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2020-11-03Changed the syntax for the "sort" function in the docstring of GeneralObject ↵zsloan
to be compatible with Python 3 syntax * wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
2020-11-03Fixed a sort used when doing the haplotype analysis to be compatible with ↵zsloan
Python 3 * wqflask/wqflask/marker_regression/display_mapping_results.py - The arguments for sort are different in Python 3, so it was changed to be compatible
2020-10-29Fixed issue with single-chromosome mapping after the bootstrap fix and fixed ↵zsloan
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
2020-10-29Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
reaper_bootstrap_fix
2020-10-29Merge pull request #469 from BonfaceKilz/bug/fix-cookies-verificationBonfaceKilz
Bug/Fix cookie verification bug
2020-10-29Merge pull request #471 from BonfaceKilz/bug/replace-map-on-strip-methodBonfaceKilz
Bug/Replace map on strip with a list comprehension that calls strip()
2020-10-28Merge pull request #470 from zsloan/mapping_chr_view_fixzsloan
Fixed error when zooming into a chromosome when mapping
2020-10-28A non-string being used as a paramter in HT.Link caused an error after the ↵zsloan
Python3 switchover, so I converted it to a string * wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string
2020-10-29Replace map on strip with a list comprehension that calls strip()BonfaceKilz
* 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.
2020-10-28Use latin-1 encoding when converting hmac secret to bytesBonfaceKilz
* 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.
2020-10-28Add new test for hmac_creation with latin-1 secretBonfaceKilz
* 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.
2020-10-28Add tests for cookie verificationBonfaceKilz
2020-10-28Merge pull request #468 from zsloan/export_fixzsloan
Fixed trait page export issue caused by Scroller
2020-10-28Fixed trait page export to work with Scroller + added metadata for ↵zsloan
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
2020-10-27Cast ProbeSet description as binary to fix encoding issue on global search pagezsloan
* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary
2020-10-27Merge pull request #466 from zsloan/show_trait_attributes_fixzsloan
Fix issue where attribute values were displayed in the wrong columns
2020-10-27Get the "first_attr_start_pos" from a samplelist instead of from each ↵zsloan
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
2020-10-27Cast post and pre-publication descriptions into binaryBonfaceKilz
* 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.
2020-10-27Merge pull request #465 from Alexanderlacuna/test-branchBonfaceKilz
add test for trait_data
2020-10-27switch from single quote to double quoteAlexanderlacuna
2020-10-27address failuresAlexanderlacuna
2020-10-27added changes to fileAlexanderlacuna
2020-10-27modified to use pep8 standardsAlexanderlacuna
2020-10-27Merge pull request #422 from BonfaceKilz/build/python3-migrationBonfaceKilz
Build/python3 migration
2020-10-26modified test fileAlexanderlacuna
2020-10-26Add page load metrics to footerBonfaceKilz
* wqflask/wqflask/__init__.py (before_request): New function. Add method for calculating total request_time to global context. * wqflask/wqflask/templates/base.html: - Display total server load time. - Display total page rendering time, and add js functionality to calculate it.
2020-10-23Fixed bootstrap results when using interval mapping for the full genome ↵zsloan
view; still need to fix for single chromosome or Mb range view * wqflask/wqflask/marker_regression/display_mapping_results.py - Fixed bootstrap results by iterating through qtlresults instead of self.genotype (the latter didn't have intervals added, resulting in the bootstrap result positions being wrong)
2020-10-23Merge pull request #462 from zsloan/fix_export_errorzsloan
Fixed trait export for situations where there's no authors/title/journal
2020-10-23Fixed trait export for situations where there's no authors/title/journalzsloan
2020-10-22Merge pull request #460 from zsloan/move_styling_to_csszsloan
Move styling to css
2020-10-21Removed code setting the maximum tick value to 1.15* the max LRS/LOD if ↵zsloan
permutations aren't used
2020-10-21Ensured all Y axis ticks in the mapping figure are below the top of the ↵zsloan
figure, but it would probably be ideal to scale things such that the top tick is at the top of the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Set LRS_LOD_Max (the top tick value) as the maximum value between the significant value (if permutations are used) and the max LRS/LOD value; previously it would set it as the significant value * 1.1 if the significant value exists and is higher than the max LRS/LOD value.
