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path: root/wqflask/base/data_set.py
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2022-08-31Delete unused modulesMunyoki Kilyungi
* wqflask/base/data_set.py: Delete "menu_main" import. * wqflask/db/call.py: Delete it. * wqflask/db/gn_server.py: Ditto. * wqflask/wqflask/submit_bnw.py: Ditto.
2022-08-31Replace fetchall, fetchone, fetch1 with database_connectionMunyoki Kilyungi
* wqflask/base/data_set.py: Replace "db.call" import with "database_connection". (create_datasets_list): Use "database_connection" to fetch data. (DatasetGroup.__init__): Ditto. (DataSet.retrieve_other_names): Ditto. (PhenotypeDataSet.setup): Remove query escaping in string and format the string. (GenotypeDataSet.setup): Ditto. (MrnaAssayDataSet.setup): Ditto. * wqflask/db/webqtlDatabaseFunction.py: Remove db.call import. (retrieve_species): Use database_connection() to fetch data. (retrieve_species_id): Ditto.
2022-08-31Remove "with Bench ..." callsMunyoki Kilyungi
"with Bench" instruments how long a function takes and generates time reports on as INFO logs. This should be done on a developer server. Should the log level be low enough, this bench marks will generate a lot of noise. Instrumentation should be done during development. * wqflask/base/data_set.py (create_datasets_list): Remove "with Bench...". * wqflask/db/call.py (fetchone): Ditto. (fetchall): Ditto. (gn_server): Ditto. * wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults.__init__): Ditto. * wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto. * wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto. * wqflask/wqflask/views.py (search_page): Ditto. (heatmap_page): Ditto. (mapping_results_page): Ditto.
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.
2022-07-12Include genotypes for F1s/reference/non-reference strains when fetchingzsloan
sample data for genotype traits
2022-04-14Add group code to loading pages when applicablezsloan
This adds the group code to phenotype traits on loading pages, and also sets the group code as an attribute of the dataset.group class.
2022-02-21Fix incorrect dataset trait data cachingzsloan
Trait data caching wasn't working correctly because it didn't account for the samplelist, causing caching to work incorrect in any situation where the target dataset's samplelist wasn't the same as that of the trait being correlated against. Trait data is stored as a dictionary where the keys are trait IDs and values are *lists* of sample values. This means that the caching needs to account for the exact same set of samples; otherwise you'll end up with samples being mismatched (since "the third sample with a value" for one dataset's trait might not be the same as "the third sample with a value" for another dataset's trait). To fix this, I added the samplelist to the functions that generate and fetch the hash file. This will require more cache files, though, so this should probably be reexamined later to make the code work with only a single cache file for each dataset.
2021-11-25Delete noisy loggingBonfaceKilz
2021-11-23resolve merge conflictsAlexander Kabui
2021-11-23pep8 formatting remove dead variablesAlexander Kabui
2021-11-17refactor sql query & date formattingAlexander Kabui
2021-11-17replace redis fetch for cached timestamp with a queryAlexander Kabui
2021-11-17isolate SQL_URI parse to a functionAlexander Kabui
2021-11-17use a dynamic value for the db_nameAlexander Kabui
2021-11-17temp disable query cachingAlexander Kabui
2021-11-16use comprehension list;fix typoAlexander Kabui
2021-11-16pep8 formatting remove debug statementsAlexander Kabui
2021-11-16test generate new filesAlexander Kabui
2021-11-16refactor:fix on the query :modify cache pointAlexander Kabui
2021-11-04check for null timestampAlexander Kabui
2021-11-04store table timestamp on redisAlexander Kabui
2021-11-04init function to get the table timestampAlexander Kabui
2021-11-04pep8 formatting ,minor fixesAlexander Kabui
2021-11-04generate filename hashAlexander Kabui
2021-11-04fetch cached resultsAlexander Kabui
2021-11-04function to cache sample resultsAlexander Kabui
2021-08-17Merge pull request #598 from zsloan/feature/add_filter_by_study_sampleszsloan
Feature/add filter by study samples
2021-08-13base: data_set: Remove unnecessary comments and logging statementsBonfaceKilz
2021-08-12Return empty list instead of None in get_study_samplelistszsloan
2021-08-12Fix the way the study_sample_lists path is set and checkedzsloan
2021-08-12add function for reading in JSON file that lists sample lists unique to each ↵zsloan
study within a group (in this case only BXD Longevity for now)
2021-06-17delete loggers and commentsAlexander Kabui
2021-06-17sort sample name by sample_idsAlexander Kabui
2021-06-17remove unused functions + minor fixesAlexander Kabui
2021-06-17minor fixAlexander Kabui
2021-06-17pep8 formattingAlexander Kabui
2021-06-17add query for fetching probeset dataAlexander Kabui
2021-06-16Added function as_dict to data_set.py for situations where we don't want to ↵zsloan
pass around the whole dataset object
2021-05-10Merge branch 'testing' into feature/integrate-correlation-apiAlexander Kabui
2021-05-10add previous endpoint for correlationAlexander Kabui
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
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'
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (Dataset.get_accession_id): Delete it.
2021-04-29base: data_set: Apply pep-8BonfaceKilz
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (riset): Delete class method.
2021-04-29base: data_set: Rewrite data_set using @dataclassBonfaceKilz
@dataclasses should be used to hold only data. Since dataset only encapsulates data, re-writing it using a dataclass makes it more readable and easier to follow.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 16:31:47 +0000