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* README.md (Development): Link to continuous deployment.
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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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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.
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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
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It's not entirely clear to me exactly why the previous logic wasn't
working correctly, but this change (that removes the user cookie when
there's no user_session after the request and returns None if there
aren't any user_details) appears to fix the issue.
The main confusing part is why the user_cookie still exists even when
not logged in
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metadata_edits.py
For some reason there were two places where it wasn't being called as a
function. Fixing this appears to have fixed the error
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There were two places this needed to be checked and I previously missed
this one
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property to user_session
Also changed the order of the dropdowns to have Sign Out after the user
drop-down, to more closely match NCBI's style
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The function returns a call to mdb.connect, which only returns the
connection object. It was throwing an error due to trying to unpack
multiple items.
One thing I noticed while looking at this is that we should probably
decide on a single way to create these connections. In some other files,
we instead use database_connection from wqflask.database (instead of the
gn3 database_connector from gn3.db_utils)
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Chore/ctl wgcna enhancements
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Passing the data into `requests.post` as a `json=...` argument will
automatically encode the data to JSON and set up the correct
Content-Type header.
The call `json.dumps(post_data)` was pre-encoding the data to a JSON
string, that was the re-encoded to JSON yet again, which is not what
we want. This commit fixes that.X
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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
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Bug/fix qtlreaper snp order
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This is meant to deal with edge cases where there's only a single coordinate for a chromosome when doing interval mapping (which causes an error, since interval mapping requires that markers be linked within each chromosome)
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