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path: root/wqflask/base/data_set.py
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2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26Rename "unicode" to "str"BonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
2020-08-20Handle module renames in the standard libraryBonfaceKilz
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>
2020-08-20Disable python2 QTLReaperBonfaceKilz
* wqflask/base/data_set.py: Remove usage of "reaper" to load datasets
2020-08-19Make Python more idiomaticBonfaceKilz
Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
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>
2020-07-27Abstract away redundant code into set_dataset_key methodBonfaceKilz
* wqflask/base/data_set.py (Dataset): - Add set_dataset_key - Remove __call__ method
2020-07-27Use the correct redis instance inside objectBonfaceKilz
* wqflask/base/data_set.py (DatasetType): Use object's redis instance
2020-07-24Merge pull request #409 from BonfaceKilz/Build/add-testszsloan
Build/add tests
2020-07-24Fixed queries that were wrongly returning Data IDs as Nszsloan
2020-07-24Inject redis instance into DatasetType classBonfaceKilz
* 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
2020-07-24Apply autopep-8BonfaceKilz
* wqflask/base/data_set.py: Apply autopep-8
2020-07-24Remove unused importBonfaceKilz
2020-06-22Fixed issue with temp traits not working for trait page functions like ↵zsloan
correlation or mapping
2020-06-17Adding all the authentication stuffzsloan
2020-05-07Fixed blatseq issue and geno correlation issueblatseq_fixzsloan
2020-05-07Committing current progress on group manager + a minor fix in dataset.pyzsloan
2020-04-27Added timeout for when/if it does the REST API query, so it doesn't hang ↵zsloan
indefinitely
2020-04-27Made change that should allow dataset structure to be loaded from Redis ↵zsloan
instead of the JSON file without breaking things
2020-04-26Removed the code that was still writing the database menu JSONzsloan
2020-04-24Replaced hard-coded instances of GN2 urls with ones pulled from settings filezsloan
2020-04-24Made a fix that should prevent the issue where new datasets cause an error ↵zsloan
when they're in search results
2020-04-06Added Mean column for phenotype traits in search and global search result tableszsloan
2020-03-27Fixed issue where GEMMA wasn't showing up for certain groupszsloan
2020-03-27Added integration for using RData files with R/qtl, plus some other changes ↵zsloan
to how it decides which mapping methods to display on the trait page
2020-02-07Users can now add and do mapping on genotype files that only include a ↵zsloan
subset of samples/strains 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
2019-12-04Added M to the possible non-number 'chromosome' nameszsloan
2019-11-21Added 3-letter codes to unpublished phenotype traits and fixed issue with ↵zsloan
ordering phenotype results from searches
2019-11-14Changed code to rebuild dataset list each time you view the trait page to ↵zsloan
avoid having to restart each time a new dataset is added. Will need to keep an eye out for any issues, but doesn't seem to affect speed much Fixed logic for UniProt link to use UniProtId instead of protein ID
2019-11-05Fixed issue with ordering items in correlation dataset select dropdownzsloan
2019-10-24Changed logic for generating drop-downs such that it shows the correct ↵zsloan
Phenotypes name when there's no accession ID
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ↵zsloan
correctly in certain situations
2019-07-23Added change to automatically update datasets list using rest api instead of ↵zsloan
json file Removed option to edit certain html pages, like news, policies, etc
2019-06-24Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should ↵zsloan
work for that now) Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text
2019-06-18Fixed issue with sorting involving 0's on trait pagezsloan
Fixed links to dataset info pages in search results and correlation results pages
2019-06-05Fixed issue that caused interval mapping to not work because the python ↵zsloan
implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) 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)
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-03-18- Added PCA traits to correlation matrix. You can't change their names yet ↵zsloan
or add them to a collection from the corr matrix page, 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
2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-05Fixed issue with getting marker info that affected heatmap and possibly ↵zsloan
other functions Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
2019-01-11Got InDel working for Variant Browserzsloan
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
2018-12-21Fixed collections so they can be very large (1000+ traits)zsloan
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
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of ↵zsloan
set width Changed to using BIMBAM files to build Marker objects in dataset.py
2018-04-06Mapping figure output now gives more accurate informationzsloan
Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-11-06Replaced Histogram and Bar Chart with Plotly version and added new Box Plot ↵zsloan
with Plotly 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
2017-06-09- Changed the way the genofile is set so different genofiles can be selected ↵zsloan
for mapping - 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
2017-04-17Added option to remove collections from collection list pagezsloan
Improved appearance of search result and collection tables
2017-04-05- Temporary traits can be created, viewed, and added to collectionszsloan
- 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
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