2020-10-20Fixing typo in JS code where "attribute_start_pos" said "attribute_start_post"zsloan
2020-10-20Fixed some problems with the previous attempt at resolving conflicts before ↵zsloan
merging (there are a lot of conflicts between this and the changes that integrated Scroller)
2020-10-20Merge branch 'testing' into move_styling_to_csszsloan
2020-10-20Added classes to replace styling in show_trait_edit_data.html to ↵zsloan
show_trait.css, replaced _ with - in class names, and changed the checkbox table cell styling to better center it * wqflask/wqflask/static/new/css/show_trait.css - Moved show_trait_edit_data.html styling to this file and changes padding for the checkbox table cell to better center it; for some reason text-align: center wasn't working and it specifically needed left-padding * wqflask/wqflask/static/new/javascript/show_trait.js - Replaced underscores with - in class names * wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Replaced underscores with - in class names
2020-10-20Replaced _ with - in class names (though this change will end up being ↵zsloan
unnecessary with the scroller changes that move the table initialization to a separate file) * wqflask/wqflask/templates/show_trait.html - Replaced underscores with - in class names
2020-10-20Replaced one class name with a more generic "inline-div" since there are ↵zsloan
other divs that only have the styling of being inline
2020-10-20Made class names consistently use - instead of _ in show_trait_edit_data.htmlzsloan
* wqflask/wqflask/templates/show_trait_edit_data.html - replaced underscores with -
2020-10-20Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-20Update how pbkdf2.pbkdf2_hex is used when encrypting passBonfaceKilz
* wqflask/wqflask/user_login.py (encode_password): - Remove unused local variable "salt". - Pass "hashfunc" as a string. - Apply Pep-8.
2020-10-20Add tests for encoding passwordBonfaceKilz
* wqflask/tests/wqflask/test_user_login.py: New tests.
2020-10-20Update pbkdf2BonfaceKilz
* wqflask/wqflask/pbkdf2.py: Remove unnecessary pbkdf2 usage docs--- it already exists in python3 stdlib--- and "__main__" section which runs the test. (imports): Delete unused imports. Add safe_str_cmp. (pbkdf2_hex): Use hashlib.pbkdf2_hmac. (safe_str_cmp): Replace with werkzeug.security.safe_str_cmp (test): Delete it. Tests moved to test_pbkdf2.py.
2020-10-20Add pbkdf2 testsBonfaceKilz
* wqflask/tests/wqflask/test_pbkdf2.py: New tests.
2020-10-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-10-19Merge branch 'testing' into scroller_testingzsloan
2020-10-19Update snpString linkBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Replace "%" strings with f-strings. Also, replace old "Href" with new htmlgen "Link" method.
2020-10-19Delete stale commentBonfaceKilz
2020-10-15Fixed issue that caused interval map setting to not work correctly for ↵zsloan
reaper mapping * wqflask/wqflask/templates/show_trait_mapping_tools.html - Mistakenly reversed true/false in the reaper Interval Map option
2020-10-15Replaced the styling in show_trait_mapping_tools.html with CSS and changed ↵zsloan
some styling to be more simple/consistent and deal better with different screen sizes * wqflask/wqflask/marker_regression/run_mapping.py - "manhattan_plot" is now passed as lower-case "true"/"false" to match the case of other boolean options * wqflask/wqflask/static/new/css/show_trait.css - Added classes for the styling in show_trait_mapping_tools.html * wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js - Changed class name "selected_covariates" to "selected-covariates" to match class naming scheme * wqflask/wqflask/static/new/javascript/show_trait.js - Changed class name "selected_covariates" to "selected-covariates" to match class naming scheme * wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Changed class names from using underscore to useing "-" to match class naming scheme * wqflask/wqflask/templates/show_trait_mapping_tools.html - Replaced styling with class names and changed some styling to be more simple/consistent
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