| Age | Commit message (Expand) | Author |
|---|
| 2022-03-08 | Fix tests, and issues caught by tests...Fix some issues caught by tests due to changes introducing the hand-off of the
partial correlations computations to an external process
Fix some issues due to the changes that introduce context managers for
database connections
Update some tests to take the above two changes into consideration
| Frederick Muriuki Muriithi |
| 2022-02-24 | gn3: Explicitly specify UTF-8 to be the file encoding....When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.
* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
*
tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
| Arun Isaac |
| 2022-02-21 | Fix minor issues introduced while fixing linting errors | Frederick Muriuki Muriithi |
| 2022-02-21 | Fix a myriad of linter issues...* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
| Frederick Muriuki Muriithi |
| 2022-02-21 | Add test to ensure samples are read correctly from .geno files...* tests/unit/db/test_genotypes2.py: New file
| Frederick Muriuki Muriithi |
| 2022-02-21 | Test partial corrs API with mix of existing and non-existing control traits...Test that the partial correlations endpoint handles a mix of existing and
non-existing control traits gracefully and issues a warning to the user.
Summary of changes:
* gn3/computations/partial_correlations.py: Issue a warning for all
non-existing control traits
* gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables
instead of comma-separated list of tables
* tests/integration/conftest.py: Add `db_conn` fixture to provide a database
connection to the tests. This will probably be changed in the future to
connect to a temporary database for tests.
* tests/integration/test_partial_correlations.py: Add test to check for
correct behaviour with a mix of existing and non-existing control traits
| Frederick Muriuki Muriithi |
| 2022-02-19 | Test partial corrs endpoint with non-existing control traits...Test that if the endpoint is queried and not a single one of the control
traits exists in the database, then the endpoint will respond with a
404 (not-found) status code.
Summary of changes:
* gn3/computations/partial_correlations.py: Check whether any control trait is
found. If none is found, return "not-found" message.
* gn3/db/partial_correlations.py: Fix bug in Geno query.
* tests/integration/test_partial_correlations.py: Add test for non-existing
control traits. Rename function to make it clearer what it is testing
for. Remove obsoleted comments.
| Frederick Muriuki Muriithi |
| 2022-02-18 | Remove erroneous test based on wrong assumptions...Related to commit 75dcfe295af57b16428c586cc11dbaa827a5feba
This commit removes the related test that was checking for the wrong thing.
| Frederick Muriuki Muriithi |
| 2022-02-18 | Test partial correlations endpoint with non-existent primary traits...Test that the partial correlations endpoint responds with an appropriate
"not-found" message and the corresponding 404 status code in the case where a
request is made and the primary trait requested for does not exist in the
database.
Summary of the changes in each file:
* gn3/api/correlation.py: generalise the building of the response
* gn3/computations/partial_correlations.py: return with a "not-found" if the
primary trait does not exist in the database
* gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions
in the case that the primary trait did not exist
* pytest.ini: register a `slow` pytest marker
* tests/integration/test_partial_correlations.py: Add a new test to check for
an appropriate 404 response in case of a primary trait that does not exist
in the database.
| Frederick Muriuki Muriithi |
| 2022-02-17 | Test partial correlations endpoint with missing data in POST request...Add a test for the partial correlations endpoint, with:
- no data in the request
- missing items in the data
Fix the bugs caught by the test
| Frederick Muriuki Muriithi |
| 2022-02-17 | Create client fixture for integration tests...Create a client fixture to help with the integration tests
| Frederick Muriuki Muriithi |
| 2022-02-17 | Use pytest's "mark" feature to categorise tests...Use pytest's `mark` feature to explicitly categorise the tests and run them
per category
| Frederick Muriuki Muriithi |
| 2022-02-17 | Add property tests for `dictify_by_samples`...Add property tests using pytest and hypothesis to test that the expected
properties hold for the
`gn3.computations.partial_correlations.dictify_by_samples`
function.
| Frederick Muriuki Muriithi |
| 2022-02-09 | Remove obsolete `PublishFreeze` table | Frederick Muriuki Muriithi |
| 2022-01-05 | test_traits.py: Update failing test | BonfaceKilz |
| 2021-12-14 | linting: Fix obvious linting issues | Frederick Muriuki Muriithi |
| 2021-12-14 | Provide expected values to use for tests | Frederick Muriuki Muriithi |
| 2021-12-10 | refactor sample r unittests | Alexander Kabui |
| 2021-12-10 | refactor unittest for normalizing sample values | Alexander Kabui |
| 2021-11-29 | Update test for data changes...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-23 | Fix a myriad of linting errors...* Fix linting errors like:
- Unused variables
- Undeclared variable errors (mostly caused by typos, and wrong names)
- Missing documentation strings for functions
etc.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Add test to query builders...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add some tests for the query builders to ensure that the queries are built
up correctly.
