| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-01-27 | Changed the glossary question mark to appear at the very end of the colum ↵ | zsloan | |
| text, in the hopes that this will show up normally for Rob | |||
| 2022-01-27 | Changed search result index column to be static (so it doesn't change when ↵ | zsloan | |
| the user sorts) | |||
| 2022-01-27 | Replaced 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 | |||
| 2022-01-27 | Moved the Show/Hide Columns text before the column buttons to save vertical ↵ | zsloan | |
| space | |||
| 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 ↵ | zsloan | |
| the Location text was being pushed to a second line (this was actually visible for me as well, not just Rob) | |||
| 2022-01-27 | Increased 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) | |||
| 2022-01-27 | Replaced 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 | |||
| 2022-01-27 | Fix 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) | |||
| 2022-01-27 | Increase Y of search result table to 1000px so more rows are visible without ↵ | zsloan | |
| scrolling | |||
| 2022-01-27 | This 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 | |||
| 2022-01-27 | Fix 'Bad substitution' issue | Frederick Muriuki Muriithi | |
| In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation. | |||
| 2022-01-26 | update live jupyter notebooks | jgart | |
| Removed bonface's notebook until seaborn gets fixed. | |||
| 2022-01-26 | wqflask: Ignore diffs with |ε| < 0.001 | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (update_phenotype): Filter out values with |ε| < 0.001 when generating the diff file. | |||
| 2022-01-26 | user_login: Remove noisy debug statement | BonfaceKilz | |
| 2022-01-25 | guix.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. | |||
| 2022-01-17 | update saunak's live jupyter notebook | jgart | |
| 2022-01-17 | update live jupyter notebooks | jgart | |
| 2022-01-11 | Removed 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) | |||
| 2022-01-06 | README: Document `guix shell' development process. | Arun Isaac | |
| * README.md: Clean up and document `guix shell' development process. | |||
| 2022-01-06 | guix.scm: Add guix.scm. | Arun Isaac | |
| * guix.scm: New file. | |||
| 2022-01-06 | README: Fix typo. | Arun Isaac | |
| * README.md: Change clinians to clinicians. | |||
| 2022-01-06 | bin: Stop execution on error. | Arun Isaac | |
| * bin/genenetwork2: Pass -e flag to sh. | |||
| 2022-01-06 | bin: 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. | |||
| 2022-01-06 | bin: 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. | |||
| 2022-01-06 | bin: 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. | |||
| 2022-01-05 | metadata_edits.py: Remove duplicate imports | BonfaceKilz | |
| 2022-01-05 | Display correct message on the # of edits | BonfaceKilz | |
| 2022-01-05 | Insert data to db by checking the tracked deletions, mods, or adds | BonfaceKilz | |
| 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. | |||
| 2022-01-05 | Check for any double-inserts or double-deletions | BonfaceKilz | |
| Track any double-inserts or double-deletions | |||
| 2022-01-05 | Remove pudb debug statements | BonfaceKilz | |
| 2022-01-05 | metadata_edits: Return early if uploaded csv has not been edited | BonfaceKilz | |
| 2022-01-05 | display_diffs: Remove in-line styling from "pre" tag | BonfaceKilz | |
| 2022-01-05 | Remove pudb line | BonfaceKilz | |
| 2022-01-05 | display_diffs: Use datatables for every table | BonfaceKilz | |
| 2022-01-05 | Make "Files for approval:" text a "h2" | BonfaceKilz | |
| 2022-01-05 | Add interface for displaying diffs in a html page | BonfaceKilz | |
| 2022-01-05 | Use datatables to display approved and rejected files | BonfaceKilz | |
| 2022-01-03 | Added 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 | |||
| 2022-01-03 | Fixed wrong logic for checking for null or empty string trait descriptions ↵ | zsloan | |
| in search results | |||
| 2021-12-23 | If phenotype metadata is cached, authenticate for those traits (otherwise ↵ | zsloan | |
| authentication happens in create_trait at line 105) | |||
| 2021-12-23 | Set new_traits_metadata so caching is used (previously was always an empty dict) | zsloan | |
| 2021-12-20 | This should fix ProbeSet trait descriptions in the search results, which ↵ | zsloan | |
| previousluy weren't showing the proper description | |||
| 2021-12-17 | Some updates to the DOL genotypes conversion script | zsloan | |
| 2021-12-15 | Edited html for index page | zsloan | |
| 2021-12-14 | Removed min-width from container div, since it seems to have preventd ↵ | zsloan | |
| horizontal scrolling when the window is small | |||
| 2021-12-14 | Includes dataset name when creating SimpleNamespace dataset_ob, since it's ↵ | zsloan | |
| needed during authentication | |||
| 2021-12-13 | Fixes 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 | |||
| 2021-12-13 | pep8 formatting | Alexander Kabui | |
 |
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| GeneNetwork (2nd generation) |
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