| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2017-02-09 | Fixed issue where I forgot to add GeneticType to the query_for_group query fo......Increased digits of some Basic Statistics values from 2 to 3
| zsloan |
| 2017-02-09 | Added genetic_type to DatasetGroup object to differentiate between which grou......Minor changes/improvements for trait page
Updated dataset_menu_structure.json
| zsloan |
| 2017-02-06 | Merge branch 'master' of github.com:zsloan/genenetwork2 | zsloan |
| 2017-02-06 | Fixed appearance of several tables (search, mapping results, sample data)...Temporarily removed second sample table for CFW traits
Fixed location of global search bar to work with wider screens
| zsloan |
| 2017-01-26 | Merge pull request #1 from genenetwork/testing...Various changes/fixes | 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 |
| 2016-12-15 | Merge pull request #234 from zsloan/master...Various changes | zsloan |
| 2016-11-18 | Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) (1054... | Lei Yan |
| 2016-11-02 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into development | 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 |
| 2016-10-29 | For those case that we have multiple genotypes we would like to add a selector. | Lei Yan |
| 2016-10-06 | Logger: add more granular debug messages | Pjotr Prins |
| 2016-10-05 | Show datasets only on debug | Pjotr Prins |
| 2016-09-13 | Run scripts from ./wqflask - just like the webserver | 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 |
| 2016-07-27 | Problem with phenotype traits should be fixed now | zsloan |
| 2016-06-26 | gn_server: simplify | Pjotr Prins |
| 2016-06-26 | gn_server: simplify | Pjotr Prins |
| 2016-06-26 | gn_server: introduced one new query to fetch a dataset record and force fetch... | Pjotr Prins |
| 2016-06-24 | Log: and document SQL calls | Pjotr Prins |
| 2016-06-23 | Logger: SQL | Pjotr Prins |
| 2016-06-23 | Log: SQL queries | Pjotr Prins |
| 2016-06-23 | Add fetchall iterator | Pjotr Prins |
| 2016-06-23 | Removed dependency on dataset_menu_structure.json | Pjotr Prins |
| 2016-06-23 | Backend: moved methods into call module | Pjotr Prins |
| 2016-06-23 | Refactored dir name dbFunction to db | Pjotr Prins |
| 2016-06-18 | Logger: replacing print statements | Pjotr Prins |
| 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 |
| 2016-04-29 | Merge | Pjotr Prins |
| 2016-04-28 | Added option to export permutation results for mapping page...Added data_scale to dataset objects and basic stats table will now check data scale when calculating range
Made interval analyst results table work with datatables
Changed the appearance of the basic stats table some by giving it a border
| zsloan |
| 2016-04-20 | -a...[PATCH 039/100] Removing commented code
| Pjotr Prins |
| 2016-04-20 | -a...[PATCH 038/100] Fix compile errors
| Pjotr Prins |
| 2016-04-20 | [PATCH 037/100] WebQtlConfig: sanitizing naming and used vars | Pjotr Prins |
| 2016-04-20 | [PATCH 033/100] Refactored file searching | Pjotr Prins |
| 2016-04-20 | [PATCH 032/100] file locating: error checking is built-in | Pjotr Prins |
| 2016-04-20 | [PATCH 024/100] Sanitizing file handling | Pjotr Prins |
| 2016-04-20 | [PATCH 023/100] WIP fixing all paths | Pjotr Prins |
| 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 |
| 2016-03-15 | Fixed the mapping figure track that lets you zoom into a smaller range...Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
| 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 |
| 2016-02-04 | Most importantly, this commit fixes an issue that caused the trait page to no......An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
| zsloan |
| 2015-11-09 | Fixed issue that caused mapping to not work; for some reason the path to pylm... | zsloan |
| 2015-10-12 | Changed the location filter for correlation page | zsloan |
| 2015-09-11 | Comment out some excessive stdout spam | DannyArends |
| 2015-09-10 | Fixed "TypeError: float argument required, not NoneType" about mean....Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
| Lei Yan |
| 2015-08-26 | Fixed issue with colums for the gene global search (still need to change for ......Fixed issue where LRS and LOD are sometimes labeled incorrectly
Changed the header of the trait page
Added link to GN1 in header
Fixxed an issue that made permutations not work with pylmm
Fixed "sign in" button when creating a collection while not logged in
| zsloan |
| 2015-07-20 | Fixed the code that generates the dataset selection drop-down for correlations...Made changes to the tables of correlation results, collections, and search results:
- Added resizeable columns to correlation results and collections, but not to search results
because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling
to the search results)
- Correlation results and collections are now in scrolling tables
- The style is the same across all of these tables now
Remaining issues:
- It doesn't seem like I can set the column width when initializing dataTables in
correlation results. I don't know why this is; it might be due to the table already being the size
of a full page. I want to be able to default to some good widths, even if the user can resize them
- I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is
due to having to put the text in a div.
| zsloan |
| 2015-07-10 | Fixed the genofile_parser.py script since some .geno files had been incorrect......Fixed GO search to work with combined searches
| zsloan |
| 2015-07-09 | Mapping methods now check for existing genotype files....Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
| zsloan |
