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2024-03-26Revert "Disable CaseAttributeId - because it needs an update to the database"Frederick Muriuki Muriithi
This reverts commit 4539ef0297bb4b8c2954f250697c237069a16d64. This commit was ignoring the historical context that led to the changes in the schema of the `CaseAttribute*` tables, and leads to errors when the database schema is updated.
2024-03-26Add missing docstrings to save/metadata_edit functions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Add "dataset.name" field to the editor form.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Only display the "edit" link when a user has edit permissions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Add a final fallback for match expression.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Use correct variable name.Munyoki Kilyungi
* gn2/wqflask/oauth2/client.py (no_token_post): "uri" does not exist. Replace it with "uri_path." Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Delete unused variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Use "require_oauth2_edit_resource_access" for edit/save endpoints.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Implement "require_oauth2_edit_resource_access" decorator.Munyoki Kilyungi
* gn2/wqflask/oauth2/checks.py (require_oauth2): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Replace "__" prefix for with "_".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Import user_logged_in from the clients module.Munyoki Kilyungi
Importing "user_logged_in" in the checks module just to export adds a layer of indirection and makes the code hard to read. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Delete repetitive statement in "render_ui".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Auto-pep8 (using flake8) file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Replace "login_required" with "require_oauth2".Munyoki Kilyungi
* gn2/wqflask/edit.py: Replace "login_required" import with "require_oauth2". (metadata_edit): Replace "login_required" with "require_oauth2". (edit): Ditto. (save): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused declared variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove typo from template.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Add extra "edit" buttons to the relevant sections.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Make the description bold.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Reset 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>
2024-03-26Prevent 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>
2024-03-26Add a hidden input form element for "section".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Replace Path construct with a format string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Add 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>
2024-03-26Replace 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>
2024-03-26Have 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>
2024-03-26Delete search dataset functionality in RDF.Munyoki Kilyungi
* gn2/wqflask/views.py (search_for_dataset): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Make 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>
2024-03-26Delete "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>
2024-03-26Add new hidden input for metadata id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Rename summary label to "edit-summary".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Add 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>
2024-03-26Add 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>
2024-03-26Add conditional for accessionId in metadata editor template.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Correctly wrap the "__build_access_checker__" function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Rename "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>
2024-03-26Delete unused page.Munyoki Kilyungi
* gn2/wqflask/views.py (display_diffs_admin): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Delete "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>
2024-03-26Integrate 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>
2024-03-22log full error messaging for gnqa ratingAlexander_Kabui
2024-03-22use icon for search historyAlexander_Kabui
2024-03-22add gnqa evaluation UIAlexander_Kabui
2024-03-22Mapping page: minor text editsPjotr Prins
2024-03-21Fix 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
2024-03-21Give more space for strain names in haplotype bandzsloan
2024-03-21Fix bug where scatterplot didn't work for temp traitszsloan
2024-03-18linnkify abstract and referencesAlexander_Kabui
2024-03-18add pumed search linkAlexander_Kabui
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-19 04:30:20 +0000