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2022-03-12Append case attributes to csv data if they existBonfaceKilz
2022-03-12db: Extend csv query to fetch case attributes...* gn3/db/traits.py (get_trait_csv_sample_data): Fetch case attribute data if it exists. BonfaceKilz
2022-03-12Revert "db: Fetch correct sample data"...This reverts commit 710769e84b3bc6a2bdd66effdbac0659272ed511. BonfaceKilz
2022-03-11Fix typing errorsFrederick Muriuki Muriithi
2022-02-21Fix minor issues introduced while fixing linting errorsFrederick 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
2022-02-21Test partial corrs API with mix of existing and non-existing control traits...Test that the partial correlations endpoint handles a mix of existing and non-existing control traits gracefully and issues a warning to the user. Summary of changes: * gn3/computations/partial_correlations.py: Issue a warning for all non-existing control traits * gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables instead of comma-separated list of tables * tests/integration/conftest.py: Add `db_conn` fixture to provide a database connection to the tests. This will probably be changed in the future to connect to a temporary database for tests. * tests/integration/test_partial_correlations.py: Add test to check for correct behaviour with a mix of existing and non-existing control traits Frederick Muriuki Muriithi
2022-02-19Test partial corrs endpoint with non-existing control traits...Test that if the endpoint is queried and not a single one of the control traits exists in the database, then the endpoint will respond with a 404 (not-found) status code. Summary of changes: * gn3/computations/partial_correlations.py: Check whether any control trait is found. If none is found, return "not-found" message. * gn3/db/partial_correlations.py: Fix bug in Geno query. * tests/integration/test_partial_correlations.py: Add test for non-existing control traits. Rename function to make it clearer what it is testing for. Remove obsoleted comments. Frederick Muriuki Muriithi
2022-02-18Remove code trying to query non-existent `TempFreeze` table...The code was migrated from GN1 with a faulty assumption that all trait types have a corresponding `*Freeze` table in the database. This assumption is not true for the `Temp` traits. This commit removes the buggy code. 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
2022-02-08db: traits: Enable deletion of individual sample values...If a user replaces an individual value with an "x", delete that date entry from the respective table. Deletion here is the only option since by default the Nstrain, PublishData and PublishSE don't accept null values. Note that deleting all 3 values is equivalent to removing the sample from the CSV file. * gn3/db/traits.py (update_sample_data): If a value is "x", delete it from the respective table. BonfaceKilz
2022-02-08db: traits: Allow insertions of "0" in resp. sample values tables...When editing values from "x" to "0"(or any other value) when editing data, an "update" statement was being run; thereby no new value was being inserted. To the end user, modifying an "x" value to something else meant that no value was being inserted. This commit fixes that by doing an insert whenever a change from "x" to "0" is performed. * gn3/db/traits.py (update_sample_data): Add insert statements whenever an "update" statement returns a 0 row-count. BonfaceKilz
2022-02-08db: traits: Insert "count" instead of "error" in "NStrain" tableBonfaceKilz
2022-02-03db: Fetch correct sample dataBonfaceKilz
2022-02-02Remove PublishFreeze from retrieve_publish_trait_info query...The PublishFreeze table isn't necessary in phenotype queries, since PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits, at least) zsloan
2022-02-02Fix bug where sample values of 0 were being treated as False...In line 91 of gn3/db/traits.py, there was an if statement "if record[key] else 'x'" that was treating values of 0 as False, so I changed it to explicitly check that values aren't None zsloan
2022-02-02Fix retrieve_publish_trait_data query...The PublishFreeeze table is actually unnecessary for this query, since the group ID (inbred_set_id) should be passed in and that ID is in the PublishXRef table (so no neeed to join with PublishFreeze) zsloan
2022-01-12Indent code correctly...Indent the code correctly. Frederick Muriuki Muriithi
2022-01-12Deduplicate query to fetch data for 'Publish' traits...The queries run in the `get_trait_csv_sample_data` and `retrieve_publish_trait_data` functions in the `gn3.db.traits` module were mostly similar. This commit changes that, by making the `get_trait_csv_sample_data` function make use of the results from calling the `retrieve_publish_trait_data` function. Frederick Muriuki Muriithi
2022-01-10Check for path existence...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2022-01-10Fix dataset retrieval query for `Geno` traits...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2022-01-10Surround statement with parens for readabilityFrederick Muriuki Muriithi
2022-01-10Convert keys to string...* Some traits have a name composed of all numerals, which leads to the names being interpreted as numbers. This commit forces them to string to avoid subtle bugs where the code fails. Frederick Muriuki Muriithi
