Age | Commit message (Collapse) | Author |
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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.
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the correlation method used
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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`.
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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:
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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.
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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.
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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:
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* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring
type of return dictionary.
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* gn3/db/datasets.py: Import List from typing.
(sparql_query): Set return type to List[Dict[str, Any]].
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* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation.
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fixme notes such as TODO, FIXME, etc. are good practice, and should not be
discouraged.
* .pylintrc (disable): Add fixme.
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* add r as a gn3 input
* calculate powers from user input
* fix merge conflict
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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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.
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* Ignore some missing library stubs
* Ignore some typing errors
* Fix obvious typing errors
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* pingouin raises an exception whenever one attempts to use it to compute the
partial correlation with data that has less than 3 samples.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Use the target dataset to load the target traits, not the primary trait's
dataset, since they might differ.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* the mysqlclient is sometimes finicky with the format specifiers, especially
in the `WHERE ... IN ...` clauses where a sequence of values is
provided. This commit explicitly sets the format specifiers for such clauses
so as to avoid sporadic failures due to differences in the form of data from
one query to the next.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Import the missing function.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Fix the code, so that it removes all control values, whose corresponding
target values are None, without throwing an error.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* In addition to the partial correlation results, this commit enables the
return of the chosen primary trait and the selected control traits. This
data is required for presentation on the results page.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Run the partial correlations against the database that the user selects, and
not the one from which the primary trait is. This was a bug in the code.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Use the correct format string paradigm: put f before opening quote.
* Provide missing space just before 'FROM' clause
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People are not using the pull request template properly. Often, the fields
remain unfilled, and the placeholders are not deleted. This is cognitively
taxing for reviewers. Also, most of our changes are better described in the
commit log than in the pull request description. And, our reviews are quite
cursory and don't need a detailed pull request description for the reviewer to
act on.
* .github/PULL_REQUEST_TEMPLATE.md: Delete file.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Provide parameters as a dict of items (which works for MySQL), rather than
as keywork arguments (as works in PostgreSQL).
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* README.md: Link CI badge to CI status page.
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* README.md: Add CI badge.
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We base this off the genenetwork3 package defined in (gn packages
genenetwork). That way, we don't have to duplicate the package definition in
multiple places.
* guix.scm (genenetwork3): Inherit from genenetwork3 package definition in (gn
packages genenetwork).
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* If the dataset name is not found, don't cause an exception, instead, return
the provided search name.
* Use the correct inner object
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* To help with debugging error conditions, provide the original name to help
with figuring out why the error was raised
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* From the collections page, the group is not present, so this commit
retrieves the group value from the primary trait.
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