phc-ingestion 0.10.20__tar.gz → 0.11.1__tar.gz

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Files changed (65) hide show
  1. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/PKG-INFO +1 -1
  2. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/metadata.py +3 -3
  3. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/ga4gh.py +3 -3
  4. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/generic/utils.py +0 -1
  5. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/pyproject.toml +1 -1
  6. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/PYPI.md +0 -0
  7. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/__init__.py +0 -0
  8. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/__init__.py +0 -0
  9. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/process.py +0 -0
  10. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/__init__.py +0 -0
  11. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/cnv.py +0 -0
  12. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/detect_genome_ref.py +0 -0
  13. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/hla.py +0 -0
  14. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/ihc.py +0 -0
  15. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/interpretation.py +0 -0
  16. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/json.py +0 -0
  17. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/specimen_details.py +0 -0
  18. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/structural.py +0 -0
  19. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/tests.py +0 -0
  20. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/tmb.py +0 -0
  21. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/tsv.py +0 -0
  22. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/vcf.py +0 -0
  23. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/__init__.py +0 -0
  24. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/process.py +0 -0
  25. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/__init__.py +0 -0
  26. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/cnv.py +0 -0
  27. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/fnv.py +0 -0
  28. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/interpretation.py +0 -0
  29. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/vcf_etl.py +0 -0
  30. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/generic/__init__.py +0 -0
  31. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/generic/process.py +0 -0
  32. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nebula/__init__.py +0 -0
  33. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nebula/constants.py +0 -0
  34. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nebula/manifest_assembler.py +0 -0
  35. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nebula/process.py +0 -0
  36. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/__init__.py +0 -0
  37. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/process.py +0 -0
  38. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/alteration_table.py +0 -0
  39. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/interpretation.py +0 -0
  40. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/manifest_helpers.py +0 -0
  41. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/nextgen_specific_genes.py +0 -0
  42. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/pre_filter_somatic_vcf.py +0 -0
  43. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/process_cnv.py +0 -0
  44. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/process_manifest.py +0 -0
  45. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/process_structural.py +0 -0
  46. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/process_vcf.py +0 -0
  47. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/nextgen/util/types.py +0 -0
  48. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/resources/GRCh37_map.csv.gz +0 -0
  49. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/resources/GRCh38_map.csv.gz +0 -0
  50. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/__init__.py +0 -0
  51. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/coords_to_genes.py +0 -0
  52. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/fetch_patient.py +0 -0
  53. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/ga4gh.py +0 -0
  54. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/gene_to_coords.py +0 -0
  55. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/lambda_client.py +0 -0
  56. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/open_maybe_gzipped.py +0 -0
  57. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/tar.py +0 -0
  58. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/shared_util/types.py +0 -0
  59. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/Variant.py +0 -0
  60. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/__init__.py +0 -0
  61. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/standardize.py +0 -0
  62. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/util/__init__.py +0 -0
  63. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/util/af_helpers.py +0 -0
  64. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/util/dp_helpers.py +0 -0
  65. {phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/vcf_standardization/util/read_write.py +0 -0
{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phc-ingestion
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- Version: 0.10.20
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+ Version: 0.11.1
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  Summary: Functions for LifeOmic PHC genomic ingestions
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  License: MIT
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  Author-email: LifeOmic Development <development@lifeomic.com>
{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/caris/util/metadata.py RENAMED
@@ -106,10 +106,10 @@ def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
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  patient = data["patientInformation"]
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  metadata["bodySiteSystem"] = "http://lifeomic.com/fhir/sequence-body-site"
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  metadata["reportID"] = get_report_id(test_details)
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- metadata["mrn"] = patient["mrn"]
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- metadata["patientLastName"] = patient["lastName"]
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+ metadata["mrn"] = patient["mrn"].strip()
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+ metadata["patientLastName"] = patient["lastName"].strip()
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- metadata["patientDOB"] = patient["dob"]
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+ metadata["patientDOB"] = patient["dob"].strip()
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  # Get physician info - ordering name, NPI, and facility
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  metadata["medFacilName"] = get_med_facil_name(physician_details)
{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/foundation/util/ga4gh.py RENAMED
@@ -180,7 +180,7 @@ def get_test_yml(
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  # Hard-code genome reference for FMI
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  genome_reference = "GRCh37"
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- mrn = get_mrn(pmi)
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+ mrn = get_mrn(pmi).strip()
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  trf = get_trf(sample)
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@@ -220,8 +220,8 @@ def get_test_yml(
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  "reportDate": reportDate,
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  "reportID": trf,
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  "mrn": mrn,
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- "patientDOB": get_date(pmi.get("DOB")),
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- "patientLastName": pmi.get("LastName"),
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+ "patientDOB": get_date(pmi.get("DOB")).strip(),
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+ "patientLastName": pmi.get("LastName").strip(),
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  "medFacilName": med_facil_info[0],
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  "medFacilID": med_facil_info[1],
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  "orderingMDName": ordering_md_info[0],
{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/ingestion/generic/utils.py RENAMED
@@ -44,7 +44,6 @@ def check_manifest(manifest_file_path: str, case_id, log: Logger):
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  Optional("plasmaTumorFraction"): str,
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  Optional("cellPurity"): float,
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  Optional("hrdStatus"): str,
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- Optional("specimenIds"): list[str],
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  }
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  )
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{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "phc-ingestion"
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- version = "0.10.20"
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+ version = "0.11.1"
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  description = "Functions for LifeOmic PHC genomic ingestions"
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  authors = [
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  { name = "LifeOmic Development", email = "development@lifeomic.com" },
{phc-ingestion-0.10.20 → phc-ingestion-0.11.1}/PYPI.md RENAMED
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