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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.
2022-01-05metadata_edits.py: Remove duplicate importsBonfaceKilz
2022-01-05Display correct message on the # of editsBonfaceKilz
2022-01-05Insert data to db by checking the tracked deletions, mods, or addsBonfaceKilz
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.
2022-01-05Check for any double-inserts or double-deletionsBonfaceKilz
Track any double-inserts or double-deletions
2022-01-05Remove pudb debug statementsBonfaceKilz
2022-01-05metadata_edits: Return early if uploaded csv has not been editedBonfaceKilz
2022-01-05display_diffs: Remove in-line styling from "pre" tagBonfaceKilz
2022-01-05Remove pudb lineBonfaceKilz
2022-01-05display_diffs: Use datatables for every tableBonfaceKilz
2022-01-05Make "Files for approval:" text a "h2"BonfaceKilz
2022-01-05Add interface for displaying diffs in a html pageBonfaceKilz
2022-01-05Use datatables to display approved and rejected filesBonfaceKilz
2022-01-03Added something that should work as a 'universal' solution for decoding ↵zsloan
trait descriptions in search results, since there were still some traits with encoding issues
2022-01-03Fixed wrong logic for checking for null or empty string trait descriptions ↵zsloan
in search results
2021-12-23If phenotype metadata is cached, authenticate for those traits (otherwise ↵zsloan
authentication happens in create_trait at line 105)
2021-12-23Set new_traits_metadata so caching is used (previously was always an empty dict)zsloan
2021-12-20This should fix ProbeSet trait descriptions in the search results, which ↵zsloan
previousluy weren't showing the proper description
2021-12-17Some updates to the DOL genotypes conversion scriptzsloan
2021-12-15Edited html for index pagezsloan
2021-12-14Removed min-width from container div, since it seems to have preventd ↵zsloan
horizontal scrolling when the window is small
2021-12-14Includes dataset name when creating SimpleNamespace dataset_ob, since it's ↵zsloan
needed during authentication
2021-12-13Fixes issue that caused LRS searches that specify position to not work ↵zsloan
properly; the queries had to be changed after integrating the change that also pulls the Max LRS info in the original query
2021-12-13pep8 formattingAlexander Kabui
2021-12-13modify endpoint for test wgcnaAlexander Kabui
2021-12-13modify template to show error generatedAlexander Kabui