| Age | Commit message (Expand) | Author |
|---|
| 2021-07-31 | sql: Add schema description....* sql/schema.org: New file.
| Arun Isaac |
| 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 | Remove extra space...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Remove extra space that was causing test to fail.
| 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 |
| 2021-07-30 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decom......Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
Fix merge conflicts in:
* gn3/db/traits.py
* tests/unit/db/test_traits.py
| Muriithi Frederick Muriuki |
| 2021-07-29 | Merge pull request #30 from genenetwork/Feature/Update-db-from-csv-data...Feature/update db from csv data | BonfaceKilz |
| 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 |
| 2021-07-29 | Retrieve 'ProbeSet' trait name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: new function (retrieve_probeset_trait_name)
* tests/unit/db/test_traits.py: test(s) for new function
Add a function to retrieve the name of a 'ProbeSet' trait in a manner
similar to genenetwork1's retrieval of the same, as implemented here
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154
Unlike in genenetwork1, we do not mutate an object, instead, we return the
values as retrieved from the database, and the caller will deal with the
returned values as appropriate.
| Muriithi Frederick Muriuki |
| 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 | db: traits: Remove publishdata column | BonfaceKilz |
| 2021-07-28 | 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 |
| 2021-07-28 | 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 |
| 2021-07-28 | Retrieve 'ProbeSet' trait name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/traits.py: new function (retrieve_probeset_trait_name)
* tests/unit/db/test_traits.py: test(s) for new function
Add a function to retrieve the name of a 'ProbeSet' trait in a manner
similar to genenetwork1's retrieval of the same, as implemented here
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154
Unlike in genenetwork1, we do not mutate an object, instead, we return the
values as retrieved from the database, and the caller will deal with the
returned values as appropriate.
| Muriithi Frederick Muriuki |
| 2021-07-26 | tests: test_db: Add test case for "update_raw" | BonfaceKilz |
| 2021-07-26 | gn3: db: Create a raw update query...* gn3/db/__init__.py (update_raw): New function.
| BonfaceKilz |
| 2021-07-26 | db: traits: Fetch sample_data from a trait in csv form | BonfaceKilz |
| 2021-07-26 | Merge branch 'main' of github.com:genenetwork/genenetwork3 | Muriithi Frederick Muriuki |
| 2021-07-26 | Fix issues caught by pylint...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix a myriad of issues caught by pylint to ensure the code passes all tests.
| Muriithi Frederick Muriuki |
| 2021-07-26 | db: traits: Remove unused functions | BonfaceKilz |
| 2021-07-26 | Check if corr_coefficient is NaN, since apparently it's stored as NaN instead... | zsloan |
| 2021-07-23 | sql: metadata_audit: Make char-set encoding explicit(utf8mb4)...See:
https://www.eversql.com/mysql-utf8-vs-utf8mb4-whats-the-difference-between-utf8-and-utf8mb4/
| BonfaceKilz |
| 2021-07-23 | Add data examples for `slink`. Implement function....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Copy the function, mostly verbatim from
genenetwork1. See:
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138
* tests/unit/computations/test_slink.py: Add a test with some example data to
test that the implementation gives the same results as that in genenetwork1
| Muriithi Frederick Muriuki |
| 2021-07-23 | Add more test data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-07-23 | Iterate through all valid pairs...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Fix the iteration construct.
Given two lists of member coordinates, such as [0, 1] and [3, 5], the
initial code would iterate over the pairs [0, 3] and [1, 5].
This commit fixes the iteration constructs such that the new code iterates
over the pairs [0, 3], [0, 5], [1, 3] and [1, 5].
| Muriithi Frederick Muriuki |
| 2021-07-23 | Extract function to flatten list of lists...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Extract the `__flatten_list_of_lists` function
since it is used in more than one place.
| Muriithi Frederick Muriuki |
| 2021-07-23 | Fix issue caught in `nearest` while testing `slink`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* While running tests for slink, to try and understand what it is doing in
order to write the appropriate tests for it, an issue arose that pointed a
blindspot in the former understanding of now `nearest` should work.
This commit fixes the issue found in both the expected data, and the code.
| Muriithi Frederick Muriuki |
| 2021-07-23 | New function (`slink`): return [] on exception...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Add minimum code to pass new test
* tests/unit/computations/test_slink.py: new test
Add test to ensure that the new `slink` function return an empty list in
case and exception is raised.
