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2022-03-12Check whether publish data already exists before inserting...* gn3/db/sample_data.py (insert_sample_data): If data already exists in the table, do not attempt an insert; otherwise, an error will be generated. BonfaceKilz
2022-03-12Fill in empty values in csv text with: "x"...* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be filled with the default value(set in the args). * tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above. BonfaceKilz
2022-03-12Fetch id's separately for the insertion edge-case...* gn3/db/sample_data (get_sample_data_ids): Add an extra condition that caters for inserts: during inserts, joins won't work when fetching the strain_id, publishdata_id, and strain_name. In this case, just create 2 separate queries to do that work. BonfaceKilz
2022-03-12Extract a strain name given a csv string and it's header...* gn3/csvcmp.py (extract_strain_name): New function. * gn3/db/sample_data (delete_sample_data): Use the aforementioned function. (insert_sample_data): Ditto. * tests/unit/test_csvcmp: Test cases for above. BonfaceKilz
2022-03-12Allow deleting case-attribute data during deletion...* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow deleting case-attribute values. BonfaceKilz
2022-03-12Allow inserting case-attribute data during inserts...* gn3/db/sample_data.py (insert_sample_data): Modify this function to allow inserting case-attribute values. BonfaceKilz
2022-03-12Fetch InbredSetId...* gn3/db/sample_data.py (get_sample_data_ids): Extend to also fetch InbredSetId. (update_sample_data): Discard the returned value of InbredSetId. (delete_sample_data): Ditto. BonfaceKilz
2022-03-12Create a new function for retrieving strain_id and publishdata_id...* gn3/db/sample_data.py: Import Any, Tuple. (get_sample_data_ids): New function that fetches the strain_id and publishdata_id of a given data point. (update_sample_data): Use `get_sample_data_ids`. (delete_sample_data): Ditto. (insert_sample_data): Ditto. BonfaceKilz
2022-03-12Move operations on sample_data to it's own moduleBonfaceKilz
2022-03-12Don't add extra key "Column" to dict if there are no changes...gn3/csvcmp.py (csv_diff): If the diff is empty, don't add an extra key "Column" to the dictionary. tests/unit/test_csvcmp (test_csv_diff_only_column_change): Add test-case for the above. BonfaceKilz
2022-03-12Fill CSV text if there are non-even rows...Should you try to run `csvdiff` against 2 csv files with either file having a non-even columns, there will be an error. As such, the csv files need to be "filled" before running `csvdiff`. * gn3/csvcmp (csv_diff): For non-even rows in the csv files, fill the csv rows. BonfaceKilz
2022-03-12Create new method for filling csv with a default value...* gn3/csvcmp.py (fill_csv): Given a csv text with uneven or incomplete fields whole length are less than width, fill them with a value which defaults to "x". * tests/unit/test_csvcmp.py (test_fill_csv): Test cases for the above. BonfaceKilz
2022-03-12Replace "all" with "and"...* gn3/csvcmp.py (remove_insignificant_edits): "all" evaluates all elements and throws an error if when `abs(float(x) - float(y)) < epsilon` is processed. Use "and" instead because of it's short-circuiting behaviour. BonfaceKilz
2022-03-12Store columns in the output dict...When inserting, deleting, or editing case-attributes, we need the column headers in order to be able to know identify the attribute of interest. * gn3/csvcmp.py (csv_diff): Add extra "Column" key in returned dict. BonfaceKilz
2022-03-12Add methods for working with csv data...gn3/csvcmp.py: New file (create_dirs_if_not_exists): From a list of dirs, create them if they don't exist. (remove_insignificant_edits): Given a dict with a "Modification" key, remove edits with "delta < ε". (csv_diff): Generate a csv_diff using the "csvdiff" tool packaged in guix. tests/unit/test_csvcmp.py: Add some tests for "gn3/csvcmp.py" BonfaceKilz
2022-03-12db: Fix error in SQL query...* gn3/db/traits.py (get_trait_csv_sample_data): Update SQL to fix runtime errors. BonfaceKilz
2022-03-12Fix pylint errorBonfaceKilz
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
2022-03-11Fix some linting issuesFrederick Muriuki Muriithi
2022-03-08Remove unused function and its testsFrederick 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
2022-02-25Fix issue where 0's were treated as False for the primary trait in...correlations In the original version of the if statement* I believe it was interpreted as "if a_val and (b_val is not None)". This caused values of 0 for a_val (the primary trait's values) to be evaluated as False. I changed it to compare both a_val and b_val to None. This seems to have fixed the issue. * if (a_val and b_val is not None) zsloan
2022-02-24gn3: computations: Call Popen with context manager....Context managers should be preferred when allocating resources. * gn3/computations/wgcna.py (stream_cmd_output): Call Popen with context manager. Arun Isaac
2022-02-24gn3: Explicitly specify UTF-8 to be the file encoding....When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument. Arun Isaac
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
2022-02-17Test 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
2022-02-17Add property tests for `dictify_by_samples`...Add property tests using pytest and hypothesis to test that the expected properties hold for the `gn3.computations.partial_correlations.dictify_by_samples` function. Frederick Muriuki Muriithi
2022-02-08Merge iterations to remove unnecessary computations...Do all the work in a single iteration to avoid unnecessary iterations that hamper performance. Frederick Muriuki Muriithi
2022-02-08Remove multiprocessing for stability...Web servers are long-running processes, and python is not very good at cleaning up after itself especially in forked processes - this leads to memory errors in the web-server after a while. This commit removes the use of multiprocessing to avoid such failures. Frederick Muriuki Muriithi
2022-02-08Give sorting functions more descriptive namesFrederick Muriuki Muriithi
2022-02-08Use multiprocessing to speed up computation...This commit refactors the code to make it possible to use multiprocessing to speed up the computation of the partial correlations. The major refactor is to move the `__compute_trait_info__` function to the top-level of the module, and provide to it all the other necessary context via the new args. Frederick Muriuki Muriithi
2022-02-08Remove unnecessary computation...In Python3 when slicing, seq[:min(some_val, len(seq))] == seq[:some_val] because Python3 will just return a copy of the entire sequence if `some_val` happens to be larger/greater than the length of the sequence. This commit removes the unnecessary call to `min()` 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