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2023-04-15Revert "Fix the way database_connection() is called"Frederick Muriuki Muriithi
This reverts commit b8b62aea1c7924e2ee7455c6fe8b34eee7cb8e74. We do need to decouple the entire `gn3.db_utils` from the `flask.current_app` object, and as such, the use of `SQL_URI` from the `utility.tools` module in GN2 was on purpose. This is also to help towards fixing issue https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
2023-04-14Handle errors for group consistent with the UI.Frederick Muriuki Muriithi
2023-04-12oauth2: Generalise JS code to work for both mRNA and Genotype datasets.Frederick Muriuki Muriithi
2023-04-12delete dead codeAlexander_Kabui
2023-04-12add code to store metadata in filesAlexander_Kabui
2023-04-11Fix bug where publication years had links even when there's no PMIDzsloan
This was just caused by the correlation code not directly being passed the PMID (and instead only being passed the link and the text), so the logic in the table code needed to be changed to check for the link instead of the PMID
2023-04-11Fix the way database_connection() is calledzsloan
I think it now gets the SQL_URI from settings
2023-04-11Fix indentation for conn.commit()zsloan
2023-04-11modify default textfile pathAlexander_Kabui
2023-04-10Add UI for searching and linking mRNA Assay datasets.Frederick Muriuki Muriithi
2023-04-10Do search. Filter out selected datasets.Frederick Muriuki Muriithi
Enable search when user types in search box. Filter out any selected datasets.
2023-04-08oauth2: Link the Genotype datasets.Frederick Muriuki Muriithi
2023-04-07Move JS to external file. Generalise functions.Frederick Muriuki Muriithi
Move the javascript to an external file to ease development. Generalise some functions to make it easier to reuse the code down the line.
2023-04-06Commit updates for phenotype/publication metadatazsloan
2023-04-06`flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`Frederick Muriuki Muriithi
Genenetwork2 configs are a tad weird, and instead of using the configs in `flask.current_app`, we need to use those in `utility.tools`.
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.Frederick Muriuki Muriithi
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
2023-04-06oauth2: UI - Enable auto-selection of datasets to be linkedFrederick Muriuki Muriithi
When a user selects a dataset in the search table, automatically add it to the link table and remove it from the search table.
2023-04-05oauth2: UI - Retain look and feel without using jQuery DataTablesFrederick Muriuki Muriithi
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.
2023-04-05oauth2: UI - Autoselect on user clickFrederick Muriuki Muriithi
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.
2023-04-05oauth2: UI - retain data in table attributesFrederick Muriuki Muriithi
Since the table data could change depending on user input, save the state in the `data-*` attributes to enable update of tables on changes.
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 typesFrederick Muriuki Muriithi
Filter out data as the user types, with a short delay to prevent searching on each and every character.
2023-03-23oauth2: data: Provide a UI for linking data, with search.Frederick Muriuki Muriithi
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.
2023-03-22Fix search result table widthzsloan
2023-03-21The mean deaults to 'N/A' for phenotypeszsloan
The previous code caused an error when the mean was N/A (when trying to take the float() of it)
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 updatedMunyoki Kilyungi
* 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.
2023-03-20Fix minor pep-8 issuesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-20Disable editing case-attributesMunyoki Kilyungi
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>
2023-03-20oauth2: Load menu and populate dropdownFrederick Muriuki Muriithi
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.
2023-03-20oauth2: Pass the offset in the queryFrederick Muriuki Muriithi
2023-03-20oauth2: phenotypes: list/link at trait levelFrederick Muriuki Muriithi
List/link the phenotypes at the trait level rather than at the dataset level.
2023-03-20corrs: Handle JSONDecodeErrorFrederick Muriuki Muriithi
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.
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 pagezsloan
Edit Sample Data and Edit Metadata are now two separate sections, and Edit Sample Data appears first
2023-03-15minor globalsearch enhancementAlexander_Kabui
2023-03-15Change global search form id to gsearchform instead of searchform (since ↵zsloan
searchform is already used for the regular search)
2023-03-15Replace REGEXP with LIKE in regular searcheszsloan
2023-03-15Fix bug caused by RRIDs parseable as intszsloan
2023-03-14fix responsivenessAlexander_Kabui
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