Age | Commit message (Collapse) | Author |
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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
* gn3/computations/partial_correlations.py: new
function (`correlations_of_all_tissue_traits`).
* gn3/db/correlations.py: delete
function (`correlations_of_all_tissue_traits`).
Move the function to `gn3.computations.partial_correlations` module and
comment out the db-access code.
Rework it to receive, as arguments, the data it previously fetched from the
database, and add comments on future rework to get the function working
again.
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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
* 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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The function `batch_computed_tissue_correlation` is a pure computations
function with no expressions accessing the database, as far as I can tell,
therefore, this commit moves the function over to the
gn3.computations.partial_correlations module that holds the pure computation
functions.
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* Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Move the partial_correlations.py module to the gn3.computations module,
since it contains the computations for partial correlations.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Remove the if clauses to simplify the code flow: use a dictionary of queries
and select the appropriate query from the dictionary instead.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Stub out `batch_computed_tissue_correlation` function to be used in
implementing the function down the line.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `correlations_of_all_tissue_traits`
function by providing a call to a non-implemented function.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `fetch_gene_symbol_tissue_value_dict_for_trait` function which is
a migration of the
`web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait`
function in GeneNetwork1.
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* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes
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Partial correlations
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* compare_tissue_correlation_absolute_values: New function. Complete. Used for
sorting of tissue correlation values
* fetch_symbol_value_pair_dict: New function. Complete. Maps gene symbols to
tissue expression data
* fetch_gene_symbol_tissue_value_dict: New function. Complete. Wrapper for
`gn3.db.correlations.fetch_symbol_value_pair_dict` function
* fetch_tissue_probeset_xref_info: New function. Complete. Retrieves the
Probeset XRef information for tissues from the database.
* correlations_of_all_tissue_traits: Stub. Dependencies not completed yet.
* build_temporary_tissue_correlations_table: Stub. Dependencies not completed
yet.
* fetch_tissue_correlations: New function. Incomplete. This function calls (a)
stub(s) function(s) which is/are under development still.
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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_all)
* tests/unit/test_data_helpers.py: tests for function
`gn3.data_helpers.partition_all`
As part of migrating some functions that access the database, this commit
extracts generic processes that can be accomplished on data, and implements
the `partition_all` function, that is equivalent to Clojure's
`partition-all` function.
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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
* Migrate:
* `web.webqtl.correlation.CorrelationPage.getTempLiteratureTable`
* `web.webqtl.correlation.CorrelationPage.fetchLitCorrelations`
from GeneNetwork1.
The first function creates and populates a temporary table with the
literature correlations data.
The second function uses the data in the newly created temporary table to
link the trait with the correlation value.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `get_filename` for the correlations, to be used to determine
whether to do fast or normal correlations.
This is a migration of the
`web.webqtl.correlation.CorrelationPage.getFileName` function in GN1
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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
* Migrate the `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID`
function in GN1 to GN3.
This is a function that retrieves data from the database, and therefore uses
a system outside of our code, therefore, the function does not have a
corresponding unit test.
This kind of function will probably need to be tested at the integration or
system tests level, where we test that our code interacts correcly with any
and all external systems that it should.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement function `find_identical_traits`
* tests/unit/test_partial_correlations.py: implement tests for function
`find_identical_traits`
Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits`
function in GN1 to here, adding in tests to ensure the migration works in a
bug-compatible version with the original.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document the issues better to help with understanding what each test checks
for.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
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* Disable minor pylint issue.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
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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.
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
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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
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* gn3/app.py: setup CORS after all the configuration sources are loaded.
* gn3/settings.py: Parse CORS_ORIGINS from the environment variables.
Enable the CORS_ORIGINS configuration to be set in the environment variables
to give the application some flexibility when launching.
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