| Age | Commit message (Expand) | Author |
|---|
| 2023-10-26 | Use auth-server for authentication...Authenticate with the Auth-server (gn-auth) to get the token to use on
the API server (GN3).
| Frederick Muriuki Muriithi |
| 2023-10-26 | Use gn-auth as the authorisation server. | Frederick Muriuki Muriithi |
| 2023-09-13 | Patch MySQLdb.escape_string to use use a connection....* wqflask/utility/db_tools.py: Delete MySQLdb.escape_. Import
get_setting, database_connection.
(escape_): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | Replace string concat with os.path.join....* wqflask/utility/tools.py (assert_writable_dir): Use "os.path.join"
to concatenate paths.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-12 | Use new session to get user (author) information...* wqflask/utility/json/__init__.py: Custom JSON for serialising UUIDs
into a JSON representantion
* wqflask/utility/json/encoders.py: Custom JSON for serialising UUIDs
into a JSON representation
* wqflask/wqflask/metadata_edits.py: Use new sessions for author
information
| Frederick Muriuki Muriithi |
| 2023-07-10 | Remove `OVERRIDES` global variable. | Frederick Muriuki Muriithi |
| 2023-07-05 | Compute the GN_VERSION in setup code not shell script | Frederick Muriuki Muriithi |
| 2023-07-05 | Config: Remove unused `OVERRIDES`...The `OVERRIDES` variable has no actual use in the application,
therefore, this commit removes it and its dependent code.
| Frederick Muriuki Muriithi |
| 2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
| 2022-12-29 | Implement "login" via OAuth2 | Frederick Muriuki Muriithi |
| 2022-10-28 | Settings: Add the `REDIS_URL` setting. | Frederick Muriuki Muriithi |
| 2022-10-28 | Declutter stdout...* wqflask/utility/tools.py: Output extraneous messages to stderr
rather than stdout to avoid cluttering the output.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Refactor: Pass user id to `check_resource_availability`...* Pass the user_id for the current user to the
`check_resource_availability` function as an argument, rather than
using the global `g.user_session.user_id` value.
| Frederick Muriuki Muriithi |
| 2022-10-12 | Account for empty strings in get_string function | zsloan |
| 2022-09-29 | Replace MonadicDictCursor with generator function....* wqflask/utility/monads.py (MonadicDictCursor): Delete class.
(sql_query_mdict): New function.
* wqflask/scripts/index.py: Import sql_query_mdict instead of
MonadicDictCursor.
(main): Use sql_query_mdict.
| Arun Isaac |
| 2022-09-29 | Remove empty first line in docstrings....* wqflask/utility/monads.py (MonadicDict, MonadicDictCursor): Remove
empty first line in docstrings.
| Arun Isaac |
| 2022-09-29 | Ignore None values early when initializing MonadicDict....* wqflask/utility/monads.py (MonadicDict.__init__): Ignore None values
early instead of converting them to Nothing and then ignoring them.
| Arun Isaac |
| 2022-09-29 | Return monadic value from MonadicDictCursor.fetchone....* wqflask/utility/monads.py (MonadicDictCursor.fetchone): Return
monadic value.
| Arun Isaac |
| 2022-09-19 | Refactor: raise appropriate error...If a file/directory does not exist, raise the builtin
`FileNotFoundError` rather than the generic `Exception`.
| Frederick Muriuki Muriithi |
| 2022-09-16 | Add example code to docstring of MonadicDictCursor....* wqflask/utility/monads.py (MonadicDictCursor): Add example code to
docstring.
| Arun Isaac |
| 2022-09-16 | Add example code to docstring of MonadicDict....* wqflask/utility/monads.py (MonadicDict): Add example code to
docstring.
| Arun Isaac |
| 2022-09-16 | Initialize empty MonadicDict by default....* wqflask/utility/monads.py (MonadicDict)[__init__]: Set default
dictionary argument to the empty dictionary.
| Arun Isaac |
| 2022-09-14 | Add monadic utilities MonadicDict and MonadicDictCursor....* wqflask/utility/monads.py: New file.
| Arun Isaac |
| 2022-09-08 | Deleting utility.logger...* wqflask/utility/logger.py: Delete.
| 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 | Replace g.db with database_connection() context manager...* wqflask/wqflask/update_search_results.py: Replace "Flask" and "g"
import with "database_connection".
