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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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Prior to this, we only checked for the json files with contained the
modifications. However, in the case of double deletions, and double
inserts, the data would have been stored in the db anyway; which is a
false representation of changes.
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