| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | 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 | 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 | Merge pull request #600 from zsloan/feature/add_more_mapping_metadata | zsloan | |
| Feature/add more mapping metadata | |||
| 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 | |||
| 2021-09-07 | Add trait hash and datetime to mapping figure | zsloan | |
| 2021-09-07 | Add timer to loading page to track how long the process has been running | zsloan | |
| 2021-09-05 | Fixed issue that caused sample data to not be fetched correctly; there's ↵ | zsloan | |
| something wrong with the 'get_probeset_data' function (not sure why this function exists) | |||
| 2021-09-03 | Allow categorical_var_list to be passed as a template variable | zsloan | |
| 2021-09-03 | Fix issue that caused javascript to not work on the R/qtl mapping result ↵ | zsloan | |
| page when permutations weren't used (because it wrongly expected the permutation histogram to always exist) | |||
| 2021-09-03 | Fix issue where values written to phenotype file for R/qtl sometimes had ↵ | zsloan | |
| trailing decimal values by grounding to 3 places past the decimal | |||
| 2021-08-25 | Fix issue where correlation results weren't included parents/f1s | zsloan | |
| 2021-08-25 | Fixed issue in get_diff_of_vals that caused the diff to be calculated wrong ↵ | zsloan | |
| (due to one set of values being rounded to 3 digits and the other not | |||
| 2021-08-25 | Add map scale option that was missing for groups with only a single genotype ↵ | zsloan | |
| file | |||
| 2021-08-25 | Fix issue that could cause an error when doing cM mapping | zsloan | |
| 2021-08-25 | Fix issue that could cause mapping_scale to not be set correctly in ↵ | zsloan | |
| show_trait.py | |||
| 2021-08-24 | README: on installing GN2 | Pjotr Prins | |
| 2021-08-24 | README: minor edits | Pjotr Prins | |
| 2021-08-24 | README: install with guix profile | Pjotr Prins | |
| 2021-08-23 | Merge pull request #599 from zsloan/bug/fix_mapping_recompute_issue | zsloan | |
| Bug/fix mapping recompute issue | |||
| 2021-08-23 | Removed unused variable from list of 'wanted' variables for mapping | zsloan | |
| 2021-08-23 | Fixed issue with the way categorical_vars and perm_strata were being passed ↵ | zsloan | |
| to the template | |||
| 2021-08-23 | Account for situations where the minimum permutation value is also above ↵ | zsloan | |
| webqtlConfig.MAXLRS; previously threw an error | |||
| 2021-08-23 | Fix get_perm_strata to usethe Ids for case attributes instead of names + ↵ | zsloan | |
| allow perm_strata to be passed to the template | |||
| 2021-08-23 | Fix the way categorical_var_list is set to account for case attribute Ids ↵ | zsloan | |
| being keys now instead of names | |||
| 2021-08-23 | Include categorical_vars in mapping_results.html so they're included when ↵ | zsloan | |
| recomputing | |||
| 2021-08-23 | For some reason sample_data was being set twice, and the second time used a ↵ | zsloan | |
| test function that does not exclude parents/f1s (causing the N to be wrong if parents/f1s exist) | |||
| 2021-08-20 | Fixed some logic in trait.py that could cause a problem if a dataset_name ↵ | zsloan | |
| was passed that wasn't Temp | |||
| 2021-08-20 | Fix issue where attempting to get the diff of vals for Temp traits was ↵ | zsloan | |
| causing an error | |||
| 2021-08-20 | startup_config.py: Add DebugToobarExtension for wsgi DEBUG mode | BonfaceKilz | |
| * wqflask/utility/startup_config.py (app_config): Add DebugToolbarExtension | |||
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