| Age | Commit message (Expand) | Author |
|---|
| 2022-07-22 | minor fixes for parsing data | Alexander_Kabui |
| 2022-07-22 | code to parse tissue correlation input | Alexander_Kabui |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui |
| 2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui |
| 2022-07-22 | minor fixes | Alexander_Kabui |
| 2022-07-11 | Allow 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 |
| 2022-06-29 | use explicit parameters | Alexander_Kabui |
| 2022-06-29 | fix issues | Alexander_Kabui |
| 2022-06-29 | pylint fixes | Alexander |
| 2022-06-29 | minor fixes | Alexander |
| 2022-06-29 | handle tmp files generation | Alexander |
| 2022-06-29 | parse output data | Alexander |
| 2022-06-29 | pep8 formatting | Alexander |
| 2022-06-29 | new variable: CORRELATION_COMMAND | Alexander |
| 2022-06-29 | init rust correlation module | Alexander |
| 2022-06-28 | Parse 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 |
| 2022-06-21 | gn3: fs_helpers: Fix pylint errors...* gn3/fs_helpers.py: Remove unused "pathlib" import.
(cache_ipfs_file): Disable "unused-argument" warting.
| BonfaceKilz |
| 2022-06-21 | gn3: fs_helpers: Remove ipfshttpclient...This library pollutes the Genenetwork2 profile with an old version
"dataclasses" thereby causing it to fail.
| BonfaceKilz |
| 2022-06-21 | Replace lint code with human-readable text...* gn3/db/correlations.py (__fetch_data__): Use a more readable code as
opposed to an error code.
| BonfaceKilz |
| 2022-06-21 | db: correlations: Ignore pylint error...* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913]
error.
| BonfaceKilz |
| 2022-06-21 | db: 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 |
| 2022-06-21 | db: 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 |
| 2022-06-20 | gn3: genodb: Retire get function....* gn3/genodb.py (get): Delete function.
(matrix): Use db.txn.get instead of get.
| Arun Isaac |
| 2022-06-20 | gn3: genodb: Match class and function names of GenotypeMatrix....* gn3/genodb.py (GenotypeMatrix): Match class and function names.
| Arun Isaac |
| 2022-06-20 | gn3: 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 |
| 2022-06-20 | gn3: genodb: Mention reading entire matrix in module docstring....* gn3/genodb.py: Mention reading entire matrix in module docstring.
| Arun Isaac |
| 2022-06-20 | Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
| Frederick Muriuki Muriithi |
| 2022-06-17 | gn3: genodb: Rename Matrix named tuple to GenotypeMatrix....* gn3/genodb.py (Matrix): Rename to GenotypeMatrix.
(matrix): Update invocation of Matrix.
| Arun Isaac |
| 2022-06-17 | gn3: genodb: Allow retrieval of the entire genotype matrix....* gn3/genodb.py: Document nparray in the module docstring.
(nparray): New function.
| Arun Isaac |
| 2022-06-17 | gn3: 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 |
| 2022-06-09 | gn3: genodb: Remove blank line in module docstring....* gn3/genodb.py: Remove blank line in module docstring.
| Arun Isaac |
| 2022-06-09 | gn3: 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 |
| 2022-06-08 | gn3: 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 |
| 2022-06-08 | gn3: 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 |
| 2022-06-08 | gn3: genodb: Open genotype database in read-only mode....* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in
read-only mode.
| Arun Isaac |
| 2022-06-08 | gn3: 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 |
| 2022-06-08 | gn3: 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 |
| 2022-06-08 | gn3: 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 |
| 2022-06-03 | gn3: Add genodb....genodb is a tiny library to read our new genotype database file format.
* gn3/genodb.py: New file.
| Arun Isaac |
| 2022-05-31 | Remove unnecessary statement | Frederick Muriuki Muriithi |
| 2022-05-31 | Extract 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 |
| 2022-05-30 | Pass 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 |
| 2022-05-27 | Move sql for CRUD operations on case-attrs from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Move sql for modifying case-attributes from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Return all the results from CaseAttributes column as is...* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import.
(get_case_attributes): Return the results of "fetchall" from the case
attributes.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing
test.
| BonfaceKilz |
| 2022-05-26 | Add Endpoint to get menu items for use in UI | Frederick Muriuki Muriithi |
| 2022-05-24 | Run partial correlations with external script...Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits
| Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Fix linting errors | Frederick Muriuki Muriithi |