(GSearch.__init__): Reformat SQL. Rename "re" to "results" since "re"
is part of the stdlib.
* wqflask/wqflask/marker_regression/rqtl_mapping.py: Replace flask.g
with database_connection.
(write_covarstruct_file): Replace g.db with database_connection().
* wqflask/wqflask/search_results.py: Replace "Flask" and "g" imports
with "database_connection" import.
(trait_info_str): Replace g.db with database_connection.
* wqflask/wqflask/docs.py (Docs): Use dababase_connection() context
manager.
(update_text): Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py:
Replace "Flask" and "g" import with "database_connection".
(DisplayMappingResults.__init__): Use database_connection.
(DisplayMappingResults.drawSNPTrackNew): Ditto.
| Munyoki Kilyungi |
| 2022-08-31 | Delete benchmark module...* wqflask/utility/benchmark.py: Delete module.
| 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 | Remove unused "string" import...* wqflask/utility/logger.py: Delete "import string".
| Munyoki Kilyungi |
| 2022-07-25 | Return config in app.config or None...Update the code to return the setting already set up in the app.config
dictionary if it exists or None if it does not exist.
| Frederick Muriuki Muriithi |
| 2022-07-04 | wqflask: Remove DebugToolbarExtension...This functionality, at least how we use it, is already provided
natively in python's pdb. Should someone need this, they can add it
manually.
* wqflask/runserver.py (app_config): Remove "flask_debugtoolbar"
import and instantiation.
* wqflask/utility/startup_config.py (app_config): Ditto.
| BonfaceKilz |
| 2022-04-04 | Return None in load_json_from_redis when the item doesn't exist...For some reason that isn't clear to me yet, a logged-in user session ID
was set even when a user wasn't logged in, causing the user session code
to attempt to fetch user information for a non-existent user ID
| zsloan |
| 2022-02-18 | wqflask: Remove python pre-2.2 checks....These checks are only relevant for python pre-2.2.
* wqflask/utility/svg.py: Remove python pre-2.2 checks.
| Arun Isaac |
| 2021-11-25 | Delete noisy logging | BonfaceKilz |
| 2021-11-04 | Removes unused import | jgart |
| 2021-10-28 | Remove all elasticsearch references in gn2 | BonfaceKilz |
| 2021-10-28 | Remove the use of '@deprecated'...This causes noisy logging.
| BonfaceKilz |
| 2021-10-25 | utility: redis_tools: Remove dead functions | BonfaceKilz |
| 2021-10-25 | authentication_tools: Mark `check_owner_or_admin` as deprecated...Use the new auth proxy tools instead.
| BonfaceKilz |
| 2021-10-25 | utility.hmac: Label "hmac_creation" as deprecated...This function is coupled to "wqflask.app", therefore requiring it's
import at the module level. This may lead circular importation issues
when working with blueprints.
| BonfaceKilz |
| 2021-10-25 | Mark `get_resource_info` as deprecated | BonfaceKilz |
| 2021-10-22 | Fix line pulling GN3_LOCAL_URL from settings | zsloan |
| 2021-10-22 | Replace hardcoded GN proxy URLs with one pulled from settings | zsloan |
| 2021-10-22 | Added proxy and local GN3 URLs in tools.py (which should be set in the settin... | zsloan |
| 2021-10-04 | Changed get_user_groups to pull both the ID and details in the for loop from ... | zsloan |
| 2021-09-10 | Removed encoding, since it's apparently not needed since the Python 3 switcho... | zsloan |
| 2021-08-23 | Account for situations where the minimum permutation value is also above webq... | zsloan |
| 2021-08-20 | startup_config.py: Add DebugToobarExtension for wsgi DEBUG mode...* wqflask/utility/startup_config.py (app_config): Add
DebugToolbarExtension
| BonfaceKilz |
| 2021-07-12 | Encode user_id as bytestring if not already bytestring to account for some us... | zsloan |
| 2021-06-17 | remove print statements | Alexander Kabui |
