| Age | Commit message (Expand) | Author |
|---|
| 2019-10-04 | Fixed issue where there was an error if the REST API used for aliases was down...Added option to download as JPEG in addition to SVG for basic stats figures
| zsloan |
| 2019-08-01 | Updated aliases to get all species aliases and remove duplicates | zsloan |
| 2019-08-01 | Added wikidata aliases...Fixed year to not be a hyperlink when no pubmed id
Fixed first column width so it doesn't go onto two lines for trait details
| zsloan |
| 2019-08-01 | Made some more aesthetic changes to various pages and charts/figures...Added some information to the mapping loading page
| zsloan |
| 2019-07-18 | Made change that should fix encoding issue, fingers crossed | zsloan |
| 2019-05-06 | Removed some unused imports of htmlgen...Fixed a bug that sometimes occurred in search results
Changed order of items on index page
| zsloan |
| 2019-03-18 | - Added PCA traits to correlation matrix. You can't change their names yet or......but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well,
but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better
way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch
- Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc
- Fixed some appearance issue where the network graph options were too wide if a trait name was too long
| zsloan |
| 2019-03-07 | Changed the way covariates are displayed when selected for mapping...Made the outlier notification appear for all mapping methods
Removed some misleading text saying "Block samples" from the Transform and Filter Data section
| zsloan |
| 2019-02-22 | Fixed some appearance issues with several tables...Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
| 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 |
| 2018-08-14 | Added cofactors to correlation scatterplot and changed it to use Plotly...Added Phenogen track to mapping results
Added comparison bar chart figure
Simplified global search to not build trait/dataset objects, which speeds thing up considerably
Fixed correlation matrix to correctly deal with 0 values
Fixed issue where anonymous collections couldn't be created if none already existed
| zsloan |
| 2018-04-06 | Mapping figure output now gives more accurate information...Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
| zsloan |
| 2017-06-12 | Fixed issue where 0.0 values would be converted into X's on the trait page | zsloan |
| 2017-05-31 | Added various tool options to correlation results page and improved table app......Fixed minor logic issue in trait.py
| zsloan |
| 2017-04-05 | - Temporary traits can be created, viewed, and added to collections...- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits
| zsloan |
| 2017-01-26 | GEMMA now works with CFW data (had to update where it looks for the input fil......Y-axis for GEMMA now says -log(p)
Updated the style of the trait sample data table in the trait page
Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs)
Updated dataset menu json file
Added option to show and hide columns to regular search page using colVis
Changed regular and global search result table styles/column widths
Began work on user trait submission code (not working yet though)
Began work on static loading page for mapping results
| zsloan |
| 2016-12-13 | Fixed a problem related to the last commit that caused a problem when loading... | 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 |
| 2016-11-15 | Fixed issue where sample values of 0 would sometimes be displayed as 'x', whi......Fixed issue where the mean would sometimes be displayed into of the additive effect
| zsloan |
| 2016-11-11 | Fixed problem that caused checkboxes to not work with Scroller search results......Improved the way the table width is set for search results page
| zsloan |
| 2016-11-02 | Added toggleable short and long labels to correlation matrix...Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
| zsloan |
| 2016-11-02 | Added Scroller functionality to regular (but not global) search, which increa......In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip
Increased table width for non-Geno DBs
Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches
Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little
Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
| zsloan |
| 2016-10-25 | Just removed some extraneous spaces in trait.py | zsloan |
| 2016-10-25 | Replaced the Download Table button for collection page with python version th......Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page
Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
| zsloan |
| 2016-09-29 | Fix global search "il6" for "Internal Server Error". Add single quotes into M... | Lei Yan |
| 2016-08-24 | Replaced post-publication description with pre-publication description for co......Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former
Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases)
Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale
Removed some unused javascript libary imports from search/global search pages
| zsloan |
| 2016-08-16 | Users can now select specific traits from collection when using collection to......To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url
Duplicate traits can no longer by added to collections
Fixed the digits for a few table columns in collection (additive effect, etc).
| zsloan |
| 2016-06-26 | Resolve conflicts | Pjotr Prins |
| 2016-06-24 | Removed function 'get_info' in trait.py that was never used and reomved 'get_... | zsloan |
| 2016-06-23 | Logger: SQL | Pjotr Prins |
| 2016-06-23 | Logger: SQL | Pjotr Prins |
| 2016-06-23 | Refactored dir name dbFunction to db | Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-06-03 | Changed appearance of tables to more easily differentiate them from the rest ......Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
| zsloan |
| 2016-05-31 | Fixed error when MrnaAssay search results didn't have a geneid | zsloan |
| 2016-05-26 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan |
| 2016-05-26 | Issue with certain samples (like BXD65a, ones were there are multiple for a s......Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments)
Fixed error when searching genotype data sets
| zsloan |
| 2016-05-23 | Reaper mapping results are now correct and account for samples with two names......R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
| zsloan |
| 2016-05-18 | Updated dataset selection dropdown menus and fixed error caused by traits wit... | zsloan |
| 2016-04-19 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development...Conflicts:
wqflask/base/trait.py
| zsloan |
| 2016-04-13 | Moved the code getting the description/location because it was throwing an er... | zsloan |
| 2016-04-13 | Global search should be able to return description and location columns now | zsloan |
| 2016-04-11 | Figured out how to load results into dataTable using AJAX, but still need to ......Added code getting the description, etc to trait.py since it was missed from last commit
| zsloan |
| 2016-04-11 | Changed the way trait data is retrieved for the global search page (it now ge......This change increases the speed by a bit (85 seconds to 66 seconds for example)
Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
| zsloan |
| 2016-03-18 | Replaced header with other information in qtl map...Began adding menu to qtl map
Fixed global search to not retrieve samples (to increase speed)
Got the vector plot working again so it can be displayed alongside the gn1-style plot
Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
| zsloan |
| 2016-03-14 | Changed the way headers look across all pages...Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
| zsloan |
| 2016-03-02 | Increased gsearch speed by removing unnecessary query for sample data...Still slower than preferable due to having to query the gn1 database for every trait in the search results
| zsloan |
| 2015-07-09 | Some phenotype searches were throwing an error due to an assert statement in ... | zsloan |
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69...Fixes #69 | zsloan |
| 2015-06-22 | fixed a few potential security issues | Artem Tarasov |
