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fix: resolve pylance issue with subscription of dict #1187

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merged 3 commits into from
Oct 25, 2023
Merged

fix: resolve pylance issue with subscription of dict #1187

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2dd4e84
fix: resolve pylance issue with subscription of dict
holtgrewe Oct 25, 2023
92ac31b
wip
holtgrewe Oct 25, 2023
f2facf5
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holtgrewe Oct 25, 2023
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52 changes: 26 additions & 26 deletions cases_import/models/executors.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,7 @@ def _import_externalfile(
fa = external_file.file_attributes
if fa.get("designation") != "quality_control":
return # can only handle QC data here
file_identifier_to_individual: dict[str, str] = {
file_identifier_to_individual: typing.Dict[str, str] = {
v: k for k, v in (external_file.identifier_map or {}).items()
}

Expand All @@ -230,7 +230,7 @@ def _import_dragen_qc_cnv_metrics(
self,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
with self.external_fs.open(external_file.path, "rt") as inputf:
io_dragen.load_cnv_metrics(
Expand All @@ -244,7 +244,7 @@ def _import_dragen_qc_fragment_length_hist(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -260,7 +260,7 @@ def _import_dragen_qc_mapping_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -276,7 +276,7 @@ def _import_dragen_qc_ploidy_estimation_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -292,7 +292,7 @@ def _import_dragen_qc_roh_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -307,7 +307,7 @@ def _import_dragen_qc_sv_metrics(
self,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
with self.external_fs.open(external_file.path, "rt") as inputf:
io_dragen.load_sv_metrics(
Expand All @@ -321,7 +321,7 @@ def _import_dragen_qc_time_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -337,7 +337,7 @@ def _import_dragen_qc_trimmer_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -352,7 +352,7 @@ def _import_dragen_qc_vc_hethom_ratio_metrics(
self,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
with self.external_fs.open(external_file.path, "rt") as inputf:
io_dragen.load_vc_hethom_ratio_metrics(
Expand All @@ -365,7 +365,7 @@ def _import_dragen_qc_vc_metrics(
self,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
with self.external_fs.open(external_file.path, "rt") as inputf:
io_dragen.load_vc_metrics(
Expand All @@ -379,7 +379,7 @@ def _import_dragen_qc_wgs_contig_mean_cov(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -395,7 +395,7 @@ def _import_dragen_qc_wgs_coverage_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -411,7 +411,7 @@ def _import_dragen_qc_wgs_fine_hist(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -427,7 +427,7 @@ def _import_dragen_qc_wgs_hist(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -443,7 +443,7 @@ def _import_dragen_qc_wgs_overall_mean_cov(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -459,7 +459,7 @@ def _import_dragen_qc_region_coverage_metrics(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
region_name = external_file.file_attributes.get("region_name", "UNKNOWN REGION")
Expand All @@ -477,7 +477,7 @@ def _import_dragen_qc_region_coverage_fine_hist(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
region_name = external_file.file_attributes.get("region_name", "UNKNOWN REGION")
Expand All @@ -495,7 +495,7 @@ def _import_dragen_qc_region_coverage_hist(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
region_name = external_file.file_attributes.get("region_name", "UNKNOWN REGION")
Expand All @@ -513,7 +513,7 @@ def _import_dragen_qc_region_coverage_overall_mean_cov(
individual_name: str,
external_file: IndividualExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
region_name = external_file.file_attributes.get("region_name", "UNKNOWN REGION")
Expand All @@ -530,7 +530,7 @@ def _import_samtools_qc_bcftools_stats(
self,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
with self.external_fs.open(external_file.path, "rt") as inputf:
io_samtools.load_bcftools_stats(
Expand All @@ -544,7 +544,7 @@ def _import_samtools_qc_samtools_flagstat(
individual_name: str,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -560,7 +560,7 @@ def _import_samtools_qc_samtools_idxstats(
individual_name: str,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -576,7 +576,7 @@ def _import_samtools_qc_samtools_stats(
individual_name: str,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -592,7 +592,7 @@ def _import_cramino_qc_cramino(
individual_name: str,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
with self.external_fs.open(external_file.path, "rt") as inputf:
Expand All @@ -608,7 +608,7 @@ def _import_ngsbits_qc_mappingqc(
individual_name: str,
external_file: PedigreeExternalFile,
caseqc: CaseQc,
file_identifier_to_individual: dict[str, str] | None = None,
file_identifier_to_individual: typing.Dict[str, str] | None = None,
):
sample_name = external_file.identifier_map.get(individual_name, individual_name)
region_name = external_file.file_attributes.get("region_name", "UNKNOWN REGION")
Expand Down
2 changes: 1 addition & 1 deletion cases_qc/io/cramino.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ def load_cramino(
sample: str,
input_file: typing.TextIO,
caseqc: models.CaseQc,
file_identifier_to_individual: dict[str, str],
file_identifier_to_individual: typing.Dict[str, str],
) -> cases_qc.models.cramino.CraminoMetrics:
"""Load a ``cramino`` output file into a ``cases_qc.models.CraminoMetrics`` record."""
parser = CraminoParser()
Expand Down
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