aboutsummaryrefslogtreecommitdiff
AgeCommit message (Expand)Author
2023-04-10Add UI for searching and linking mRNA Assay datasets.Frederick Muriuki Muriithi
2023-04-10Do search. Filter out selected datasets....Enable search when user types in search box. Filter out any selected datasets. Frederick Muriuki Muriithi
2023-04-08oauth2: Link the Genotype datasets.Frederick Muriuki Muriithi
2023-04-07Move JS to external file. Generalise functions....Move the javascript to an external file to ease development. Generalise some functions to make it easier to reuse the code down the line. Frederick Muriuki Muriithi
2023-04-06Commit updates for phenotype/publication metadatazsloan
2023-04-06`flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`...Genenetwork2 configs are a tad weird, and instead of using the configs in `flask.current_app`, we need to use those in `utility.tools`. Frederick Muriuki Muriithi
2023-04-06correlations: Provide more output to enable debug of errors.Frederick Muriuki Muriithi
2023-04-06Remove use of deprecated `gn3.db_utils.database_connector` function....Remove use of deprecated function and fix a myriad of bugs that rise from its removal. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils Frederick Muriuki Muriithi
2023-04-06oauth2: UI - Enable auto-selection of datasets to be linked...When a user selects a dataset in the search table, automatically add it to the link table and remove it from the search table. Frederick Muriuki Muriithi
2023-04-05oauth2: UI - Retain look and feel without using jQuery DataTables...Simplify the implementation by dropping the use of the jQuery DataTables plugin - this avoids a lot of arising bugs while retaining the UI look and feel until we have something working. Frederick Muriuki Muriithi
2023-04-05oauth2: UI - Autoselect on user click...Try auto-selecting datasets on user click: not successful at this point. There are some weird bugs with the DataTables that I have not been able to resolve yet. Frederick Muriuki Muriithi
2023-04-05oauth2: UI - retain data in table attributes...Since the table data could change depending on user input, save the state in the `data-*` attributes to enable update of tables on changes. Frederick Muriuki Muriithi
2023-04-04oauth2: Provide UI for linking genotype datasets.Frederick Muriuki Muriithi
2023-04-03Add conn.commit() for metadata editszsloan
2023-03-28Re-add md5.min.js to search result templatezsloan
2023-03-28Only include 'cytochrome AND P450' as part of the placeholder textzsloan
2023-03-25oauth2: Add UI to use to link dataFrederick Muriuki Muriithi
2023-03-24oauth2: data: setup search as user types...Filter out data as the user types, with a short delay to prevent searching on each and every character. Frederick Muriuki Muriithi
2023-03-23oauth2: data: Provide a UI for linking data, with search....Provide a UI for the phenotype datasets with a search interface (currently inactive) that is eventually going to allow for linking the traits to user groups. Frederick Muriuki Muriithi
2023-03-22Fix search result table widthzsloan
2023-03-21The mean deaults to 'N/A' for phenotypes...The previous code caused an error when the mean was N/A (when trying to take the float() of it) zsloan
2023-03-21Remove session['user_details'] references since they seem to cause an errorzsloan
2023-03-21Replace twitter-post-fetcher with Twitter's provided timeline linkzsloan
2023-03-20Add link to diff page when sample-data is updated...* wqflask/wqflask/metadata_edits.py (update_phenotype): Add url to diff page in flash message. * wqflask/wqflask/templates/edit_phenotype.html: Render flash message with HTML. Munyoki Kilyungi
2023-03-20Fix minor pep-8 issues...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-03-20Disable editing case-attributes...ATM, editing case-attributes is very buggy. * wqflask/tests/integration/wqflask/test_metadata_edits.py: Delete. * wqflask/wqflask/decorators.py: Remove: gn3.authentication.get_groups_by_user_uid import. (case_attributes_edit_access): Delete. * wqflask/tests/integration/wqflask/test_metadata_edits.py: Remove wqflask.decorators.case_attributes_edit_access, gn3.db.case_attributes.get_case_attributes, gn3.db.case_attributes.get_unreviewed_diffs, gn3.db.case_attributes.insert_case_attribute_audit, gn3.db.case_attributes.reject_case_attribute and gn3.db.case_attributes.approve_case_attribute. (display_phenotype_metadata): Remove headers arg when rendering template. (update_phenotype): Remove case attribute headers list when updating a phenotype. (show_case_attribute_columns, update_case_attributes): Delete. (reject_case_attribute_data, approve_case_attribute_data): Ditto. * wqflask/wqflask/templates/edit_phenotype.html: Remove link that shows all the listed case-attributes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-03-20oauth2: Load menu and populate dropdown...In order to enable searching through the existing datasets for linking with the auth system, we need a way to filter the data. In this commit, I load the menu and load it onto a dropdown box as a proof of concept to give an idea of some of the filters I can use down the road to fetch the data. This commit breaks the data-linking code. I will need to rework the data-linking code entirely to get it working again. Frederick Muriuki Muriithi
2023-03-20oauth2: Pass the offset in the queryFrederick Muriuki Muriithi
2023-03-20oauth2: phenotypes: list/link at trait level...List/link the phenotypes at the trait level rather than at the dataset level. Frederick Muriuki Muriithi
2023-03-20corrs: Handle JSONDecodeError...In the case that the JSON output from the correlations computation is malformed, we capture that into a new exception an re-raise it to help with debugging and fixing issues. Frederick Muriuki Muriithi
2023-03-18oauth2: resources: toggle whether a resource is public or not.Frederick Muriuki Muriithi
2023-03-18oauth2: resources: Disallow duplicate resource names.Frederick Muriuki Muriithi
2023-03-17Fix correlation bug caused by a NULL UPDATE_TIME in the DBzsloan
2023-03-16Make the two Submit Change buttons consistentzsloan
2023-03-16Edit dataset dropdown JS to handle Species sub-categorieszsloan
2023-03-16Change the UI for the phenotype editing page...Edit Sample Data and Edit Metadata are now two separate sections, and Edit Sample Data appears first zsloan
2023-03-15minor globalsearch enhancementAlexander_Kabui
2023-03-15Change global search form id to gsearchform instead of searchform (since sear...zsloan
2023-03-15Replace REGEXP with LIKE in regular searcheszsloan
2023-03-15Fix bug caused by RRIDs parseable as intszsloan
2023-03-14fix responsivenessAlexander_Kabui
2023-03-14add shadow and border effect autocompleteAlexander_Kabui
2023-03-10oauth2: Extend scope for GN2 oauth2 client.Frederick Muriuki Muriithi
2023-03-09Merge pull request #772 from genenetwork/chores/code-refactoring...Chores/code refactoringAlexander Kabui
2023-03-09code cleanupchores/code-refactoringAlexander_Kabui
2023-03-09delete recent search handlerAlexander_Kabui
2023-03-09Merge pull request #771 from genenetwork/chores/ui-enhancements...Chores/UI enhancementsAlexander Kabui
2023-03-09fix miniform search idAlexander_Kabui
2023-03-09link to hint page;update form selectorAlexander_Kabui
2023-03-08Add DataAnalyzer.py script to maintenance scriptszsloan