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2021-09-20Move "Clustered Heatmap" button to separate formFrederick 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.
2021-09-20Implement proof-of-concept code to submit dataFrederick 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.
2021-09-20Provide UI elements for clustered heatmap generationFrederick 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.
2021-09-16wqflask: views: Redirect to the correct URL after phenotype updateBonfaceKilz
2021-09-14Replace / with _ in the mapping results filename, due to / causing issues ↵zsloan
with being translated to directories
2021-09-14Replace / with _ in the file hashes in rqtl_mapping.py, since they get ↵zsloan
translated to directories
2021-09-13Change mapping export filename to use the path passed from run_mapping, ↵zsloan
instead of the generic mapping_results.csv
2021-09-13Change mapping export filename to use the trait hashzsloan
2021-09-13Add trait name and trait hash to exported mapping resultszsloan
2021-09-13Include some extra metadata in the mapping page details (in addition to the ↵zsloan
figure itself)
2021-09-13Change Genotype File text to only show the meaningful genotype deescriptionzsloan
2021-09-13Temporarily point the View in GN1 button to gn1-lily.genenetwork.org since ↵zsloan
some features aren't working on gn1.genenetwork.org yet
2021-09-11Add Jupyter Notebook Launcher to Tools dropdown menujgart
2021-09-10Fix 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
2021-09-10Removed 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)
2021-09-09Change trait name to display name in the metadata at the top of the page (so ↵zsloan
group codes will be includes in phenotype IDs
2021-09-09Replaced trait name with trait display name in display_mapping_results so ↵zsloan
the group codes will be includes in phenotype IDs
2021-09-07Add trait hash and datetime to mapping figurezsloan
2021-09-07Add timer to loading page to track how long the process has been runningzsloan
2021-09-05Fixed 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)
2021-09-03Allow categorical_var_list to be passed as a template variablezsloan
2021-09-03Fix 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)
2021-09-03Fix issue where values written to phenotype file for R/qtl sometimes had ↵zsloan
trailing decimal values by grounding to 3 places past the decimal
2021-08-25Fix issue where correlation results weren't included parents/f1szsloan
2021-08-25Fixed 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
2021-08-25Add map scale option that was missing for groups with only a single genotype ↵zsloan
file
2021-08-25Fix issue that could cause an error when doing cM mappingzsloan
2021-08-25Fix issue that could cause mapping_scale to not be set correctly in ↵zsloan
show_trait.py
2021-08-23Removed unused variable from list of 'wanted' variables for mappingzsloan
2021-08-23Fixed issue with the way categorical_vars and perm_strata were being passed ↵zsloan
to the template
2021-08-23Account for situations where the minimum permutation value is also above ↵zsloan
webqtlConfig.MAXLRS; previously threw an error
2021-08-23Fix get_perm_strata to usethe Ids for case attributes instead of names + ↵zsloan
allow perm_strata to be passed to the template
2021-08-23Fix the way categorical_var_list is set to account for case attribute Ids ↵zsloan
being keys now instead of names
2021-08-23Include categorical_vars in mapping_results.html so they're included when ↵zsloan
recomputing
2021-08-23For 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)
2021-08-20Fixed some logic in trait.py that could cause a problem if a dataset_name ↵zsloan
was passed that wasn't Temp
2021-08-20Fix issue where attempting to get the diff of vals for Temp traits was ↵zsloan
causing an error
2021-08-20startup_config.py: Add DebugToobarExtension for wsgi DEBUG modeBonfaceKilz
* wqflask/utility/startup_config.py (app_config): Add DebugToolbarExtension
2021-08-19Change color for Submit button when selecting covariates + move Back button ↵zsloan
to the far right
2021-08-19Fixed R/qtl 'select covariates' buttons to be the same as the changed ones ↵zsloan
for GEMMA
2021-08-19Fixed issue in JS that caused filter_by_value to not work for case attributeszsloan
2021-08-19Fixed the way the drop-down for Filter by Value set values for the case ↵zsloan
attributes
2021-08-19Added type='button' to the mapping compute buttons in order to prevent them ↵zsloan
from being submitted twice
2021-08-19Add hash of vals and diff of vals to template_vars passed to loading page in ↵zsloan
views.py
2021-08-19Fix issues caused by the attribute keys being ids instead of names + fix ↵zsloan
issue caused by an attribute cell being empty
2021-08-19Exclude attributes with only one distinct value as wellzsloan
2021-08-19Removed some unnecessary empty lines from loading.html JSzsloan
2021-08-19Added function for getting the diff of sample values before and after user ↵zsloan
changes to show_trait.py
2021-08-19Added hash of sample values and table of changed values to the loading pagezsloan
2021-08-19Added option to make collection default in the colorbox pop-upzsloan
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 21:23:47 +0000