Skip to content

Commit

Permalink
fix: namespaced string issue from 2207-07-01
Browse files Browse the repository at this point in the history
  • Loading branch information
@holtgrewe
holtgrewe committed Jul 1, 2024
1 parent 715f281 commit 7eec141
Show file tree
Hide file tree
Showing 6 changed files with 2,507 additions and 21 deletions.
50 changes: 29 additions & 21 deletions clinvar_data/conversion/dict_to_pb.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,14 @@ def ensure_str(value: str | dict[str, str]) -> str:
return value


def ensure_str_optional(value: None | str | dict[str, str]) -> None | str:
"""Similar to ``ensure_str`` but allows ``None``."""
if value is None:
return None
else:
return ensure_str(value)


class ConvertGeneVariantRelationship:
"""Static method helper for converting XML data to to ``GeneVariantRelationship``."""

Expand Down Expand Up @@ -1669,7 +1677,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AggregatedGermlineClassifi
tag_germline_classification["ReviewStatus"]
)
)
description: str | None = tag_germline_classification.get("Description")
description: str | None = ensure_str_optional(tag_germline_classification.get("Description"))
explanation: Comment | None = None
if "Explanation" in tag_germline_classification:
explanation = ConvertComment.xmldict_data_to_pb(
Expand Down Expand Up @@ -1764,7 +1772,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AggregatedSomaticClinicalI
tag_somatic_clinical_impact["ReviewStatus"]
)
)
description: str | None = tag_somatic_clinical_impact.get("Description")
description: str | None = ensure_str_optional(tag_somatic_clinical_impact.get("Description"))

# Parse out Citation, XRef, Comment tags.
cxcs = cls.parse_citations_xrefs_comments(tag_somatic_clinical_impact)
Expand Down Expand Up @@ -1848,7 +1856,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AggregatedOncogenicityClas
tag_oncogenicity_classification["ReviewStatus"]
)
)
description: str | None = tag_oncogenicity_classification.get("Description")
description: str | None = ensure_str_optional(tag_oncogenicity_classification.get("Description"))

# Parse out Citation, XRef, Comment tags.
cxcs = cls.parse_citations_xrefs_comments(tag_oncogenicity_classification)
Expand Down Expand Up @@ -1977,7 +1985,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> ClinicalSignificance:
review_status = ConvertSubmitterReviewStatus.xmldict_data_to_pb(
tag_clinical_significance["ReviewStatus"]
)
description: str | None = tag_clinical_significance.get("Description")
description: str | None = ensure_str_optional(tag_clinical_significance.get("Description"))
explanation: Comment | None = None
if "Explanation" in tag_clinical_significance:
explanation = ConvertComment.xmldict_data_to_pb(
Expand Down Expand Up @@ -2187,18 +2195,18 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> ClassificationScv:
ensure_str(tag_classification["ReviewStatus"])
)
)
germline_classification: str | None = tag_classification.get("GermlineClassification")
germline_classification: str | None = ensure_str_optional(tag_classification.get("GermlineClassification"))
somatic_clinical_impact: ClassificationScv.SomaticClinicalImpact | None = None
if "SomaticClinicalImpact" in tag_classification:
somatic_clinical_impact = cls.convert_somatic_clinical_impact(
{"SomaticClinicalImpact": tag_classification["SomaticClinicalImpact"]}
)
oncogenicity_classification: str | None = tag_classification.get(
oncogenicity_classification: str | None = ensure_str_optional(tag_classification.get(
"OncogenicityClassification"
)
explanation_of_classification: str | None = tag_classification.get(
))
explanation_of_classification: str | None = ensure_str_optional(tag_classification.get(
"ExplanationOfClassification"
)
))
classification_scores: list[ClassificationScv.ClassificationScore] | None = None
if "ClassificationScore" in tag_classification:
classification_scores = [
Expand Down Expand Up @@ -2785,7 +2793,7 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> FamilyData:
assert "FamilyData" in tag
tag_inner: dict[str, Any] = tag["FamilyData"]

family_history: str | None = tag_inner.get("FamilyHistory")
family_history: str | None = ensure_str_optional(tag_inner.get("FamilyHistory"))
num_families: int | None = None
if "@NumFamilies" in tag_inner:
num_families = int(tag_inner["@NumFamilies"])
Expand Down Expand Up @@ -3016,8 +3024,8 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> Sample:
if "Origin" in tag_sample:
origin = ConvertOrigin.xmldict_data_to_pb(ensure_str(tag_sample["Origin"]))

