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2021-10-25Implement `fetch_literature_correlations` and depedenciesFrederick Muriuki Muriithi
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.
2021-10-25Implement `get_filename` for correlationsFrederick Muriuki Muriithi
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
2021-10-21Implement `translate_to_mouse_gene_id` functionFrederick Muriuki Muriithi
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.
2021-10-21Implement `find_identical_traits` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement function `find_identical_traits` * tests/unit/test_partial_correlations.py: implement tests for function `find_identical_traits` Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits` function in GN1 to here, adding in tests to ensure the migration works in a bug-compatible version with the original.
2021-10-19Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-10-19Implement remaining `fix_samples` functionalityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `fix_samples` function * tests/unit/test_partial_correlations.py: implement tests for `fix_samples` function Implement the remaining partial migration for the `web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
2021-10-19Fix some linting issuesFrederick Muriuki Muriithi
2021-10-19Allow CORS_ORIGINS to be configurable via the environmentFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * gn3/app.py: setup CORS after all the configuration sources are loaded. * gn3/settings.py: Parse CORS_ORIGINS from the environment variables. Enable the CORS_ORIGINS configuration to be set in the environment variables to give the application some flexibility when launching.
2021-10-19Enable vertical and horizontal heatmapsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the request endpoint, so that it produces a vertical or horizontal heatmap depending on the user's request.
2021-10-19Enable vertical orientation of heatmapsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the code to enable the generation of the heatmap in both the horizontal and vertical orientations.
2021-10-19Swap axis labelsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Switch the axis labels to make them less confusing for the user.
2021-10-19Add typing. Simplify arguments.Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Add type-hints to the functions * Merge the axis data and labels to simpler dict arguments to reduce number of parameters to the function.
2021-10-19Remove file I/O statementsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Remove file I/O from the function. If file I/O is needed, it will be provided outside of this function.
2021-10-19Implement `dictify_by_samples`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `dictify_by_samples` function * tests/unit/test_partial_correlations.py: implement tests for `dictify_by_samples` function Implement the `dictify_by_samples` function as a partial migration of the `web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
2021-10-18Implement `control_samples` function as is in GN1Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement `control_samples` function * tests/unit/test_partial_correlations.py: add tests for `control_samples` function Implement the function `control_samples` and make it mostly bug-compatible with the `web/webqtl/correlation/correlationFunction.controlStrain` function in GN1. This implementation in GN3 does not do any calls to the database. It will rely on other functions to provide the data from the database to it.
2021-10-18Move `export_informative` function to `gn3.db.traits` moduleFrederick Muriuki Muriithi
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.
2021-10-18Move 'export_trait_data' to 'gn3.db.traits' moduleFrederick Muriuki Muriithi
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.
2021-10-18Migrate `export_informative` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement a mostly, bug-compatible `export_informative` function as part of migrating the partial correlations feature over to GN3 from GN1 * tests/unit/test_partial_correlations.py: Implement tests to ensure the code work in a similar manner as that one in GN1.
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
bug/fix_rqtl_covariates
2021-09-28Provide loci names to heatmapFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the loci names to the heatmaps so that hovering over the heatmap cells displays the associated locus name.
2021-09-28Retrieve loci names ordered by chromosomesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps.py: implement function * tests/unit/test_heatmaps.py: add test Add a function to retrieve the loci names from the traits, ordered by chromosomes, in alphabetical order. This is useful to provide the user with more information on hovering over the heatmap cells: each cell will now display the locus name, trait name and value associated with it.
2021-09-28Approximate single-spectrum colour scale in GN1Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * To provide a somewhat similar experience to GeneNetwork1, this commit approximates the single-spectrum colour scale in GeneNetwork1 for the heatmaps in GeneNetwork3. Work to get the multiple-spectrum colour sc(ales/hemes) will be done in other commits, since that might require digging even deeper into Plotly's guts to figure out.
