| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-10-06 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵ | Frederick Muriuki Muriithi | |
| clustered_heatmaps | |||
| 2021-10-06 | Enable selection of heatmap orientation | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Provide the user with the UI elements to enable them select the orientation of the heatmap that will be produced. | |||
| 2021-10-06 | tests: test_run_mapping: Add missing "name" attribute to tests | BonfaceKilz | |
| 2021-10-06 | tests: test_run_mapping: Add missing calls | BonfaceKilz | |
| After adding the missing attribute to "self.trait", we need to also need to update some missing calls. | |||
| 2021-10-06 | tests: test_run_mapping: Fix failing assert when getting perm strata | BonfaceKilz | |
| 2021-10-06 | tests: test_run_mapping: Add missing attribute to "self.trait" | BonfaceKilz | |
| 2021-10-06 | tests: test_run_mapping: Add missing positional argument "vals_hash" | BonfaceKilz | |
| 2021-10-04 | Changed get_user_groups to pull both the ID and details in the for loop from ↵ | zsloan | |
| group_list by using group_list.items() | |||
| 2021-10-04 | Add group link for user member groups | zsloan | |
| 2021-10-04 | wqflask: resource_manager: Remove logger | BonfaceKilz | |
| 2021-10-04 | Remove "_scripts.html" and all it's references | BonfaceKilz | |
| 2021-10-04 | new_security: login_user.html: Delete commented out block | BonfaceKilz | |
| 2021-10-04 | Replace hard-coded e-mails with gn-proxy queries | BonfaceKilz | |
| * wqflask/wqflask/decorators.py (edit_access_required.wrap): Query the proxy to see the access rights of a given user. | |||
| 2021-10-04 | Rename "admin_login_required" to "edit_access_required" | BonfaceKilz | |
| 2021-09-27 | Apply pep-8 formatting | BonfaceKilz | |
| 2021-09-27 | Remove variable-- named after a python keyword-- called "list" | BonfaceKilz | |
| 2021-09-27 | Remove lengthy stack trace for 404, 400, 408 status codes | BonfaceKilz | |
| The stack trace causes the log file to grow into unmanageable sizes over time. | |||
| 2021-09-25 | Add progress indicator. Handle errors. | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add a progress indicator to show the user that there is some progress happening, so that they can wait. Add a function to handle any errors that arise. | |||
| 2021-09-25 | Remove hard-coded URL; use configured URL | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * etc/default_settings.py: remove duplicate configuration variable * wqflask/wqflask/collect.py: use the configured url for the API server Use the configured URL rather that the hard-coded URL that was used for testing out the clustered heatmap generation. | |||
| 2021-09-23 | Clear any existing image on subsequent clicks | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * If the user clicks on the "Clustered Heatmap" button, the system should remove any previously existing clustered heatmap image and replace it with the new image. | |||
| 2021-09-23 | Move the heatmap display area to before the table | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move the heatmap area to before the data table, so that once the heatmap is generated, it shows up before the table, and the user is able to see what happened. | |||
| 2021-09-22 | Removed the Control for (marker) option from R/qtl for now since Danny ↵ | zsloan | |
| mentioned it isn't working correctly | |||
| 2021-09-22 | Fixed issue where the control marker parameter was being passed incorrectly ↵ | zsloan | |
| to GN3 (should be just 'control' but was previously passed as 'control_marker') | |||
| 2021-09-22 | Only show most search page options if results exist; otherwise provide a ↵ | zsloan | |
| link back to the home page | |||
| 2021-09-22 | Added type='button' to the Delete Collection button within collections/view, ↵ | zsloan | |
| since without it it attempts to submit the form encapsulating the button (export in this case) | |||
| 2021-09-22 | Remove references to reaper_version and code for running old qtlreaper | zsloan | |
| 2021-09-22 | Cleanup code | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove unnecessary console.log(...) statements that were used in development * Re-arrange the html elements * Rename element id | |||
| 2021-09-22 | Test heatmap creation from serialized figure | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Attempt using the figure, serialized as JSON, to display the clustered heatmap. | |||
| 2021-09-20 | Returned the GN1 url to gn1.genenetwork.org since it's apparently working ↵ | zsloan | |
| well enough again now that some issues have been fixed | |||
| 2021-09-20 | Removed the reaper_version selection option, since original qtlreaper is no ↵ | zsloan | |
| longer supported | |||
| 2021-09-20 | Added back the option to edit privileges on trait pages, since the metadata ↵ | zsloan | |
| edit button had replaced it | |||
| 2021-09-20 | Prevent the default submit action | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Prevent the default submit action. | |||
| 2021-09-20 | Fix id used. | Frederick Muriuki Muriithi | |
| 2021-09-20 | Move "Clustered Heatmap" button to separate form | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move the button out of the "export_form" into a new "heatmaps_form" to avoid some weird JS interaction that showed up. | |||
| 2021-09-20 | Implement proof-of-concept code to submit data | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement some javascript to activate the "Clustered Heatmap" button. This commit provides a proof-of-concept implementation to help with identifying the requirements for sending and receiving of the heatmaps data. | |||
| 2021-09-20 | Provide UI elements for clustered heatmap generation | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * wqflask/wqflask/collect.py: provide hard-coded URL for testing * wqflask/wqflask/templates/collections/view.html: provide button Provide a button to trigger the heatmap generation. As a test, we also provide a hard-coded URL for the API endpoint to get the heatmap data. | |||
| 2021-09-16 | wqflask: views: Redirect to the correct URL after phenotype update | BonfaceKilz | |
| 2021-09-14 | Replace / with _ in the mapping results filename, due to / causing issues ↵ | zsloan | |
| with being translated to directories | |||
| 2021-09-14 | Replace / with _ in the file hashes in rqtl_mapping.py, since they get ↵ | zsloan | |
| translated to directories | |||
| 2021-09-13 | Change mapping export filename to use the path passed from run_mapping, ↵ | zsloan | |
| instead of the generic mapping_results.csv | |||
| 2021-09-13 | Change mapping export filename to use the trait hash | zsloan | |
| 2021-09-13 | Add trait name and trait hash to exported mapping results | zsloan | |
| 2021-09-13 | Include some extra metadata in the mapping page details (in addition to the ↵ | zsloan | |
| figure itself) | |||
| 2021-09-13 | Change Genotype File text to only show the meaningful genotype deescription | zsloan | |
| 2021-09-13 | Temporarily point the View in GN1 button to gn1-lily.genenetwork.org since ↵ | zsloan | |
| some features aren't working on gn1.genenetwork.org yet | |||
| 2021-09-11 | Add Jupyter Notebook Launcher to Tools dropdown menu | jgart | |
| 2021-09-10 | Fix issue with the way the template was checking if genofile_string was set; ↵ | zsloan | |
| it was receiving an empty string, so the previous logic made it think there was a genofile string when there wasn't one | |||
| 2021-09-10 | Removed encoding, since it's apparently not needed since the Python 3 ↵ | zsloan | |
| switchover (and was causing there to be no matches between user IDs and groups) | |||
| 2021-09-09 | Change trait name to display name in the metadata at the top of the page (so ↵ | zsloan | |
| group codes will be includes in phenotype IDs | |||
| 2021-09-09 | Replaced trait name with trait display name in display_mapping_results so ↵ | zsloan | |
| the group codes will be includes in phenotype IDs | |||
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