| Frederick Muriuki Muriithi |
| 2021-11-19 | Avoid rounding: compare floats approximately...Notes:
https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918
* As mentioned in the notes, rather than rounding to an arbitrary number of
decimal places, it is a much better practice to use approximate comparisons
of floats for the tests.
| Frederick Muriuki Muriithi |
| 2021-11-19 | Replace use of assert_allclose. Disable linter error...Notes:
https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918
* From the notes above, the assert_allclose is a better function for figuring
out what failed, unlike the allclose that simply just returns a True/False
value.
This commit restores the use of the assert_allclose function, and then
disables the linter error due to the fact that there is no use of the `self`
keyword.
| Frederick Muriuki Muriithi |
| 2021-11-18 | Fix some linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Fix some obvious linting errors and remove obsolete code
| Frederick Muriuki Muriithi |
| 2021-11-18 | Replace code migrated from R with pingouin functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Replace the code that was in the process of being migrated from R in
GeneNetwork1 with calls to pingouin functions that achieve the same thing.
Since the functions in this case are computing correlations and partial
correlations, rather than having home-rolled functions to do that, this
commit makes use of the tried and tested pingouin functions.
This avoids complicating our code with edge-case checks, and leverages the
performance optimisations done in pingouin.
| Frederick Muriuki Muriithi |
| 2021-11-15 | Fix bugs in recursive partial correlations...* gn3/computations/partial_correlations.py: Remove rounding. Fix computation
of remaining covariates
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt:
reduce the number of covariates to between one (1) and three (3)
* tests/unit/computations/test_partial_correlations.py: fix some minor bugs
It turns out that the computation complexity increases exponentially, with
the number of covariates. Therefore, to get a somewhat sensible test time,
while retaining a large-ish number of tests, this commit reduces the number
of covariates to between 1 and 3.
| Frederick Muriuki Muriithi |
| 2021-11-15 | Fix the columns in built data frame...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* When the z value is a Sequence of sequences of values, each of the internal
sequences should form a column of its own, and not a row, as it was
originally set up to do.
| Frederick Muriuki Muriithi |
| 2021-11-12 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-11-12 | Pass in parser function for flexibility...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* To improve the usefulness of already existing code, provide the parser
function as an argument to the `parse_input_line` function.
This was found to be useful when writing code to compare the `pcor.test`
function in GN1 and the `pingouin.partial_corr` function.
The format of the data generated when getting results for the `pcor.test`
function shared a lot with that of the `pcor.rec` function, but it was
different in a few, places, and the differences were non-trivial, needing
different parsing processes.
In such a case, it was found necessary to just pass in the function to do
the actual parsing, rather than create code with the same form as the
existing one, save for the function being called.
| Frederick Muriuki Muriithi |
| 2021-11-11 | Reimplement correlations2.compute_correlation using pearsonr....correlations2.compute_correlation computes the Pearson correlation
coefficient. Outsource this computation to scipy.stats.pearsonr. When the
inputs are constant, the Pearson correlation coefficient does not exist and is
represented by NaN. Update the tests to reflect this.
* gn3/computations/correlations2.py: Remove import of sqrt from math.
(compute_correlation): Reimplement using scipy.stats.pearsonr.
* tests/unit/computations/test_correlation.py: Import math.
(TestCorrelation.test_compute_correlation): When inputs are constant, set
expected correlation coefficient to NaN.
| Arun Isaac |
| 2021-11-11 | Compare floats approximately....Floating point numbers should only be compared approximately. Different
implementations of functions might produce slightly different results.
* tests/unit/computations/test_correlation.py: Import assert_almost_equal from
numpy.testing.
(TestCorrelation.test_compute_correlation): Compare floats using
assert_almost_equal instead of assertEqual.
* tests/unit/test_heatmaps.py: Import assert_allclose from numpy.testing.
