| Age | Commit message (Expand) | Author |
|---|
| 2021-12-13 | Return the primary and control traits in addition to results...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.
| Frederick Muriuki Muriithi |
| 2021-12-13 | Run partial correlations against chosen database...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.
| Frederick Muriuki Muriithi |
| 2021-12-13 | Fix errors with query...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
| Frederick Muriuki Muriithi |
| 2021-12-10 | Fix parameters...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).
| Frederick Muriuki Muriithi |
| 2021-12-10 | format normalize function doc string | Alexander Kabui |
| 2021-12-10 | minor pr fixes | Alexander Kabui |
| 2021-12-10 | rename variables | Alexander Kabui |
| 2021-12-10 | try and catch for non matching sample keys | Alexander Kabui |
| 2021-12-10 | update function docs for normalizing strain values | Alexander Kabui |
| 2021-12-10 | fix bug:unpacking error when generator returns empty list | Alexander Kabui |
| 2021-12-09 | Prevent error on no result. Fix indexing...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
| Frederick Muriuki Muriithi |
| 2021-12-09 | Provide clearer error message...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
| Frederick Muriuki Muriithi |
| 2021-12-08 | Provide group from primary trait...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.
| Frederick Muriuki Muriithi |
| 2021-12-06 | Merge branch 'main' of github.com:genenetwork/genenetwork3 | Frederick Muriuki Muriithi |
| 2021-12-02 | Implement dataset metadata API endpoint....* 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.
| Arun Isaac |
| 2021-11-29 | Merge branch 'main' into partial-correlations | Muriithi Frederick Muriuki |
| 2021-11-29 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-29 | Provide entry-point function for the partial correlations...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).
| Frederick Muriuki Muriithi |
| 2021-11-29 | Fix bugs in data...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
| Frederick Muriuki Muriithi |
| 2021-11-29 | Update return type...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.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Return only values...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.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Update typing notations on functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-29 | Fix query parametrisation...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.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Retrieve the species name given the group...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).
| Frederick Muriuki Muriithi |
| 2021-11-29 | db: traits: Support additions and deletions from csv file | BonfaceKilz |
| 2021-11-29 | db: traits: Remove trailing ".0" in int values | BonfaceKilz |
| 2021-11-29 | db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload.
| BonfaceKilz |
| 2021-11-25 | db: traits: Support additions and deletions from csv file | BonfaceKilz |
| 2021-11-24 | db: traits: Remove trailing ".0" in int values | BonfaceKilz |
| 2021-11-23 | db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload.
| BonfaceKilz |
| 2021-11-23 | Fix a myriad of linting errors...* Fix linting errors like:
- Unused variables
- Undeclared variable errors (mostly caused by typos, and wrong names)
- Missing documentation strings for functions
etc.
| Frederick Muriuki Muriithi |
| 2021-11-23 | Migrate `getPartialCorrelationsNormal`...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
| Frederick Muriuki Muriithi |
| 2021-11-23 | Update documentation for functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document functions for posterity.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Add test to query builders...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.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Migrate `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function...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.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Make the DB connection argument the first...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.
| Frederick Muriuki Muriithi |
| 2021-11-20 | Merge pull request #56 from genenetwork/partial-correlations...Partial correlations | Muriithi Frederick Muriuki |
| 2021-11-19 | Avoid rounding: compare floats approximately...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.
| Frederick Muriuki Muriithi |
| 2021-11-18 | Fix some linting errors...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
| Frederick Muriuki Muriithi |
| 2021-11-18 | Replace code migrated from R with pingouin functions...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.
| Frederick Muriuki Muriithi |
| 2021-11-16 | Remove sqlalchemy....* 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.
| Arun Isaac |
| 2021-11-15 | Fix bugs in recursive partial correlations...* gn3/computations/partial_correlations.py: Remove rounding. Fix computation
of remaining covariates
*
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.
| Frederick Muriuki Muriithi |
| 2021-11-15 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-11-15 | Fix the columns in built data frame...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.
| Frederick Muriuki Muriithi |
| 2021-11-13 | Do not shadow global symbol uuid....* 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.
| Arun Isaac |
| 2021-11-13 | Reformat condition on a single line....* gn3/authentication.py (get_user_info_by_key): Reformat so that condition is
on a single line.
| Arun Isaac |
| 2021-11-13 | Do not use dangerous default argument []....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.
| Arun Isaac |
| 2021-11-12 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-11-11 | Remove redundant check on the Pearson correlation coefficient....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.
| Arun Isaac |
| 2021-11-11 | Reimplement correlations2.compute_correlation using pearsonr....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.
| Arun Isaac |
