| Age | Commit message (Expand) | Author |
|---|
| 2023-05-16 | auth: View collection details from GN3 endpoint...Retrieve a specific collection's details from the GN3 endpoint rather
than from the session, as was done previously.
| Frederick Muriuki Muriithi |
| 2023-05-15 | Create new collection via GN3 API...* wqflask/wqflask/collect.py: Send data to the GN3 API to create the
new collections.
* wqflask/wqflask/oauth2/client.py: Ensure request is sent as a json
request.
* wqflask/wqflask/static/new/javascript/search_results.js: use "POST"
rather than "GET" and send the traits also, in addition to the hash
| Frederick Muriuki Muriithi |
| 2023-05-12 | auth: Fetch anonymous collections from separate endpoint. | Frederick Muriuki Muriithi |
| 2023-05-12 | auth: Integrate sessions with auth...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
| Frederick Muriuki Muriithi |
| 2023-05-10 | auth: Fetch user collections from GN3...Fetch the user collections from GN3 for users that have authenticated.
| Frederick Muriuki Muriithi |
| 2023-05-10 | auth: bug-fix: Call `logged_in` function...The `logged_in` symbol was changed from a plain variable into a
function, so we need to call it to get its actual value.
| Frederick Muriuki Muriithi |
| 2023-05-09 | Integrate OAuth2 auth with GN2 UI...Update the templates to make use of the OAuth2 authentication rather
than the older authentication that used Redis.
hook-up-auth-to-traits-page | Frederick Muriuki Muriithi |
| 2023-05-09 | auth: Handle authentication using the "Authorization Code Flow" | Frederick Muriuki Muriithi |
| 2023-05-08 | oauth2: UI - Remove `Edit` element...The `Edit` button was unnecessary, since the `View` button gives the
user access to a UI that allows them to edit the role.
| Frederick Muriuki Muriithi |
| 2023-05-08 | oauth2: Fix UI failure on authorisation errors...Surround the UI elements with the check for any authorisation errors
to avoid trying to access non-existent data (this leads to an
exception).
| Frederick Muriuki Muriithi |
| 2023-05-08 | oauth2: Add auth-checking wrapper to `/show_trait?...` page...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.
| Frederick Muriuki Muriithi |
| 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...For some reason xanchor=right does this
| zsloan |
| 2023-04-28 | Enable passing dataid for correlation results...This allows the scatterplots to use edited sample data
| zsloan |
| 2023-04-28 | Use cached sample data in scatter plots (when applicable) | zsloan |
| 2023-04-28 | Cache trait sample data for mapping...This is so edited sample values can be used in the additive effect scatterplots
| zsloan |
| 2023-04-25 | auth: disable UI elements for non-editable roles...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.
| Frederick Muriuki Muriithi |
| 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...Add missing `wqflask.oauth2.ui` module
Make arguments to the menu-generation macro mandatory going forward.
| Frederick Muriuki Muriithi |
| 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...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-19 | oauth2: UI: Enable selecting and deselecting items for linking...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.
| Frederick Muriuki Muriithi |
| 2023-04-18 | Merge pull request #774 from genenetwork/chores/minor-fixes...Chores/minor fixes | Alexander Kabui |
| 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 ch... | Alexander_Kabui |
| 2023-04-18 | Add a web url to genewiki entries for GN...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-17 | Add genewiki page...* wqflask/wqflask/templates/generif.html: New template.
* wqflask/wqflask/views.py (display_diffs_users): New route.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-17 | oauth2: Build code to do search...At this point, the code fails with a 404, despite the appropriate
endpoint existing. Will need further debugging.
| Frederick Muriuki Muriithi |
| 2023-04-15 | Revert "Fix the way database_connection() is called"...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
| Frederick Muriuki Muriithi |
| 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...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
| zsloan |
| 2023-04-11 | Fix the way database_connection() is called...I think it now gets the SQL_URI from settings
| zsloan |
| 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....Enable search when user types in search box. Filter out any selected
datasets.
| Frederick Muriuki Muriithi |
