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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.
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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.
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* 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.
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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
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The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).
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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
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This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
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This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
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This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
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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
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regex, for validating the Select Rows input
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read and explicitly inverts start_index and end_index when the former is greater than the latter
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change_buttons because it's referenced in many other files
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hit Enter in the Select Rows text area
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a little vertical space
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text, in the hopes that this will show up normally for Rob
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the user sorts)
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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
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space
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the Location text was being pushed to a second line (this was actually visible for me as well, not just Rob)
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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)
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superscript question mark, since the icon was appearing strangely in some browsers (namely Rob's) but in a while I couldn't reproducd
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the Chr column (and the chr_num column isn't always populated for certain Genotype datasets)
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scrolling
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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
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In posix shell, string indexing is undefined. This commit replaces the
string indexing with a more portable implementation.
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Removed bonface's notebook until seaborn gets fixed.
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* wqflask/wqflask/metadata_edits.py (update_phenotype): Filter out
values with |ε| < 0.001 when generating the diff file.
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The package definition was likely copied from the genenetwork3 repo
resulting in this error.
* guix.scm: Inherit package from genenetwork2, not genenetwork3.
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from being able to access all rows (which caused functions like Select All to only select the first 100-200 rows)
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* README.md: Clean up and document `guix shell' development process.
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* guix.scm: New file.
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* README.md: Change clinians to clinicians.
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* bin/genenetwork2: Pass -e flag to sh.
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/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.
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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.
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`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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