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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
2022-01-27Reordered search result options as described in Rob's 1/19/2022 e-mailzsloan
2022-01-27Make glossary link question marks italicized and redzsloan
2022-01-27Made the search result table wider for genotype results, since previously ↵zsloan
the Location text was being pushed to a second line (this was actually visible for me as well, not just Rob)
2022-01-27Increased the width of the location columns a bit, since they were being ↵zsloan
pushed onto a second line in some browsers (specifically Robs, but couldn't reproduce in mine, so I just changed it to something that should work for him)
2022-01-27Replaced the info icon in the Peak LOD and Effect Size columns with a ↵zsloan
superscript question mark, since the icon was appearing strangely in some browsers (namely Rob's) but in a while I couldn't reproducd
2022-01-27Fix issue where Geno query was fetching from the chr_num column instead of ↵zsloan
the Chr column (and the chr_num column isn't always populated for certain Genotype datasets)
2022-01-27Increase Y of search result table to 1000px so more rows are visible without ↵zsloan
scrolling
2022-01-27This fixes an issue where you couldn't select more than 150-200 rows when ↵zsloan
submitting search result traits to a collection; it previously just used JQuery and needed to be changed to use DataTables API to select from rows
2022-01-27Fix 'Bad substitution' issueFrederick Muriuki Muriithi
In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation.
2022-01-26update live jupyter notebooksjgart
Removed bonface's notebook until seaborn gets fixed.
2022-01-26wqflask: Ignore diffs with |ε| < 0.001BonfaceKilz
* wqflask/wqflask/metadata_edits.py (update_phenotype): Filter out values with |ε| < 0.001 when generating the diff file.
2022-01-26user_login: Remove noisy debug statementBonfaceKilz
2022-01-25guix.scm: Inherit package from genenetwork2, not genenetwork3.Arun Isaac
The package definition was likely copied from the genenetwork3 repo resulting in this error. * guix.scm: Inherit package from genenetwork2, not genenetwork3.
2022-01-17update saunak's live jupyter notebookjgart
2022-01-17update live jupyter notebooksjgart
2022-01-11Removed the deferRender setting, since it appears to revent DataTables API ↵zsloan
from being able to access all rows (which caused functions like Select All to only select the first 100-200 rows)
2022-01-06README: Document `guix shell' development process.Arun Isaac
* README.md: Clean up and document `guix shell' development process.
2022-01-06guix.scm: Add guix.scm.Arun Isaac
* guix.scm: New file.
2022-01-06README: Fix typo.Arun Isaac
* README.md: Change clinians to clinicians.
2022-01-06bin: Stop execution on error.Arun Isaac
* bin/genenetwork2: Pass -e flag to sh.
2022-01-06bin: Set shebang to sh instead of bash.Arun Isaac
/bin/sh is present on Guix System and other distros while /bin/bash is present only on other distros. * bin/genenetwork2: Set shebang to sh instead of bash.
2022-01-06bin: Do not set environment variables set by guix shell.Arun Isaac
The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
2022-01-06bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.Arun Isaac
`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
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