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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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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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end)
Not sure how best to do this; I just had the sort algorithm change "M" to "z" (which will always be sorted last, behind X and Y)
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The parameter should never be interval if pair_scan is being run; not checking for this causes the --interval tag to pointlessly be included when running pair-scan, which also interferes with caching
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Previously it would always register as True, due to being in the start_vars
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Replace pca rpy2 code
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- Limit number of full names to 2 followed by "et al."
- Fix wrong logic that was using the full length of the authors string instead of the truncated length when determining the width of the column, resulting in it always being at least 500px wide
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looks strange
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Previously authentication didn't work correctly if users had "edit" privileges, because the code specifically looked for just "view"; this changes it to check for either "view" or "edit"
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* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is
created.
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These tests touch on core data-structures in gn2; and there's a chance
that refactoring said data-structures may break many things.
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* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper
database connection instead of the db connection attached at "g.db".
* wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto.
* wqflask/wqflask/api/correlation.py: Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
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* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger".
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If the GN2_SETTINGS environment variable, is for some reason, not set,
and the application actually ever tries to get a connection to the
database, then use the default settings/configuration file.
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Also made a large number of other fixes that proved necessary during
testing
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Also store parents/type metadata from source genofiles
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- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles
- references to the app context are removed in favor of just taking input as arguments or environment variables
- Updated example commands
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generate_new_genofiles function
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- Removed some unused code
- Strip marker genotype to avoid newline character at end
- Convert zip to list for marker genotypes
- Add typing to group_samples
- Rename strain_genofile to source_genofile
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gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
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