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With the reorganisation, a number of module paths changed, and need to
be updated. This commit fixes a few obvious ones.
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For example, in bin/genenetwork2 etc/default_settings.py -c -m pytest,
remove only up to -c.
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We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Add an option to help with running the application under pdb, and add
some documentation to help other developers figure it out.
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Only add a value to the path if it is actually set
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redis needs to be started and managed as a separate service. We create
a flag NO_REDIS so that it can be so. If NO_REDIS is not defined, the
present behavior of starting redis remains. Thus current use cases are
not broken.
* bin/genenetwork2: Allow for not starting redis with the NO_REDIS
flag.
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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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In posix shell, string indexing is undefined. This commit replaces the
string indexing with a more portable implementation.
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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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Also use
the jitter switch.
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Run:
```
find . -type f -print0 | xargs -0 sed -i \
"s|lib/python2.7/site-packages|lib/python3.8/site-packages|g"
```
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Removed some unused JS libraries
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Put transform/blocking tools into their own tab (still need to change formatting of tab's contents)
Improved appearance of search result page table (still need to change a few other tables)
Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool
Basic Stats figures now load when the user clicks the tab, to improve initial page load time
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just clicking their row in collection
- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
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https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
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PYTHONPATH needed as
it is now in the Guix build.
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* Add some code to set up the path for the python-elasticsearch module.
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