Add the new `slink` function with minimum amount of code needed to pass the
test.
| Muriithi Frederick Muriuki |
| 2021-07-23 | Add dummy module documentation...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Add initial dummy module documentation in form of
a python docstring
Update the names of what would be private methods/function to start with a
double-underscore (__) so that they do not show up in the default python
documentation.
| Muriithi Frederick Muriuki |
| 2021-07-23 | Add docstring for `nearest' function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: add documentation for the `nearest` function in
the `gn3.computations.slink` module in the form of a (hopefully correct)
python docstring.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Get shortest distance from two lists/tuples of member coordinates...* gn3/computations/slink.py: add code to ensure new test passes
* tests/unit/computations/test_slink.py: new test
This one is a little weird: from
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L57-L63
It gets rid of the last coordinates in both the lists of the member
coordinates, and uses the remaining coordinates to find the shortest
members.
For example, given the following member coordinates:
- i=[0,1,2] and j=[5,7,9], it uses [0,1] and [5,7]
- i=[3,6,1] and j=[7,13], it uses [3,6] and [7]
to find the shortest distances.
I (fredmanglis) am not sure why it does it this way, since I'd have expected
it to use all the coordinates, however, since at this time we need to retain
bug-compatibility with the older code, I have done it as it is done in the
old code.
I also add a statement to raise an exception in the case where i and j are
not lists of integers, or integers
| Muriithi Frederick Muriuki |
| 2021-07-22 | Extract common `is_list_or_tuple' function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Extract the common function `is_list_or_tuple' making it accessible to later
parts of the code.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Test for shortest distance between members in a list and coordinate...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: add code to pass new test
* tests/unit/computations/test_slink.py: new test
Given a list of members in a group, and a coordinate for a member in the
same group, find the distance of the closest member from the given
coordinate in the group.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Merge branch 'main' of github.com:genenetwork/genenetwork3 | Muriithi Frederick Muriuki |
| 2021-07-22 | Check that given list and both coordinates, we get shortest distance...* gn3/computations/slink.py: Add code to compute the distance given the
coordinate of both members on the parent list/tuple
* tests/unit/computations/test_slink.py:
* Change the name of the tests to more closely correspond to the business
requirement the test is checking for
* Update the comments to indicate some more things that might need to be
done in the future
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that all distances are positive or zero...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: check that all distances between the 'somethings'
are all either zero or positive.
* tests/unit/computations/test_slink.py:
* Remove data with all distances positive or zero, since it would fail the
test
* Change the expected message to more closely correspond to the business
logic
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that distance from A to B is same as from B to A...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: check that the distance from child A to B is the
same as distance from child B to A. If not, throw an exception.
* tests/unit/computations/test_slink.py:
* Change the name of the test to more closely correspond to the business
logic being tested.
* Update the data in a separate test such that it does not error out due to
failing to fulfill the expectations of separate requirement.
- pass tests
- Rename test
- Fix errors: distances same both directions
| Muriithi Frederick Muriuki |
| 2021-07-22 | Move sql updates into dir | Pjotr Prins |
| 2021-07-22 | Check that child distance from itself is zero...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Check that a child's distance from itself is
zero. If not, throw an exception.
The children lists are a list of distances of "something" from other
"somethings". There is still some need to establish what those "somethings"
are, so that the test names can reflect the ideas that are actually being
tested for.
* tests/unit/computations/test_slink.py: Change the name of the test so that
it more closely corresponds to the business logic it is actually testing,
and not the mechanics of testing the idea.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check the child lengths are same as length of parent...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Check that the child lists/tuples are the same length as the parent
list/tuple. If any of the children is not the same length as the parent,
throw and exception.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Add docstring...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add docstring to the function, useful for generating automated developer
documentation.
We also surround the guard functions with some notification comments, to
mark possible future places where change might be done.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that list and its direct children are not empty...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to pass the test that the list/tuple passed to `nearest' and its
direct children lists/tuples are not empty.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Implement check for lists or tuples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Implement the code to pass the check that a list of lists is passed to the
`nearest' function.
| Muriithi Frederick Muriuki |