(TestHeatmap.test_cluster_traits): Use assert_allclose instead of assertEqual.
| Arun Isaac |
| 2021-11-11 | pep8 formatting;update unittests | Alexander Kabui |
| 2021-11-09 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-11-09 | Implement remaining part of `partial_correlation_recursive` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: implement remaining portion of
`partial_correlation_recursive` function.
* tests/unit/computations/test_partial_correlations.py: add parsing for new
data format and update tests
| Frederick Muriuki Muriithi |
| 2021-11-09 | Update test data: have both vectors and matrices...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Delete the older test data that was only testing with `z` being a vector and
replace it with data that has `z` being a vector or matrix from data item to
data item.
| Frederick Muriuki Muriithi |
| 2021-11-09 | Add new data processing utility...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: New function (`partition_by`)
* tests/unit/test_data_helpers.py: Tests for new function
Add a function that approximates Clojure's `partition-by` function, to help
with processing the data in a more functional way.
| Frederick Muriuki Muriithi |
| 2021-11-04 | test_partial_correlations: skip failing tests...Fix these later. I need a passing test suite so as to update the gn2 docker
image.
| BonfaceKilz |
| 2021-11-04 | Create blackbox tests for some functions migrated from R...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new stub
functions (partial_correlation_matrix, partial_correlation_recursive)
*
tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv:
blackbox sample data and results for variance-covariance matrix method
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv:
blackbox sample data and results for recursive method
* tests/unit/computations/test_partial_correlations.py: Tests for new function
Provide some blackbox testing sample data for checking the operation of the
functions migrated from R.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Retrieve indices of the selected samples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New
function (good_dataset_samples_indexes).
* tests/unit/computations/test_partial_correlations.py: Tests for new
function (good_dataset_samples_indexes)
Get the indices of the selected samples. This is a partial migration of the
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
function in GN1.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Parse single line from CSV file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: New function (parse_csv_line)
* tests/unit/test_data_helpers.py: Add tests for new function (parse_csv_line)
Add a function to parse a single line from a CSV file.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Specify ten (10) decimal places...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: specify 10 decimal places
* tests/unit/computations/test_partial_correlations.py: update examples
Slight differences in python implementations, possibly hardware and
operating systems could cause the value of float (double) values to be
different in the less significant parts of the decimal places.
This commit limits the usable part of the decimals to the first 10 decimal
places for now.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Fix some linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-04 | Implement `tissue_correlation` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New function (tissue_correlation)
* tests/unit/test_partial_correlations.py ->
tests/unit/computations/test_partial_correlations.py: Move module. Implement
tests for new function
Migrate the `cal_tissue_corr` function embedded in the
`web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
GN1 and implement tests to ensure it works correctly.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Partially implement `partial_correlation_recursive`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Implement one path for the
`gn3.computations.partial_correlations.partial_correlation_recursive`
function.
* gn3/settings.py: Add a setting for how many decimal places to round to
* tests/unit/computations/test_partial_correlations.py: Update test to take
the number of decimal places into consideration
Implement a single path (where the z value is a vector and not a matrix) for
the `partial_correlation_recursive` function.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Implement `build_data_frame`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new function (`build_data_frame`)
* tests/unit/computations/test_partial_correlations.py: Add tests for new
function
Add a new function to build a pandas DataFrame object from the provided
values:
- x: a vector of floats (represented with a tuple of floats)
- y: a vector of floats (represented with a tuple of floats)
- z: a vector OR matrix of floats (represented with a tuple of floats or a
tuple of tuples of floats)
| Frederick Muriuki Muriithi |
| 2021-11-04 | Create blackbox tests for some functions migrated from R...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new stub
functions (partial_correlation_matrix, partial_correlation_recursive)
*
tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv:
blackbox sample data and results for variance-covariance matrix method
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv:
blackbox sample data and results for recursive method
* tests/unit/computations/test_partial_correlations.py: Tests for new function
Provide some blackbox testing sample data for checking the operation of the
functions migrated from R.
| Frederick Muriuki Muriithi |
| 2021-11-01 | Add test cases for gn3.authentication | BonfaceKilz |
| 2021-11-01 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-11-01 | Retrieve indices of the selected samples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New
function (good_dataset_samples_indexes).
* tests/unit/computations/test_partial_correlations.py: Tests for new
function (good_dataset_samples_indexes)
Get the indices of the selected samples. This is a partial migration of the
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
function in GN1.
| Frederick Muriuki Muriithi |
