| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-03-26 | Reset repo and pull then write changes before committing. | Munyoki Kilyungi | |
| * gn2/wqflask/edit.py: Import session_info. (save_dataset_metadata): Add author as an argument. Reset repo and pull then write changes before committing. Split strings before __run_cmd is called. (metadata_edit): Rename "metadata" -> "__metadata". (save): Save the output to the correct path. Pass author to "save_dataset_metadata". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Prevent shell injection by disabling shell invocation in subprocess. | Munyoki Kilyungi | |
| See: <https://stackoverflow.com/questions/52019920/python3-sanitizing-user-input-passed-to-shell-as-parameter> for more information. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add a hidden input form element for "section". | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Replace Path construct with a format string. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add missing "curry" to __run_cmd. | Munyoki Kilyungi | |
| This is required to be able to pass __run_cmd through a pipeline. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Replace Path.join with urljoin for url paths. | Munyoki Kilyungi | |
| * gn2/wqflask/edit.py: Import urljoin. (metadata_edit): Replace Path with urljoin. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Have one template for datasets. | Munyoki Kilyungi | |
| * gn2/wqflask/templates/metadata/dataset.html: Move this ... * gn2/wqflask/templates/dataset.html: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Delete search dataset functionality in RDF. | Munyoki Kilyungi | |
| * gn2/wqflask/views.py (search_for_dataset): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Make GN3_LOCAL_URL local to avoid circular imports. | Munyoki Kilyungi | |
| * gn2/wqflask/edit.py: Move GN3_LOCAL_URL ... (metadata_edit): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Delete "raise_unimplemented". | Munyoki Kilyungi | |
| * gn2/wqflask/oauth2/groups.py: Remove unused "raise_unimplemented" import. * gn2/wqflask/oauth2/request_utils.py (raise_unimplemented): Delete function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add new hidden input for metadata id. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Rename summary label to "edit-summary". | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add function for saving metadata in git. | Munyoki Kilyungi | |
| * gn2/wqflask/edit.py (save_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add classified-under to hidden form inputs. | Munyoki Kilyungi | |
| * gn2/wqflask/templates/metadata/editor.html: Add "classified-under" form element. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Add conditional for accessionId in metadata editor template. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Correctly wrap the "__build_access_checker__" function. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Remove unused imports. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Rename "required_access" to "required_trait_access". | Munyoki Kilyungi | |
| * gn2/wqflask/decorators.py (required_access): Rename this to ... (required_trait_access): ... this. * gn2/wqflask/metadata_edits.py: Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Delete unused page. | Munyoki Kilyungi | |
| * gn2/wqflask/views.py (display_diffs_admin): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Remove unused imports. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Delete "edit_access_required" decorator. | Munyoki Kilyungi | |
| * gn2/wqflask/decorators.py (edit_access_required): Delete. * gn2/wqflask/resource_manager.py: Delete references to "edit_access_required". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-26 | Integrate CKEditor into metadata editing. | Munyoki Kilyungi | |
| * gn2/wqflask/__init__.py: Register blueprint endpoint for metadata edits. * gn2/wqflask/edit.py (metadata_edit): New function. (save): Ditto. * gn2/wqflask/templates/metadata/dataset.html: New template. * gn2/wqflask/templates/metadata/editor.html: New template. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-03-22 | log full error messaging for gnqa rating | Alexander_Kabui | |
| 2024-03-22 | use icon for search history | Alexander_Kabui | |
| 2024-03-22 | add gnqa evaluation UI | Alexander_Kabui | |
| 2024-03-22 | Mapping page: minor text edits | Pjotr Prins | |
| 2024-03-22 | Update ProbeSetSE table schema. | Frederick Muriuki Muriithi | |
| 2024-03-21 | Fix issue where Haplotype band could overlap with Homology band (plus other ↵ | zsloan | |
| spacing issues related to the Homology band) Change Homology track colors to be more color-blind friendly | |||
| 2024-03-21 | Give more space for strain names in haplotype band | zsloan | |
| 2024-03-21 | Fix bug where scatterplot didn't work for temp traits | zsloan | |
| 2024-03-18 | Merge pull request #835 from genenetwork/feature/pub-data-ui | Alexander Kabui | |
| add pub data UI | |||
| 2024-03-18 | linnkify abstract and references | Alexander_Kabui | |
| 2024-03-18 | add pumed search link | Alexander_Kabui | |
| 2024-03-18 | add pubdata ui | Alexander_Kabui | |
| 2024-03-14 | Disable CaseAttributeId - because it needs an update to the database | GN2 | |
| and it is not clear why. @bonfacem. | |||
| 2024-03-13 | Make some improvements to the collections list template | zsloan | |
| 2024-03-13 | Add options to select by index/attr (instead of just block) | zsloan | |
| 2024-03-07 | fix bugs. | Frederick Muriuki Muriithi | |
| 2024-03-06 | Check whether `GN2_SETTINGS` is provided before using default | Frederick Muriuki Muriithi | |
| 2024-03-06 | Use AUTH_SERVER_URL setting from flask.current_app not gn2.utility.tools | Frederick Muriuki Muriithi | |
| 2024-03-06 | Bug: Break circular import | Frederick Muriuki Muriithi | |
| 2024-03-05 | disable login requirement for gnqa on cd | Alexander_Kabui | |
| * reason gnqa and gn-auth are currently unstable | |||
| 2024-03-05 | Fix missed bug: Don't use `gn2.utility.tools` for configs. | Frederick Muriuki Muriithi | |
| 2024-03-05 | configs: Fetch configs from app not `gn2.utility.tools` | Frederick Muriuki Muriithi | |
| Fetch configurations from the application, rather than from the `gn2.utility.tools` module that does not get the updated values from the secrets file. | |||
| 2024-03-05 | Pick secrets from config file. | Frederick Muriuki Muriithi | |
| 2024-03-04 | Include ALL html templates. | Frederick Muriuki Muriithi | |
| 2024-03-02 | Doc database layout | Pjotr Prins | |
| 2024-03-02 | doc: databasing | Pjotr Prins | |
| 2024-02-29 | Fix URI to query | Frederick Muriuki Muriithi | |
| 2024-02-21 | Merge pull request #834 from genenetwork/chores/replace-js-external-links | Alexander Kabui | |
| Replacing JS External Links with Guix Packages | |||
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