| Age | Commit message (Expand) | Author |
|---|
| 2021-11-04 | Move the function to computations module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The function `batch_computed_tissue_correlation` is a pure computations
function with no expressions accessing the database, as far as I can tell,
therefore, this commit moves the function over to the
gn3.computations.partial_correlations module that holds the pure computation
functions.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Remove if clauses: replace with dict...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Remove the if clauses to simplify the code flow: use a dictionary of queries
and select the appropriate query from the dictionary instead.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Stub out `batch_computed_tissue_correlation` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Stub out `batch_computed_tissue_correlation` function to be used in
implementing the function down the line.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Complete `correlations_of_all_tissue_traits`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `correlations_of_all_tissue_traits`
function by providing a call to a non-implemented function.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Implement `fetch_gene_symbol_tissue_value_dict_for_trait`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `fetch_gene_symbol_tissue_value_dict_for_trait` function which is
a migration of the
`web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait`
function in GeneNetwork1.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Start implementation of `fetch_tissue_correlations` and dependencies...* compare_tissue_correlation_absolute_values: New function. Complete. Used for
sorting of tissue correlation values
* fetch_symbol_value_pair_dict: New function. Complete. Maps gene symbols to
tissue expression data
* fetch_gene_symbol_tissue_value_dict: New function. Complete. Wrapper for
`gn3.db.correlations.fetch_symbol_value_pair_dict` function
* fetch_tissue_probeset_xref_info: New function. Complete. Retrieves the
Probeset XRef information for tissues from the database.
* correlations_of_all_tissue_traits: Stub. Dependencies not completed yet.
* build_temporary_tissue_correlations_table: Stub. Dependencies not completed
yet.
* fetch_tissue_correlations: New function. Incomplete. This function calls (a)
stub(s) function(s) which is/are under development still.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Implement `fetch_literature_correlations` and depedencies...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate:
* `web.webqtl.correlation.CorrelationPage.getTempLiteratureTable`
* `web.webqtl.correlation.CorrelationPage.fetchLitCorrelations`
from GeneNetwork1.
The first function creates and populates a temporary table with the
literature correlations data.
The second function uses the data in the newly created temporary table to
link the trait with the correlation value.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Implement `get_filename` for correlations...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `get_filename` for the correlations, to be used to determine
whether to do fast or normal correlations.
This is a migration of the
`web.webqtl.correlation.CorrelationPage.getFileName` function in GN1
| Frederick Muriuki Muriithi |
| 2021-10-21 | Implement `translate_to_mouse_gene_id` 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.translateToMouseGeneID`
function in GN1 to GN3.
This is a function that retrieves data from the database, and therefore uses
a system outside of our code, therefore, the function does not have a
corresponding unit test.
This kind of function will probably need to be tested at the integration or
system tests level, where we test that our code interacts correcly with any
and all external systems that it should.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `strain` to `sample`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the terminology used: use `sample` in place of `strain` according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-22 | Fix typing issues...* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix pylint errors...* Add missing function and module docstrings
* Remove unused imports
* Fix import order
* Rework some code sections to fix issues
* Disable some pylint errors.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix a number of linting issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Frederick Muriuki Muriithi |
| 2021-09-01 | Fix linting and typing issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-09-01 | Built top-level genotype file parsing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse data lines into markers...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse data lines in file to genetic markers.
* tests/unit/db/test_genotypes.py: test that parsing works.
Add some tests to check that the parsing of the markers works as expected,
and add the code to actually parse the markers.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Implement parsing of genotype labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype labels
* tests/unit/db/test_genotypes.py: test that genotype labels are parsed
correctly
As part of parsing the genotype files into usable python data structures,
this commit adds a function to parse the label lines (beginning with "@")
into the appropriate values.
| Muriithi Frederick Muriuki |
| 2021-08-31 | Fix linting errors, minor bugs and reorganise code...* Fix some linting errors and some minor bugs caught by the linter.
Move the `random_string` function to separate module for use in multiple
places in the code.
| Muriithi Frederick Muriuki |
| 2021-08-31 | Update `heatmap_data` function: remove extraneous data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: update function
* gn3/db/traits.py: new function
Remove extraneous data and arguments from the function.
- Load the genotype file
- Generate traits file
- Provide both raw traits data, and exported traits data in return
| Muriithi Frederick Muriuki |
| 2021-08-31 | Provide utilities for genotype files...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: New module
* gn3/settings.py: Add new configuration variable
* qtlfilesexport.py: Test out new code
Add a module containing functions dealing with the genotype files.
Add a configuration variable to point to the location of the genotype files.
| 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 | 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 |
| 2021-08-09 | 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 |
| 2021-08-05 | 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 | 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 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 | db: traits: Remove publishdata column | BonfaceKilz |
