phc-ingestion 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

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Files changed (8) hide show
  1. ingestion/broad/utils.py +1 -0
  2. ingestion/generic/utils.py +1 -0
  3. ingestion/nebula/manifest_assembler.py +1 -1
  4. ingestion/nextgen/util/manifest_helpers.py +3 -1
  5. ingestion/nextgen/util/process_manifest.py +1 -1
  6. {phc_ingestion-1.0.3.dist-info → phc_ingestion-1.0.5.dist-info}/METADATA +1 -1
  7. {phc_ingestion-1.0.3.dist-info → phc_ingestion-1.0.5.dist-info}/RECORD +8 -8
  8. {phc_ingestion-1.0.3.dist-info → phc_ingestion-1.0.5.dist-info}/WHEEL +0 -0
ingestion/broad/utils.py CHANGED
@@ -64,6 +64,7 @@ def check_manifest(manifest_file_path: str, case_id, log: Logger):
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  raise e
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  # Add duplicate fields from supplied ones to fit formatting
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+ manifest["mrn"] = manifest["mrn"].strip()
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  manifest["patientInfo"]["identifiers"] = [
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  {
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  "codingCode": "MR",
ingestion/generic/utils.py CHANGED
@@ -64,6 +64,7 @@ def check_manifest(manifest_file_path: str, case_id, log: Logger):
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  raise e
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  # Add duplicate fields from supplied ones to fit formatting
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+ manifest["mrn"] = manifest["mrn"].strip()
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  manifest["patientInfo"]["identifiers"] = [
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  {
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  "codingCode": "MR",
ingestion/nebula/manifest_assembler.py CHANGED
@@ -131,7 +131,7 @@ class ManifestAssembler:
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  if not identifier:
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  return ""
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- return identifier.get("value", "")
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+ return identifier.get("value", "").strip()
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  def __parse_human_name(self, human_name: list[HumanName] | None):
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  if not human_name:
ingestion/nextgen/util/manifest_helpers.py CHANGED
@@ -25,7 +25,9 @@ def parse_patient_name(line: str) -> str:
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  def parse_sample_number(line: str) -> str:
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- return parse_pattern(r"^.*Specimen #: (\d*-?R?) .*$", line, "sample number")
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+ return parse_pattern(
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+ r"^.*Specimen #: (\d+(?:-[A-Za-z0-9]+)?(?:-?R)?) .*$", line, "sample number"
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+ )
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  def parse_body_site(line: str) -> str:
ingestion/nextgen/util/process_manifest.py CHANGED
@@ -87,7 +87,7 @@ def extract_patient_data(patient_info_lines: list[str]):
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  if "mrn" not in patient_data and "MRN #" in line:
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  mrnArray = line.split(" ")
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- mrn = search_and_grab(mrnArray, "MRN", 2)
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+ mrn = search_and_grab(mrnArray, "MRN", 2).strip()
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  patient_data["mrn"] = mrn
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  patient_data["patientInfo"]["identifiers"] = [
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  {
{phc_ingestion-1.0.3.dist-info → phc_ingestion-1.0.5.dist-info}/METADATA 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: 1.0.3
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+ Version: 1.0.5
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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-1.0.3.dist-info → phc_ingestion-1.0.5.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
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  ingestion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ingestion/broad/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ingestion/broad/process.py,sha256=IrtnANQlbPpI7aza-N_v8qMyxBOX17jq904wDNq7Nng,1803
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- ingestion/broad/utils.py,sha256=YHzbmB0tP-aQjvY9vRSn8iOhailleYwvctDbB0IEKb8,2853
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+ ingestion/broad/utils.py,sha256=QghE7y5Tz4m-sB1trKmMOMEHdf53CK9zVIeAOAu9QUU,2899
