| Age | Commit message (Expand) | Author |
|---|
| 2022-03-12 | Append case attributes to csv data if they exist | BonfaceKilz |
| 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 |
| 2022-02-18 | 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 |
| 2022-02-17 | 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 |
| 2022-02-09 | Remove obsolete `PublishFreeze` table | Frederick Muriuki Muriithi |
| 2022-01-05 | test_traits.py: Update failing test | BonfaceKilz |
| 2021-12-14 | Provide expected values to use for tests | 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 |
| 2021-10-19 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-23 | Refactor: Move common sample data to separate file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Move common sample test data into a separate file where it can be imported
from, to prevent pylint error R0801 which proved tricky to silence in any
other way.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-15 | Add missing sample file for tests...* tests/unit/db/data/genotypes/genotype_sample1.geno: new file
Add a missing sample data file needed for unit tests.
| Frederick Muriuki Muriithi |
| 2021-09-01 | Fix linting and typing issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-09-01 | Built top-level genotype file parsing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse data lines into markers...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse data lines in file to genetic markers.
* tests/unit/db/test_genotypes.py: test that parsing works.
Add some tests to check that the parsing of the markers works as expected,
and add the code to actually parse the markers.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Implement parsing of genotype labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype labels
* tests/unit/db/test_genotypes.py: test that genotype labels are parsed
correctly
As part of parsing the genotype files into usable python data structures,
this commit adds a function to parse the label lines (beginning with "@")
into the appropriate values.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Set up the trait dataset type correctly...* gn3/db/traits.py: setup `trait_dataset_type`
* tests/unit/db/test_traits.py: fix tests
The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's
dataset, and not the trait itself. This commit updates the code to take this
into consideration.
The dataset type is also set up from a trait's full name, therefore this
commit removes the `trait_type` argument from the `retrieve_trait_info`
function.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add module, class and function docstrings
* Deactivate some irrelevant pylint errors
* Fix indentations and line-lengths
| Muriithi Frederick Muriuki |
| 2021-08-08 | Update tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix tests to take current changes into consideration.
| Muriithi Frederick Muriuki |
| 2021-08-05 | Reorganise the database code...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Reorganise the code to separate the datasets from the traits, and to more
closely conform to the same flow as that in GN1
| Muriithi Frederick Muriuki |
| 2021-08-05 | Build up trait_name items from full name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The full name of the traits from search contains multiple parts to it, and
as such, we use it to retrieve the appropriate data and set it up in the
final trait_info dictionary that is produced.
| Muriithi Frederick Muriuki |
| 2021-08-04 | Fix issues caught by pylint...* gn3/computations/slink.py: remove unused imports
* gn3/db/traits.py: remove unnecessary `else` clauses
* tests/unit/db/test_traits.py: add docstrings for functions
| Muriithi Frederick Muriuki |
| 2021-08-04 | Retrieve the RISet and RISet ID values...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Retrieve the RISet and RISet ID values from the database.
| Muriithi Frederick Muriuki |
| 2021-08-04 | Add tests for post-processing functions...Issues:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add missing tests for some post-processing functions
| Muriithi Frederick Muriuki |
| 2021-08-04 | Update tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the tests to deal with changes in the code.
| Muriithi Frederick Muriuki |
| 2021-07-30 | Remove extra space...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Remove extra space that was causing test to fail.
| Muriithi Frederick Muriuki |
| 2021-07-30 | Return dict from query functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: return dicts rather than tuples/list
* tests/unit/db/test_traits.py: Update tests
Return dicts with the key-value pairs set up so as to ease with the data
manipulation down the pipeline.
This is also useful to help with the retrieval of all other extra
information that was left out in the first iteration.
This commit also updates the tests by ensuring they expect dicts rather than
tuples.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Merge branch 'main' into Feature/Update-db-from-csv-data | BonfaceKilz |
| 2021-07-29 | Delete "update_raw" and it's test-cases | BonfaceKilz |
| 2021-07-29 | Add method for updating values from a sample dataset...* gn3/db/traits.py (update_sample_data): New function.
* tests/unit/db/test_traits.py: New test cases for ^^.
| BonfaceKilz |
| 2021-07-29 | Retrieve trait information...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: add functions to retrieve traits information
* tests/unit/db/test_traits.py: add tests for new function
Add functions to retrieve traits information as is done in genenetwork1
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
At this point, the data retrieval functions are probably incomplete, as
there is more of the `retrieveInfo` function in GN1 that has not been
considered as of this commit.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Make name retrieval more general...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: make function more general
* tests/unit/db/test_traits.py: parametrize the tests
Make the name retrieval more general for the different types of traits by
changing the column specification and table as appropriate.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Retrieve 'ProbeSet' trait name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: new function (retrieve_probeset_trait_name)
* tests/unit/db/test_traits.py: test(s) for new function
Add a function to retrieve the name of a 'ProbeSet' trait in a manner
similar to genenetwork1's retrieval of the same, as implemented here
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154
Unlike in genenetwork1, we do not mutate an object, instead, we return the
values as retrieved from the database, and the caller will deal with the
returned values as appropriate.
| Muriithi Frederick Muriuki |
| 2021-07-26 | tests: test_db: Add test case for "update_raw" | BonfaceKilz |
| 2021-07-10 | Fix pylint issues | BonfaceKilz |
| 2021-07-10 | db: test_db: Test that a fetch is correct when columns are specified | BonfaceKilz |
| 2021-06-07 | db: test_db: Add extra variable in test data for "id" | BonfaceKilz |
| 2021-06-07 | Rename json_data column to json_diff_data | BonfaceKilz |
| 2021-06-07 | tests: test_db: Add a test-case for fetchall | BonfaceKilz |
| 2021-06-07 | tests: test_db: Rename TestPhenotype | BonfaceKilz |
| 2021-06-07 | tests: test_phenotype: Rename to test_db | BonfaceKilz |
| 2021-06-03 | Use prepared statements for FETCH sql function | BonfaceKilz |
| 2021-06-03 | Use prepared statements for UPDATE sql function | BonfaceKilz |
