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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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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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Feature/add rqtl pairscan
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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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Add missing argument to the command in the documentation
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The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org.
* README.md: Update CI badge subdomain.
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Chore/gn2 enhancements
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Replace pca rpy2 code
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* test/requests/test-website.py: Run "black test/requests/test
test-website.py".
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* test/requests/test-website.py: Delete parser option "-i" for running
integration tests.
(integration_tests): Delete it.
(integration_suite): Ditto.
(run_integration_tests): Ditto.
* test/requests/test_registration.py: Delete it.
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* test/requests/test-website: These imports were deleted in an earlier
PR here: <https://github.com/genenetwork/genenetwork2/pull/574>
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* test/requests/test-website.py: Delete "from wqflask import
app". This has the undesired effect of starting an instance of
Genenetwork2.
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Document the configurations for the service, and how to use them when
invoking the service.
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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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Add documentation on how to run the tests - this was no clear from the
existing documentation up to this point.
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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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