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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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* guix.scm: Import (gnu packages rdf).
(genenetwork3)[propagated-inputs]: Add python-sparqlwrapper.
* gn3/settings.py (SPARQL_ENDPOINT): New variable.
* gn3/api/general.py: Import datasets from gn3.db.
(dataset_metadata): New API endpoint.
* gn3/db/datasets.py: Import re, Template from string, Dict and Optional from
typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from
gn3.settings.
(sparql_query, dataset_metadata): New functions.
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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
* Provide the entry-point function to the partial correlation feature. This is
the function that ochestrates the fetching of the data, and processing it
for output by the API endpoint (to be implemented).
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Process the db_name and db_type values.
* Return data correctly
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the complete filename when found, or the boolean value False, when it
is not found.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the values from the database, not the tuples.
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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
* Pass parameters to the query the way the MySQL driver expects.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate the `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies`
in GeneNetwork1 to `gn3.db.species.species_name` in GeneNetwork3 to enable
the retrieval of the species name, given the group name (formerly RISet).
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In excel, "\n\n" is replaced with ",,,," during upload.
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In excel, "\n\n" is replaced with ",,,," during upload.
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* Fix linting errors like:
- Unused variables
- Undeclared variable errors (mostly caused by typos, and wrong names)
- Missing documentation strings for functions
etc.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate the
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal`
function in GN1.
* Remove function obsoleted by newer implementation of the code
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document functions for posterity.
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate the
`web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function from
GN1 to GN3.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* To make the code more composable down the line, make the database connection
argument the first argument for functions that access the database, since
they will always require the connection.
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Partial correlations
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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.
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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
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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.
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* gn3/settings.py (SQLALCHEMY_TRACK_MODIFICATIONS): Delete variable.
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs.
* setup.py: Remove sqlalchemy-stubs from install_requires.
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* gn3/computations/partial_correlations.py: Remove rounding. Fix computation
of remaining covariates
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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.
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partial-correlations
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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.
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* gn3/authentication.py (get_groups_by_user_uid): Rename local symbol uuid to
group_uuid.
(get_user_info_by_key): Rename local symbol uuid to user_uuid.
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* gn3/authentication.py (get_user_info_by_key): Reformat so that condition is
on a single line.
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Default arguments get evaluated only once when the function is defined, and
are then shared across all instances of the function. If the argument is then
mutated, this can cause hard to find bugs. See
https://docs.python.org/3/tutorial/controlflow.html#default-argument-values
* gn3/authentication.py (create_group): Do not use [] as the default argument.
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partial-correlations
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The Pearson correlation coefficient always has a value between -1 and 1. So,
this check is redundant.
* gn3/heatmaps.py (cluster_traits.__compute_corr): Remove redundant check on
the Pearson correlation coefficient.
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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.
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* gn3/computations/correlations2.py: Remove import of reduce from functools.
(__items_with_values): Reimplement using list comprehension.
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partial-correlations
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