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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add the `check_for_literature_info` and
`check_symbol_for_tissue_correlation` functions to check for the presence of
specific data.
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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/db/correlations.py: Remove the
`compare_tissue_correlation_absolute_values` function which is no longer
needed.
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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: Remove comments after updating
usage of the function at call point
* gn3/db/correlations.py: Complete the implementation of the
`build_temporary_tissue_correlations_table` function
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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
* 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
* 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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* 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
* 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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