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2023-10-06Provide keyword argument.Frederick Muriuki Muriithi
2023-10-06Pass in configs/settings as function argumentsFrederick Muriuki Muriithi
To avoid reliance of `flask.current_app.config` or on `gn3.settings` modules globally, this commit passes in the appropriate configurations as arguments to the relevant functions.
2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-15Fetch genotypes from virtuosoMunyoki Kilyungi
* gn3/api/metadata.py: Import get_genotype_metadata. (genotype): New end-point. * gn3/db/rdf.py (get_phenotype_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Fetch phenotypes from virtuosoMunyoki Kilyungi
* gn3/api/metadata.py: Import get_phenotype_metadata. (phenotype): New end-point. * gn3/db/rdf.py (get_phenotype_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Correct publication function docstringMunyoki Kilyungi
* gn3/api/metadata.py (publication): Update docstring. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-07Add publication end-pointMunyoki Kilyungi
* gn3/api/metadata.py: Import get_publication_metadata (publication): New endpoint. * gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-07Remove trait_metadata endpointMunyoki Kilyungi
* gn3/api/metadata.py: Remove get_trait_metadata import. (trait_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Rename dataset_metadata -> datasetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-17Create new endpoint for fetching GeneRIF entriesMunyoki Kilyungi
* gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES. (get_genewiki_entries): New endpoint. * gn3/db/rdf.py: Add new constant for storing rdf prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-06Remove deprecated `gn3.db_utils.database_connector` functionFrederick Muriuki Muriithi
Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
2023-03-01Fetch sampledataMunyoki Kilyungi
* gn3/api/sampledata.py (get_sampledata): New end-point. * gn3/app.py: Register above end-point. * gn3/settings.py: Add new conf variable for LMDB. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Create API endpoint for fetching trait metadataMunyoki Kilyungi
* gn3/api/metadata.py (dataset_metadata): New function and endpoint. (jsonify_dataset_metadata): Rename to dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-01-24search: Use decimals, not floats, when converting to megabases.Arun Isaac
* gn3/api/search.py (parse_location_field): Use decimals, not floats, when converting to megabases.
2023-01-24search: Support SI suffixes and point locations.Arun Isaac
* gn3/api/search.py (parse_position_field): New function. (parse_query): Associate the position prefix with the parse_position_field field processor.
2023-01-24search: Abstract out parsing of position spec into separate function.Arun Isaac
* gn3/api/search.py (parse_position): New function. (parse_location_field): Use parse_position. * tests/unit/test_search.py: Import parse_position from gn3.api.search. (test_parse_position_close_to_zero_location): New test.
2023-01-24search: Alias the position prefix with pos.Arun Isaac
* gn3/api/search.py (parse_query): Alias the position prefix with pos.
2023-01-24search: Rename the mb prefix to position.Arun Isaac
* gn3/api/search.py (parse_query): Rename the mb prefix to position.
2023-01-24search: Assume triplets mean synteny is requested.Arun Isaac
* gn3/api/search.py (query_subqueries, query_terms, parse_synteny_field, is_synteny_on, remove_synteny_field): Delete functions. (parse_query): Assume triplets mean synteny is requested.
2023-01-24search: Use comprehension when splitting location.Arun Isaac
* gn3/api/search.py (parse_location_field): Use comprehension.
2023-01-20mypy: minor fixes to typing errorsFrederick Muriuki Muriithi
2023-01-19search: Downcase before applying SI suffix.Arun Isaac
* gn3/api/search.py (apply_si_suffix): Downcase before applying SI suffix.
2023-01-19search: Use decimals, not floats, to manipulate range limits.Arun Isaac
Decimals are exact and do not introduce tiny errors in the range limits like floats are wont to do. * gn3/api/search.py: Import Decimal from decimal. (apply_si_suffix): Use decimals, not floats, to manipulate range limits.
2023-01-19search: Only look for SI suffix in the last character.Arun Isaac
Suffixes are the last character, not everything but the last character. * gn3/api/search.py (apply_si_suffix): Only look for SI suffix in the last character.
2023-01-19search: Apply SI suffix only if last character is an actual suffix.Arun Isaac
Prior to this commit, when there was no SI suffix (such as in a plain suffix-less number), the last digit would be dropped! * gn3/api/search.py (apply_si_suffix): Apply SI suffix only if last character is an actual suffix.
2023-01-18search: Ensure limits of chromosomal interval is non-negative.Arun Isaac
* gn3/api/search.py (parse_location_field): Ensure limits of chromosomal interval is non-negative.
2023-01-18search: Convert point locations to a +/- 50 kbase range.Arun Isaac
* gn3/api/search.py (parse_location_field): Convert point locations to a +/- 50 kbase range.
2023-01-18Pass species and species prefix as a single query argument.Arun Isaac
* gn3/api/search.py (parse_location_field): Accept a single species query argument instead of separate species and species prefix arguments. (parse_query): Pass parse_location_field a single species query argument.
