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Also refactor the way the exports and BNW submission are done
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Modify the code to request computation of partial correlations with
selected traits rather than a complete dataset.
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* 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.
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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.
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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.
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relative to other figures
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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)
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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.
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window is less wide than it
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This is necessary for the coloring of the gene band rectangles to work
correctly (because a query it runs needs the BXD strain ID)
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the page from being too far to the right
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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.
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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.
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* 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>
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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.
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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.
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* 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.
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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.
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Remove code for connecting to the database that is not actually used
in the application in any sensible form.
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* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns):
Create a connection and pass it to "get_case_attributes".
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* wqflask/wqflask/metadata_edits.py: Run "black -l 79
wqflask/wqflask/metadata_edits.py"
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* 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.
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