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2023-07-12Bug: Set the `data_exists` variable within the context managerFrederick Muriuki Muriithi
The `cursor.fetchone()` call that was used as the condition to the `if` was called outside of the context manager, and therefore would always give a non-truthy value at best and an inconsistent result at worst. This commit gets the value before the context manager has exited and stores it for later use.
2023-07-12Bug: Retrieve configs from app, not environmentFrederick Muriuki Muriithi
Retrieve the configuration values from the application object, not from the environment. We are assured of having the configuration values set in the application - we do not have that assurance for the environment.
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>
2023-06-12Delete unused importMunyoki Kilyungi
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>
2023-06-12Delete unused get_trait_metadata functionMunyoki Kilyungi
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>
2023-06-07Nest duplicate entries into a list from a sparql resultMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Pass geoSeries as a URLMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Rename gn:geoPlatform -> gn:geoPlatformUrlMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Match how dataset metadata is fetched with GN1Munyoki Kilyungi
* gn3/db/rdf.py (sparql_query): Parse CONSTRUCTS and SELECTS differently. (strip_url): Rename to ... (get_url_local_name): ... this. (get_dataset_metadata): Fetch extra fields in RDF. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Replace taxon prefix with ncbiTaxon which references NCBIMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Replace SELECT with CONSTRUCT when fetching a dataset's metadataMunyoki Kilyungi
* gn3/db/rdf.py: Importh pymonad.Nothing. (get_dataset_metadata): Replace SELECT with CONSTRUCT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Create a function for stripping the last bit from a URLMunyoki Kilyungi
* gn3/db/rdf.py: Import unquote and urlparse. (strip_url): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-22Use string literal concatenation to make genofile_path line shorterzsloan
2023-05-22Fix quotes when setting genofile_pathzsloan
2023-05-22Fix return typing for get_trait_sample_datazsloan
2023-05-22Change type from 'any' to 'Any'zsloan
2023-05-22Use f-string for setting genofile_pathzsloan
Also set default value for os.environ.get("GENENETWORK_FILES")
2023-05-22Include encoding in open statement to address pylint W1514zsloan
2023-05-22Initialize 'line'; previous pylint complained because line might not be ↵zsloan
initialized (if the genofile was empty, for example)
2023-05-22Use 'with open()' syntaxzsloan
Initialize samplelist variable
2023-05-22Remove unused variable this_datazsloan
2023-05-22Include all samples in trait sample datazsloan
This is necessary in order to allow for editing the values of samples that don't currently have values
2023-05-22Fix sample data CSV query to only fetch distinct sampleszsloan
There's probably a better way to fix this query (it was previously returning each sample twice), but DISTINCT was the easiest way I could come up with
2023-05-22Fix get_trait_sample_data functionzsloan
2023-05-22Fix retrieve_sample_list function to correctly get genofile_pathzsloan
2023-05-22Commit update/insert queries, since they don't seem to be executed otherwise ↵zsloan
after the recent changes to the DB
2023-05-22Add function for retrieving group name (given group ID)zsloan
2023-05-22Add function for retrieving phenotype sample data as dictzsloan
2023-05-22Add function for retrieving samplelist from .geno filezsloan
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>
2023-03-20Disable fetching case-attributes when getting sample dataMunyoki Kilyungi
* gn3/db/sample_data.py: Remove 're' import. (get_trait_csv_sample_data): Remove fetching sample data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-17Add conn.commit() to queries in sample_data.pyzsloan
2023-03-17Change get_all_species query to order by Familyzsloan
2023-03-01Open lmdb path in readonly modeMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions, get_nth_matrix, get_current_matrix): Open lmdb in readonly mode. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Fetch trait metadata from RDFMunyoki Kilyungi
* gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Get the N-th matrix given N, an index valueMunyoki Kilyungi
* gn3/db/matrix.py (get_nth_matrix): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Get total number of versions that a database hasMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Add method to fetch the current matrixMunyoki Kilyungi
* gn3/db/matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.Frederick Muriuki Muriithi
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import
2022-12-08Remove unused importFrederick Muriuki Muriithi
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.
2022-11-16Inject SPARQLWrapper as a parameterMunyoki Kilyungi
* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto.
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.
2022-11-02Fix pylint and mypy errorsMunyoki Kilyungi
* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query directly to cursor.execute. Rename value to _value in for loop to make mypy pass. * gn3/db_utils.py (Connection): Add class docstring. (Connection.cursor): Add docstring. * mypy.ini: Add an entry for xapian.
2022-08-23Remove conn.commit() and conn.rollback()Munyoki Kilyungi
* gn3/db/__init__.py (update): Delete conn.commit() and conn.rollback() (insert): Ditto. * gn3/db/case_attributes.py (insert_case_attribute_audit): Ditto. (reject_case_attribute): Ditto. (approve_case_attribute): Ditto. * gn3/db/sample_data.py (update_sample_data): Ditto. (delete_sample_data): Ditto. (insert_sample_data): Ditto.
2022-06-21Replace lint code with human-readable textBonfaceKilz
* gn3/db/correlations.py (__fetch_data__): Use a more readable code as opposed to an error code.
2022-06-21db: correlations: Ignore pylint errorBonfaceKilz
* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913] error.
2022-06-21db: correlations: Ignore typesBonfaceKilz
* gn3/db/correlations.py (__build_query__): Ignore the "sample_ids" and "joins" types when calling build_query_sgo_lit_corr (fetch_all_database_data): Ignore the return type. TODO: Ping Alex/Arun to fix this.
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