ethnicity: str | None = tag_sample.get("Ethnicity")
geographic_origin: str | None = tag_sample.get("GeographicOrigin")
ethnicity: str | None = ensure_str_optional(tag_sample.get("Ethnicity"))
geographic_origin: str | None = ensure_str_optional(tag_sample.get("GeographicOrigin"))
val_tissue: str | dict[str, str] | None = tag_sample.get("Tissue")
if val_tissue:
tissue = ensure_str(val_tissue)
Expand All @@ -3033,14 +3041,14 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> Sample:
somatic_variant_allele_fraction: str | None = None
if "SomaticVariantAlleleFraction" in tag_sample:
somatic_variant_allele_fraction = tag_sample["SomaticVariantAlleleFraction"]
cell_line: str | None = tag_sample.get("CellLine")
cell_line: str | None = ensure_str_optional(tag_sample.get("CellLine"))
species: Species | None = None
if "Species" in tag_sample:
species = ConvertSpecies.xmldict_data_to_pb(tag_sample)
ages: list[Sample.Age] | None = None
if "Age" in tag_sample:
ages = [cls.convert_age({"Age": entry}) for entry in cls.ensure_list(tag_sample["Age"])]
strain: str | None = tag_sample.get("Strain")
strain: str | None = ensure_str_optional(tag_sample.get("Strain"))
affected_status: Sample.AffectedStatus.ValueType | None = None
if "AffectedStatus" in tag_sample:
affected_status = cls.convert_affected_status(ensure_str(tag_sample["AffectedStatus"]))
Expand Down Expand Up @@ -3462,7 +3470,7 @@ def xmldict_data_to_pb(cls, value: dict[str, Any]) -> AlleleScv: # noqa: C901
if "Name" in tag_sa:
assert isinstance(tag_sa["Name"], (dict, str)), f"is: {tag_sa['Name']}"
name = ConvertOtherName.xmldict_data_to_pb({"Name": tag_sa["Name"]})
variant_type: str | None = tag_sa.get("VariantType")
variant_type: str | None = ensure_str_optional(tag_sa.get("VariantType"))
location: Location | None = None
if "Location" in tag_sa:
location = ConvertLocation.xmldict_data_to_pb({"Location": tag_sa["Location"]})
Expand Down Expand Up @@ -3581,7 +3589,7 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> HaplotypeScv:
ConvertAlleleScv.xmldict_data_to_pb({"SimpleAllele": entry})
for entry in cls.ensure_list(tag_genotype["SimpleAllele"])
]
name: str | None = tag_genotype.get("Name")
name: str | None = ensure_str_optional(tag_genotype.get("Name"))
other_names: list[OtherName] | None = None
if "OtherNameList" in tag_genotype:
other_names = [
Expand Down Expand Up @@ -3677,7 +3685,7 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> GenotypeScv:
ConvertHaplotypeScv.xmldict_data_to_pb({"Haplotype": entry})
for entry in cls.ensure_list(tag_genotype["Haplotype"])
]
name: str | None = tag_genotype.get("Name")
name: str | None = ensure_str_optional(tag_genotype.get("Name"))
other_names: list[OtherName] | None = None
if "OtherNameList" in tag_genotype:
other_names = [
Expand Down Expand Up @@ -4141,8 +4149,8 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> ClinicalAssertion: # noqa:
ConvertCitation.xmldict_data_to_pb({"Citation": entry})
for entry in cls.ensure_list(tag_ca["CitationList"]["Citation"])
]
study_name: str | None = tag_ca.get("StudyName")
study_description: str | None = tag_ca.get("StudyDescription")
study_name: str | None = ensure_str_optional(tag_ca.get("StudyName"))
study_description: str | None = ensure_str_optional(tag_ca.get("StudyDescription"))
comments: list[Comment] | None = None
if "Comment" in tag_ca:
comments = [
Expand Down Expand Up @@ -4247,7 +4255,7 @@ def convert_gene(cls, tag: dict[str, Any]) -> Allele.Gene:
properties: list[str] | None = None
if "Property" in tag_gene:
properties = [entry for entry in cls.ensure_list(tag_gene["Property"])]
symbol: str | None = tag_gene.get("Symbol")
symbol: str | None = ensure_str_optional(tag_gene.get("Symbol"))
full_name: str = tag_gene["@FullName"]
gene_id: int = int(tag_gene["@GeneID"])
hgnc_id: str | None = None
Expand Down Expand Up @@ -4348,7 +4356,7 @@ def xmldict_data_to_pb(cls, tag: dict[str, Any]) -> Allele:
for entry in cls.ensure_list(tag_allele["GeneList"]["Gene"])
]
name: str = tag_allele["Name"]
canonical_spdi: str | None = tag_allele.get("CanonicalSPDI")
canonical_spdi: str | None = ensure_str_optional(tag_allele.get("CanonicalSPDI"))
variant_types: list[str] | None = None
if "VariantType" in tag_allele:
variant_types = [entry for entry in cls.ensure_list(tag_allele["VariantType"])]
Expand Down
Loading

0 comments on commit 7eec141

Please sign in to comment.