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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
2024-03-18add pubdata uiAlexander_Kabui
2024-03-14Disable CaseAttributeId - because it needs an update to the databaseGN2
and it is not clear why. @bonfacem.
2024-03-13Make some improvements to the collections list templatezsloan
2024-03-13Add options to select by index/attr (instead of just block)zsloan
2024-03-07fix bugs.Frederick Muriuki Muriithi
2024-03-06Use AUTH_SERVER_URL setting from flask.current_app not gn2.utility.toolsFrederick Muriuki Muriithi
2024-03-06Bug: Break circular importFrederick Muriuki Muriithi
2024-03-05disable login requirement for gnqa on cdAlexander_Kabui
* reason gnqa and gn-auth are currently unstable
2024-03-05Fix missed bug: Don't use `gn2.utility.tools` for configs.Frederick Muriuki Muriithi
2024-03-05configs: 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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 23:33:45 +0000