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* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
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* gn3/db/sample_data.py: Run "python black -l 79 ..."
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* gn3/csvcmp.py (parse_csv_column): New function.
* tests/unit/test_csvcmp.py: Test case for the above.
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* gn3/csvcmp.py: Run "black -l 79 ..."
* tests/unit/db/test_sample_data.py: Ditto.
* tests/unit/test_csvcmp.py: Ditto.
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returning a string"
This reverts commit b93b22386056347d8002dd2e403425beeb4657cd.
The appropriate fix should have been in GN2. The original statement
args = request.get_json()
was correct, since `request.get_json()` should return a python object parsed
from the JSON string in the request. Unfortunately, GN2 was encoding the
request data two times, which led to the call returning a JSON-encoded string
instead of the expected object.
The issue has been fixed in GN2 and therefore, the "fix" here can be reverted.
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Remove unused modules from the `use-modules` arguments.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* Remove a module that is no longer in use
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returning a string
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Implement a fixture that:
* Creates a new test database
* Copies over table structure from existing database
* Gets connection to new test database and returns it
* Cleans up after itself when the tests have run
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See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126>
* gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also,
manually fix other pylint issues.
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Feature/add rqtl pairscan
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https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan
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Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)
Also added a couple more verbose prints
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position in pair-scan results + return only the sorted top 500 results
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selected
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it's needed to store the proximal/distal markers for each position
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Dict and List respectively used for the pair scan figure and the table showing the results
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we need the list of markers/pseudomarkers and their positions)
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api/rqtl.py
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in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
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step-size to 10cM for pair-scan
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(pairscan) is used
- For pairscan default to using step 20 (subject to change, but some
step is required during calc.genoprob to make it run fast enough)
- Added some new verbose prints
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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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There was a subtle bug where "csvdiff" generated an error related to
"different column headings" caused something akin to diffing: "a, b \n, ..."
with "a, b\n, ...".
* gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing.
* tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to
capture aforementioned bug.
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* gn3/csvcmp.py (clean_csv_text): New function.
* tests/unit/test_csvcmp.py: Import "csv_text".
(test_clean_csv_text): Test case for the above.
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* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca
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* gn3/csvcmp.py (extract_invalid_csv_headers): New function.
* tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers".
(test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the
above.
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* gn3/csvcmp.py: Import "Any" and "List".
(get_allowable_sampledata_headers): New function.
* tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers".
(test_get_allowable_csv_headers): Test case for the above.
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* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92
that broke this.
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