| Age | Commit message (Expand) | Author |
|---|
| 2023-05-22 | Include all samples in trait sample data...This is necessary in order to allow for editing the values of samples that don't currently have values
| zsloan |
| 2023-05-22 | Fix sample data CSV query to only fetch distinct samples...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
| zsloan |
| 2023-05-22 | Fix get_trait_sample_data function | zsloan |
| 2023-05-22 | Fix retrieve_sample_list function to correctly get genofile_path | zsloan |
| 2023-05-22 | Commit update/insert queries, since they don't seem to be executed otherwise ... | zsloan |
| 2023-05-22 | Add function for retrieving group name (given group ID) | zsloan |
| 2023-05-22 | Add function for retrieving phenotype sample data as dict | zsloan |
| 2023-05-22 | Add function for retrieving samplelist from .geno file | zsloan |
| 2023-04-17 | Create new endpoint for fetching GeneRIF entries...* 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>
| Munyoki Kilyungi |
| 2023-03-20 | Disable fetching case-attributes when getting sample data...* 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>
| Munyoki Kilyungi |
| 2023-03-17 | Add conn.commit() to queries in sample_data.py | zsloan |
| 2023-03-17 | Change get_all_species query to order by Family | zsloan |
| 2023-03-01 | Open lmdb path in readonly mode...* 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>
| Munyoki Kilyungi |
| 2023-03-01 | Fetch trait metadata from RDF...* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | Get the N-th matrix given N, an index value...* gn3/db/matrix.py (get_nth_matrix): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | Get total number of versions that a database has...* gn3/db/matrix.py (get_total_versions): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | Add method to fetch the current matrix...* gn3/db/matrix.py: New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2022-12-21 | gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts....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
| Frederick Muriuki Muriithi |
| 2022-12-08 | Remove unused import | Frederick Muriuki Muriithi |
| 2022-12-06 | Use a dataset's name to fetch it's metadata from RDF...* 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.
| Munyoki Kilyungi |
| 2022-11-16 | Inject SPARQLWrapper as a parameter...* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import.
(sparql_query): Inject SPARQLWrapper.
(get_dataset_metadata): Ditto.
| Munyoki Kilyungi |
| 2022-11-02 | Re-implement RDF related code to use monads in its own module...* 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.
| Munyoki Kilyungi |
| 2022-11-02 | Fix pylint and mypy errors...* 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.
| Munyoki Kilyungi |
| 2022-08-23 | Remove conn.commit() and conn.rollback()...* 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.
| Munyoki Kilyungi |
| 2022-06-21 | Replace lint code with human-readable text...* gn3/db/correlations.py (__fetch_data__): Use a more readable code as
opposed to an error code.
| BonfaceKilz |
| 2022-06-21 | db: correlations: Ignore pylint error...* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913]
error.
| BonfaceKilz |
| 2022-06-21 | db: correlations: Ignore types...* 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.
| BonfaceKilz |
| 2022-06-21 | db: datasets.py: Ignore results from sparql.queryAndConvert...ATM, it's very difficult to work the correct type that is returned. Ignore
this for now and fix this later.
| BonfaceKilz |
| 2022-05-31 | Extract utility functions from `fetch_all_database_data`...Extract the utility functions to help with understanding the what the
`fetch_all_database_data` function is doing. This helps with maintenance.
| Frederick Muriuki Muriithi |
| 2022-05-27 | Move sql for CRUD operations on case-attrs from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Move sql for modifying case-attributes from gn2 to gn3 | BonfaceKilz |
| 2022-05-27 | Return all the results from CaseAttributes column as is...* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import.
(get_case_attributes): Return the results of "fetchall" from the case
attributes.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing
test.
| BonfaceKilz |
| 2022-05-26 | Add Endpoint to get menu items for use in UI | Frederick Muriuki Muriithi |
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi |
| 2022-05-05 | Compute partial correlation with selected traits...Compute partial correlations against a selection of traits rather than against
an entire dataset.
| Frederick Muriuki Muriithi |
| 2022-04-12 | Strip any newline, tab or carriage-return chars from sample data...* gn3/db/sample_data.py (get_trait_csv_sample_data): Strip out "\n", "\t", or
"\r" from the sample data. See:
<https://issues.genenetwork.org/issues/csv-error-ITP_10001-longevity-data-set.html>
| BonfaceKilz |
| 2022-04-07 | Fix pylint errors | BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during insertions...* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Use case attribute id inside brackets if present during updates...* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
| BonfaceKilz |
| 2022-04-07 | Add method for fetching the case_attributes...* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
| BonfaceKilz |
| 2022-04-07 | Run python black on file...* gn3/db/sample_data.py: Run "python black -l 79 ..."
| BonfaceKilz |
| 2022-03-14 | Dummy White Space commit to fix laminar | BonfaceKilz |
| 2022-03-12 | Remove unused imports | BonfaceKilz |
| 2022-03-12 | Fix mypy issues | BonfaceKilz |
| 2022-03-12 | Fix pylint issues | BonfaceKilz |
| 2022-03-12 | Store the first element as strain_id | BonfaceKilz |
| 2022-03-12 | Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Apply auto-pep8 to sample_data.py and it's test file | BonfaceKilz |
| 2022-03-12 | Add missing return type-annotations...* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return
type for type annotations.
(insert_sample_data): Ditto.
| BonfaceKilz |