2023-01-18auth: Fix tests after enforcing FOREIGN KEY constraintFrederick Muriuki Muriithi
Fix a number of tests and fixtures that were not conforming to the FOREIGN KEY constraints: * Each test that creates a new "object" needs to clean up after itself * Each fixture that sets up test data needs to clean up after itself
2023-01-18Tolerate WEIGHT operator in parsed search queries.Arun Isaac
* gn3/api/search.py (remove_synteny_field): Tolerate WEIGHT operator in parsed search queries.
2023-01-18Implement synteny search.Arun Isaac
* gn3/api/search.py: Import gzip, Path from pathlib and curry from pymonad.tools. (IntervalLiftoverFunction): New variable. (query_subqueries, query_terms, field_processor_or, liftover, liftover_interval, parse_synteny_field, is_synteny_on, remove_synteny_field): New functions. (parse_location_field): Generalize to support synteny searches. (parse_query): Support synteny search queries. (search_results): Pass synteny files directory to parse_query.
2023-01-18Support location shorthands in search queries.Arun Isaac
* gn3/api/search.py: Import partial and reduce from functools. Import Callable from typing. (ChromosomalPosition, ChromosomalInterval, FieldProcessor): New classes. (apply_si_suffix, combine_queries, parse_location_field, interval_start, interval_end): New functions. (parse_query): Add field processors for location shorthands.
2023-01-18Split off search query parsing into separate function.Arun Isaac
* gn3/api/search.py (parse_query): New function. (search_results): Use parse_query.
2022-12-06Use a dataset's name to fetch it's metadata from RDFMunyoki Kilyungi
* gn3/api/metadata.py (jsonify_dataset_metadata): Rewrite metadata end-point to use a dataset's name instead of it's accession_id. * gn3/db/rdf.py (get_dataset_metadata): Replace accession_id with name. Use one single RDF query instead of multiple queries.
2022-11-28Catch a URLError when virtuoso isn't running at allMunyoki Kilyungi
* gn3/api/metadata.py: Import URLError. (jsonify_dataset_metadata): Add URLError in except block.
2022-11-28Fix pylint errorsMunyoki Kilyungi
* gn3/api/general.py: Delete rdf import. Delete trailing white spaces. * gn3/api/metadata.py: Delete trailing white spaces.
2022-11-28Fail gracefully when virtuoso is not accessibleMunyoki Kilyungi
* gn3/api/metadata.py: import RemoteDisconnected. (jsonify_dataset_metadata): Wrap get_dataset_metadata in try block.
2022-11-23Create a new REST endpoint for fetching a phenotype's metadataMunyoki Kilyungi
* gn3/api/general.py: (dataset_metadata) Delete. * gn3/api/metadata.py: Import Blueprint, jsonify, current_app, SPARQLWrapper and get_dataset_metadata. (metadata): New Blueprint (jsonify_dataset_metadata): New function/end-point. * gn3/app.py: Import metadata (create_app): Register metadata blueprint.
2022-11-02Re-implement RDF related code to use monads in its own moduleMunyoki Kilyungi
* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf. (dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with rdf.get_dataset_metadata. * gn3/db/datasets.py: Remove unused imports. (sparql_query, dataset_metadata): Delete. * gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
2022-10-28Use Xapian index path from app settings.Arun Isaac
App settings should be accessed from current_app. It should not be hard-coded to a variable in a module. * gn3/db_utils.py: Do not import XAPIAN_DB_PATH from gn3.settings. (xapian_database): Accept path argument. * gn3/api/search.py: Import current_app from flask. (search_results): Pass Xapian index path to xapian_database.
2022-10-28Add search.Arun Isaac
* gn3/api/search.py: New file. * gn3/app.py: Register the search blueprint.
2022-07-28Add command to run the sample correlations in an external processFrederick Muriuki Muriithi
2022-05-26Add Endpoint to get menu items for use in UIFrederick Muriuki Muriithi
2022-05-24Run partial correlations with external scriptFrederick Muriuki Muriithi
Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits
2022-05-24New script to compute partial correlationsFrederick Muriuki Muriithi
* Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order.
2022-05-21Fix linting errorsFrederick Muriuki Muriithi
2022-05-16Run computation in one-shot asynchronous processFrederick Muriuki Muriithi
After reworking the worker/runner to have a one-shot mode, add a function that queues up the task and then runs the worker in the one-shot mode to process the computation in the background.
2022-05-06Fix linting and typing errorsFrederick Muriuki Muriithi
2022-05-06Hook up pcorrs with target traits computationsFrederick Muriuki Muriithi
Enable the endpoint to actually compute partial correlations with selected target traits rather than against an entire dataset. Fix some issues caused by recent refactor that broke pcorrs against a dataset
2022-03-30Revert "Run json.loads on request.get_json, since request.get_json was just ↵Frederick Muriuki Muriithi
returning a string" This reverts commit b93b22386056347d8002dd2e403425beeb4657cd. The appropriate fix should have been in GN2. The original statement args = request.get_json() was correct, since `request.get_json()` should return a python object parsed from the JSON string in the request. Unfortunately, GN2 was encoding the request data two times, which led to the call returning a JSON-encoded string instead of the expected object. The issue has been fixed in GN2 and therefore, the "fix" here can be reverted.
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