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* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
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self.datasets property because the group name was used as the key (instead of the group name + "Publish", which is the full dataset name for phenotypes)
* wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
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* wqflask/base/data_set.py - TempDataSet class contained some code
referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
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datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
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* wqflask/base/data_set.py (Dataset):
- Add set_dataset_key
- Remove __call__ method
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* wqflask/base/data_set.py (DatasetType): Use object's redis instance
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Build/add tests
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* 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
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* wqflask/base/data_set.py: Apply autopep-8
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correlation or mapping
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indefinitely
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instead of the JSON file without breaking things
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when they're in search results
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to how it decides which mapping methods to display on the trait page
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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
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ordering phenotype results from searches
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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
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Phenotypes name when there's no accession ID
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correctly in certain situations
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json file
Removed option to edit certain html pages, like news, policies, etc
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work for that now)
Fixed position digits and row highlighting on interval analyst table
Updated default MAF to 0.05
Updated footer text
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Fixed links to dataset info pages in search results and correlation results pages
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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)
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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
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other functions
Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
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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
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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
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set width
Changed to using BIMBAM files to build Marker objects in dataset.py
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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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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
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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
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Improved appearance of search result and collection tables
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- 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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for non-mRNA Assay datasets
Increased digits of some Basic Statistics values from 2 to 3
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groups should show dominance effect
Minor changes/improvements for trait page
Updated dataset_menu_structure.json
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