| Age | Commit message (Expand) | Author |
|---|
| 2020-08-26 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-08-24 | Remove unused imports...* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is
does not have py3 support so it's important to remove references to it.
| BonfaceKilz |
| 2020-08-24 | The function draw_rotated_text_ was writing an image to /tmp, which GN2...user apparently doesn't have access to, so I replaced it with a link to
the dynamically set TEMPDIR
* wqflask/utility/pillow_utils.py - Replaced "/tmp/" in image location
with TEMPDIR
| zsloan |
| 2020-08-23 | Use Python3 string methods...* wqflask/utility/webqtlUtil.py (genRandStr): Replace "string.letters" with
"string.ascii_letters".
| BonfaceKilz |
| 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 |
| 2020-08-19 | 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 | Rename xrange() to range() and wrap existing range() calls with list...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
| BonfaceKilz |
| 2020-08-19 | Wrap `raise` statements in parenthesis...Run `2to3-3.8 -f raise -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
| BonfaceKilz |
| 2020-08-19 | Convert the old not-equal syntax, <>, to !=...Run `2to3-3.8 -f ne -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
| BonfaceKilz |
| 2020-08-19 | Fix dictionary iteration methods...Run `2to3-3.8 -f dict -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and
<https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
| BonfaceKilz |
| 2020-08-19 | Remove erroneous `if .. else` branch...* wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error
if either height or width is not defined. Fixes parsing error when running
`2to3-3.8 -f apply -w .`
| BonfaceKilz |
| 2020-08-19 | Wrap `map()` in a `list` call...Run `2to3-3.8 -f map -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
| BonfaceKilz |
| 2020-08-18 | Apply pep8...* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running
`2to3-3.8 -w .`:
````
RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403)
````
| BonfaceKilz |
| 2020-08-18 | Replace "<>" with "!="...* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
| BonfaceKilz |
| 2020-08-18 | Wrap print statements in parentheses | BonfaceKilz |
| 2020-08-18 | Fix malformed docstring...* wqflask/utility/Plot.py: Update docstring.
| BonfaceKilz |
| 2020-08-08 | Add draw_open_polygon() utility...* wqflask/utility/pillow_utils.py: New method.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use draw_rotated_text()...Use the new draw_rotated_text() function to draw the text rotated as was
formerly done.
* wqflask/utility/Plot.py (plotBar): Use draw_rotated_text().
* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults) Use draw_rotated_text().
| Muriithi Frederick Muriuki |
| 2020-08-08 | Create new utility module for drawing...* wqflask/utility/pillow_utils.py: Create a module to hold some utility
functions for drawing with Pillow. Initialise the module with a function to draw
rotated text.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Fix font paths...* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Migrate code from Piddle to Pillow...* wqflask/wqflask/marker_regression/display_mapping_results.py: Add font files
(DisplayMappingResults): Update the code from the Piddle way of things to the
Pillow way of things, for example, replace:
- pid.drawRect(...) with im_drawer.rectangle(...)
- pid.drawString(...) with im_drawer.text(...)
- pid.drawPolygon(...) with im_drawer.polygon(...) etc.
* wqflask/utility/Plot.py: Migrate code from the older, unsupported Piddle to
the newer Pillow library.
| Muriithi Frederick Muriuki |
| 2020-07-29 | Fixed error that occured for new resources in check_admin...* wqflask/utility/authentication_tools.py: the code forgot to get
resource_info when a resource wasn't in Redis yet, causing an error when
it was referenced, so I added a line getting the resource info (and also
a couple comments for other lines related to authentication)
| zsloan |
| 2020-07-25 | The variable is never defined, so let's default to "none" | Pjotr Prins |
| 2020-07-24 | Merge pull request #409 from BonfaceKilz/Build/add-tests...Build/add tests | zsloan |
| 2020-07-24 | Revert "Add work-around for failed imports in unittest"...This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
| BonfaceKilz |
| 2020-07-24 | Add work-around for failed imports in unittest...* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app`
and the gn2 script will use `from wqflask import app`
| BonfaceKilz |
| 2020-07-24 | Apply autopep-8...* wqflask/utility/formatting.py: apply it
| BonfaceKilz |
| 2020-07-24 | Add zero to num_repr dictionary...* wqflask/utility/formatting.py(numify): Update `num_repr` to have a zero
| BonfaceKilz |
| 2020-07-24 | Remove redundant variable...* wqflask/utility/corr_result_helpers.py(normalize_values_with_values):
Remove `num_overlap`
| BonfaceKilz |
| 2020-07-24 | Remove unused assert...* wqflask/utility/corr_result_helpers.py(normalize_values):
At no one point will that assert be hit
| BonfaceKilz |
| 2020-07-24 | Remove unused doc-tests...* wqflask/utility/corr_result_helpers.py: Delete doc-test
| BonfaceKilz |
| 2020-07-24 | Simplify normalize_values...* wqflask/utility/corr_result_helpers.py(normalize_values): Replace loop with
zip form
| BonfaceKilz |
| 2020-07-24 | Remove unused doc-tests...* wqflask/utility/chunks.py: Remove test code from module
| BonfaceKilz |
| 2020-07-24 | Revert "Add work-around for failed imports in unittest"...This reverts commit d5e87fa6fe7546b46790f512d984a5501223082f.
| BonfaceKilz |
| 2020-07-24 | Add work-around for failed imports in unittest...* wqflask/utility/tools.py: Unittests will use `from wqflask.wqflask import app`
and the gn2 script will use `from wqflask import app`
| BonfaceKilz |
| 2020-07-22 | It should add new resources to Redis automatically now | zsloan |
| 2020-07-16 | Expose elastic-search variables for tests to pass | BonfaceKilz |
| 2020-07-08 | Removed remaining unused references to the old qtlreaper | zsloan |
| 2020-07-06 | Fixed some of the logic with how traits are authenticated to avoid situation ... | zsloan |
| 2020-06-24 | Temporary partial fix to issue of resources without info; need to add somethi... | zsloan |
| 2020-06-20 | Fixed ports for proxy (though I need to add the port to global variables) and... | zsloan |
| 2020-06-20 | Added some admin functionality and fixed issue with temp traits | zsloan |
| 2020-06-17 | A user's id is now set as a parameter if it doesn't already existauthentication_test | zsloan |
| 2020-06-17 | Adding all the authentication stuff | zsloan |
| 2020-06-05 | Commiting other current group/resource management code, plus the new files | zsloan |
| 2020-06-04 | Really should have split this into many more commits:...- 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
| zsloan |
| 2020-05-28 | Added lines calling proxy for publish datasets + added some resource redis qu... | zsloan |
| 2020-05-12 | Merging Danny's changes and Bonface's changes to js imports | zsloan |
| 2020-05-12 | Added change for F2s in r/qtl and fixed minor issue in save_user in redis_tools | zsloan |
