| Age | Commit message (Expand) | Author |
|---|
| 2022-02-08 | Merge iterations to remove unnecessary computations...Do all the work in a single iteration to avoid unnecessary iterations that
hamper performance.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Remove multiprocessing for stability...Web servers are long-running processes, and python is not very good at
cleaning up after itself especially in forked processes - this leads to memory
errors in the web-server after a while.
This commit removes the use of multiprocessing to avoid such failures.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Give sorting functions more descriptive names | Frederick Muriuki Muriithi |
| 2022-02-08 | Use multiprocessing to speed up computation...This commit refactors the code to make it possible to use multiprocessing to
speed up the computation of the partial correlations.
The major refactor is to move the `__compute_trait_info__` function to the
top-level of the module, and provide to it all the other necessary context via
the new args.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Remove unnecessary computation...In Python3 when slicing,
seq[:min(some_val, len(seq))] == seq[:some_val]
because Python3 will just return a copy of the entire sequence if `some_val`
happens to be larger/greater than the length of the sequence.
This commit removes the unnecessary call to `min()`
| Frederick Muriuki Muriithi |
| 2022-02-02 | refactor code for invoking ctl script | Alexander Kabui |
| 2022-02-02 | pep8 formatting | Alexander Kabui |
| 2022-02-02 | new line fix | Alexander Kabui |
| 2022-02-02 | fix comprehension list | Alexander Kabui |
| 2022-01-22 | process ctl plot data img | Alexander Kabui |
| 2022-01-22 | read stdout data;handle exceptions | Alexander Kabui |
| 2022-01-22 | init file to call ctl script | Alexander Kabui |
| 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 |
| 2022-01-10 | 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 | 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 | Remove all pairs with 'None' as the value...* Remove all key-value pairs whose value is None.
| 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 | 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 |
| 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 |
| 2021-12-24 | Return the correlation method used...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the correlation method used
| Frederick Muriuki Muriithi |
| 2021-12-24 | Reduce the total amount of data to be output...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* There is a lot of data that is not necessary in the final result. This
commit removes that data, retaining only data relevant for the display.
| Frederick Muriuki Muriithi |
| 2021-12-24 | Add dataset type to the results...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The dataset type is relevant for the display of the data, therefore, this
commit presents the dataset type as part of the results.
| Frederick Muriuki Muriithi |
| 2021-12-17 | Add "success" status to final computation results...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-12-14 | linting: Fix obvious linting issues | Frederick Muriuki Muriithi |
| 2021-12-14 | mypy: ignore some imports and errors...* Ignore some missing library stubs
* Ignore some typing errors
* Fix obvious typing errors
| Frederick Muriuki Muriithi |
| 2021-12-14 | Adds type hint for normalize_values function | jgart |
| 2021-12-14 | TO REVERT: Add logging to see data frame | Frederick Muriuki Muriithi |
| 2021-12-14 | Remove any items with less than 3 samples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* pingouin raises an exception whenever one attempts to use it to compute the
partial correlation with data that has less than 3 samples.
| Frederick Muriuki Muriithi |
| 2021-12-14 | Fix dataset: use target dataset not primary...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Use the target dataset to load the target traits, not the primary trait's
dataset, since they might differ.
| Frederick Muriuki Muriithi |
| 2021-12-13 | Provide missing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Import the missing function.
| Frederick Muriuki Muriithi |
| 2021-12-13 | Fix the removal of controls for corresponding Nones in targets...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Fix the code, so that it removes all control values, whose corresponding
target values are None, without throwing an error.
| Frederick Muriuki Muriithi |
| 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 |
| 2021-12-10 | 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 |
| 2021-12-08 | 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 |
| 2021-11-29 | 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 |
| 2021-11-23 | 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 |
