| Age | Commit message (Expand) | Author |
|---|
| 2020-06-20 | Added some admin functionality and fixed issue with temp traits | zsloan |
| 2020-06-17 | A user's id is now set as a parameter if it doesn't already existauthentication_test | zsloan |
| 2020-06-17 | Adding all the authentication stuff | zsloan |
| 2020-06-05 | Commiting other current group/resource management code, plus the new files | zsloan |
| 2020-03-10 | Added back macaque monkey to dropdown generation, not sure why it was removed... | zsloan |
| 2019-12-09 | Fixed minor issue that caused the sample list to be fetched incorrectly for a... | 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to be able to show multiple datasets under the ......Fixed issue where full description was given for some unpublished traits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 |
| 2018-12-21 | Fixed collections so they can be very large (1000+ traits)...Added option to submit traits in collection to BNW
Fixed issue with "x" values for user-submitted traits
Fixed issue where post-publications descriptions were wrongly appearing in global search results
| 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 |
| 2018-11-20 | Added option to select chromosome from trait page when mapping...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
| zsloan |
| 2018-10-11 | - Added fix for GEMMA LOCO...- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
| 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 |
| 2018-05-17 | Added script to quantile normalize a data set and enter its normalized sample......Added option to replace trait page sample/strain values with normalized ones
Began editing Lei's scatterplot code
Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
| zsloan |
| 2018-04-23 | Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter in......Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
| 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 |
| 2018-04-09 | Removed unused code from convert_geno_to_bimbam.py and corestats.py | 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 |
| 2017-09-07 | Added the script to convert bimbam to kinship matrices | zsloan |
| 2017-09-05 | Added file converting genofiles to bimbam | 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 |
| 2017-02-08 | Changed the way .fam files are written/read, which fixes the issue with GEMMA... | zsloan |
| 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 |
| 2016-09-30 | Add missing __init__.py | Pjotr Prins |
| 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 |
| 2016-07-16 | README: added info | 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 |
| 2016-06-18 | Disable setting sys.paths | 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 |
| 2016-04-20 | [PATCH 037/100] WebQtlConfig: sanitizing naming and used vars | Pjotr Prins |
| 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 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | 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 |
| 2016-01-26 | Removed a bunch of files/directories/packages that are no longer used and som... | zsloan |
