| Age | Commit message (Collapse) | Author |
|---|
|
* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf.
(dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with
rdf.get_dataset_metadata.
* gn3/db/datasets.py: Remove unused imports.
(sparql_query, dataset_metadata): Delete.
* gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
|
|
* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query
directly to cursor.execute. Rename value to _value in for loop to
make mypy pass.
* gn3/db_utils.py (Connection): Add class docstring.
(Connection.cursor): Add docstring.
* mypy.ini: Add an entry for xapian.
|
|
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.
|
|
* gn3/db_utils.py (Connection): Disable missing-class-docstring,
missing-function-docstring and too-few-public-methods pylint checks.
|
|
* gn3/api/search.py: New file.
* gn3/app.py: Register the search blueprint.
|
|
* 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.
|
|
* gn3/genodb.py (matrix): Reshape column major genotype database storage as
ncols x nrows instead of as nrows x ncols.
|
|
|
|
* gn3/monads.py: Import SSDictCursor from MySQLdb.cursors.
(query_sql): Add server_side argument.
|
|
* 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.
|
|
* gn3/monads.py: New file.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
|
|
|
|
|
|
* 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.
|
|
|
|
Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
|
|
|
|
* 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.
|
|
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.
|
|
|
|
* Always return dict
* Fix internal '__parse_line__' to always have a valid return
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* remove extra iteration that is unnecessary
* remove unnecessary variables
|
|
* 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
|
|
|
|
* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Allow the resources (endpoints) to be accessible from anywhere on the internet
by default, while still allowing for restriction via CLI environment variable
on a case by case basis.
|
