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2022-07-28Update sample correlations code to use multiprocessingFrederick Muriuki Muriithi
* To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module.
2022-07-22mypy fixesAlexander_Kabui
2022-07-22pep8 fixesAlexander_Kabui
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22import rust_correlation when running gn3 as libAlexander_Kabui
2022-07-22compute num overlapAlexander_Kabui
2022-07-22fix for bug splitting list dataAlexander_Kabui
2022-07-22minor fixes for parsing dataAlexander_Kabui
2022-07-22code to parse tissue correlation inputAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22code to fetch correct sample corr dataAlexander_Kabui
2022-07-22delete dead_code;rename variablesAlexander_Kabui
2022-07-22minor fixesAlexander_Kabui
2022-07-11Allow CORS everywhere by defaultFrederick Muriuki Muriithi
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.
2022-06-29use explicit parametersAlexander_Kabui
2022-06-29fix issuesAlexander_Kabui
2022-06-29pylint fixesAlexander
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 rust correlation moduleAlexander
2022-06-28Parse the method from UI before passing it to external processFrederick Muriuki Muriithi
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
2022-06-21gn3: fs_helpers: Fix pylint errorsBonfaceKilz
* gn3/fs_helpers.py: Remove unused "pathlib" import. (cache_ipfs_file): Disable "unused-argument" warting.
2022-06-21gn3: fs_helpers: Remove ipfshttpclientBonfaceKilz
This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail.
2022-06-21Replace lint code with human-readable textBonfaceKilz
* gn3/db/correlations.py (__fetch_data__): Use a more readable code as opposed to an error code.
2022-06-21db: correlations: Ignore pylint errorBonfaceKilz
* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913] error.
2022-06-21db: correlations: Ignore typesBonfaceKilz
* 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.
2022-06-21db: datasets.py: Ignore results from sparql.queryAndConvertBonfaceKilz
ATM, it's very difficult to work the correct type that is returned. Ignore this for now and fix this later.
2022-06-20gn3: genodb: Retire get function.Arun Isaac
* gn3/genodb.py (get): Delete function. (matrix): Use db.txn.get instead of get.
2022-06-20gn3: genodb: Match class and function names of GenotypeMatrix.Arun Isaac
* gn3/genodb.py (GenotypeMatrix): Match class and function names.
2022-06-20gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix.Arun Isaac
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.
2022-06-20gn3: genodb: Mention reading entire matrix in module docstring.Arun Isaac
* gn3/genodb.py: Mention reading entire matrix in module docstring.
2022-06-20Restrict partial correlation method choicesFrederick Muriuki Muriithi
- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations
2022-06-17gn3: genodb: Rename Matrix named tuple to GenotypeMatrix.Arun Isaac
* gn3/genodb.py (Matrix): Rename to GenotypeMatrix. (matrix): Update invocation of Matrix.
2022-06-17gn3: genodb: Allow retrieval of the entire genotype matrix.Arun Isaac
* gn3/genodb.py: Document nparray in the module docstring. (nparray): New function.
2022-06-17gn3: genodb: Read optimized storage for the current matrix.Arun Isaac
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.
2022-06-09gn3: genodb: Remove blank line in module docstring.Arun Isaac
* gn3/genodb.py: Remove blank line in module docstring.
2022-06-09gn3: genodb: Rewrite without classes.Arun Isaac
We rewrite genodb using only functions. This makes for much more readable code. * gn3/genodb.py: Rewrite without classes.
2022-06-08gn3: genodb: Support reading columns.Arun Isaac
* gn3/genodb.py (Matrix.__init__): Retrieve column pointers from database. (row): Abstract out vector access code to ... (Matrix.__vector): ... here. (Matrix.column): New method.
2022-06-08gn3: genodb: Read only the most recent genotype matrix.Arun Isaac
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.
2022-06-08gn3: genodb: Open genotype database in read-only mode.Arun Isaac
* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in read-only mode.
2022-06-08gn3: genodb: Do not create genotype database if it does not exist.Arun Isaac
* gn3/genodb.py (GenotypeDatabase.__init__): Do not create genotype database if it does not exist.
2022-06-08gn3: genodb: Decide on little endianness.Arun Isaac
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.
2022-06-08gn3: genodb: Do not terminate database strings with null.Arun Isaac
* gn3/genodb.py (GenotypeDatabase.get_metadata, GenotypeDatabase.matrix): Do not terminate database strings with the null character.
2022-06-03gn3: Add genodb.Arun Isaac
genodb is a tiny library to read our new genotype database file format. * gn3/genodb.py: New file.
2022-05-31Remove unnecessary statementFrederick Muriuki Muriithi
2022-05-31Extract utility functions from `fetch_all_database_data`Frederick Muriuki Muriithi
Extract the utility functions to help with understanding the what the `fetch_all_database_data` function is doing. This helps with maintenance.
2022-05-30Pass trait data as args to `fix_strains` and fix some bugsFrederick Muriuki Muriithi
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.
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