| Age | Commit message (Expand) | Author |
|---|
| 2021-08-27 | Rework strains and trait values retrieval...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Rework the strains and values retrieval function to more closely correspond
to the working of the original code in GN1
| Muriithi Frederick Muriuki |
| 2021-08-20 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_gener... | Muriithi Frederick Muriuki |
| 2021-08-20 | Fix typing issue(s) caught by mypy...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Use `Sequence` type not `Iterator` type
| Muriithi Frederick Muriuki |
| 2021-08-20 | Retrieve the strains with valid values...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: add function to get strains with values
* tests/unit/computations/test_heatmap.py: new tests
Add function to get the strains whose values are not `None` from the
`trait_data` object passed in.
This migrates
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221
into a separate function that can handle that and be tested independently of
any other code.
| Muriithi Frederick Muriuki |
| 2021-08-20 | Add tests for ordering and implement function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: implement new ordering function
* tests/unit/computations/test_heatmap.py: add new tests
Implement the ordering function to migrate the setup of the `neworder`
variable from GN1 to GN3.
This migration is incomplete, since there is dependence on the return from
the `web.webqtl.heatmap.Heatmap.draw` function in form of the `d_1` variable
in some of the paths.
The thing is, this `d_1` variable, and the `xoffset` variable seem to be
used for laying out things on the drawn heatmap, and might actually end up
not being needed for the new system using plotly, which has other ways of
laying out things on the drawing.
For now though, this commit "shims" the presence of these values until when
the use of these variables is confirmed as present or absent in the new GN3
system.
| Muriithi Frederick Muriuki |
| 2021-08-20 | Minor correlation fixes (#36)...* fix key error for (*tissue_cor) tissue correlation
* update tests for tissue correlation
* rename speed_compute to fast_compute
* pep8 formatting | Alexander Kabui |
| 2021-08-18 | Test the clustering...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix clustering bugs
* tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues.
Test and fix the clustering function.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Fix obvious linting errors...* Fix linting errors that do not change the function of the code.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Make child sequence a list...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Since the `slink` function assigns values to the `listcopy` variable and its
children, this commit ensures that the sequence is a list to allow for the
assignment.
If the child-sequence is a tuple, that would lead to an exception.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Provide top-level `riset` key-value pair...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the expected, top-level `riset` key-value pair and eliminate the
redundant key-value pair.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Add tests and fix errors caught with tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: fix errors
* tests/unit/computations/test_heatmap.py: new tests
Add new tests with the expected source data format, and expected results.
Fix all errors that were caught by running the tests
| Muriithi Frederick Muriuki |
| 2021-08-18 | Fix errors: add in missing parenthesis...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Call the `cursor.fetchone()` function to get results. Without the
parenthesis, the code was trying to use the function itself as the results,
which was a bug, and would lead to failure.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Initialise heatmap generation module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to
test out plotly features on the command-line.
* guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Test the clustering...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix clustering bugs
* tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues.
Test and fix the clustering function.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Fix obvious linting errors...* Fix linting errors that do not change the function of the code.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Make child sequence a list...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Since the `slink` function assigns values to the `listcopy` variable and its
children, this commit ensures that the sequence is a list to allow for the
assignment.
If the child-sequence is a tuple, that would lead to an exception.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Provide top-level `riset` key-value pair...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the expected, top-level `riset` key-value pair and eliminate the
redundant key-value pair.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Add tests and fix errors caught with tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: fix errors
* tests/unit/computations/test_heatmap.py: new tests
Add new tests with the expected source data format, and expected results.
Fix all errors that were caught by running the tests
| Muriithi Frederick Muriuki |
| 2021-08-17 | Fix errors: add in missing parenthesis...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Call the `cursor.fetchone()` function to get results. Without the
parenthesis, the code was trying to use the function itself as the results,
which was a bug, and would lead to failure.
| Muriithi Frederick Muriuki |
| 2021-08-16 | Merge branch 'main' into heatmap_generation | Muriithi Frederick Muriuki |
| 2021-08-16 | Merge pull request #32 from genenetwork/heatmap_decompose_db_retrieval...Heatmap decompose db retrieval | BonfaceKilz |
| 2021-08-12 | Initialise heatmap generation module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to
test out plotly features on the command-line.
* guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix some errors caught by the linter.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Import missing definitions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Import some missing definitions.
| Muriithi Frederick Muriuki |
| 2021-08-11 | use normal function for correlation (#34)...* use normal function for correlation + rename functions
* update test for sample correlation
* use normal function for tissue correlation + rename functions | Alexander Kabui |
| 2021-08-09 | Build up the heatmap data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to compute and organise the data that will be used to draw the
final heatmap.
This varies significantly in how it works from the original, but it still
tries to retain the general flow of data.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Set up the trait dataset type correctly...* gn3/db/traits.py: setup `trait_dataset_type`
* tests/unit/db/test_traits.py: fix tests
The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's
dataset, and not the trait itself. This commit updates the code to take this
into consideration.
