| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-05-16 | Enable running the worker in "one-shot" mode...Enable the running of the worker script in one-shot mode.
| 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 |
| 2022-05-05 | Link to continuous deployment in README....* README.md: Link to continuous deployment.
| Arun Isaac |
| 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 |
| 2022-04-12 | Test that a carriage return is removed when generating csv...* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data".
(test_get_trait_csv_sample_data): New test function.
| 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 | guix.scm: Remove unused modules....Remove unused modules from the `use-modules` arguments.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| 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 |
| 2022-03-24 | Test Fixture: Create new test database and get connection to it...Implement a fixture that:
* Creates a new test database
* Copies over table structure from existing database
* Gets connection to new test database and returns it
* Cleans up after itself when the tests have run
| Frederick Muriuki Muriithi |
| 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 | Merge pull request #29 from zsloan/feature/add_rqtl_pairscan...Feature/add rqtl pairscan | zsloan |
| 2022-03-22 | Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenet... | zsloan |
| 2022-03-22 | Change order of if statements for running genoprob command...Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)
Also added a couple more verbose prints
| zsloan |
| 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 |
| 2022-03-22 | Create pairscan_for_figure and pairscan_for_table functions that return the D... | zsloan |
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2022-03-22 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ... | zsloan |
| 2022-03-22 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i... | zsloan |
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo...(pairscan) is used
- For pairscan default to using step 20 (subject to change, but some
step is required during calc.genoprob to make it run fast enough)
- Added some new verbose prints
| zsloan |
