Some changes to cset_upload.py to allow site observation short codes #527
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
NB! this probably still won't work! I suspect the file I was given is broken and I cannot test it further
alanbchristie
approved these changes
Feb 12, 2024
alanbchristie
added a commit
that referenced
this pull request
Feb 19, 2024
* 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 * 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 * Site observation groups for shortcodes now by experiment * 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> --------- 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>
alanbchristie
added a commit
that referenced
this pull request
Feb 29, 2024
* 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]> --------- 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>
alanbchristie
added a commit
that referenced
this pull request
Mar 5, 2024
* 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) --------- 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>
alanbchristie
added a commit
that referenced
this pull request
Mar 12, 2024
* 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]> --------- 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]>
alanbchristie
added a commit
that referenced
this pull request
Mar 12, 2024
* 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]>
alanbchristie
added a commit
that referenced
this pull request
Mar 13, 2024
* 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]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Probably the upload still won't work but I cannot test it further because I suspect the test file is broken