| Age | Commit message (Expand) | Author |
|---|
| 2021-03-17 | Added the RRID urls for mouse and rat to webqtlConfig | zsloan |
| 2021-03-03 | Checked if pre_publication_description is NULL, because there was an error re... | zsloan |
| 2021-02-18 | Changed DEFAULT_PERMISSIONS AND SUPER_PERMISSIONS to not have permissions be ... | zsloan |
| 2021-02-18 | Fixed missing colon | zsloan |
| 2021-02-18 | Fixed checking permissions in trait.py | zsloan |
| 2021-02-18 | Fixed SUPER_PRIVILEGES and DEFAULT_PRIVILEGES | zsloan |
| 2021-02-11 | Removed some log statements | zsloan |
| 2021-02-11 | Ensure trait description_display is set | zsloan |
| 2020-12-07 | Changed the logic in create_trait so that permissions should always be set, a... | zsloan |
| 2020-12-01 | Merge pull request #482 from zsloan/feature/corr_table_changes...Feature/corr table changes | zsloan |
| 2020-11-18 | Fixed issue where the cofactor trait descriptions didn't work correctly...for genotype/snp cofactors (the code previously only accounted for
probeset/phenotype cofactors, so it was treating genotypes/snps like
phenotype traits)
| zsloan |
| 2020-11-18 | Fixed issue that was causing scatterplot cofactors to not work if the...cofactors were genotypes (because it tried to get the
"description_display" which doesn't exist for genotype traits)
| zsloan |
| 2020-11-11 | Switched checking if a trait is confidential to checking if it has a pubmed I... | zsloan |
| 2020-11-03 | Changed the syntax for the "sort" function in the docstring of GeneralObject ......* wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
| zsloan |
| 2020-10-27 | Get the "first_attr_start_pos" from a samplelist instead of from each individ......* 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
| zsloan |
| 2020-10-20 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-10-19 | Merge branch 'testing' into scroller_testing | zsloan |
| 2020-10-12 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-10-09 | Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collections...Tests/add extra tests for collections | BonfaceKilz |
| 2020-10-09 | Apply PEP 8 to buffer...* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
| BonfaceKilz |
| 2020-10-08 | Fixed remaining issue that applies to all dataset types...* 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
| zsloan |
| 2020-10-08 | Fixed issue where new phenotype groups wouldn't be saved to the self.datasets......* 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
| zsloan |
| 2020-10-02 | Ignore utf-8 encoding errors...* wqflask/base/trait.py (retrieve_trait_info): Add extra param to
ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position
0: invalid start byte" thrown in Python3.
| BonfaceKilz |
| 2020-10-01 | Convert trait attributes to utf-8 strings if they were bytes | BonfaceKilz |
| 2020-09-30 | Removed unused code from TempDataSet class...* 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
| zsloan |
| 2020-09-28 | Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2... | BonfaceKilz |
| 2020-09-28 | Fix casting error...* 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)*.
| BonfaceKilz |
| 2020-09-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-09-28 | Fix casting error...* 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)*.
| BonfaceKilz |
| 2020-09-28 | Convert None to "" in if statement...* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
| BonfaceKilz |
| 2020-09-18 | Made a bunch of changes to move trait page DataTables initialization to...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
| zsloan |
| 2020-09-17 | Convert "target_string" to a str type...* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string"
to a str, otherwise an exception will be thrown if it's None.
| BonfaceKilz |
| 2020-09-17 | Apply pep8...* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
| BonfaceKilz |
| 2020-08-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-08-27 | Remove python2 string processing to utf-8...* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods.
* wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
| BonfaceKilz |
| 2020-08-27 | Replace mysqldb's "escape" with the one from utils.db_tools...Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra
step of converting the binary string to a string.
| BonfaceKilz |
| 2020-08-27 | Remove redundant methods which are defined elsewhere...* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are
defined in "utility.db_tools"
| BonfaceKilz |
| 2020-08-27 | Remove unused imports | BonfaceKilz |
| 2020-08-27 | Replace "string.split" & "string.join" with python's inbuilt methods | BonfaceKilz |
| 2020-08-26 | Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
| BonfaceKilz |
| 2020-08-26 | Replace "__cmp__" with "__eq__" magic method...* wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See:
<https://stackoverflow.com/questions/8276983/why-cant-i-use-the-method-cmp-in-python-3-as-for-python-2>
| BonfaceKilz |
| 2020-08-26 | Rename "unicode" to "str"...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
| BonfaceKilz |
| 2020-08-25 | Fixed issue in DatasetType that caused an error when trying to load new...datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
| zsloan |
| 2020-08-20 | Handle module renames in the standard library...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>
| BonfaceKilz |
| 2020-08-20 | Disable python2 QTLReaper...* wqflask/base/data_set.py: Remove usage of "reaper" to load datasets
| BonfaceKilz |
| 2020-08-20 | Add backward support for urllib...* wqflask/base/trait.py: Remove unused imports
* wqflask/db/call.py (Bench): Add urllib2 fallback for python2
| BonfaceKilz |
| 2020-08-19 | Remove extra whitespace(or add it) from comma separated items...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 2020-08-19 | Make Python more idiomatic...Run `2to3-3.8 -f idioms -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
| BonfaceKilz |
| 2020-08-19 | Handle the rename of urllib and urllib2 to the urllib package...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 2020-08-19 | Replace backtick repr with the repr() function...* wqflask/base/trait.py: See
<https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
| BonfaceKilz |
