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2022-01-22add endpoint for ctlAlexander Kabui
2022-01-22init file to call ctl scriptAlexander Kabui
2022-01-22generate lineplotAlexander Kabui
2022-01-22minor fix:read input data from json fileAlexander Kabui
2022-01-22export json dataAlexander Kabui
2022-01-22get significant interactionsAlexander Kabui
2022-01-22perform the ctl scanAlexander Kabui
2022-01-22fetch genotypes and phenotype filesAlexander Kabui
2022-01-22init script ctl analysisAlexander Kabui
2022-01-21README: Update link to CI badge.Arun Isaac
The CI has been moved to penguin2, and this is accompanied by a URI change. * README.md: Update link to CI badge.
2022-01-12Update return type. Remove duplicate import.Frederick Muriuki Muriithi
The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import.
2022-01-12Indent code correctlyFrederick Muriuki Muriithi
Indent the code correctly.
2022-01-12Deduplicate query to fetch data for 'Publish' traitsFrederick Muriuki Muriithi
The queries run in the `get_trait_csv_sample_data` and `retrieve_publish_trait_data` functions in the `gn3.db.traits` module were mostly similar. This commit changes that, by making the `get_trait_csv_sample_data` function make use of the results from calling the `retrieve_publish_trait_data` function.
2022-01-10Check for path existenceFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10Fix dataset retrieval query for `Geno` traitsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10Use the correct letter case for the keysFrederick Muriuki Muriithi
* Use the correct case for the keys inorder to retrieve the correct values.
2022-01-10Surround statement with parens for readabilityFrederick Muriuki Muriithi
2022-01-10Indicate that string is an f-stringFrederick Muriuki Muriithi
* The string had the f-string syntax to format the values to be inserted into the string, but was missing the 'f' before the opening quotes to signify to python that this was an f-string. This commit fixes that.
2022-01-10Convert keys to stringFrederick Muriuki Muriithi
* Some traits have a name composed of all numerals, which leads to the names being interpreted as numbers. This commit forces them to string to avoid subtle bugs where the code fails.
2022-01-10Remove all pairs with 'None' as the valueFrederick Muriuki Muriithi
* Remove all key-value pairs whose value is None.
2022-01-10Fix error in query: Replace '=' with 'IN'Frederick Muriuki Muriithi
2022-01-10Replace unoptimised function with optimised oneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace unoptimised function with one optimised to give better performance. The optimisation done here is to fetch multiple items/traits from the database per query, rather than the original form, which fetched a single item/trait from the database per query.
2022-01-10Silence `duplicate-code` linting notificationsFrederick Muriuki Muriithi
2022-01-10Convert NaN to NoneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Comment: https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159 * Convert NaN values to None to avoid possible bugs with the string replace method used before.
2022-01-10Add optimised entry for partial correlationsFrederick Muriuki Muriithi
Issue: * Function `gn3.computations.partial_correlations_optimised.partial_correlations_entry` is a copy of the `gn3.computations.partial_correlation.partial_correlations_entry` function that is optimised for better performance. The optimised function is intended to replace the unoptimised one, but it is included in this commit for comparison purposes, and to maintain some historical context for doing it this way.
2022-01-10Rework database functions to fetch multiple itemsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In an attempt to optimise the performance of the partial correlations feature, this commit reworks some database access functions to fetch multiple items from the database, per query, unlike their original forms which would fetch a single item per query. This reduces queries to the database, and should hopefully improve the responsiveness of the partial correlations feature.
2022-01-05Merge pull request #64 from jgarte/type-hint-normalize-valuesBonfaceKilz
Adds type hint for normalize_values function
2022-01-05Merge pull request #69 from ↵BonfaceKilz
genenetwork/fix/check-for-duplicates-before-deletions-or-insertions Fix/check for duplicates before deletions or insertions
2022-01-05Merge branch 'main' into fix/check-for-duplicates-before-deletions-or-insertionsBonfaceKilz
2022-01-05Fix pylint errorsBonfaceKilz
2022-01-05test_traits.py: Update failing testBonfaceKilz
2022-01-04traits.py: Don't use "value" to check if a record existsBonfaceKilz
The problem with using the "value" record is that it's a floating point number. See <https://www.bonfacemunyoki.com/post/2021-10-21-comparing-floating-point-numbers/> on why comparing floating point numbers can be an issue.
2022-01-04traits.py: Return early during an insert if the give record existsBonfaceKilz
Sometimes, a user will try to insert data twice, on in some instances, 2 different users will attempt the same inserts of the same records separately. In such cases, ignore the insert, and return early.
2022-01-04traits.py Delete a record only if it existsBonfaceKilz
In the case when the user tries to delete the same data twice, prior to this commit, an error was being generated. This commit remedies this by checking if a record exists prior to deleting it.
2022-01-01guix_deployPjotr Prins
2022-01-01guix_deployPjotr Prins
2021-12-24Fix typing errorsFrederick Muriuki Muriithi
2021-12-24Fix linting errorsFrederick Muriuki Muriithi
2021-12-24Fix sortingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Update the sorting algorithm, for literature and tissue correlations so that it sorts the results by the correlation value first then by the p-value next.
2021-12-24Return the correlation method usedFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the correlation method used
2021-12-24Replace `NaN` with `null` in JSON stringFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * `NaN` is not a valid JSON value, and leads to errors in the code. This commit replaces all `NaN` values with `null`.
2021-12-24Encode the data to JSON and set the status codeFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Encode bytes objects to string * Encode NaN values to "null" * gn3/api/correlation.py:
2021-12-24Reduce the total amount of data to be outputFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * There is a lot of data that is not necessary in the final result. This commit removes that data, retaining only data relevant for the display.
2021-12-24Add dataset type to the resultsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The dataset type is relevant for the display of the data, therefore, this commit presents the dataset type as part of the results.
2021-12-24Add API endpoint for partial correlationsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add an API endpoint for the partial correlation. * gn3/api/correlation.py:
2021-12-23db: Assist mypy with explicit type declaration.Arun Isaac
* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring type of return dictionary.
2021-12-23db: Fix sparql_query return type.Arun Isaac
* gn3/db/datasets.py: Import List from typing. (sparql_query): Set return type to List[Dict[str, Any]].
2021-12-23db: Fix wrong continued indentation.Arun Isaac
* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation.
2021-12-23pylintrc: Disable fixme check.Arun Isaac
fixme notes such as TODO, FIXME, etc. are good practice, and should not be discouraged. * .pylintrc (disable): Add fixme.
2021-12-22Refactor wgcna (#63)Alexander Kabui
* add r as a gn3 input * calculate powers from user input * fix merge conflict
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 22:46:27 +0000