2022-01-10Fix error in query: Replace '=' with 'IN'Frederick Muriuki Muriithi
2022-01-10Rework database functions to fetch multiple items...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In an attempt to optimise the performance of the partial correlations feature, this commit reworks some database access functions to fetch multiple items from the database, per query, unlike their original forms which would fetch a single item per query. This reduces queries to the database, and should hopefully improve the responsiveness of the partial correlations feature. Frederick Muriuki Muriithi
2022-01-05Merge branch 'main' into fix/check-for-duplicates-before-deletions-or-insertionsBonfaceKilz
2022-01-04traits.py: Don't use "value" to check if a record exists...The problem with using the "value" record is that it's a floating point number. See <https://www.bonfacemunyoki.com/post/2021-10-21-comparing-floating-point-numbers/> on why comparing floating point numbers can be an issue. BonfaceKilz
2022-01-04traits.py: Return early during an insert if the give record exists...Sometimes, a user will try to insert data twice, on in some instances, 2 different users will attempt the same inserts of the same records separately. In such cases, ignore the insert, and return early. BonfaceKilz
2022-01-04traits.py Delete a record only if it exists...In the case when the user tries to delete the same data twice, prior to this commit, an error was being generated. This commit remedies this by checking if a record exists prior to deleting it. BonfaceKilz
2021-12-23db: Assist mypy with explicit type declaration....* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring type of return dictionary. Arun Isaac
2021-12-23db: Fix sparql_query return type....* gn3/db/datasets.py: Import List from typing. (sparql_query): Set return type to List[Dict[str, Any]]. Arun Isaac
2021-12-23db: Fix wrong continued indentation....* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation. Arun Isaac
2021-12-14linting: Fix obvious linting issuesFrederick Muriuki Muriithi
2021-12-14Fix bug: expects int, gets object - Fixed.Frederick Muriuki Muriithi
2021-12-14mypy: ignore some imports and errors...* Ignore some missing library stubs * Ignore some typing errors * Fix obvious typing errors Frederick Muriuki Muriithi
2021-12-14Set explicit formatting for sequences in queries...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * the mysqlclient is sometimes finicky with the format specifiers, especially in the `WHERE ... IN ...` clauses where a sequence of values is provided. This commit explicitly sets the format specifiers for such clauses so as to avoid sporadic failures due to differences in the form of data from one query to the next. Frederick Muriuki Muriithi
2021-12-13Fix errors with query...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Use the correct format string paradigm: put f before opening quote. * Provide missing space just before 'FROM' clause Frederick Muriuki Muriithi
2021-12-10Fix parameters...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Provide parameters as a dict of items (which works for MySQL), rather than as keywork arguments (as works in PostgreSQL). Frederick Muriuki Muriithi
2021-12-09Prevent error on no result. Fix indexing...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * If the dataset name is not found, don't cause an exception, instead, return the provided search name. * Use the correct inner object Frederick Muriuki Muriithi
2021-12-09Provide clearer error message...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To help with debugging error conditions, provide the original name to help with figuring out why the error was raised Frederick Muriuki Muriithi
2021-12-06Merge branch 'main' of github.com:genenetwork/genenetwork3Frederick 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
2021-11-29Merge branch 'main' into partial-correlationsMuriithi Frederick Muriuki
2021-11-29Fix linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-29Provide entry-point function for the partial correlations...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Provide the entry-point function to the partial correlation feature. This is the function that ochestrates the fetching of the data, and processing it for output by the API endpoint (to be implemented). Frederick Muriuki Muriithi
2021-11-29Fix bugs in data...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Process the db_name and db_type values. * Return data correctly Frederick Muriuki Muriithi
2021-11-29Update return type...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the complete filename when found, or the boolean value False, when it is not found. Frederick Muriuki Muriithi
2021-11-29Return only values...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the values from the database, not the tuples. Frederick Muriuki Muriithi
2021-11-29Update typing notations on functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-29Fix query parametrisation...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Pass parameters to the query the way the MySQL driver expects. Frederick Muriuki Muriithi