Age | Commit message (Collapse) | Author |
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* jquery.qtip.css: Delete it.
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Correlation errors fix
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the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover)
* wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis
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samples + traits that user doesn't have permission to access
* wqflask/wqflask/correlation/show_corr_results.py - Moved the num_overlap check so that it never attempts to calculate the correlation if it's too low + checked if trait_object is None in the main loop (since it would be returned as None if the user doesn't have permissions
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Adding more Test for show_trait module
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test-branch
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the potential to cause an axis tick to appear above the figure
* wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis
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Mapping Y Axis Fix
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the potential to cause an axis tick to appear above the figure
* wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis
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test-branch
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Reaper bootstrap fix
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error that occurred if either bootstrap or permutations were set to 0
* wqflask/wqflask/marker_regression/display_mapping_results.py - Cast self.qtlresults 'chr' as a string since the comparison between it and the chromosome names was faililng due to numeric chromosomes being int type + used a list comprehension that converts None to an empty string when creating a comma-joined string from the list of mapping output files
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reaper_bootstrap_fix
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test-branch
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Bug/Fix cookie verification bug
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Bug/Replace map on strip with a list comprehension that calls strip()
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Fixed error when zooming into a chromosome when mapping
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Python3 switchover, so I converted it to a string
* wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string
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* scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map
string.strip on a list of strings. Instead use a list comprehension
and apply strip() on each element of the list.
* wqflask/wqflask/marker_regression/plink_mapping.py: Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
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* wqflask/utility/hmac.py (hmac_creation): Use latin-1 when
serializing the hmac secret. This ensures that the behaviour
of *verify_cookie* remains the same as in the python2 tip.
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* wqflask/tests/utility/test_hmac.py (test_hmac_creation_with_cookie):
New test. For this test, use a secret that behaves differently when
encoded to either utf-8 or latin-1.
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Fixed trait page export issue caused by Scroller
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non-Phenotype traits and column headers
* wqflask/wqflask/show_trait/export_trait_data.py - Added metadata for non-Phenotype traits and column headers (which didn't previously exist)
* wqflask/wqflask/static/new/javascript/show_trait.js - Changed export_sample_table_data to use DataTables API instead of just selecting from the DOM with JQuery
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Remaining gsearch encoding fix for ProbeSet description
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* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary
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Fix issue where attribute values were displayed in the wrong columns
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individual sample, because it was previously causing problems when only some samples had an N
* wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos
* wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed
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* wqflask/wqflask/gsearch.py (GSearch): There's an exception thrown
when the decode method is called on that description string. If the
casting is absent, and the decode statements are removed, the some
characters get broken.
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add test for trait_data
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Build/python3 migration
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