| Age | Commit message (Expand) | Author |
|---|
| 2022-09-06 | Fix a few problems with ind_genofile conversion script | zsloan |
| 2022-08-31 | Remove usage of "logger" and un-necessary comments wrt the same...Logging is used to introspect variables or notify the commencement of
a given operation. Logging should only be used to log errors. Also,
most of the logging is either "logger.debug" or "logger.info"; and
this won't show up in production/testing since we need a logging level
above "WARNING" for them to show up.
* wqflask/base/data_set.py (create_datasets_list): Remove logger.
(Markers.add_pvalues): Ditto.
(DataSet.retrieve_other_names): Ditto.
* wqflask/base/mrna_assay_tissue_data.py: Ditto.
* wqflask/base/webqtlCaseData.py: Ditto.
* wqflask/db/call.py (fetch1): Ditto.
(gn_server): Ditto.
* wqflask/db/gn_server.py: Ditto.
* wqflask/maintenance/set_resource_defaults.py: Ditto.
* wqflask/utility/Plot.py (find_outliers): Ditto.
* wqflask/utility/gen_geno_ob.py: Ditto.
* wqflask/utility/helper_functions.py: Ditto.
* wqflask/utility/pillow_utils.py: Ditto.
* wqflask/utility/redis_tools.py: Ditto.
* wqflask/wqflask/api/gen_menu.py (get_groups): Ditto.
* wqflask/wqflask/api/mapping.py: Ditto.
* wqflask/wqflask/api/router.py (get_dataset_info): Ditto.
* wqflask/wqflask/collect.py (report_change): Ditto.
* wqflask/wqflask/correlation/corr_scatter_plot.py: Ditto.
* wqflask/wqflask/ctl/ctl_analysis.py (CTL): Ditto.
(CTL.__init__): Ditto.
(CTL.run_analysis): Ditto.
(CTL.process_results): Ditto.
* wqflask/wqflask/db_info.py: Ditto.
* wqflask/wqflask/do_search.py (DoSearch.execute): Ditto.
(DoSearch.mescape): Ditto.
(DoSearch.get_search): Ditto.
(MrnaAssaySearch.run_combined): Ditto.
(MrnaAssaySearch.run): Ditto.
(PhenotypeSearch.run_combined): Ditto.
(GenotypeSearch.get_where_clause): Ditto.
(LrsSearch.get_where_clause): Ditto.
(MeanSearch.run): Ditto.
(RangeSearch.get_where_clause): Ditto.
(PvalueSearch.run): Ditto.
* wqflask/wqflask/docs.py: Ditto.
* wqflask/wqflask/export_traits.py: Ditto.
* wqflask/wqflask/external_tools/send_to_bnw.py: Ditto.
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Ditto.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/heatmap/heatmap.py: Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Ditto.
* wqflask/wqflask/marker_regression/gemma_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/plink_mapping.py (run_plink): Ditto.
* wqflask/wqflask/marker_regression/qtlreaper_mapping.py (run_reaper): Ditto.
* wqflask/wqflask/marker_regression/rqtl_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto.
* wqflask/wqflask/parser.py (parse): Ditto.
* wqflask/wqflask/search_results.py (SearchResultPage.__init__): Ditto.
* wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto.
* wqflask/wqflask/user_login.py (send_email): Ditto.
(logout): Ditto.
(forgot_password_submit): Ditto.
(password_reset): Ditto.
(password_reset_step2): Ditto.
(register): Ditto.
* wqflask/wqflask/user_session.py (create_signed_cookie): Ditto.
| Munyoki Kilyungi |
| 2022-03-17 | Create a db connection correctly...* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is
created.
