| Age | Commit message (Expand) | Author |
|---|
| 2022-09-20 | Decompose file into separate modules...To ease future refactors on the code, decompose the file into a module
with multiple modules that can be refactored semi-independently.
refactor-data_set_py-20220920 | Frederick Muriuki Muriithi |
| 2022-09-12 | Fix query: Add comma to separate columns. | Frederick Muriuki Muriithi |
| 2022-09-12 | Fix query: remove wrongly-placed comma | Frederick Muriuki Muriithi |
| 2022-09-12 | Check db resultset before indexing into it...The assumption that the resultset will never be empty was leading to a
lot of errors.
| Frederick Muriuki Muriithi |
| 2022-09-09 | Fix bug in retrieve_other_names...After a recent change, it always tries to unpack 6 values from the
query, but it should only be unpacking 4 values if not type ProbeSet (so
it was throwing an error for anything not ProbeSet)
| zsloan |
| 2022-09-09 | tissue:fetch for query formatting | Alexander_Kabui |
| 2022-09-09 | Retain only a single import of the same module | Frederick Muriuki Muriithi |
| 2022-09-09 | Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlations...Bug/fix broken correlations | Muriithi Frederick Muriuki |
| 2022-09-09 | Fetch sample values correctly...* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data):
Fix indentation.
| Munyoki Kilyungi |
| 2022-09-09 | Add missing import...* wqflask/base/trait.py: Import utility.hmac
| Munyoki Kilyungi |
| 2022-09-09 | Import missing module. | Frederick Muriuki Muriithi |
| 2022-09-09 | Filter out Samples without values | Frederick Muriuki Muriithi |
| 2022-09-09 | Use `database_connection()`...Call the `database_connection()` function to get a connection to the
database.
| Frederick Muriuki Muriithi |
| 2022-09-09 | Replace `g.db.execute` with `cursor.execute` | Frederick Muriuki Muriithi |
| 2022-09-08 | Simplify how chromosomes are fetched...* wqflask/base/species.py: Import "Any" and "Union".
(TheSpecies): Add type hints. Get rid of redundant "if ... else"
statement.
(IndChromosome.mb_length): Add type hints.
(Chromosomes): Inject conn and add type hints.
| Munyoki Kilyungi |
| 2022-09-08 | Remove redundant cursor.fetchone()...* wqflask/base/data_set.py (DataSet.retrieve_other_names): Call
cursor.fetchone() only once.
| Munyoki Kilyungi |
| 2022-09-08 | Use "%s" in sql query...* wqflask/base/mrna_assay_tissue_data.py: Delete db_tools.
(MrnaAssayTissueData.get_symbol_values_pairs): Re-format query.
* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py:
(test_get_trait_symbol_and_tissue_values): Add test for above.
| Munyoki Kilyungi |
| 2022-09-08 | Inject database connection to mrna_assay_tissue_data class...* wqflask/base/mrna_assay_tissue_data.py: Imports: Delete
database_connection, escape, and database_connector.
(MrnaAssayTissueData): Inject conn. Re-format queries. Rework 'if
... else' logic. Re-work how results are assigned to
'self.data[symbol]' - remove dot-notation.
(MrnaAssayTissueData.get_symbol_values_pairs): Move box-comments to
doc-string. Rework how results are assigned to 'symbol_values_dict' -
remove dot-notation.
* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
(test_mrna_assay_tissue_data_initialisation): New test.
* wqflask/wqflask/correlation/correlation_functions.py: Import
database_connection.
(get_trait_symbol_and_tissue_values): Inject conn object.
| Munyoki Kilyungi |
| 2022-09-08 | Fix sql queries..."%s" should only be used outside table names and column names
otherwise a string literal will be inserted thereby leading to errors
in the sql statements.
* wqflask/base/data_set.py (geno_mrna_confidentiality): Use f-strings
for table/columns/clause.
* wqflask/base/trait.py (retrieve_trait_info): Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py
(SnpBrowser.get_browser_results): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Add missing "," in cursor.execute()...* wqflask/base/data_set.py (DatasetGroup.get_mapping_methods): Fix
failing query by adding a missing ",".
| Munyoki Kilyungi |
| 2022-09-08 | Remove intermediate variables that are only used once...* wqflask/base/data_set.py (DatasetGroup.__init__): Remove "query"
variable.
(DataSet.chunk_dataset): Fix indentation.
* wqflask/wqflask/search_results.py (get_GO_symbols): Remove
"this_term" variable.
* wqflask/wqflask/views.py (search_page): Remove "the_search"
variable.
| Munyoki Kilyungi |
| 2022-09-08 | Delete dead imports...* wqflask/base/data_set.py: Remove un-used imports.
* wqflask/base/trait.py: Ditto.
wqflask/tests/wqflask/show_trait/test_show_trait.py: Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Ditto.
* wqflask/wqflask/views: Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* wqflask/base/data_set.py (DatasetType.set_dataset_key): Replace g.db
with "database_connection()".
(DatasetGroup.get_mapping_methods): Ditto.
(DataSet.get_accession_id): Ditto.
(DataSet.retrieve_other_names): Rework "if ... else" logic to get rid
of "query" and "_vars" variables. Also, nest "try ... except" block
within "database_connection".
(DataSet.chunk_dataset): Replace g.db with "database_connection()".
(DataSet.get_probeset_data): Ditto.
