| Age | Commit message (Expand) | Author |
|---|
| 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 | refactor sample r unittests | Alexander Kabui |
| 2021-12-10 | refactor unittest for normalizing sample values | Alexander Kabui |
| 2021-12-10 | fix bug:unpacking error when generator returns empty list | Alexander Kabui |
| 2021-12-09 | README: Link CI badge to CI status page....* README.md: Link CI badge to CI status page.
| Arun Isaac |
| 2021-12-09 | README: Add CI badge....* README.md: Add CI badge.
| Arun Isaac |
| 2021-12-09 | guix.scm: Inherit from (gn packages genenetwork)....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).
| Arun Isaac |
| 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 |
| 2021-12-06 | Merge branch 'partial-correlations' | Frederick Muriuki Muriithi |
| 2021-12-02 | Add a Guix operating-system configuration....* guix-system.scm: New file.
| Arun Isaac |
| 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 | Update test for data changes...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 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 | Add SQL statement to update json_diff | 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 | Add SQL statement to update json_diff | 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 | Replace guix environment with guix shell....* README.md, guix.scm: Replace guix environment with guix shell.
| Arun Isaac |
| 2021-11-19 | Do not recommend GUIX_PACKAGE_PATH....* guix.scm: Do not recommend GUIX_PACKAGE_PATH.
| Arun Isaac |
| 2021-11-19 | Remove gemma specific instructions from guix.scm....* guix.scm: Remove gemma specific instructions.
| Arun Isaac |
| 2021-11-19 | Sort inputs in package definition....* guix.scm (genenetwork3)[propagated-inputs]: Sort.
| Arun Isaac |
| 2021-11-19 | Remove duplicated python-plotly dependency....* guix.scm (genenetwork3)[propagated-inputs]: Remove python-plotly.
| Arun Isaac |
| 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 |
| 2021-11-19 | Replace use of assert_allclose. Disable linter error...Notes:
https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918
* From the notes above, the assert_allclose is a better function for figuring
out what failed, unlike the allclose that simply just returns a True/False
value.
This commit restores the use of the assert_allclose function, and then
disables the linter error due to the fact that there is no use of the `self`
keyword.
| Frederick Muriuki Muriithi |
| 2021-11-19 | Use latest version of Pengouin...Notes:
https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918
* Pingouin 0.3.12 is buggy, as noted in the comment noted above. One of the
bugs is that the Spearman correlations might give the wrong results under
some circumstances.
This commit removes the pinned version so that the system gets the latest
version for testing.
| 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 |
