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2022-02-09fetch pheno input dataAlexander Kabui
2022-02-09parse geno input dataAlexander Kabui
2022-02-09parse input dataAlexander Kabui
2022-02-09init py file:call gn3 ctl apiAlexander Kabui
2022-02-09add ui template for ctlAlexander Kabui
2022-02-07Double quote shell variables to prevent globbing and word splittingFrederick Muriuki Muriithi
2022-02-07Add 'api' to root of partial correlations URLFrederick Muriuki Muriithi
Add api to the root of the partial correlations URL, making it: /api/correlations/partial rather than: /correlations/partial
2022-02-05Update live jupyter notebooksjgart
2022-02-02Add covarstruct for rqtl mappingzsloan
Added a function for generating a covarstruct file required for R/qtl mapping This file contains info on whether each covariate is categorical or numerical and is generated by querying the TraitMetadata table in the DB
2022-01-31wqflask: Use a more semantic name when downloading samplesBonfaceKilz
* wqflask/wqflask/metadata_edits.py (get_sample_data_as_csv): Save csv file to be downloaded as "sample-name-<dataset_id>.csv" instead of "myplot.csv"
2022-01-29Fix bug: rho/r not set appropriatelyFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The column heading, and the "data-column-heading" values depend on the correlation method. The initial idea had been to set these values up from the server. With the use of Javascript, however, the system defaults to using `r`, which is a bug when the method is any of the Spearman's methods.
2022-01-29Include the "Locus" in the displayFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Provide missing argumentFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Fix check for non-existent valuesFrederick Muriuki Muriithi
2022-01-29Hide template row instead of deleting itFrederick Muriuki Muriithi
2022-01-29Add more items to trait stringFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Update styling: Display traits in a tabular-like formFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Display the trait details in a tabular-life form without using a table.
2022-01-29Include template to get rid of repetitive template codeFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The generation of input elements that relate to the traits is very similar, therefore this commit pulls it out into a separate template that can be included where needed.
2022-01-29Display results for Geno and ProbeSet tablesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add function to display the results for the **Geno** and **ProbeSet** tables.
2022-01-29Improve UI elementsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Force results area to use up the entire width of the page * Set background colour and line-height of header row * Add some padding to the cells * Reorganise layout * Set up appropriate classes for .with-trait items
2022-01-29Format numbers for displayFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Format the numbers for display, to reduce the number of columns needed for display.
2022-01-29Display data for "Publish" datasetsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Display the correlations results for "Publish" datasets.
2022-01-29Add templates for the results tablesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add templates for the tables that will display the results.
2022-01-29Add elements to display results. Provide PoC JSFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add some html elements to be used to display the results of running the partial correlations * Provide some initial proof-of-concept javascript code to animate the various elements and to use for displaying both successful and error results.
2022-01-29Use list rather than tupleFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Using a tuple, rather than a list for the HTTP methods in the route definition causes an error. This fixes that by using a list.
2022-01-29Skip the target traits selection stepFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Skip the target traits selection step, and only allow running the partial correlations against one of the available databases.
2022-01-29Implement better stylingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Separate the form elements that allow selection from the elements that display previous selections. This allows styling of the "active" area of the form in a different way from the "display" area of the form, allowing the user to see information on their previous choices, even while making further selections for the partial correlations.
2022-01-29Automate setting of the development GN3 repoFrederick Muriuki Muriithi
* When developing the GN2 code, there are times we need to use the latest code in GN3, and rather than manually editing the `bin/genenetwork` file every time we need that, this commit enables the use of an environment variable. In this case, launching the application with something like: $ env GN3_DEV_REPO_PATH="$HOME/genenetwork3" ...\ ./bin/genenetwork2 ./the_settings.py -gunicorn-dev will add the path to the development version to the PYTHONPATH. If the GN3_DEV_REPO_PATH variable is not set, then the PYTHONPATH is not altered, and would be as if there is no development version of GN3 in use.
2022-01-29Add "Partial Correlations" UI elements on collections pageFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add UI elements to trigger the partial correlations feature * Connect partial correlation view to the application * Point to correct application element for gunicorn
2022-01-28Update PYTHONPATHzsloan
The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).
2022-01-28Revert 'bin: Set shebang to sh instead of bash'zsloan
It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash): ./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpected
2022-01-28Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."Arun Isaac
This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
2022-01-28Revert "bin: Do not set environment variables set by guix shell."Arun Isaac
This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
2022-01-28Revert "README: Document `guix shell' development process."Arun Isaac
This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
2022-01-27Highlight rows selected by filterByIndexzsloan
This adds the "selected" class to rows selected by filterByIndex, which adds highlighting to them I also made the variables in this part of the code camel cased
2022-01-27Changed var to letzsloan
2022-01-27Removed unused variables codezsloan
2022-01-27Added the div for showing the error when the Select Rows text has wrong syntaxzsloan
2022-01-27Replaced the try/catch with something checking for the correct pattern with ↵zsloan
regex, for validating the Select Rows input
2022-01-27Added a comment explaining what the parseIndexString function doeszsloan
2022-01-27Replaced a confusing for loop with something that is (hopefully) easier to ↵zsloan
read and explicitly inverts start_index and end_index when the former is greater than the latter
2022-01-27Changed functions in search_results.js to be camelCased, except for ↵zsloan
change_buttons because it's referenced in many other files
2022-01-27Removed unnecessary variable from for-loop in parse_index_stringzsloan
2022-01-27Changed the placeholder text for the table search to Search Forzsloan
2022-01-27Added some JS disabling form submission on hitting Enter, so that users can ↵zsloan
hit Enter in the Select Rows text area
2022-01-27Moved the Show/Hide Columns text onto the same line as the buttons, to save ↵zsloan
a little vertical space
2022-01-27Changed the glossary question mark to appear at the very end of the colum ↵zsloan
text, in the hopes that this will show up normally for Rob
2022-01-27Changed search result index column to be static (so it doesn't change when ↵zsloan
the user sorts)
2022-01-27Replaced the Select Top feature with one that functions more like the Block ↵zsloan
By Index feature from the trait page; you can now use text indicating index ranges or specific indices, and the filter triggers on either hitting Enter or clicking outside of the text area
2022-01-27Moved the Show/Hide Columns text before the column buttons to save vertical ↵zsloan
space
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