(DataSet.get_trait_data): Ditto.
(PhenotypeDataSet.get_trait_info): Ditto.
(PhenotypeDataSet.retrieve_sample_data): Ditto.
(GenotypeDataSet.retrieve_sample_data): Ditto.
(MrnaAssayDataSet.get_trait_info): Ditto.
(MrnaAssayDataSet.retrieve_sample_data): Ditto.
(MrnaAssayDataSet.retrieve_genes): Ditto.
(TempDataSet): Ditto.
(geno_mrna_confidentiality): Ditto.
(query_table_timestamp): Ditto.
* wqflask/wqflask/api/router.py: Replace "flask.g" with
database_connection import.
(get_species_list): Replace g.db
with "database_connection()".
(get_species_info): Ditto.
(get_groups_list): Ditto.
(get_group_info): Ditto.
(get_datasets_for_group): Ditto.
(get_dataset_info): Ditto.
(fetch_traits): Ditto.
(all_sample_data): Ditto.
(trait_sample_data): Ditto.
(get_trait_info): Ditto.
(get_dataset_trait_ids): Ditto.
(get_samplelist): Ditto.
(get_group_id_from_dataset): Ditto.
(get_group_id): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Delete logger import...* wqflask/base/trait.py: Remove utility.logger
| Munyoki Kilyungi |
| 2022-09-08 | Replace assertion with Value Error for non-existent dataset...* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in
ValueError.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection.
(MrnaAssayTissueData.__init__): Use database_connection.
(MrnaAssayTissueData.get_symbol_values_pairs): Ditto.
* wqflask/base/species.py: Replace "Flask.g" imports with
"database_connection".
(Chromosomes.chromosomes): Use database_connection.
* wqflask/base/trait.py: Import database_connection.
(retrieve_trait_info): Use database_connection.
* wqflask/utility/authentication_tools.py: Replace "flask.g" with
database_connection.
(get_group_code): Use database_connection.
* wqflask/utility/helper_functions.py: Replace "flask.g" with
"database_connection".
(get_species_groups): Use database_connection.
* wqflask/wqflask/db_info.py: Replace "Flask" and "g" with
"database_connection".
(InfoPage.get_info): Use database_connection.
* wqflask/wqflask/do_search.py (DoSearch.execute): Use
database_connection().
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace
"Flask" and "g" import with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace
"Flask, g" imports with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with
database_connection.
(GSearch.__init__): Use database_connection.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes):
Use database_connection().
* wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import"
with database_connection.
(SampleList.get_attributes): Use database_connection.
(SampleList.get_extra_attribute_values): Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g"
import with database_connection.
(ShowTrait.__init__): Use database_connection.
(ShowTrait.get_external_links): Ditto.
(get_nearest_marker): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Merge pull request #727 from Alexanderlacuna/feature/use-textfiles...use text files for Probeset | Alexander Kabui |
| 2022-09-07 | catch general errors this will recreate the file | Alexander_Kabui |
| 2022-09-06 | Fix error with dataset menu query in data_set.py...I'm only using g.db.execute here because using cursor is throwing an
error and I don't want to change the way this query is currently written
since I didn't write it (I believe it was initially written using
g.db.execute and whoever wrote it just forgot to put the g.db.execute,
since previously it just called "fetchall")
| zsloan |
| 2022-09-06 | Merge branch 'testing' into feature/generalize_tables | zsloan |
| 2022-09-06 | Set up the self.* variables from query results...Set up the appropriate self.* variables from the results of running
the appropriate query.
| Frederick Muriuki Muriithi |
| 2022-09-06 | Use dataset name if dataset group name is not set. | Frederick Muriuki Muriithi |
| 2022-08-31 | Delete unused modules...* 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.
| Munyoki Kilyungi |
| 2022-08-31 | Replace fetchall, fetchone, fetch1 with database_connection...* 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.
| Munyoki Kilyungi |
| 2022-08-31 | Remove "with Bench ..." calls..."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.
| Munyoki Kilyungi |
| 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 |
| 2022-08-31 | add new environment variable:TEXTDIR | Alexander_Kabui |
| 2022-07-12 | Include genotypes for F1s/reference/non-reference strains when fetching...sample data for genotype traits
| zsloan |
| 2022-06-23 | Change jsonable in GeneralTrait so that it passes all necessary table...information
| zsloan |
| 2022-06-23 | Convert trait.view to string for conversion to JSON...It's originally a boolean, which causes an error when passed to the JS
code as JSON
| zsloan |
| 2022-06-13 | Check for chromosome of 'Un' and print location as 'Not available' in such cases | zsloan |
| 2022-04-14 | Add group code to loading pages when applicable...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.
| zsloan |
| 2022-03-25 | Fix issues that prevented genotype traits from being added to collections...Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function
| zsloan |
| 2022-02-21 | Fix incorrect dataset trait data caching...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.
| zsloan |
| 2021-11-25 | Delete noisy logging | BonfaceKilz |
| 2021-11-23 | resolve merge conflicts | Alexander Kabui |
| 2021-11-23 | pep8 formatting remove dead variables | Alexander Kabui |
| 2021-11-17 | refactor sql query & date formatting | Alexander Kabui |
| 2021-11-17 | replace redis fetch for cached timestamp with a query | Alexander Kabui |
| 2021-11-17 | isolate SQL_URI parse to a function | Alexander Kabui |
