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* tests/unit/test_monads.py (test_monadic_dict): Add basic test-cases
for MonadicDict.
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This allows Maybe[T] to be used as a type. Both Nothing and Just are
of type Maybe.
* mypy.ini: Add default location for stub files.
* stubs/pymonad/__init__.pyi: New file.
* stubs/pymonad/maybe.pyi: Ditto.
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App settings should be accessed from current_app. It should not be hard-coded
to a variable in a module.
* gn3/db_utils.py: Do not import XAPIAN_DB_PATH from gn3.settings.
(xapian_database): Accept path argument.
* gn3/api/search.py: Import current_app from flask.
(search_results): Pass Xapian index path to xapian_database.
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* gn3/db_utils.py (Connection): Disable missing-class-docstring,
missing-function-docstring and too-few-public-methods pylint checks.
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* gn3/api/search.py: New file.
* gn3/app.py: Register the search blueprint.
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* gn3/settings.py (XAPIAN_DB_PATH): New variable.
* gn3/db_utils.py: Import xapian and XAPIAN_DB_PATH from gn3.settings.
(xapian_database): New function.
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* gn3/genodb.py (matrix): Reshape column major genotype database storage as
ncols x nrows instead of as nrows x ncols.
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* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
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* gn3/monads.py: Import SSDictCursor from MySQLdb.cursors.
(query_sql): Add server_side argument.
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* gn3/db_utils.py: Import contextlib. Import Any, Iterator, Protocol and Tuple
from typing.
(database_connector): Deprecate function.
(Connection): New class.
(database_connection): New function.
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* gn3/monads.py: New file.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function
was parsing data from a file, and then converting the parsed values into a
comma-separated string for output, despite the fact that the data parsed is
not output in this specific function. This is a really bad idea, and leads
to errors showing up down the line, far removed from the cause.
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Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
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* README.md: Update link to continuous deployment.
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* gn3/db/__init__.py (update): Delete conn.commit() and conn.rollback()
(insert): Ditto.
* gn3/db/case_attributes.py (insert_case_attribute_audit): Ditto.
(reject_case_attribute): Ditto.
(approve_case_attribute): Ditto.
* gn3/db/sample_data.py (update_sample_data): Ditto.
(delete_sample_data): Ditto.
(insert_sample_data): Ditto.
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By default, MySQL/Mariadb connects at port 3306, however, the configuration
variable `SQL_URI` could contain a different port. In that case, this commit
allows the system to connect to the non-default port.
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* Always return dict
* Fix internal '__parse_line__' to always have a valid return
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* remove extra iteration that is unnecessary
* remove unnecessary variables
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* README.md: update mypy's invocation
* scripts/argparse_actions.py: new file - implement custom FileCheck action
for argparse
* scripts/sample_correlations.py: new file - implement new script to run
sample correlations in an external process
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* gn3/computations/correlations.py: rename function
* mypy.ini: deactivate mypy error about missing imports
* tests/integration/test_correlation.py: mock correct function
* tests/unit/computations/test_correlation.py: test correct function
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* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
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