The dataset type is also set up from a trait's full name, therefore this
commit removes the `trait_type` argument from the `retrieve_trait_info`
function.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Retrieve the trait data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add functions to retrieve the `value`, `variance`, and `ndata` values for
any given trait.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Add missing arguments. Fix typo....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix minor bugs in the code.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add module, class and function docstrings
* Deactivate some irrelevant pylint errors
* Fix indentations and line-lengths
| Muriithi Frederick Muriuki |
| 2021-08-08 | Only load extra data if the traits have basic info...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Only load the extra trait data if the basic trait information is found.
| Muriithi Frederick Muriuki |
| 2021-08-08 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decom... | Muriithi Frederick Muriuki |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
| 2021-08-05 | db: traits: Return unique values when fetching sample data | BonfaceKilz |
| 2021-08-05 | Reorganise the database code...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Reorganise the code to separate the datasets from the traits, and to more
closely conform to the same flow as that in GN1
| Muriithi Frederick Muriuki |
| 2021-08-05 | Build up trait_name items from full name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The full name of the traits from search contains multiple parts to it, and
as such, we use it to retrieve the appropriate data and set it up in the
final trait_info dictionary that is produced.
| Muriithi Frederick Muriuki |
| 2021-08-04 | Fix issues caught by pylint...* gn3/computations/slink.py: remove unused imports
* gn3/db/traits.py: remove unnecessary `else` clauses
* tests/unit/db/test_traits.py: add docstrings for functions
| Muriithi Frederick Muriuki |
| 2021-08-04 | Retrieve the RISet and RISet ID values...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Retrieve the RISet and RISet ID values from the database.
| Muriithi Frederick Muriuki |
| 2021-08-04 | Add tests for post-processing functions...Issues:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add missing tests for some post-processing functions
| Muriithi Frederick Muriuki |
| 2021-08-04 | Avoid string interpolation: use prepared statement...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Following Arun's comment at
https://github.com/genenetwork/genenetwork3/pull/31#issuecomment-890915813
this commit eliminates string interpolation, and adds a map of tables for
the various types of traits dataset names
| Muriithi Frederick Muriuki |
| 2021-07-30 | Rework db functions to enable postprocessing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Rework the database functions to return a dict of key-value pairs, which
eases the postprocessing of the trait information.
The postprocessing is mainly to try an maintain data compatibility with the
code that is at the following locations:
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py
This was mainly a proof-of-concept, and the functions do not have testing
added for them: there is therefore need to add testing for the new
functions, and probably even rework them if they are found to be
complicated.
| Muriithi Frederick Muriuki |
| 2021-07-30 | Add module for common utilities...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/function_helpers.py: new file
Provides a new module to hold common programming utilities that are generic
enough that they will find use across the entire application.
The first utility function provided in this commit is the `compose`
function, whose purpose, as indicated by its name, is to take a number of
functions and compose them into a single function, which when called, will
return the same result that would have been got had the user called the
functions in a chain from right to left.
| Muriithi Frederick Muriuki |
| 2021-07-30 | Return dict from query functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: return dicts rather than tuples/list
* tests/unit/db/test_traits.py: Update tests
Return dicts with the key-value pairs set up so as to ease with the data
manipulation down the pipeline.
This is also useful to help with the retrieval of all other extra
information that was left out in the first iteration.
This commit also updates the tests by ensuring they expect dicts rather than
tuples.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Merge branch 'main' into Feature/Update-db-from-csv-data | BonfaceKilz |
| 2021-07-29 | Delete "update_raw" and it's test-cases | BonfaceKilz |
| 2021-07-29 | Add method for updating values from a sample dataset...* gn3/db/traits.py (update_sample_data): New function.
* tests/unit/db/test_traits.py: New test cases for ^^.
| BonfaceKilz |
| 2021-07-29 | Add partial type annotations for slink module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add some type annotations for the `nearest` function.
* Leave some comments regarding the issues experienced when trying to add some
typing annotations to the function to help with future endeavours of the
same.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Add type annotations to the function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add some type annotations to the functions to reduce the chances of bugs
creeping into the code.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Retrieve trait information...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: add functions to retrieve traits information
* tests/unit/db/test_traits.py: add tests for new function
Add functions to retrieve traits information as is done in genenetwork1
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
At this point, the data retrieval functions are probably incomplete, as
there is more of the `retrieveInfo` function in GN1 that has not been
considered as of this commit.
| Muriithi Frederick Muriuki |
| 2021-07-29 | Make name retrieval more general...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: make function more general
* tests/unit/db/test_traits.py: parametrize the tests
Make the name retrieval more general for the different types of traits by
changing the column specification and table as appropriate.
| Muriithi Frederick Muriuki |
