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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
2022-05-30Pass trait data as args to `fix_strains` and fix some bugs...The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function. Frederick Muriuki Muriithi
2022-05-27Move sql for CRUD operations on case-attrs from gn2 to gn3BonfaceKilz
2022-05-27Move sql for modifying case-attributes from gn2 to gn3BonfaceKilz
2022-05-27sql: caseattributes_audit.sql: New file...Create new table that stores edits related to case-attributes. BonfaceKilz