| Age | Commit message (Expand) | Author |
|---|
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-01-24 | search: Use decimals, not floats, when converting to megabases....* gn3/api/search.py (parse_location_field): Use decimals, not floats, when
converting to megabases.
| Arun Isaac |
| 2023-01-24 | search: Support SI suffixes and point locations....* gn3/api/search.py (parse_position_field): New function.
(parse_query): Associate the position prefix with the parse_position_field
field processor.
| Arun Isaac |
| 2023-01-24 | search: Abstract out parsing of position spec into separate function....* 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.
| Arun Isaac |
| 2023-01-24 | search: Alias the position prefix with pos....* gn3/api/search.py (parse_query): Alias the position prefix with pos.
| Arun Isaac |
| 2023-01-24 | search: Rename the mb prefix to position....* gn3/api/search.py (parse_query): Rename the mb prefix to position.
| Arun Isaac |
| 2023-01-24 | search: Assume triplets mean synteny is requested....* 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.
| Arun Isaac |
| 2023-01-24 | search: Use comprehension when splitting location....* gn3/api/search.py (parse_location_field): Use comprehension.
| Arun Isaac |
| 2023-01-20 | mypy: minor fixes to typing errors | Frederick Muriuki Muriithi |
| 2023-01-19 | search: Downcase before applying SI suffix....* gn3/api/search.py (apply_si_suffix): Downcase before applying SI suffix.
| Arun Isaac |
| 2023-01-19 | search: Use decimals, not floats, to manipulate range limits....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.
| Arun Isaac |
| 2023-01-19 | search: Only look for SI suffix in the last character....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.
| Arun Isaac |
| 2023-01-19 | search: Apply SI suffix only if last character is an actual suffix....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.
| Arun Isaac |
| 2023-01-18 | search: Ensure limits of chromosomal interval is non-negative....* gn3/api/search.py (parse_location_field): Ensure limits of chromosomal
interval is non-negative.
| Arun Isaac |
| 2023-01-18 | search: Convert point locations to a +/- 50 kbase range....* gn3/api/search.py (parse_location_field): Convert point locations to a +/-
50 kbase range.
| Arun Isaac |
| 2023-01-18 | Pass species and species prefix as a single query argument....* 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.
| Arun Isaac |
| 2023-01-18 | auth: Fix tests after enforcing FOREIGN KEY constraint...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
| Frederick Muriuki Muriithi |
| 2023-01-18 | Tolerate WEIGHT operator in parsed search queries....* gn3/api/search.py (remove_synteny_field): Tolerate WEIGHT operator in parsed
search queries.
| Arun Isaac |
| 2023-01-18 | Implement synteny search....* 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.
| Arun Isaac |
| 2023-01-18 | Support location shorthands in search queries....* 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.
| Arun Isaac |
| 2023-01-18 | Split off search query parsing into separate function....* gn3/api/search.py (parse_query): New function.
(search_results): Use parse_query.
| Arun Isaac |
| 2022-10-28 | Use Xapian index path from app settings....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.
| Arun Isaac |
| 2022-10-28 | Add search....* gn3/api/search.py: New file.
* gn3/app.py: Register the search blueprint.
| Arun Isaac |
