Aligns production with latest staging #545
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…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
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
Short code prefix and tooltip read from yaml file (issue 1334)
TODO: add all the yamls
* 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 (issue 1327)
Renamed canon- and conf site tags
* 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 <alan.christie@matildapeak.com> * feat: Adds support for private keys on SSH tunnel * fix: Fixes key-based logic --------- Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Download zip; ligand sdfs now in aligned_files not in missing_sdfs
RHS upload backend side functional
Increased loglevel to error on unexpected exceptions block
…vice (#544) Co-authored-by: Alan Christie <alan.christie@matildapeak.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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
Only populated on creation, updates won't touch it
kaliif
approved these changes
Mar 1, 2024
Changes metadata.csv format in download and adds 'upload_name' attribute to tag model (issues 1343 and 1355)
- 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
Updates to api/download_structures endpoint (issue 1326)
Added parsing directives to DownloadStructuresserializer
Consecutive numbering of observations under canon site
SiteObservatdion.tag split to tag and tag_prefix (1361)
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