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2022-08-31Remove usage of "logger" and un-necessary comments wrt the sameMunyoki Kilyungi
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.
2022-03-17Create a db connection correctlyBonfaceKilz
* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is created.
2022-03-16Remove unnecessary print statementzsloan
2022-03-16Replace top comment with docstringzsloan
2022-03-16Add code generating the new genotype fileszsloan
Also made a large number of other fixes that proved necessary during testing
2022-03-16Generate JSON file for target genotypeszsloan
Also store parents/type metadata from source genofiles
2022-03-16Fix the way target/source genofiles were being processed + some other changeszsloan
- 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
2022-03-16Add function for mapping strain to sample pos + begin creating ↵zsloan
generate_new_genofiles function
2022-03-16Add function for getting strain name from sample namezsloan
2022-03-16Change EOL from CRLF to LFzsloan
2022-03-16Minor changes/bug fixeszsloan
- 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
2022-03-16Add in-progress gen_ind_genofiles.pyzsloan
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
2022-03-10Use context manager with database connectionFrederick Muriuki Muriithi
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.
2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
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
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
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
2021-04-29Run `sed -i 's/(object)//g'`BonfaceKilz
See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-20Handle module renames in the standard libraryBonfaceKilz
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>
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Rename xrange() to range() and wrap existing range() calls with listBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
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>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
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>
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ↵zsloan
where a trait is authenticated twice
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-06-17A user's id is now set as a parameter if it doesn't already existauthentication_testzsloan
2020-06-17Adding all the authentication stuffzsloan
2020-06-05Commiting other current group/resource management code, plus the new fileszsloan
2020-03-10Added back macaque monkey to dropdown generation, not sure why it was ↵zsloan
removed; need to ask Rob
2019-12-09Fixed minor issue that caused the sample list to be fetched incorrectly for ↵zsloan
a group groups
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ↵zsloan
correctly in certain situations
2019-05-14Added all of the third party links from GN1zsloan
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)
2019-04-04Fixed issue where dataset_menu_structure.json included some groups with no ↵zsloan
visible datasets
2019-04-03Fixed an issue that caused global phenotype search to often not work and ↵zsloan
certain phenotype datasets to not show up in drop-downs
2019-03-27Changed gen_select_dataset.py to be able to show multiple datasets under the ↵zsloan
Phenotype type (for example the GI Tract Metabolome data) 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
2018-12-21Fixed collections so they can be very large (1000+ traits)zsloan
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
2018-12-05Fixed issue where SNP track for mapping did not appear correctlyzsloan
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
2018-11-20Added option to select chromosome from trait page when mappingzsloan
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
2018-10-11- Added fix for GEMMA LOCOzsloan
- 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
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
just clicking their row in collection - 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")
2018-05-25Fixed issue causing anonymous collections to not work on my branch and ↵zsloan
staging, though still not sure why it's working on production without that change 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
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
sample data into ElasticSearch 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)
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵zsloan
instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 14:04:18 +0000