| Age | Commit message (Expand) | Author |
|---|
| 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 | 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 |
| 2023-04-08 | oauth2: Link the Genotype datasets. | Frederick Muriuki Muriithi |
| 2023-04-07 | Move JS to external file. Generalise functions....Move the javascript to an external file to ease development.
Generalise some functions to make it easier to reuse the code down the line.
| Frederick Muriuki Muriithi |
| 2023-04-06 | Commit updates for phenotype/publication metadata | zsloan |
| 2023-04-06 | `flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`...Genenetwork2 configs are a tad weird, and instead of using the configs
in `flask.current_app`, we need to use those in `utility.tools`.
| Frederick Muriuki Muriithi |
| 2023-04-06 | correlations: Provide more output to enable debug of errors. | Frederick Muriuki Muriithi |
| 2023-04-06 | Remove use of deprecated `gn3.db_utils.database_connector` function....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
| Frederick Muriuki Muriithi |
| 2023-04-06 | oauth2: UI - Enable auto-selection of datasets to be linked...When a user selects a dataset in the search table, automatically add
it to the link table and remove it from the search table.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - Retain look and feel without using jQuery DataTables...Simplify the implementation by dropping the use of the jQuery
DataTables plugin - this avoids a lot of arising bugs while retaining
the UI look and feel until we have something working.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - Autoselect on user click...Try auto-selecting datasets on user click: not successful at this
point.
There are some weird bugs with the DataTables that I have not been
able to resolve yet.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - retain data in table attributes...Since the table data could change depending on user input, save the
state in the `data-*` attributes to enable update of tables on
changes.
| Frederick Muriuki Muriithi |
| 2023-04-04 | oauth2: Provide UI for linking genotype datasets. | Frederick Muriuki Muriithi |
