| Age | Commit message (Expand) | Author |
|---|
| 2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
| 2022-03-10 | Use context manager with database connection...Use the `with` context manager with database connections and cursors
to ensure that they are closed once they are no longer needed.
Where it was not feasible to use the `with` context manager without a
huge refactor/rewrite, the cursors and connections are closed manually.
| Frederick Muriuki Muriithi |
| 2021-04-30 | autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E501 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E20-E27...Run:
python -m autopep8 --in-place --recrusive ./ --select\
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\
E242,E251,E252,E26,E265,E266,E27 -p 3
| BonfaceKilz |
| 2020-08-26 | Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
| BonfaceKilz |
| 2020-08-20 | Handle module renames in the standard library...Run:
```
2to3-3.8 -f imports -w . && \
2to3-3.8 -f imports2 -w .
```
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and
<https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
| BonfaceKilz |
| 2020-08-19 | Remove extra whitespace(or add it) from comma separated items...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 2020-08-19 | Fix dictionary iteration methods...Run `2to3-3.8 -f dict -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and
<https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
| BonfaceKilz |
| 2020-03-10 | Added back macaque monkey to dropdown generation, not sure why it was removed... | zsloan |
| 2019-10-18 | Added UniProt link and fixed issue that caused sample lists to not be formed ... | zsloan |
| 2019-05-14 | Added all of the third party links from GN1...Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets
Added icon for smartphones/tablets
Made error more informative for main search
Added gene symbol column to collections (need to add something that removes the column if it's all empty)
| zsloan |
| 2019-04-04 | Fixed issue where dataset_menu_structure.json included some groups with no vi... | zsloan |
| 2019-04-03 | Fixed an issue that caused global phenotype search to often not work and cert... | zsloan |
| 2019-03-27 | Changed gen_select_dataset.py to be able to show multiple datasets under the ......Fixed issue where full description was given for some unpublished traits
Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something
| zsloan |
| 2018-12-05 | Fixed issue where SNP track for mapping did not appear correctly...Updated style for a variety of tables
Moved transform/blocking tools for trait sample table into its own tab
Added some new customization options to network graph
Started work on implementing third party link-outs
Updated drop-down generation script to order datasets according to CreateTime
| zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- 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")
| zsloan |
| 2018-05-25 | Fixed issue causing anonymous collections to not work on my branch and stagin......Added script to convert the dryad format genotype files to BIMBAM
removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
| zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-12 | README and docs | Pjotr Prins |
| 2018-04-09 | Removed unused code from get_select_dataset.py and get_group_samplelists.py s... | zsloan |
| 2017-12-06 | Fixed drop-down group order | zsloan |
| 2017-12-04 | Fixed drop-down scripts to more appropriately deal with BXD300 groups (though......Added some header data to mapping output file
Fixed links in Network Group nodes/edges
| zsloan |
| 2017-11-06 | Replaced Histogram and Bar Chart with Plotly version and added new Box Plot w......GEMMA now has option to select genotypes
Updated dataset select dropdowns to be ordered correctly
Fixed dataset select dropdowns for correlations to not show confidential datasets
Added Skewness and Kurtosis to Basic Statistics table
Fixed Verify and RNA-seq buttons on trait page
Temporarily hardcoded Reference page until we get it to link with database
| zsloan |
| 2017-05-21 | Merge from the diet branch.... * refactored ./bin/genenetwork2 and /etc/default_settings
- better detection of Guix
- removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
- removing some default settings, such as PYLMM_COMMAND
- rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
- added GUIX_JS_PATH for JS modules
* Added documentation on installing binary GN2
* Updated Twitter board to latest version in Guix - it had broken
* Updated many tools in the latest Guix profile
| Pjotr Prins |
| 2016-12-12 | Moved a bunch of functions out of the GeneralTrait class that didn't need to ......Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)
Removed some unused code from show_trait.py
changed appearance of table headers some, though needs a little more work
Updated dataset_menu_structure.json
| zsloan |
| 2016-09-13 | Fixed the path for the json file in gen_select_dataset.py since it was wrong ......Added "Reset" option to network graph that returns all the nodes/edges
Made the visualization options area in the network graph a little wider
| zsloan |
| 2016-09-13 | Run scripts from ./wqflask - just like the webserver | Pjotr Prins |
| 2016-09-10 | Comment | Pjotr Prins |
| 2016-09-10 | Support for running maintenance scripts so they can pick up all webserver set......Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
| Pjotr Prins |
| 2016-06-19 | Renamed settings so they are grouped together | Pjotr Prins |
| 2016-06-18 | Changed file permssions to non-executable | Pjotr Prins |
| 2016-06-17 | Conflict | Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-06-16 | Generating the menu is now obsolete | Pjotr Prins |
| 2016-04-20 | More hard-coded | pjotrp |
| 2016-02-18 | Edited gen_select_dataset to remove confidential datasets...Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
| zsloan |
| 2016-01-29 | Info button should now work for phenotype and genotype datasets | zsloan |
| 2016-01-27 | Added info button to Dataset dropdown on index page...Fixed script that generates dataset dropdown json file to include accession id
Fixed dataset link on search results page
| zsloan |
| 2015-05-11 | Fixed gen_select_dataset so that it does not include Phenotype and...Genotype groups when the corresponding data sets do not exist
Interval Mapping no longer shows up for human traits
Fixed the appearance of the mirror links on the main page
| zsloan |
| 2014-06-25 | Added Karl's correlation matrix code...Improved the "scatterplot matrix" feature on the trait page so that
it matches the chosen trait against every selected trait
| Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page
| Zachary Sloan |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user
password, etc
| Zachary Sloan |
| 2013-07-19 | Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist
| Zachary Sloan |
| 2013-07-18 | Added Amelie's rat data genotypes...Got human mapping mostly working
Fixed dataset dropdown menus
| Zachary Sloan |
| 2013-07-18 | Merge branch 'master' of https://github.com/zsloan/genenetwork...Conflicts:
wqflask/base/webqtlConfigLocal.py
wqflask/maintenance/gen_select_dataset.py
wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
| Zachary Sloan |
| 2013-07-18 | Added to installation notes...Removed webqtlConfigLocal file containing passwords
Updated main page dropdown menus (dataset_menu_structure.json)
| Zachary Sloan |
| 2013-07-17 | Fixed gen_select_dataset.py...Appended redis installation info to notes
| Zachary Sloan |
| 2012-10-25 | Got the Make Default option working on the home page | Zachary Sloan |