| BonfaceKilz |
| 2022-03-16 | Remove unnecessary print statement | zsloan |
| 2022-03-16 | Replace top comment with docstring | zsloan |
| 2022-03-16 | Add code generating the new genotype files...Also made a large number of other fixes that proved necessary during
testing
| zsloan |
| 2022-03-16 | Generate JSON file for target genotypes...Also store parents/type metadata from source genofiles
| zsloan |
| 2022-03-16 | Fix the way target/source genofiles were being processed + some other changes...- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles
- references to the app context are removed in favor of just taking input as arguments or environment variables
- Updated example commands
| zsloan |
| 2022-03-16 | Add function for mapping strain to sample pos + begin creating generate_new_g... | zsloan |
| 2022-03-16 | Add function for getting strain name from sample name | zsloan |
| 2022-03-16 | Change EOL from CRLF to LF | zsloan |
| 2022-03-16 | Minor changes/bug fixes...- Removed some unused code
- Strip marker genotype to avoid newline character at end
- Convert zip to list for marker genotypes
- Add typing to group_samples
- Rename strain_genofile to source_genofile
| zsloan |
| 2022-03-16 | Add in-progress gen_ind_genofiles.py...gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
| zsloan |
| 2022-03-10 | Use context manager with database connection...Use the `with` context manager with database connections and cursors
to ensure that they are closed once they are no longer needed.
Where it was not feasible to use the `with` context manager without a
huge refactor/rewrite, the cursors and connections are closed manually.
| Frederick Muriuki Muriithi |
| 2021-10-28 | Remove all elasticsearch references in gn2 | BonfaceKilz |
| 2021-04-30 | autopep8: Run autopep8 100 times with target rules...Rules used are:
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242,
E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,
E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121,
E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
| BonfaceKilz |
| 2021-04-30 | autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E101, E11 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix W504 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix W291, W292, W293, W391 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E70 and E701 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E501 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E20-E27...Run:
python -m autopep8 --in-place --recrusive ./ --select\
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\
E242,E251,E252,E26,E265,E266,E27 -p 3
| BonfaceKilz |
| 2021-04-29 | Run `sed -i 's/(object)//g'`...See: https://is.gd/pL7IJF
Ran:
find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
| BonfaceKilz |
| 2020-08-26 | Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
| BonfaceKilz |
| 2020-08-20 | 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 | 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 | Replace `izip` with python's built-in equivalent...Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports>
and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
| 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 |
| 2020-07-06 | Fixed some of the logic with how traits are authenticated to avoid situation ... | 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 |
| 2020-03-10 | Added back macaque monkey to dropdown generation, not sure why it was removed... | zsloan |
| 2019-12-09 | Fixed minor issue that caused the sample list to be fetched incorrectly for a... | zsloan |
| 2019-10-18 | Added UniProt link and fixed issue that caused sample lists to not be formed ... | zsloan |
| 2019-05-14 | Added all of the third party links from GN1...Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets
Added icon for smartphones/tablets
Made error more informative for main search
Added gene symbol column to collections (need to add something that removes the column if it's all empty)
| zsloan |
| 2019-04-04 | Fixed issue where dataset_menu_structure.json included some groups with no vi... | zsloan |
| 2019-04-03 | Fixed an issue that caused global phenotype search to often not work and cert... | zsloan |
| 2019-03-27 | Changed gen_select_dataset.py to be able to show multiple datasets under the ......Fixed issue where full description was given for some unpublished traits
Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something
| zsloan |
| 2018-12-21 | Fixed collections so they can be very large (1000+ traits)...Added option to submit traits in collection to BNW
Fixed issue with "x" values for user-submitted traits
Fixed issue where post-publications descriptions were wrongly appearing in global search results
| zsloan |
| 2018-12-05 | Fixed issue where SNP track for mapping did not appear correctly...Updated style for a variety of tables
Moved transform/blocking tools for trait sample table into its own tab
Added some new customization options to network graph
Started work on implementing third party link-outs
Updated drop-down generation script to order datasets according to CreateTime
| zsloan |
| 2018-11-20 | Added option to select chromosome from trait page when mapping...Put transform/blocking tools into their own tab (still need to change formatting of tab's contents)
Improved appearance of search result page table (still need to change a few other tables)
Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool
Basic Stats figures now load when the user clicks the tab, to improve initial page load time
| zsloan |
| 2018-10-11 | - Added fix for GEMMA LOCO...- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
| zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
| zsloan |
| 2018-05-25 | Fixed issue causing anonymous collections to not work on my branch and stagin......Added script to convert the dryad format genotype files to BIMBAM
removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
| zsloan |
| 2018-05-17 | Added script to quantile normalize a data set and enter its normalized sample......Added option to replace trait page sample/strain values with normalized ones
Began editing Lei's scatterplot code
Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
| zsloan |
