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2021-08-20Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_generation
2021-08-20Fix typing issue(s) caught by mypyMuriithi Frederick Muriuki
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
2021-08-20Retrieve the strains with valid valuesMuriithi Frederick Muriuki
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.
2021-08-20Add tests for ordering and implement functionMuriithi Frederick Muriuki
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.
2021-08-20Minor correlation fixes (#36)Alexander Kabui
* fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formatting
2021-08-18Test the clusteringMuriithi Frederick Muriuki
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.
2021-08-18Fix obvious linting errorsMuriithi Frederick Muriuki
* Fix linting errors that do not change the function of the code.
2021-08-18Make child sequence a listMuriithi Frederick Muriuki
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.
2021-08-18Provide top-level `riset` key-value pairMuriithi Frederick Muriuki
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.
2021-08-18Add tests and fix errors caught with testsMuriithi Frederick Muriuki
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
2021-08-18Fix errors: add in missing parenthesisMuriithi Frederick Muriuki
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.
2021-08-18Initialise heatmap generation moduleMuriithi Frederick Muriuki
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.
2021-08-17Test the clusteringMuriithi Frederick Muriuki
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.
2021-08-17Fix obvious linting errorsMuriithi Frederick Muriuki
* Fix linting errors that do not change the function of the code.
2021-08-17Make child sequence a listMuriithi Frederick Muriuki
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.
2021-08-17Provide top-level `riset` key-value pairMuriithi Frederick Muriuki
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.
2021-08-17Add tests and fix errors caught with testsMuriithi Frederick Muriuki
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
2021-08-17Fix errors: add in missing parenthesisMuriithi Frederick Muriuki
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.
2021-08-16Merge branch 'main' into heatmap_generationMuriithi Frederick Muriuki
2021-08-16Merge pull request #32 from genenetwork/heatmap_decompose_db_retrievalBonfaceKilz
Heatmap decompose db retrieval
2021-08-12Initialise heatmap generation moduleMuriithi Frederick Muriuki
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.
2021-08-12Fix linting errorsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix some errors caught by the linter.
2021-08-12Import missing definitionsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Import some missing definitions.
2021-08-11use normal function for correlation (#34)Alexander Kabui
* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functions
2021-08-09Build up the heatmap dataMuriithi Frederick Muriuki
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.
2021-08-09Set up the trait dataset type correctlyMuriithi Frederick Muriuki
* 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.
2021-08-09Retrieve the trait dataMuriithi Frederick Muriuki
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.
2021-08-09Add missing arguments. Fix typo.Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix minor bugs in the code.
2021-08-09Fix linting errorsMuriithi Frederick Muriuki
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
2021-08-08Update testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix tests to take current changes into consideration.
2021-08-08Only load extra data if the traits have basic infoMuriithi Frederick Muriuki
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.
2021-08-08Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-07Add gunicorn support for productionPjotr Prins
2021-08-07Update info on running guix containerPjotr Prins
2021-08-05db: traits: Return unique values when fetching sample dataBonfaceKilz
2021-08-05Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-05Reorganise the database codeMuriithi Frederick Muriuki
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
2021-08-05Build up trait_name items from full nameMuriithi Frederick Muriuki
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.
2021-08-04Fix issues caught by pylintMuriithi Frederick Muriuki
* 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
2021-08-04Retrieve the RISet and RISet ID valuesMuriithi Frederick Muriuki
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.
2021-08-04Add tests for post-processing functionsMuriithi Frederick Muriuki
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
2021-08-04sql: Add documentation extracted from within the database.Arun Isaac
It turns out there is documentation of the database within the database itself. I have dumped that it into an org file. * sql/schema-from-in-db-documentation.org: New file.
2021-08-04Update testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the tests to deal with changes in the code.
2021-08-04Avoid string interpolation: use prepared statementMuriithi Frederick Muriuki
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
2021-08-04Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-03guix.scm: Add csvdiff as a propagated inputBonfaceKilz
2021-08-02sql: Document the table Strain.Arun Isaac
* sql/schema.org (Strain): New section.
2021-07-31sql: Add schema description.Arun Isaac
* sql/schema.org: New file.
2021-07-30Rework db functions to enable postprocessingMuriithi Frederick Muriuki
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.
2021-07-30Remove extra spaceMuriithi Frederick Muriuki
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.
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