| Age | Commit message (Expand) | Author |
|---|
| 2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
| 2023-05-19 | auth: Use auth privileges to control UI display...Use the privileges from the authorisation endpoint to control which
elements of the UI are displayed to the user.
* wqflask/base/trait.py: Remove unused import
* wqflask/wqflask/show_trait/show_trait.py: Unhook from GN-PROXY
* wqflask/wqflask/templates/show_trait.html: Display or hide UI
elements depending on the privileges the user has.
* wqflask/wqflask/templates/show_trait_details.html: Display or hide
UI elements depending on the privileges the user has.
* wqflask/wqflask/views.py: Pass privileges, user, and resource
details on to the UI template to be used for controlling UI element
display.
| Frederick Muriuki Muriithi |
| 2023-02-17 | Use abbreviation as symbol for phenotypes in collection page | zsloan |
| 2023-02-17 | Default trait abbreviation to N/A and only set to pre/post_publication_abbrev... | zsloan |
| 2023-02-14 | Fix collection page error when ProbeSet/Publish traits don't have a mean | zsloan |
| 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 |
| 2022-10-27 | init fix for querying for datasets | Alexander_Kabui |
| 2022-10-20 | Cleanup: Remove unused code...* Commit 49580eb9cd47bb2ce15fd44be11bb9580d85efef removed the use of
the gn-proxy, but left some code that was used expressly for use
with the gn-proxy. This commit removes that code.
| Frederick Muriuki Muriithi |
| 2022-10-18 | Change logic in retrieve_trait_info to account for situations where a marker ... | zsloan |
| 2022-10-12 | Use SQL to fetch trait metadata instead of gn-proxy, since it's dramatically ... | zsloan |
| 2022-10-12 | Include chr/mb values in jsonable trait | zsloan |
| 2022-10-04 | Add more information to exception to help in debugging | Frederick Muriuki Muriithi |
| 2022-09-25 | Fix issue where the display name was used in the hmac for phenotype traits | zsloan |
| 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 | Add missing import...* wqflask/base/trait.py: Import utility.hmac
| Munyoki Kilyungi |
| 2022-09-09 | Import missing module. | Frederick Muriuki Muriithi |
| 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 | 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 | 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 |
| 2022-06-23 | 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 |
| 2022-03-25 | 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 |
| 2021-10-22 | Replace hardcoded GN proxy URLs in trait.py with one pulled from settings | zsloan |
| 2021-08-20 | Fixed some logic in trait.py that could cause a problem if a dataset_name was... | zsloan |
| 2021-06-16 | Changed the function jsonable in trait.py to return a couple extra fields + t... | zsloan |
| 2021-04-30 | autopep8: Fix W504 | BonfaceKilz |
| 2021-04-29 | Merge branch 'testing' into Feature/Add-upload-data-forms | 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 |
| 2021-04-29 | base: trait: Remove unused function...* wqflask/base/trait.py (jsonable_table_row): Delete it.
| BonfaceKilz |
| 2021-04-28 | Added something to jsonable in trait.py to account for temp traits (this is n... | zsloan |
| 2021-03-03 | Checked if pre_publication_description is NULL, because there was an error re... | zsloan |
| 2021-02-18 | Fixed missing colon | zsloan |
| 2021-02-18 | Fixed checking permissions in trait.py | zsloan |
| 2021-02-11 | Ensure trait description_display is set | zsloan |
| 2020-12-07 | Changed the logic in create_trait so that permissions should always be set, a... | zsloan |
| 2020-12-01 | Merge pull request #482 from zsloan/feature/corr_table_changes...Feature/corr table changes | zsloan |
| 2020-11-18 | Fixed issue where the cofactor trait descriptions didn't work correctly...for genotype/snp cofactors (the code previously only accounted for
probeset/phenotype cofactors, so it was treating genotypes/snps like
phenotype traits)
| zsloan |
| 2020-11-18 | Fixed issue that was causing scatterplot cofactors to not work if the...cofactors were genotypes (because it tried to get the
"description_display" which doesn't exist for genotype traits)
| zsloan |
| 2020-11-11 | Switched checking if a trait is confidential to checking if it has a pubmed I... | zsloan |
| 2020-10-12 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-10-09 | Apply PEP 8 to buffer...* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
| BonfaceKilz |
| 2020-10-02 | Ignore utf-8 encoding errors...* wqflask/base/trait.py (retrieve_trait_info): Add extra param to
ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position
0: invalid start byte" thrown in Python3.
| BonfaceKilz |
| 2020-10-01 | Convert trait attributes to utf-8 strings if they were bytes | BonfaceKilz |
| 2020-09-28 | Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2... | BonfaceKilz |
| 2020-09-28 | Fix casting error...* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
| BonfaceKilz |
| 2020-09-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
