| Age | Commit message (Expand) | Author |
|---|
| 2022-01-29 | Skip the target traits selection step...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.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Implement better styling...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.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Automate setting of the development GN3 repo...* 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.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Add "Partial Correlations" UI elements on collections page...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
| Frederick Muriuki Muriithi |
| 2022-01-28 | Update PYTHONPATH...The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production). | zsloan |
| 2022-01-28 | Revert 'bin: Set shebang to sh instead of bash'...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 | zsloan |
| 2022-01-28 | Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."...This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
| Arun Isaac |
| 2022-01-28 | Revert "bin: Do not set environment variables set by guix shell."...This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
| Arun Isaac |
| 2022-01-28 | Revert "README: Document `guix shell' development process."...This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
| Arun Isaac |
| 2022-01-27 | Highlight rows selected by filterByIndex...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
| zsloan |
| 2022-01-27 | Changed var to let | zsloan |
| 2022-01-27 | Removed unused variables code | zsloan |
| 2022-01-27 | Added the div for showing the error when the Select Rows text has wrong syntax | zsloan |
| 2022-01-27 | Replaced the try/catch with something checking for the correct pattern with r... | zsloan |
| 2022-01-27 | Added a comment explaining what the parseIndexString function does | zsloan |
| 2022-01-27 | Replaced a confusing for loop with something that is (hopefully) easier to re... | zsloan |
| 2022-01-27 | Changed functions in search_results.js to be camelCased, except for change_bu... | zsloan |
| 2022-01-27 | Removed unnecessary variable from for-loop in parse_index_string | zsloan |
| 2022-01-27 | Changed the placeholder text for the table search to Search For | zsloan |
| 2022-01-27 | Added some JS disabling form submission on hitting Enter, so that users can h... | zsloan |
| 2022-01-27 | Moved the Show/Hide Columns text onto the same line as the buttons, to save a... | zsloan |
| 2022-01-27 | Changed the glossary question mark to appear at the very end of the colum tex... | zsloan |
| 2022-01-27 | Changed search result index column to be static (so it doesn't change when th... | zsloan |
| 2022-01-27 | Replaced the Select Top feature with one that functions more like the Block B... | zsloan |
| 2022-01-27 | Moved the Show/Hide Columns text before the column buttons to save vertical s... | zsloan |
| 2022-01-27 | Reordered search result options as described in Rob's 1/19/2022 e-mail | zsloan |
| 2022-01-27 | Make glossary link question marks italicized and red | zsloan |
| 2022-01-27 | Made the search result table wider for genotype results, since previously the... | zsloan |
| 2022-01-27 | Increased the width of the location columns a bit, since they were being push... | zsloan |
| 2022-01-27 | Replaced the info icon in the Peak LOD and Effect Size columns with a supersc... | zsloan |
| 2022-01-27 | Fix issue where Geno query was fetching from the chr_num column instead of th... | zsloan |
| 2022-01-27 | Increase Y of search result table to 1000px so more rows are visible without ... | zsloan |
| 2022-01-27 | This fixes an issue where you couldn't select more than 150-200 rows when sub... | zsloan |
| 2022-01-27 | Fix 'Bad substitution' issue...In posix shell, string indexing is undefined. This commit replaces the
string indexing with a more portable implementation.
| Frederick Muriuki Muriithi |
| 2022-01-26 | update live jupyter notebooks...Removed bonface's notebook until seaborn gets fixed.
| jgart |
| 2022-01-26 | wqflask: Ignore diffs with |ε| < 0.001...* wqflask/wqflask/metadata_edits.py (update_phenotype): Filter out
values with |ε| < 0.001 when generating the diff file.
| BonfaceKilz |
| 2022-01-26 | user_login: Remove noisy debug statement | BonfaceKilz |
| 2022-01-25 | guix.scm: Inherit package from genenetwork2, not genenetwork3....The package definition was likely copied from the genenetwork3 repo
resulting in this error.
* guix.scm: Inherit package from genenetwork2, not genenetwork3.
| Arun Isaac |
| 2022-01-17 | update saunak's live jupyter notebook | jgart |
| 2022-01-17 | update live jupyter notebooks | jgart |
| 2022-01-14 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/ad... | zsloan |
| 2022-01-11 | Removed the deferRender setting, since it appears to revent DataTables API fr... | zsloan |
| 2022-01-06 | README: Document `guix shell' development process....* README.md: Clean up and document `guix shell' development process.
| Arun Isaac |
| 2022-01-06 | guix.scm: Add guix.scm....* guix.scm: New file.
| Arun Isaac |
| 2022-01-06 | README: Fix typo....* README.md: Change clinians to clinicians.
| Arun Isaac |
| 2022-01-06 | bin: Stop execution on error....* bin/genenetwork2: Pass -e flag to sh.
| Arun Isaac |
| 2022-01-06 | bin: Set shebang to sh instead of bash..../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.
| Arun Isaac |
| 2022-01-06 | bin: Do not set environment variables set by guix shell....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.
| Arun Isaac |
| 2022-01-06 | bin: Set GN2_PROFILE from GUIX_ENVIRONMENT....`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.
| Arun Isaac |
| 2022-01-05 | metadata_edits.py: Remove duplicate imports | BonfaceKilz |
