aboutsummaryrefslogtreecommitdiff
path: root/gn3/api
AgeCommit message (Expand)Author
2022-03-28Run json.loads on request.get_json, since request.get_json was just returning...zsloan
2022-03-22Fixes pylint errorszsloan
2022-03-22Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s...zsloan
2022-03-22Added genofile name to inputs for processing R/qtl pair-scan results, since i...zsloan
2022-03-22Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ...zsloan
2022-03-22Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i...zsloan
2022-03-11Fix some linting issuesFrederick Muriuki Muriithi
2022-03-08Fix tests, and issues caught by tests...Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration Frederick Muriuki Muriithi
2022-03-08Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure that those connections are closed once the call is completed. This hopefully avoids the 'too many connections' error Frederick Muriuki Muriithi
2022-03-04Automatically decode Redis stringsFrederick Muriuki Muriithi
2022-03-03Add endpoint for checking state of external processes...Long-running computations are handed off to external processes. This avoids timeouts in the webserver, and also reduces chances of instability of the webserver. The results of these long-running computations are needed eventually, so this commit provides a way to check for the state of the computation, and the results if any. Frederick Muriuki Muriithi
2022-03-03Run partial correlations in an external process...Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the *genenetwork3* path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run Frederick Muriuki Muriithi
2022-02-21Fix a myriad of linter issues...* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes Frederick Muriuki Muriithi
2022-02-18Test partial correlations endpoint with non-existent primary traits...Test that the partial correlations endpoint responds with an appropriate "not-found" message and the corresponding 404 status code in the case where a request is made and the primary trait requested for does not exist in the database. Summary of the changes in each file: * gn3/api/correlation.py: generalise the building of the response * gn3/computations/partial_correlations.py: return with a "not-found" if the primary trait does not exist in the database * gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions in the case that the primary trait did not exist * pytest.ini: register a `slow` pytest marker * tests/integration/test_partial_correlations.py: Add a new test to check for an appropriate 404 response in case of a primary trait that does not exist in the database. Frederick Muriuki Muriithi
2022-02-17Test partial correlations endpoint with missing data in POST request...Add a test for the partial correlations endpoint, with: - no data in the request - missing items in the data Fix the bugs caught by the test Frederick Muriuki Muriithi
2022-02-02response object error fixAlexander Kabui
2022-02-02pep8 formattingAlexander Kabui
2022-02-02return 401 on request failAlexander Kabui
2022-02-02pep8 formattingAlexander Kabui
2022-02-02new line fixAlexander Kabui
2022-01-22generate required json data for ctl apiAlexander Kabui
2022-01-22add endpoint for ctlAlexander Kabui
2022-01-10Convert NaN to None...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Comment: https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159 * Convert NaN values to None to avoid possible bugs with the string replace method used before. Frederick Muriuki Muriithi
2021-12-24Replace `NaN` with `null` in JSON string...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * `NaN` is not a valid JSON value, and leads to errors in the code. This commit replaces all `NaN` values with `null`. Frederick Muriuki Muriithi
2021-12-24Encode the data to JSON and set the status code...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Encode bytes objects to string * Encode NaN values to "null" * gn3/api/correlation.py: Frederick Muriuki Muriithi
2021-12-24Add API endpoint for partial correlations...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add an API endpoint for the partial correlation. * gn3/api/correlation.py: Frederick Muriuki Muriithi
2021-12-17Add API endpoint for partial correlations...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add an API endpoint for the partial correlation. Frederick Muriuki Muriithi
2021-12-02Implement dataset metadata API endpoint....* guix.scm: Import (gnu packages rdf). (genenetwork3)[propagated-inputs]: Add python-sparqlwrapper. * gn3/settings.py (SPARQL_ENDPOINT): New variable. * gn3/api/general.py: Import datasets from gn3.db. (dataset_metadata): New API endpoint. * gn3/db/datasets.py: Import re, Template from string, Dict and Optional from typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from gn3.settings. (sparql_query, dataset_metadata): New functions. Arun Isaac
2021-10-19Enable vertical and horizontal heatmaps...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. Frederick Muriuki Muriithi
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f...zsloan
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27Remove unnecessary variable....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 Frederick Muriuki Muriithi
2021-09-23minor fixes for endpointAlexander Kabui
2021-09-22Fix 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
2021-09-22Update check: Heatmaps need at least 2 items...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. Frederick Muriuki Muriithi
2021-09-22Return serialized plotly figure...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. Frederick Muriuki Muriithi
2021-09-22jsonify resultsAlexander Kabui
2021-09-20Enable Cross-Origin Resource Sharing...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. Frederick Muriuki Muriithi
2021-09-20Return only the data...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. Frederick Muriuki Muriithi
2021-09-17Return path to generated filename for now...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. Frederick Muriuki Muriithi
2021-09-16pass user input to call scriptAlexander Kabui
2021-09-16Intergrate the heatmap generation with the API...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. Frederick Muriuki Muriithi
2021-09-16add initial endpoint for wgcnaAlexander Kabui
2021-09-03Add covarstruct as a possible keyword for the rqtl_wrapper.R script (not inte...zsloan
2021-08-18Fix obvious linting errors...* Fix linting errors that do not change the function of the code. Muriithi Frederick Muriuki
2021-08-17Fix obvious linting errors...* Fix linting errors that do not change the function of the code. Muriithi Frederick Muriuki
2021-08-11use normal function for correlation (#34)...* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functionsAlexander Kabui
2021-08-07Add gunicorn support for productionPjotr Prins
2021-06-18Fixed pylint issueszsloan
2021-06-18Fixed issue where all bool kwargs were always being passed to generate_rqtl_c...zsloan
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 23:34:22 +0000