phc-ingestion 0.10.8__py3-none-any.whl → 0.10.9__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ingestion/nebula/manifest_assembler.py +1 -1
- ingestion/nebula/process.py +3 -0
- {phc_ingestion-0.10.8.dist-info → phc_ingestion-0.10.9.dist-info}/METADATA +1 -1
- {phc_ingestion-0.10.8.dist-info → phc_ingestion-0.10.9.dist-info}/RECORD +5 -5
- {phc_ingestion-0.10.8.dist-info → phc_ingestion-0.10.9.dist-info}/WHEEL +0 -0
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@@ -160,7 +160,7 @@ class ManifestAssembler:
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raise RuntimeError(f"Patient with kit id {self.kit_id} not found")
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patient_birth_date = patient.get("birthDate")
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if not patient_birth_date:
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raise RuntimeError("Patient birth date is
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raise RuntimeError("Patient birth date is required to create a manifest")
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organization: Organization | None = self.__fetch_resource_by_type_and_reference(
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"Organization", patient.get("managingOrganization")
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ingestion/nebula/process.py
CHANGED
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@@ -1,6 +1,7 @@
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import os
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from ingestion.nebula.constants import NEBULA_TEST_TYPE
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from ingestion.shared_util.ga4gh import create_yaml
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from ingestion.vcf_standardization.standardize import standardize_vcf
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from lifeomic_logging import scoped_logger
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from ingestion.nebula.manifest_assembler import ManifestAssembler
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@@ -43,6 +44,8 @@ def process(vcf_file, out_path, file_name, source_file_id, ingestion_id, account
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}
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]
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create_yaml(manifest, file_name)
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# Hard-code genome reference for Nebula VCFs
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genome_reference = "GRCh38"
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@@ -28,8 +28,8 @@ ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,
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ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
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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=
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ingestion/nebula/process.py,sha256=
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ingestion/nebula/manifest_assembler.py,sha256=NaFxmWYiIUXOabP8TTaH3JkvwELVB7Z-TUMN4j_MoaM,6972
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ingestion/nebula/process.py,sha256=NhlaMl6q2nTocWZvTUVMKaq1IghiZKyqSjnWApchnAU,2331
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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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@@ -59,6 +59,6 @@ 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-0.10.
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phc_ingestion-0.10.
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phc_ingestion-0.10.
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phc_ingestion-0.10.9.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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phc_ingestion-0.10.9.dist-info/METADATA,sha256=5qVLQFXYsuhBOyl6rtGdZ-_YHSCBeX1Zyut3QiMJnI4,677
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phc_ingestion-0.10.9.dist-info/RECORD,,
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File without changes
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