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2022-05-06Make the results table dataTable classFrederick Muriuki Muriithi
2022-05-06Display the trait name in the header during editsBonfaceKilz
2022-05-06Move "Update History" to it's own pageBonfaceKilz
* wqflask/wqflask/metadata_edits.py (edit_phenotype): Move the logic for fetching the diff data from here to... (show_history): ... here. * wqflask/wqflask/templates/edit_phenotype.html: Move html section for displaying recent edits from here to ... * wqflask/wqflask/templates/edit_history.html: ... here.
2022-05-06Align the submit button to the leftBonfaceKilz
2022-05-06Remove the "Reset" buttonBonfaceKilz
2022-05-06Re-order the form fields to match the APA citation styleBonfaceKilz
2022-05-06Fix typos; "Pre" and "Post", as prefixes, aren't standalone wordsBonfaceKilz
2022-05-06Remove the "Sequence" form fieldBonfaceKilz
2022-05-06Adjust the row-size of the "Authors" field to 3BonfaceKilz
2022-05-06Shrink the rows of the "Volume" field to 1BonfaceKilz
2022-05-05Change mm9 to mm10 for creating the UCSC Genome Browser linkzsloan
2022-05-05Link to continuous deployment in README.Arun Isaac
* README.md (Development): Link to continuous deployment.
2022-05-04Add text-field for the "Volume" of a PublicationBonfaceKilz
2022-05-03Replace references of "publish_xref.pubmed_id" with "publication.id"BonfaceKilz
See: https://issues.genenetwork.org/issues/edit-metadata-bugs.html * wqflask/wqflask/metadata_edits (edit_phenotype): When diffing, should there be a null, use a "" during page display. Also, use the "publication.id_" instead of "publication.pubmed_id" when updating a publication. * wqflask/wqflask/templates/edit_phenotype.html: In the HTML form, use values of "publication" instead of "publish_xref" when referring to a publication.
2022-05-03Put contents into "container" divs to get similar stylingFrederick Muriuki Muriithi
Put the contents of the partial correlations pages between the <div class="container"></div> tags to take advantage of the existing styling of the content, especially regarding margins and paddings.
2022-04-30Add tool-button-container class to tool button div in correlation resultszsloan
2022-04-29Add non-CaseAttribute allowable headerszsloan
2022-04-29Set headers since it seems to have not been set before getting referencedzsloan
2022-04-26Add left float to permutation histogram so it appears correctlyzsloan
relative to other figures
2022-04-21Change searches to interpret any string starting with c/C as chromosomezsloan
Previously search terms with chromosome as a parameter would only search for Chr or chr specifically; this changes them to detect any string starting with a C/c (so it would detect, for example, 'ch4' as chromosome 4)
2022-04-21Fix error caused by traits without LRS values on collection pagezsloan
2022-04-21Fix issue with collection page exportzsloan
There were some extra spaces/newline characters in the checkbox table cell that were causing the javascript fetching trait info to not work correctly (it was trying to select the first item in the table cell, which in this case was the space/newline characters instead of the checkbox itself). Removing those characters seem to fix the export.
2022-04-20Fix issue where mapping figure wasn't horizontally scrolling when thezsloan
window is less wide than it
2022-04-20Remove extra template bracketzsloan
2022-04-19Add scatterplot link for additive effect in mapping resultszsloan
2022-04-18Add BXD-Micturition to BXD-equivalent groupszsloan
This is necessary for the coloring of the gene band rectangles to work correctly (because a query it runs needs the BXD strain ID)
2022-04-14Adjust mapping results page to prevent the mapping options at the top ofzsloan
the page from being too far to the right
2022-04-14Add group code to loading pages when applicablezsloan
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.
2022-04-14Increase tool-button-container min-widthzsloan
This increases the min-width for the search/collection page tool button container, since previously the Partial Correlation button would get shoved below when the window was too narrow. It needed to be increased to account for that button.
2022-04-14wqflask: Mock db connection when fetching case attributesBonfaceKilz
* wqflask/tests/integration/wqflask/test_metadata_edits.py (test_show_case_attributes): Mock "database_connection". Fixes this failing test: <https://ci.genenetwork.org/jobs/genenetwork2/223>
2022-04-14Register the port in the app configsFrederick Muriuki Muriithi
2022-04-14Provide db port when presentFrederick Muriuki Muriithi
Sometimes the system uses a port to connect to the database, rather than a socket, so if the port is present, provide it as part of the connection arguments.
2022-04-14Trigger the CI after mariadb restartFrederick Muriuki Muriithi
2022-04-14Use `MySQLdb.connect` rather than `MySQLdb.Connect`Frederick Muriuki Muriithi
2022-04-14Debug: Add logging to track db connection creation and stoppingdebug-too-many-connections-errorFrederick Muriuki Muriithi
As part of debugging the "Too many connections" error to the database, this commit adds logging to track the creation of connections to the database, and their eventual closing.
2022-04-12Replace get_allowable_sampledata_headers with get_case_attributesBonfaceKilz
* wqflask/wqflask/metadata_edits.py: Remove "get_allowable_sampledata_headers" import. (display_phenotype_metadata): Use "get_case_attributes" to fetch all the allowable case attributes.
2022-04-12List out case-attrs from database; and add link to case-attr pageBonfaceKilz
2022-04-12Don't create db engine for static filesFrederick Muriuki Muriithi
There is no need to create a database engine for requests for static files like CSS files and javascript files. This commit checks for and skips the creation of the engine for such requests.
2022-04-12Remove unused database codeFrederick Muriuki Muriithi
Remove code for connecting to the database that is not actually used in the application in any sensible form.
2022-04-07Add submit buttons to the top of the edit pageBonfaceKilz
2022-04-07Fix "Pubmed" spelling to "PubMed"BonfaceKilz
2022-04-07Add left space to content by making the "form" a containerBonfaceKilz
2022-04-07Remove ":" after a headerBonfaceKilz
2022-04-07Make case-attribute table a "data table"BonfaceKilz
2022-04-07Pass missing "conn" when getting case attributesBonfaceKilz
* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Create a connection and pass it to "get_case_attributes".
2022-04-07Run python-black on fileBonfaceKilz
* wqflask/wqflask/metadata_edits.py: Run "black -l 79 wqflask/wqflask/metadata_edits.py"
2022-04-07Create a new page to display case-attributes and their descriptionsBonfaceKilz
* wqflask/wqflask/metadata_edits.py: Import "gn3.db.sample_data.get_case_attributes". (show_case_attribute_columns): New function/ end-point to show case-attributes. * wqflask/tests/integration/wqflask/test_metadata_edits.py: New integration tests for the above. * wqflask/tests/integration/wqflask/__init__.py: New file. * wqflask/wqflask/templates/case_attributes.html: New template file to display the above.
2022-04-06Changed some styling for the edit_phenotype templatezsloan
2022-04-05Fix combined searches involving aliaseszsloan
The logic for building the SQL query wasn't working correctly when aliases were involved. The query also checks for a gene symbol's aliases in the DB, but this wasn't properly handling the AND/OR logic, leading to no results being shown when doing a "Get Combined" search involving a gene symbol. This also removed some unused code related to aliases.
2022-04-04Return None in load_json_from_redis when the item doesn't existzsloan
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 14:18:17 +0000