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  ingestion/caris/__init__.py,sha256=sFHl6qZWaacTbCFyikkIkuC-z459m5XQ7kwwoCw7HK8,61
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  ingestion/caris/process.py,sha256=7GaSTg9LjqSn7iTNbY3FJIPFvVjkd6wgXiVC00pn-7A,1411
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  ingestion/caris/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -28,20 +28,20 @@ ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd
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  ingestion/foundation/util/vcf_etl.py,sha256=GXV5JXswwdyHEEdPsM3Qq8tDPFkvZajrZn5chWgF53k,2266
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  ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
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- ingestion/generic/utils.py,sha256=YHzbmB0tP-aQjvY9vRSn8iOhailleYwvctDbB0IEKb8,2853
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+ ingestion/generic/utils.py,sha256=QghE7y5Tz4m-sB1trKmMOMEHdf53CK9zVIeAOAu9QUU,2899
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  ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
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  ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
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- ingestion/nebula/manifest_assembler.py,sha256=kcRSy6pixHkuVEK9QSoM-i6ZdLWMSYXw39eKGHvam34,7995
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+ ingestion/nebula/manifest_assembler.py,sha256=ZqppEe4n8tgh3118Jdq4rmaz5TCejNAbUATAZWx2QVM,8003
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  ingestion/nebula/process.py,sha256=N9OuipynGV_XgEL3nO5I_-di1tk9szOy8LqsyNTw0E0,2323
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  ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
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  ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
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  ingestion/nextgen/util/alteration_table.py,sha256=JTWBL1Fqj_pGsH5vwuVEnCUJle2wOBk6VYImHYCF9vg,6129
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  ingestion/nextgen/util/interpretation.py,sha256=a_B8jVjJXjkrN0hNzB260WNlZdY-BkL26LyLZcYP20A,950
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- ingestion/nextgen/util/manifest_helpers.py,sha256=zucNhbSss6IuU-kf3tpVoSxV27iSNQohGSMUXQQePSc,2729
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+ ingestion/nextgen/util/manifest_helpers.py,sha256=Eo89CBRDrMGLIq2OBkKS9lH5yL4pgMUOysle1TL9qr8,2765
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  ingestion/nextgen/util/nextgen_specific_genes.py,sha256=1jFcqvtYAlJ7eBwOBm1UC2TzAbjHjdlvPBUzxr1G8dY,1206
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  ingestion/nextgen/util/pre_filter_somatic_vcf.py,sha256=mIaUihmGLbS38D4Gy_Qtf1lFAfW0A-LgAgQmsrEiI-M,3529
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  ingestion/nextgen/util/process_cnv.py,sha256=MIirc8e0k6lsaTZkRM3U3L3IvbrcHmKQ4xlIu585514,2430
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- ingestion/nextgen/util/process_manifest.py,sha256=RsHzDGL1OBea2raoEHACo8owRodIFpX3xVE-aFOoyrg,8428
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+ ingestion/nextgen/util/process_manifest.py,sha256=feyJXt045e8NVwii0vHyZ7RdSfARs9Q205dgMz4d9DM,8436
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  ingestion/nextgen/util/process_structural.py,sha256=FKjkK7BkIlocnLs8rFCjrMC39FCQnD0nQCeWvi7cRoA,7539
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  ingestion/nextgen/util/process_vcf.py,sha256=ZZURSMnZhHDpFahzijZ4MvCfSWTPdIktzmnCKVVUbGs,7768
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  ingestion/nextgen/util/types.py,sha256=SSzt5gv-kss1PR45eQUelypWrGI-dAfQMO3GSD-T-Wg,22
@@ -63,6 +63,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
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  ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
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  ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
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  ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
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- phc_ingestion-1.0.3.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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- phc_ingestion-1.0.3.dist-info/METADATA,sha256=3B6vgXo5LbPEbaAxeCDBfhynbjPtpUd9KKSTpaO-S5Q,676
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- phc_ingestion-1.0.3.dist-info/RECORD,,
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+ phc_ingestion-1.0.5.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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+ phc_ingestion-1.0.5.dist-info/METADATA,sha256=lnKLnHLkhAEChPtanrK1bkL4iRXOxGkvZdFvf0QgdUQ,676
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+ phc_ingestion-1.0.5.dist-info/RECORD,,