diff options
| -rw-r--r-- | quality_control/checks.py | 12 | ||||
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 3 | ||||
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 3 |
3 files changed, 13 insertions, 5 deletions
diff --git a/quality_control/checks.py b/quality_control/checks.py index bb05e31..f01bdd4 100644 --- a/quality_control/checks.py +++ b/quality_control/checks.py @@ -4,7 +4,11 @@ from typing import Optional from .errors import InvalidValue -def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern: +def decimal_places_pattern( + mini: int, + maxi: Optional[int] = None, + allow_negative_values: bool = False +) -> re.Pattern: """ Generate a regular expression for checking numbers @@ -40,8 +44,10 @@ def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern: raise ValueError(*exc.args) from exc return re.compile( - r"^(" - r"0+" # All zeroes, no decimal places + r"^" + + (r"-?" if allow_negative_values else r"") + + r"(" + + r"0+" # All zeroes, no decimal places + r"|0+\.0+" # 0.00… + r"|[0-9]+\.?0*" # Whole numbers, or all zeroes after decimal point + r"|[0-9]+\.[0-9]{" diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index 31eb715..72cd641 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -212,7 +212,8 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments _delay = 1 headers = { "Authorization": f"Bearer {token}", - "Content-Type": "application/json" + "Content-Type": "application/json", + "Accept": "application/json" } def authserveruri(endpoint): return urljoin(authserver, endpoint) diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 084c876..e65bbcc 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -252,7 +252,8 @@ def decimal_points_error(# pylint: disable=[too-many-arguments,too-many-position decimal_places: int = 1 ) -> Optional[InvalidValue]: """Returns an error if the value does not meet the checks.""" - if not bool(decimal_places_pattern(decimal_places).match(cellvalue)): + if not bool(decimal_places_pattern( + decimal_places, allow_negative_values=True).match(cellvalue)): return InvalidValue(filename, rowtitle, coltitle, cellvalue, message) return None |