| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-05-21 | Use multiprocessing to improve performance | Frederick Muriuki Muriithi |
| 2022-05-21 | Process primary, target and control traits in a single iteration...Rework the code to process the traits in a single iteration to improve
performance.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Return generator object rather than tuples...Return generator objects rather than pre-computed tuples to reduce the number
of iterations needed to process the data, and thus improve the performance of
the system somewhat.
| Frederick Muriuki Muriithi |
| 2022-05-16 | Run computation in one-shot asynchronous process...After reworking the worker/runner to have a one-shot mode, add a function that
queues up the task and then runs the worker in the one-shot mode to process
the computation in the background.
| Frederick Muriuki Muriithi |
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi |
| 2022-05-06 | Hook up pcorrs with target traits computations...Enable the endpoint to actually compute partial correlations with selected
target traits rather than against an entire dataset.
Fix some issues caused by recent refactor that broke pcorrs against a dataset
| Frederick Muriuki Muriithi |
| 2022-05-05 | Compute partial correlation with selected traits...Compute partial correlations against a selection of traits rather than against
an entire dataset.
| Frederick Muriuki Muriithi |
| 2022-05-05 | Extract common error checking. Rename function....* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
| Frederick Muriuki Muriithi |
| 2022-05-03 | Refactor: Remove unnecessary loop...Remove an unnecessary looping construct to help with speeding up the partial
correlations somewhat.
| Frederick Muriuki Muriithi |
| 2022-04-29 | Replace whole header with the longest one, instead of just the...non-CaseAttribute headers (before this caused issues if someone was
adding case attributes to a file that already contained some case
attributes)
| zsloan |
| 2022-04-29 | Get max string length instead when comparing headers...Apparently max(string1, string2) in Python gets the strong that is
highest alphabetically, but I'm pretty sure this line was intenteded
to get the header with the most items (which this commit doesn't fully
address; you could still end up with a situation where some case
attributes were removed while others were added, though that should be
rare)
| zsloan |
| 2022-04-12 | Delete "get_allowable_sampledata_headers"...* gn3/csvcmp.py (get_allowable_sampledata_headers): Delete it.
* tests/unit/test_csvcmp.py: Remove "get_allowable_sampledata_headers" import.
(test_get_allowable_csv_headers): Delete it.
| BonfaceKilz |
| 2022-04-12 | Strip any newline, tab or carriage-return chars from sample data...* gn3/db/sample_data.py (get_trait_csv_sample_data): Strip out "\n", "\t", or
"\r" from the sample data. See:
<https://issues.genenetwork.org/issues/csv-error-ITP_10001-longevity-data-set.html>
| BonfaceKilz |
| 2022-04-07 | Fix pylint errors | BonfaceKilz |
| 2022-04-07 | Fix mypy error | BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during updates...* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Add method for fetching the case_attributes...* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
| BonfaceKilz |
| 2022-04-07 | Run python black on file...* gn3/db/sample_data.py: Run "python black -l 79 ..."
| BonfaceKilz |
| 2022-04-07 | Add method for parsing a csv header from uploaded sample-data file...* gn3/csvcmp.py (parse_csv_column): New function.
* tests/unit/test_csvcmp.py: Test case for the above.
| BonfaceKilz |
| 2022-04-01 | Run python-black in file...* gn3/csvcmp.py: Run "black -l 79 ..."
* tests/unit/db/test_sample_data.py: Ditto.
* tests/unit/test_csvcmp.py: Ditto.
| BonfaceKilz |
| 2022-03-30 | Revert "Run json.loads on request.get_json, since request.get_json was just r......This reverts commit b93b22386056347d8002dd2e403425beeb4657cd.
The appropriate fix should have been in GN2. The original statement
args = request.get_json()
was correct, since `request.get_json()` should return a python object parsed
from the JSON string in the request. Unfortunately, GN2 was encoding the
request data two times, which led to the call returning a JSON-encoded string
instead of the expected object.
The issue has been fixed in GN2 and therefore, the "fix" here can be reverted.
| Frederick Muriuki Muriithi |
| 2022-03-29 | Remove unused module...* Remove a module that is no longer in use
| Frederick Muriuki Muriithi |
| 2022-03-28 | Run json.loads on request.get_json, since request.get_json was just returning... | zsloan |
| 2022-03-23 | Run python-black on file and fix other pylint issues....See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126>
* gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also,
manually fix other pylint issues.
| BonfaceKilz |
| 2022-03-22 | Fixes pylint errors | zsloan |
| 2022-03-22 | Fixed mypy typing errors | zsloan |
| 2022-03-22 | Tried to make the docstrings more consistent | zsloan |
| 2022-03-22 | Add typing to some functions | zsloan |
| 2022-03-22 | Add functions for getting proximal/distal markers for each pseudomarker posit... | zsloan |
| 2022-03-22 | Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s... | zsloan |
| 2022-03-22 | Added genofile name to inputs for processing R/qtl pair-scan results, since i... | zsloan |
| 2022-03-22 | Removed quotes from beginning and end of chromosome string | zsloan |
| 2022-03-22 | Fixed a cople function calls to use the updated function names | zsloan |
