| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | 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 | |||
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