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2022-07-22delete dead_code;rename variablesAlexander_Kabui
2022-07-22add unittestsAlexander_Kabui
2022-07-22minor fixesAlexander_Kabui
2022-07-11Allow CORS everywhere by default...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. Frederick Muriuki Muriithi
2022-06-29use explicit parametersAlexander_Kabui
2022-06-29fix issuesAlexander_Kabui
2022-06-29lint test fileAlexander
2022-06-29pylint fixesAlexander
2022-06-29add testsAlexander
2022-06-29add test dataAlexander
2022-06-29minor fixesAlexander
2022-06-29handle tmp files generationAlexander
2022-06-29parse output dataAlexander
2022-06-29pep8 formattingAlexander
2022-06-29new variable: CORRELATION_COMMANDAlexander
2022-06-29init test correlation rust moduleAlexander
2022-06-29init rust correlation moduleAlexander
2022-06-28Parse the method from UI before passing it to external process...To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods Frederick Muriuki Muriithi
2022-06-21tests: test_file_utils: Replace pytest.mark.skip with unittest.skip..."python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3. BonfaceKilz
2022-06-21setup.py: Remove commented out "ipfshttpclient" lineBonfaceKilz
2022-06-21gn3: fs_helpers: Fix pylint errors...* gn3/fs_helpers.py: Remove unused "pathlib" import. (cache_ipfs_file): Disable "unused-argument" warting. BonfaceKilz
2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto. BonfaceKilz
2022-06-21gn3: fs_helpers: Remove ipfshttpclient...This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail. BonfaceKilz
2022-06-21setup.py: Remove ipfshttpclientBonfaceKilz
2022-06-21integration: test_gemma: Skip "GemmaAPITest"BonfaceKilz
2022-06-21Replace lint code with human-readable text...* gn3/db/correlations.py (__fetch_data__): Use a more readable code as opposed to an error code. BonfaceKilz
2022-06-21db: correlations: Ignore pylint error...* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913] error. BonfaceKilz
2022-06-21db: correlations: Ignore types...* gn3/db/correlations.py (__build_query__): Ignore the "sample_ids" and "joins" types when calling build_query_sgo_lit_corr (fetch_all_database_data): Ignore the return type. TODO: Ping Alex/Arun to fix this. BonfaceKilz
2022-06-21db: datasets.py: Ignore results from sparql.queryAndConvert...ATM, it's very difficult to work the correct type that is returned. Ignore this for now and fix this later. BonfaceKilz
2022-06-21mypy.ini: Ignore missing lmdb mypy stubsBonfaceKilz
2022-06-20Update README: export env variables explicitlyFrederick Muriuki Muriithi
2022-06-20gn3: genodb: Retire get function....* gn3/genodb.py (get): Delete function. (matrix): Use db.txn.get instead of get. Arun Isaac
2022-06-20gn3: genodb: Match class and function names of GenotypeMatrix....* gn3/genodb.py (GenotypeMatrix): Match class and function names. Arun Isaac
2022-06-20gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix....db is unused. nrows and ncols are available in the array and transpose numpy arrays. * gn3/genodb.py (GenotypeMatrix)[db, nrows, ncols]: Delete fields. * gn3/genodb.py (matrix): Do not initialize db, nrows and ncols fields. Arun Isaac
2022-06-20gn3: genodb: Mention reading entire matrix in module docstring....* gn3/genodb.py: Mention reading entire matrix in module docstring. Arun Isaac
2022-06-20Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations Frederick Muriuki Muriithi
2022-06-17gn3: genodb: Rename Matrix named tuple to GenotypeMatrix....* gn3/genodb.py (Matrix): Rename to GenotypeMatrix. (matrix): Update invocation of Matrix. Arun Isaac
2022-06-17gn3: genodb: Allow retrieval of the entire genotype matrix....* gn3/genodb.py: Document nparray in the module docstring. (nparray): New function. Arun Isaac
2022-06-17gn3: genodb: Read optimized storage for the current matrix....The genotype database now stores the current version of the matrix alone in a read-optimized form, while storing the older versions of the matrix in a more compressed form. We are only interested in the current version of the matrix. So, always use the read optimized storage. * gn3/genodb.py (Matrix)[row_pointers, column_pointers]: Delete fields. [array, transpose]: New fields. * gn3/genodb.py (matrix, row, column): Read from read-optimized storage. (vector_ref): Delete function. Arun Isaac
2022-06-09gn3: genodb: Remove blank line in module docstring....* gn3/genodb.py: Remove blank line in module docstring. Arun Isaac
2022-06-09gn3: genodb: Rewrite without classes....We rewrite genodb using only functions. This makes for much more readable code. * gn3/genodb.py: Rewrite without classes. Arun Isaac
2022-06-08gn3: genodb: Support reading columns....* gn3/genodb.py (Matrix.__init__): Retrieve column pointers from database. (row): Abstract out vector access code to ... (Matrix.__vector): ... here. (Matrix.column): New method. Arun Isaac
2022-06-08gn3: genodb: Read only the most recent genotype matrix....The genotype database format now supports versioning of matrices. So, we update genodb.py to return only the most recent genotype matrix. * gn3/genodb.py (GenotypeDatabase.matrix): Return only the most recent genotype matrix. Arun Isaac
2022-06-08gn3: genodb: Open genotype database in read-only mode....* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in read-only mode. Arun Isaac
2022-06-08gn3: genodb: Do not create genotype database if it does not exist....* gn3/genodb.py (GenotypeDatabase.__init__): Do not create genotype database if it does not exist. Arun Isaac
2022-06-08gn3: genodb: Decide on little endianness....It has been decided that the genotype database will use little endianness wherever applicable. * gn3/genodb.py (Matrix.__init__): Remove TODO note to decide on endianness. Arun Isaac
2022-06-08gn3: genodb: Do not terminate database strings with null....* gn3/genodb.py (GenotypeDatabase.get_metadata, GenotypeDatabase.matrix): Do not terminate database strings with the null character. Arun Isaac
2022-06-03gn3: Add genodb....genodb is a tiny library to read our new genotype database file format. * gn3/genodb.py: New file. Arun Isaac
2022-05-31Remove unnecessary statementFrederick Muriuki Muriithi
2022-05-31Extract utility functions from `fetch_all_database_data`...Extract the utility functions to help with understanding the what the `fetch_all_database_data` function is doing. This helps with maintenance. Frederick Muriuki Muriithi