2021-09-27add file not found exceptionAlexander Kabui
2021-09-27return str error for exceptionAlexander Kabui
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27Remove unnecessary variable.Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix issue according to review https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714549781
2021-09-27Narrow the exception and add commentsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Only catch the `FileExistsError` allowing any other exception to pass through. This tries to conform a little to the review at https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714552696
2021-09-27Update terminology: `riset` to `group`Frederick Muriuki Muriithi
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
2021-09-27Update terminology: `strain` to `sample`Frederick Muriuki Muriithi
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
2021-09-23minor fixes for endpointAlexander Kabui
2021-09-23Return r error if returncode!=0Alexander Kabui
2021-09-23read generated files from r and return outputAlexander Kabui
2021-09-22Fix more pylint errorsFrederick Muriuki Muriithi
2021-09-22Fix typing issuesFrederick Muriuki Muriithi
* Ignore some errors * Update typing definitions for some portions of code * Add missing imports
2021-09-22Fix pylint errorsFrederick Muriuki Muriithi
* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors.
2021-09-22Update check: Heatmaps need at least 2 itemsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the check to look for at least 2 traits before trying to generate the heatmap.
2021-09-22Return serialized plotly figureFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Serialize the figure to JSON * gn3/heatmaps.py: Return the figure object Serialize the Plotly figure into JSON, and return that, so that it can be used on the client to display the image.
2021-09-22jsonify resultsAlexander Kabui
2021-09-20Enable Cross-Origin Resource SharingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Fix bugs in data parsing * gn3/app.py: enable CORS * gn3/settings.py: add flask-cors configurations * guix.scm: Add flask-cors dependency For easier testing of the heatmaps generation feature, this commit activates the cross-origin resource sharing for all "localhost" origins.
2021-09-20Return only the dataFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Parse incoming data to build up correct trait names and respond with only the computed heatmap data. * gn3/heatmaps.py: Return only the computed data for heatmaps and clustering. Since GN3 is supposed to handle only the data, and db-access, this commit ensures that GN3 responds to the client with only the computed heatmap data, and does not try to generate the heatmaps themselves. The generation of the heatmaps will be delegated to the UI clients, such as GeneNetwork2.
2021-09-17Fix a number of linting issuesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-09-17Return path to generated filename for nowFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * To help with demonstrating that the code is producing the expected output, for now, we return the path to the generated html file that displays the interactive heatmap. At this point, it is mostly useful in the development environment. Moving forward, we might have to actually stream the raw html, or if we can get the Kaleido library packaged for GNU Guix, stream the images binary data instead.
2021-09-17Fix some layout issues and update colorscaleFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the plot layouts and size to display the dendrogram and individual chromosome heatmaps side by side * Update the colour scale to begin with the grays rather than absolute black
2021-09-17Create dendrogram to show clustering treeFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the clustering data to be used for the creation of the clustering dendrogram in the final clustered heatmap plot.
2021-09-16Add WGCNA_SCRIT env to settingsAlexander Kabui
2021-09-16pass user input to call scriptAlexander Kabui
2021-09-16Intergrate the heatmap generation with the APIFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Intergrate the heatmap generation code on the /api/heatmaps/clustered endpoint. The endpoint should take a json query of the form: {"traits_names": [ ... ] } where the "traits_name" value is a list of the full names of traits. A sample query to the endpoint could be something like the following: curl -i -X POST "http://localhost:8080/api/heatmaps/clustered" \ -H "Accept: application/json" \ -H "Content-Type: application/json" \ -d '{ "traits_names": [ "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672", "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338", "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576", "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577", "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121", "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541", "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722", "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722", "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064", "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463" ] }' which should respond with a json response containing the raw binary string for the png format and possibly another for the svg format.
2021-09-16Fix minor bugsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a few minor bugs left over from the integration of code from the proof-of-concept code.
2021-09-16Add missing importsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add missing imports that are needed in the code.
2021-09-16run cmd and add exception handlerAlexander Kabui
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