| Age | Commit message (Expand) | Author |
|---|
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart |
| 2022-01-24 | README: Add pylint and mypy CI badges....We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
| Arun Isaac |
| 2022-01-22 | minor refactoring | Alexander Kabui |
| 2022-01-22 | function override:fix target specific output file for network | Alexander Kabui |
| 2022-01-22 | generate network | Alexander Kabui |
| 2022-01-22 | process ctl plot data img | Alexander Kabui |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui |
| 2022-01-22 | read stdout data;handle exceptions | Alexander Kabui |
| 2022-01-22 | generate required json data for ctl api | Alexander Kabui |
| 2022-01-22 | fixes for ctl script:generate ctl ctl_significant json | Alexander Kabui |
| 2022-01-22 | bugfixes for script;create pheno and geno objects | Alexander Kabui |
| 2022-01-22 | add endpoint for ctl | Alexander Kabui |
| 2022-01-22 | init file to call ctl script | Alexander Kabui |
| 2022-01-22 | generate lineplot | Alexander Kabui |
| 2022-01-22 | minor fix:read input data from json file | Alexander Kabui |
| 2022-01-22 | export json data | Alexander Kabui |
| 2022-01-22 | get significant interactions | Alexander Kabui |
| 2022-01-22 | perform the ctl scan | Alexander Kabui |
| 2022-01-22 | fetch genotypes and phenotype files | Alexander Kabui |
| 2022-01-22 | init script ctl analysis | Alexander Kabui |
| 2022-01-21 | README: Update link to CI badge....The CI has been moved to penguin2, and this is accompanied by a URI change.
* README.md: Update link to CI badge.
| Arun Isaac |
| 2022-01-12 | Update return type. Remove duplicate import....The function is a generator function, since it uses a `yield` statement, and
thus returns a generator object, that contains a tuple object. This fixes
that. We also remove a duplicate import.
| Frederick Muriuki Muriithi |
| 2022-01-12 | Indent code correctly...Indent the code correctly.
| Frederick Muriuki Muriithi |
| 2022-01-12 | Deduplicate query to fetch data for 'Publish' traits...The queries run in the `get_trait_csv_sample_data` and
`retrieve_publish_trait_data` functions in the `gn3.db.traits` module were
mostly similar. This commit changes that, by making the
`get_trait_csv_sample_data` function make use of the results from calling the
`retrieve_publish_trait_data` function.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Check for path existence...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-10 | Fix dataset retrieval query for `Geno` traits...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-10 | Use the correct letter case for the keys...* Use the correct case for the keys inorder to retrieve the correct values.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Surround statement with parens for readability | Frederick Muriuki Muriithi |
| 2022-01-10 | Indicate that string is an f-string...* The string had the f-string syntax to format the values to be inserted into
the string, but was missing the 'f' before the opening quotes to signify to
python that this was an f-string. This commit fixes that.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Convert keys to string...* Some traits have a name composed of all numerals, which leads to the names
being interpreted as numbers. This commit forces them to string to avoid
subtle bugs where the code fails.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Remove all pairs with 'None' as the value...* Remove all key-value pairs whose value is None.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Fix error in query: Replace '=' with 'IN' | Frederick Muriuki Muriithi |
| 2022-01-10 | Replace unoptimised function with optimised one...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Replace unoptimised function with one optimised to give better performance.
The optimisation done here is to fetch multiple items/traits from the
database per query, rather than the original form, which fetched a single
item/trait from the database per query.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Silence `duplicate-code` linting notifications | Frederick Muriuki Muriithi |
| 2022-01-10 | Convert NaN to None...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
Comment:
https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159
* Convert NaN values to None to avoid possible bugs with the string replace
method used before.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Add optimised entry for partial correlations...Issue:
* Function
`gn3.computations.partial_correlations_optimised.partial_correlations_entry`
is a copy of the
`gn3.computations.partial_correlation.partial_correlations_entry`
function that is optimised for better performance.
The optimised function is intended to replace the unoptimised one, but it is
included in this commit for comparison purposes, and to maintain some
historical context for doing it this way.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Rework database functions to fetch multiple items...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* In an attempt to optimise the performance of the partial correlations
feature, this commit reworks some database access functions to fetch
multiple items from the database, per query, unlike their original forms
which would fetch a single item per query.
This reduces queries to the database, and should hopefully improve the
responsiveness of the partial correlations feature.
| Frederick Muriuki Muriithi |
| 2022-01-05 | Merge pull request #64 from jgarte/type-hint-normalize-values...Adds type hint for normalize_values function | BonfaceKilz |
| 2022-01-05 | Merge pull request #69 from genenetwork/fix/check-for-duplicates-before-delet......Fix/check for duplicates before deletions or insertions | BonfaceKilz |
| 2022-01-05 | Merge branch 'main' into fix/check-for-duplicates-before-deletions-or-insertions | BonfaceKilz |
| 2022-01-05 | Fix pylint errors | BonfaceKilz |
| 2022-01-05 | test_traits.py: Update failing test | BonfaceKilz |
| 2022-01-04 | traits.py: Don't use "value" to check if a record exists...The problem with using the "value" record is that it's a floating point
number. See
<https://www.bonfacemunyoki.com/post/2021-10-21-comparing-floating-point-numbers/>
on why comparing floating point numbers can be an issue.
| BonfaceKilz |
| 2022-01-04 | traits.py: Return early during an insert if the give record exists...Sometimes, a user will try to insert data twice, on in some instances, 2
different users will attempt the same inserts of the same records separately.
In such cases, ignore the insert, and return early.
| BonfaceKilz |
| 2022-01-04 | traits.py Delete a record only if it exists...In the case when the user tries to delete the same data twice, prior to this
commit, an error was being generated. This commit remedies this by checking
if a record exists prior to deleting it.
| BonfaceKilz |
| 2022-01-01 | guix_deploy | Pjotr Prins |
| 2022-01-01 | guix_deploy | Pjotr Prins |
| 2021-12-24 | Fix typing errors | Frederick Muriuki Muriithi |
| 2021-12-24 | Fix linting errors | Frederick Muriuki Muriithi |
| 2021-12-24 | Fix sorting...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Update the sorting algorithm, for literature and tissue correlations so that
it sorts the results by the correlation value first then by the p-value
next.
| Frederick Muriuki Muriithi |
