| Age | Commit message (Expand) | Author |
|---|
| 2020-08-19 | Replace `izip` with python's built-in equivalent...Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports>
and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
| BonfaceKilz |
| 2020-07-27 | Abstract away redundant code into set_dataset_key method...* wqflask/base/data_set.py (Dataset):
- Add set_dataset_key
- Remove __call__ method
| BonfaceKilz |
| 2020-07-27 | Use the correct redis instance inside object...* wqflask/base/data_set.py (DatasetType): Use object's redis instance
| BonfaceKilz |
| 2020-07-24 | Merge pull request #409 from BonfaceKilz/Build/add-tests...Build/add tests | zsloan |
| 2020-07-24 | Fixed queries that were wrongly returning Data IDs as Ns | zsloan |
| 2020-07-24 | Inject redis instance into DatasetType class...* wqflask/base/data_set.py(DatasetType):
- Rename Redis instance to r to avoid confusion and name collisions
- Inject the redis instance into Dataset_Types class to make it easier to test
- Rename Dataset_Types class to DatasetType class
| BonfaceKilz |
| 2020-07-24 | Apply autopep-8...* wqflask/base/data_set.py: Apply autopep-8
| BonfaceKilz |
| 2020-07-24 | Remove unused import | BonfaceKilz |
| 2020-06-22 | Fixed issue with temp traits not working for trait page functions like correl... | zsloan |
| 2020-06-17 | Adding all the authentication stuff | zsloan |
| 2020-05-07 | Fixed blatseq issue and geno correlation issueblatseq_fix | zsloan |
| 2020-05-07 | Committing current progress on group manager + a minor fix in dataset.py | zsloan |
| 2020-04-27 | Added timeout for when/if it does the REST API query, so it doesn't hang inde... | zsloan |
| 2020-04-27 | Made change that should allow dataset structure to be loaded from Redis inste... | zsloan |
| 2020-04-26 | Removed the code that was still writing the database menu JSON | zsloan |
| 2020-04-24 | Replaced hard-coded instances of GN2 urls with ones pulled from settings file | zsloan |
| 2020-04-24 | Made a fix that should prevent the issue where new datasets cause an error wh... | zsloan |
| 2020-04-06 | Added Mean column for phenotype traits in search and global search result tables | zsloan |
| 2020-03-27 | Fixed issue where GEMMA wasn't showing up for certain groups | zsloan |
| 2020-03-27 | Added integration for using RData files with R/qtl, plus some other changes t... | zsloan |
| 2020-02-07 | Users can now add and do mapping on genotype files that only include a subset......Also filtered the results used by Christian's genome browser, so now it should have an easier time loading when dealing with larger numbers of markers
| zsloan |
| 2019-12-04 | Added M to the possible non-number 'chromosome' names | zsloan |
| 2019-11-21 | Added 3-letter codes to unpublished phenotype traits and fixed issue with ord... | zsloan |
| 2019-11-14 | Changed code to rebuild dataset list each time you view the trait page to avo......Fixed logic for UniProt link to use UniProtId instead of protein ID
| zsloan |
| 2019-11-05 | Fixed issue with ordering items in correlation dataset select dropdown | zsloan |
| 2019-10-24 | Changed logic for generating drop-downs such that it shows the correct Phenot... | zsloan |
| 2019-10-18 | Added UniProt link and fixed issue that caused sample lists to not be formed ... | zsloan |
| 2019-07-23 | Added change to automatically update datasets list using rest api instead of ......Removed option to edit certain html pages, like news, policies, etc
| zsloan |
| 2019-06-24 | Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should work......Fixed position digits and row highlighting on interval analyst table
Updated default MAF to 0.05
Updated footer text
| zsloan |
| 2019-06-18 | Fixed issue with sorting involving 0's on trait page...Fixed links to dataset info pages in search results and correlation results pages
| zsloan |
| 2019-06-05 | Fixed issue that caused interval mapping to not work because the python imple......Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
| zsloan |
| 2019-05-24 | Replaced qtlreaper Dataset object with python object | 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 |
| 2019-02-13 | Removed pylmm references and related functions | Pjotr Prins |
| 2019-02-05 | Fixed issue with getting marker info that affected heatmap and possibly other......Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
| zsloan |
| 2019-01-11 | Got InDel working for Variant Browser...Changed Variant Browser to display gene name under "Domain" when the user searches a gene term and rows are mislabeled "Intergenic"
Fixed Chr option to display correct chromosomes for different species
Fixed order for correlation drop-down on trait page
Fixed some appearance issues with the mapping results table
Improved appearance of correlation scatterplot page
| 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 |
| 2018-04-19 | Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py
| 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 |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins |
| 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 |
| 2017-06-09 | - Changed the way the genofile is set so different genofiles can be selected ......- Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples
- Mapping results page now displays the genofile in the information section
- Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species)
- Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set
- Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options)
- Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable)
- Changed the glossary links for LRS and Additive Effect columns for Gene Global Search
- Improved appearance for Phenotype Global Search results
- Temporarily removed Mapping options/features that don't work from the trait page
| zsloan |
| 2017-04-17 | Added option to remove collections from collection list page...Improved appearance of search result and collection tables
| 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 |
| 2017-02-09 | 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 |
