| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-05-12 | auth: Integrate sessions with auth | Frederick Muriuki Muriithi | |
| Rework the sessions to do what was handled by the soon-to-be-obsolete `wqflask.user_sessions` module. This is necessary in order to retain the expected functionality of the user collections, especially: * anonymous user collections * authenticated user collections * import of anonymous collections when user authenticates | |||
| 2023-05-10 | auth: Fetch user collections from GN3 | Frederick Muriuki Muriithi | |
| Fetch the user collections from GN3 for users that have authenticated. | |||
| 2023-05-10 | auth: bug-fix: Call `logged_in` function | Frederick Muriuki Muriithi | |
| The `logged_in` symbol was changed from a plain variable into a function, so we need to call it to get its actual value. | |||
| 2023-05-09 | Integrate OAuth2 auth with GN2 UIhook-up-auth-to-traits-page | Frederick Muriuki Muriithi | |
| Update the templates to make use of the OAuth2 authentication rather than the older authentication that used Redis. | |||
| 2023-05-09 | auth: Handle authentication using the "Authorization Code Flow" | Frederick Muriuki Muriithi | |
| 2023-05-08 | oauth2: UI - Remove `Edit` element | Frederick Muriuki Muriithi | |
| The `Edit` button was unnecessary, since the `View` button gives the user access to a UI that allows them to edit the role. | |||
| 2023-05-08 | oauth2: Fix UI failure on authorisation errors | Frederick Muriuki Muriithi | |
| Surround the UI elements with the check for any authorisation errors to avoid trying to access non-existent data (this leads to an exception). | |||
| 2023-05-08 | oauth2: Add auth-checking wrapper to `/show_trait?...` page | Frederick Muriuki Muriithi | |
| As a proof-of-concept, add some sort of wrapper to check whether the user has access to the given trait/dataset. This will probably need some improvement to check for edit access, curation access, etc. | |||
| 2023-05-04 | Fix bug where global search had wrong checkbox values | zsloan | |
| 2023-05-03 | Add table for editing sample values/SE/N | zsloan | |
| 2023-05-01 | Left-align histogram title | zsloan | |
| For some reason xanchor=right does this | |||
| 2023-04-28 | Enable passing dataid for correlation results | zsloan | |
| This allows the scatterplots to use edited sample data | |||
| 2023-04-28 | Use cached sample data in scatter plots (when applicable) | zsloan | |
| 2023-04-28 | Cache trait sample data for mapping | zsloan | |
| This is so edited sample values can be used in the additive effect scatterplots | |||
| 2023-04-25 | auth: disable UI elements for non-editable roles | Frederick Muriuki Muriithi | |
| If a role is not user-editable, disable the UI elements that allow editting of the role to prevent that as an option in the first place. | |||
| 2023-04-21 | oauth2: BugFixes: Fix redirect. Add Dataset Name. | Frederick Muriuki Muriithi | |
| 2023-04-21 | oauth2: Update to enable linking of phenotypes. | Frederick Muriuki Muriithi | |
| 2023-04-21 | oauth: Update UI for phenotype resources. | Frederick Muriuki Muriithi | |
| 2023-04-20 | Fix bugs: Add missing module. Make args mandatory | Frederick Muriuki Muriithi | |
| Add missing `wqflask.oauth2.ui` module Make arguments to the menu-generation macro mandatory going forward. | |||
| 2023-04-20 | oauth2: Render UI uniformly across all templates. | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: Provide missing species_name | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: fix bug with error handling. | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: Link the data | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: update UI on successful search. | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: phenotypes: Enable search from user input. | Frederick Muriuki Muriithi | |
| 2023-04-19 | Remove dead text in GeneRIF page | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-19 | oauth2: UI: Enable selecting and deselecting items for linking | Frederick Muriuki Muriithi | |
| This commit generalises the code for selecting and deselecting items making it usable even for the phenotype traits. Now we can switch items from the search table to the linking table and vice versa. | |||
| 2023-04-18 | Merge pull request #774 from genenetwork/chores/minor-fixes | Alexander Kabui | |
| Chores/minor fixes | |||
| 2023-04-18 | import code cleanup | Alexander_Kabui | |
| 2023-04-18 | metadata caching code integration | Alexander_Kabui | |
| 2023-04-18 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | Alexander_Kabui | |
| chores/minor-fixes | |||
| 2023-04-18 | Add a web url to genewiki entries for GN | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-18 | oauth2: update UI and js to display initial search results. | Frederick Muriuki Muriithi | |
| 2023-04-17 | Add a link to the GN2 GeneWiki page | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Add genewiki page | Munyoki Kilyungi | |
| * wqflask/wqflask/templates/generif.html: New template. * wqflask/wqflask/views.py (display_diffs_users): New route. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | oauth2: Build code to do search | Frederick Muriuki Muriithi | |
| At this point, the code fails with a 404, despite the appropriate endpoint existing. Will need further debugging. | |||
| 2023-04-15 | Revert "Fix the way database_connection() is called" | Frederick Muriuki Muriithi | |
| This reverts commit b8b62aea1c7924e2ee7455c6fe8b34eee7cb8e74. We do need to decouple the entire `gn3.db_utils` from the `flask.current_app` object, and as such, the use of `SQL_URI` from the `utility.tools` module in GN2 was on purpose. This is also to help towards fixing issue https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils | |||
| 2023-04-14 | Handle errors for group consistent with the UI. | Frederick Muriuki Muriithi | |
| 2023-04-12 | oauth2: Generalise JS code to work for both mRNA and Genotype datasets. | Frederick Muriuki Muriithi | |
| 2023-04-12 | delete dead code | Alexander_Kabui | |
| 2023-04-12 | add code to store metadata in files | Alexander_Kabui | |
| 2023-04-11 | Fix bug where publication years had links even when there's no PMID | zsloan | |
| This was just caused by the correlation code not directly being passed the PMID (and instead only being passed the link and the text), so the logic in the table code needed to be changed to check for the link instead of the PMID | |||
| 2023-04-11 | Fix the way database_connection() is called | zsloan | |
| I think it now gets the SQL_URI from settings | |||
| 2023-04-11 | Fix indentation for conn.commit() | zsloan | |
| 2023-04-11 | modify default textfile path | Alexander_Kabui | |
| 2023-04-10 | Add UI for searching and linking mRNA Assay datasets. | Frederick Muriuki Muriithi | |
| 2023-04-10 | Do search. Filter out selected datasets. | Frederick Muriuki Muriithi | |
| Enable search when user types in search box. Filter out any selected datasets. | |||
| 2023-04-08 | oauth2: Link the Genotype datasets. | Frederick Muriuki Muriithi | |
| 2023-04-07 | Move JS to external file. Generalise functions. | Frederick Muriuki Muriithi | |
| Move the javascript to an external file to ease development. Generalise some functions to make it easier to reuse the code down the line. | |||
| 2023-04-06 | Commit updates for phenotype/publication metadata | zsloan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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