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2023-05-09Integrate OAuth2 auth with GN2 UIhook-up-auth-to-traits-pageFrederick Muriuki Muriithi
Update the templates to make use of the OAuth2 authentication rather than the older authentication that used Redis.
2023-05-09auth: Handle authentication using the "Authorization Code Flow"Frederick Muriuki Muriithi
2023-05-08oauth2: UI - Remove `Edit` elementFrederick 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.
2023-05-08oauth2: Fix UI failure on authorisation errorsFrederick 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).
2023-05-08oauth2: Add auth-checking wrapper to `/show_trait?...` pageFrederick 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.
2023-05-04Fix bug where global search had wrong checkbox valueszsloan
2023-05-03Add table for editing sample values/SE/Nzsloan
2023-05-01Left-align histogram titlezsloan
For some reason xanchor=right does this
2023-04-28Enable passing dataid for correlation resultszsloan
This allows the scatterplots to use edited sample data
2023-04-28Use cached sample data in scatter plots (when applicable)zsloan
2023-04-28Cache trait sample data for mappingzsloan
This is so edited sample values can be used in the additive effect scatterplots
2023-04-25auth: disable UI elements for non-editable rolesFrederick 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.
2023-04-21oauth2: BugFixes: Fix redirect. Add Dataset Name.Frederick Muriuki Muriithi
2023-04-21oauth2: Update to enable linking of phenotypes.Frederick Muriuki Muriithi
2023-04-21oauth: Update UI for phenotype resources.Frederick Muriuki Muriithi
2023-04-20Fix bugs: Add missing module. Make args mandatoryFrederick Muriuki Muriithi
Add missing `wqflask.oauth2.ui` module Make arguments to the menu-generation macro mandatory going forward.
2023-04-20oauth2: Render UI uniformly across all templates.Frederick Muriuki Muriithi
2023-04-19oauth2: Provide missing species_nameFrederick Muriuki Muriithi
2023-04-19oauth2: fix bug with error handling.Frederick Muriuki Muriithi
2023-04-19oauth2: Link the dataFrederick Muriuki Muriithi
2023-04-19oauth2: update UI on successful search.Frederick Muriuki Muriithi
2023-04-19oauth2: phenotypes: Enable search from user input.Frederick Muriuki Muriithi
2023-04-19Remove dead text in GeneRIF pageMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-19oauth2: UI: Enable selecting and deselecting items for linkingFrederick 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.
2023-04-18import code cleanupAlexander_Kabui
2023-04-18metadata caching code integrationAlexander_Kabui
2023-04-18Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Alexander_Kabui
chores/minor-fixes
2023-04-18Add a web url to genewiki entries for GNMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-18oauth2: update UI and js to display initial search results.Frederick Muriuki Muriithi
2023-04-17Add a link to the GN2 GeneWiki pageMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-17Add genewiki pageMunyoki 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>
2023-04-17oauth2: Build code to do searchFrederick Muriuki Muriithi
At this point, the code fails with a 404, despite the appropriate endpoint existing. Will need further debugging.
2023-04-15Revert "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
2023-04-14Handle errors for group consistent with the UI.Frederick Muriuki Muriithi
2023-04-12oauth2: Generalise JS code to work for both mRNA and Genotype datasets.Frederick Muriuki Muriithi
2023-04-12delete dead codeAlexander_Kabui
2023-04-12add code to store metadata in filesAlexander_Kabui
2023-04-11Fix bug where publication years had links even when there's no PMIDzsloan
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
2023-04-11Fix the way database_connection() is calledzsloan
I think it now gets the SQL_URI from settings
2023-04-11Fix indentation for conn.commit()zsloan
2023-04-11modify default textfile pathAlexander_Kabui
2023-04-10Add UI for searching and linking mRNA Assay datasets.Frederick Muriuki Muriithi
2023-04-10Do search. Filter out selected datasets.Frederick Muriuki Muriithi
Enable search when user types in search box. Filter out any selected datasets.
2023-04-08oauth2: Link the Genotype datasets.Frederick Muriuki Muriithi
2023-04-07Move 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.
2023-04-06Commit updates for phenotype/publication metadatazsloan
2023-04-06`flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`Frederick Muriuki Muriithi
Genenetwork2 configs are a tad weird, and instead of using the configs in `flask.current_app`, we need to use those in `utility.tools`.
2023-04-06correlations: Provide more output to enable debug of errors.Frederick Muriuki Muriithi
2023-04-06Remove use of deprecated `gn3.db_utils.database_connector` function.Frederick Muriuki Muriithi
Remove use of deprecated function and fix a myriad of bugs that rise from its removal. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
2023-04-06oauth2: UI - Enable auto-selection of datasets to be linkedFrederick Muriuki Muriithi
When a user selects a dataset in the search table, automatically add it to the link table and remove it from the search table.
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