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2020-10-19Merge branch 'testing' into scroller_testingzsloan
2020-10-09Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collectionsBonfaceKilz
Tests/add extra tests for collections
2020-10-09Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto
2020-10-08Fixed remaining issue that applies to all dataset typeszsloan
* 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
2020-10-08Fixed issue where new phenotype groups wouldn't be saved to the ↵zsloan
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
2020-09-30Removed unused code from TempDataSet classzsloan
* 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
2020-09-28Fix casting errorBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*.
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-18Made a bunch of changes to move trait page DataTables initialization tozsloan
a separate file (initialize_show_trait_tables.js). The biggest complication was getting the order of attributes in the rows to sync with the order of atribute namees in the column headers. Previously this logic was all in the template. * wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a very awkward solution to passing the column position into the column render function in situations where there are case attribute columns (which can be variable in number) * wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names" in js_data with "attributes" (which allows the JS access to more information) and also pass new se_exists and has_num_cases variables with js_data, so the javascript has access to whether or not those columns exist in the table * wqflask/wqflask/static/new/javascript/show_trait.js - Change case attribute-related logic to use js_data.attributes instead of js_data.attribute_names * wqflask/wqflask/templates/show_trait.html - Removed table initialization from template * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - new file that initializes tables and reproduces what the template logic used to do with JS logic
2020-08-25Fixed issue in DatasetType that caused an error when trying to load newzsloan
datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error
2020-07-27Clean up webqtlCaseData classBonfaceKilz
* wqflask/base/webqtlCaseData.py (webqtlCaseData): - Remove obsolete 'Object' from Class inheritance - Replace 'str' with 'case_data_string' variable- it collides with python in-builts - Use pythonic 'is Not None' form - Remove redundancy in 'if' forms - Update copyright header
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
2020-07-25Removing bimbam check. We'll get rid of bimbam anyway.Pjotr Prins
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
2020-07-24Remove unreachable conditionalBonfaceKilz
* wqflask/base/GeneralObject.py(__getattr__): remove if statement that is unreachable
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
2020-07-24Apply autopep-8BonfaceKilz
* wqflask/base/GeneralObject.py: Replace tabs with 4 spaces
2020-07-24Remove unused importBonfaceKilz
2020-07-24Added binary casting to phenotype trait info query to fix unicode issuezsloan
2020-07-21Fixed issue that caused group codes to be wrong sometimeszsloan
2020-07-14Added binary casting to phenotype trait info query to fix unicode issuezsloan
2020-07-08Removed remaining unused references to the old qtlreaperzsloan
2020-07-06Temporarily commented out the line in trait.py doing the encoding until we ↵zsloan
figure out the real solution to that issue
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ↵zsloan
where a trait is authenticated twice
2020-06-29Change that hopefully fixes some encoding stuffzsloan
2020-06-24Temporary partial fix to issue of resources without info; need to add ↵zsloan
something that automatically inserts resources with default privileges
2020-06-22Fixed issue with temp traits not working for trait page functions like ↵zsloan
correlation or mapping
2020-06-20Fixed ports for proxy (though I need to add the port to global variables) ↵zsloan
and also simplified the check_owner_or_admin function a little
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-06-17Adding all the authentication stuffzsloan
2020-06-05Commiting other current group/resource management code, plus the new fileszsloan
2020-06-04Added back in trait info queries for situations where the proxy isn't runningzsloan
2020-06-04Really should have split this into many more commits:zsloan
- Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code
2020-05-28Added lines calling proxy for publish datasets + added some resource redis ↵zsloan
queries and a missing import for the hmac functions
2020-05-21Made search result table width variable again and fixed row highlighting, ↵zsloan
though later I need to go through and redo a bunch of CSS stuff
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
2020-03-09I think this should complete consolidating all the collections code.zsloan
2020-03-03Forgot to replace code referring to hmac function user_managerzsloan
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