (#534) * Centralised environment variables (#529) * refactor: Restructured settings.py * docs: Minor tweaks * refactor: Move security and infection config to settings * refactor: b/e & f/e/ tags now in settings (also fixed f/e tag value) * refactor: Move Neo4j config to settings * refactor: More variables into settings * refactor: Moved remaining config * docs: Adds configuration guide as comments * docs: Variable prefix now 'stack_' not 'stack_env_' --------- Co-authored-by: Alan Christie <[email protected]> * feat: Adds support for private keys on SSH tunnel * fix: Fixes key-based logic --------- Co-authored-by: Alan Christie <[email protected]> * build(deps): bump cryptography from 42.0.0 to 42.0.2 (#533) Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.0 to 42.0.2. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@42.0.0...42.0.2) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: Updates documentation (#536) Co-authored-by: Alan Christie <[email protected]> * build(deps): bump django from 3.2.20 to 3.2.24 (#535) Bumps [django](https://github.com/django/django) from 3.2.20 to 3.2.24. - [Commits](django/django@3.2.20...3.2.24) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: reverting wrong changes * fix: reverting wrong changes (#538) * stashing * add site observation's ligand sdf to aligned_files * fix: custom pdb now downloadable * fix: increased loglevel to error on unexpected exceptions block * fix: Discourse service check now checks API key before creating a service (#544) Co-authored-by: Alan Christie <[email protected]> * build(deps): bump cryptography from 42.0.2 to 42.0.4 (#539) Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.2 to 42.0.4. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@42.0.2...42.0.4) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * metadata.csv populated Started working on issue 1355 as well, it's too tightly coupled. Some work remaining re that: - when tag created in UI, make sure upload_name attribute is populated * upload_name automatically pouplated when creating tags in UI Only populated on creation, updates won't touch it * changes to api/download_structures - apo_file, bound_file, sdf_info and smiles_info merged into all_aligned_structures - added pdb_info field NB! download_structures was requred to provide ligand_pdb as well. This wasn't tracked previously, so I added field to SiteObservation model. Meaning there's a migration and on stack deployment data needs to be wiped and reuploaded * don't download neighbourhoods.yaml unless trans_matrix_info is checked * fixed error handling (errors.csv) and not returning combined sdf * fix: Added parsing directives to DownloadStructuresserializer * Consecutive numbering of observations under canon site * SiteObservatdion.tag split to tag and tag_prefix (1361) * fix: crystallographic_files folders in download now sans suffix (#550) * fix: tag names underdand prefix in download's metadata.csv * fix: return all proteins listed in api/download_structures * fix: fixed 'All structures' option not working in download dialog * Migrations for new file fields * Issue 1326 - mol and smiles added to download bundle NB! not prodction/staging ready, still contains a hack for testing because XCA doesn't provide all the attributes. * Target loader should handle empty code_prefix and tooltip 'Should' because haven't tested yet with real data * Column 'Downloaded' to metadata.csv in downloads * fix: restore 'upload_name' in site obvs tags to prefix-tag format * Removed ligand_smiles workaround All necessary files are now tracked by the database and returned in download. * fix: Add force_error_display to connection functions (default False) (#559) Co-authored-by: Alan Christie <[email protected]> * Align production with staging (#555) (#560) * Some changes to cset_upload.py to allow site observation short codes (#527) * stashing * fix: cset_upload.py updated to allow new-style site observation codes NB! this probably still won't work! I suspect the file I was given is broken and I cannot test it further * stashing * stashing * Short code prefix and tooltip to backend Target loader now reads short code prefix and tooltip from meta_aligner.yaml. Tooltip is saved to Experiment model. TODO: make tooltip available via API * Prefix tooltip now serverd by api/site_observation * stashing * Site observation groups for shortcodes now by experiment * feat: download structure fixed TODO: add all the yamls * All yaml files added to download * New format to download zip (issue 1326) (#530) * stashing * stashing * feat: download structure fixed TODO: add all the yamls * All yaml files added to download * cset_upload.py: lhs_pdb renamed to ref_pdb * Renamed canon- and conf site tags * Adds support for key-based SSH connections (#534) * Centralised environment variables (#529) * refactor: Restructured settings.py * docs: Minor tweaks * refactor: Move security and infection config to settings * refactor: b/e & f/e/ tags now in settings (also fixed f/e tag value) * refactor: Move Neo4j config to settings * refactor: More variables into settings * refactor: Moved remaining config * docs: Adds configuration guide as comments * docs: Variable prefix now 'stack_' not 'stack_env_' --------- * feat: Adds support for private keys on SSH tunnel * fix: Fixes key-based logic --------- * build(deps): bump cryptography from 42.0.0 to 42.0.2 (#533) Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.0 to 42.0.2. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@42.0.0...42.0.2) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... * docs: Updates documentation (#536) * build(deps): bump django from 3.2.20 to 3.2.24 (#535) Bumps [django](https://github.com/django/django) from 3.2.20 to 3.2.24. - [Commits](django/django@3.2.20...3.2.24) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... * fix: reverting wrong changes * fix: reverting wrong changes (#538) * stashing * add site observation's ligand sdf to aligned_files * fix: custom pdb now downloadable * fix: increased loglevel to error on unexpected exceptions block * fix: Discourse service check now checks API key before creating a service (#544) * build(deps): bump cryptography from 42.0.2 to 42.0.4 (#539) Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.2 to 42.0.4. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@42.0.2...42.0.4) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... * metadata.csv populated Started working on issue 1355 as well, it's too tightly coupled. Some work remaining re that: - when tag created in UI, make sure upload_name attribute is populated * upload_name automatically pouplated when creating tags in UI Only populated on creation, updates won't touch it * changes to api/download_structures - apo_file, bound_file, sdf_info and smiles_info merged into all_aligned_structures - added pdb_info field NB! download_structures was requred to provide ligand_pdb as well. This wasn't tracked previously, so I added field to SiteObservation model. Meaning there's a migration and on stack deployment data needs to be wiped and reuploaded * don't download neighbourhoods.yaml unless trans_matrix_info is checked * fixed error handling (errors.csv) and not returning combined sdf * fix: Added parsing directives to DownloadStructuresserializer * Consecutive numbering of observations under canon site * SiteObservatdion.tag split to tag and tag_prefix (1361) * fix: crystallographic_files folders in download now sans suffix (#550) * fix: tag names underdand prefix in download's metadata.csv * fix: return all proteins listed in api/download_structures * fix: fixed 'All structures' option not working in download dialog * Migrations for new file fields * Issue 1326 - mol and smiles added to download bundle NB! not prodction/staging ready, still contains a hack for testing because XCA doesn't provide all the attributes. * Target loader should handle empty code_prefix and tooltip 'Should' because haven't tested yet with real data * Column 'Downloaded' to metadata.csv in downloads * fix: restore 'upload_name' in site obvs tags to prefix-tag format * Removed ligand_smiles workaround All necessary files are now tracked by the database and returned in download. * fix: Add force_error_display to connection functions (default False) (#559) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Kalev Takkis <[email protected]> Co-authored-by: Warren Thompson <[email protected]> Co-authored-by: Alan Christie <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Warren Thompson <[email protected]> * Add DISABLE_RESTRICT_PROPOSALS_TO_MEMBERSHIP (#561) * feat: Add DISABLE_RESTRICT_PROPOSALS_TO_MEMBERSHIP * style: Minor log tweak --------- Co-authored-by: Alan Christie <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Kalev Takkis <[email protected]> Co-authored-by: Warren Thompson <[email protected]> Co-authored-by: Alan Christie <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Warren Thompson <[email protected]>
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