AdvancedAnalysisFileParser 0.1.0__py3-none-any.whl

AdvancedAnalysisFileParser/Test/smn_silent_carrier_risk.json

@@ -0,0 +1,101 @@
+{
+  "softwareVersion": "dragen v05.121.779.4.4.4",
+  "sampleId": "22WVHMLT4_5_270UDI-idt-UMI",
+  "genomeBuild": "hg38",
+  "phenotypeDatabaseSources": [
+    "PharmCAT Phenotypes Version: Snapshot-2022.09.15"
+  ],
+  "cyp2b6": {
+    "genotype": "*1/*29",
+    "genotypeFilter": "PASS",
+    "phenotypeDatabaseAnnotation": "Intermediate Metabolizer"
+  },
+  "lpa": {
+    "kiv2CopyNumber": 39.45213332616308,
+    "refMarkerAlleleCopyNumber": null,
+    "altMarkerAlleleCopyNumber": null,
+    "type": "Homozygous REF markers call",
+    "variants": [
+      {
+        "hgvs": "LPA:4925G>A",
+        "qual": 0.0,
+        "altCopyNumber": 0,
+        "altCopyNumberQuality": 150.0
+      },
+      {
+        "hgvs": "LPA:4733G>A",
+        "qual": 0.0,
+        "altCopyNumber": 0,
+        "altCopyNumberQuality": 150.0
+      }
+    ]
+  },
+  "rh": {
+    "totalCopyNumber": 4,
+    "rhdCopyNumber": 2,
+    "rhceCopyNumber": 2,
+    "variants": [
+      {
+        "hgvs": "NC_000001.11g.25405596_25409676con25283766_25287797",
+        "qual": 26.086525474041604,
+        "altCopyNumber": 1,
+        "altCopyNumberQuality": 150.0
+      }
+    ]
+  },
+  "cyp21a2": {
+    "totalCopyNumber": 3,
+    "deletionBreakpointInGene": false,
+    "recombinantHaplotypes": [
+      "",
+      ""
+    ],
+    "variants": []
+  },
+  "cyp2d6": {
+    "totalCopyNumber": 3,
+    "genotype": "*1/*5",
+    "genotypeFilter": "PASS",
+    "genotypeQuality": 150,
+    "phenotypeDatabaseAnnotation": "Intermediate Metabolizer",
+    "variants": [
+      {
+        "alleleId": "g.42126938C>T",
+        "alleleCopyNumber": 2,
+        "genotypeQuality": 21,
+        "filter": "PASS"
+      }
+    ]
+  },
+  "gba": {
+    "totalCopyNumber": 4,
+    "deletionBreakpointInGene": null,
+    "recombinantHaplotypes": [
+      "",
+      ""
+    ],
+    "variants": []
+  },
+  "hba": {
+    "totalCopyNumber": 4,
+    "genotype": "aa/aa",
+    "genotypeQuality": 56,
+    "genotypeFilter": "PASS",
+    "variants": []
+  },
+  "smn": {
+    "fullLengthCopyNumber": 3,
+    "totalCopyNumber": 4,
+    "smn1CopyNumber": 2,
+    "smn2CopyNumber": 1,
+    "smn2Delta78CopyNumber": 1,
+    "fullLengthCopyNumberFloat": "2.59",
+    "totalCopyNumberFloat": "3.56",
+    "variants": [
+      {
+        "alleleId": "NM_000344.4:c.*3+80T>G",
+        "alleleCopyNumber": 1
+      }
+    ]
+  }
+}

AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py

@@ -0,0 +1,342 @@
+import json
+import logging
+import os
+import pytest
+from AdvancedAnalysisFileParser import JsonDict
+from AdvancedAnalysisFileParser import AdvancedAnalysisParser
+
+# Always resolve the test data directory relative to this file
+TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "Test")
+
+# Define test contexts for parametrization
+TEST_CONTEXTS = [
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["dummy_warnset_1.targeted.json"]
+            },
+            "expected": {
+                "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>positive for hemoglobin H disease</b>"},
+                "SMN": {"warning": "Based on the SMN Caller, this sample is positive for Spinal Muscular Atrophy"},
+                "GBA": {"warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"}
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["dummy_warnset_2.targeted.json"]
+            },
+            "expected": {
+                "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>carrier</b>"},
+                "SMN": {"warning": "Based on the SMN Caller, this sample is carrier for Spinal Muscular Atrophy"},
+                "GBA": {"warning": "Multiple GBA variants detected; phase is unknown (could be in cis or in trans). Interpret cautiously."}
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["dummy_warnset_3.targeted.json"]
+            },
+            "expected": {
+                "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>silent carrier</b>"},
+                "SMN": {"warning": "Based on the SMN Caller, this sample has increased risk of being a silent carrier (2+0) for Spinal Muscular Atrophy"},
+                "GBA": {"warning": "Based on the GBA Caller, this sample is carrier for Gaucher disease"}
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["dummy_gba_phase_unknown_one_recomb_plus_variant.targeted.json"]
+            },
+            "expected": {
+                "GBA": {"warning": "Multiple GBA variants detected; phase is unknown (could be in cis or in trans). Interpret cautiously."}
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["dummy_gba_carrier_one_recomb_only.targeted.json"]
+            },
+            "expected": {
+                "GBA": {"warning": "Based on the GBA Caller, this sample is carrier for Gaucher disease"}
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["gba_carrier_1.json"]
+            },
+            "expected": {
+                "GBA": {
+                    "warning": "Based on the GBA Caller, this sample is carrier for Gaucher disease"
+                }
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["gba_positive_1.json"]
+            },
+            "expected": {
+                "GBA": {
+                    "warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"
+                }
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["smn_carrier.json"]
+            },
+            "expected": {
+                "SMN": {
+                    "warning": "Based on the SMN Caller, this sample is carrier for Spinal Muscular Atrophy"
+                }
+            }
+        },
+        {
+            "request": {
+                "output_json": "out.json",
+                "input_dir": TEST_DATA_DIR,
+                "output_dir": TEST_DATA_DIR,
+                "input_files": ["smn_positive.json"]
+            },
+            "expected": {
+                "SMN": {
+                    "warning": "Based on the SMN Caller, this sample is positive for Spinal Muscular Atrophy"
+                }
+            }
+        },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba_positive_1.json"]
+        },
+        "expected": {
+            "GBA": {
+                "warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"
+            }
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_carrier_1.json"]
+        },
+        "expected": {
+            "HBA": {
+                "warning": "Based on HBA Special Caller, this sample is defined as <b>carrier</b>"
+            }
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_hemoglobin_h_disease.json"]
+        },
+        "expected": {
+            "HBA": {
+                "warning": "Based on HBA Special Caller, this sample is defined as <b>positive for hemoglobin H disease</b>"
+            }
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_silent_carrier.json"]
+        },
+        "expected": {
+            "HBA": {
+                "warning": "Based on HBA Special Caller, this sample is defined as <b>silent carrier</b>"
+            }
+        }
+    },
+      {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba_carrier_2.json"]
+        },
+        "expected": {
+            "GBA": {"warning": "Based on the GBA Caller, this sample is carrier for Gaucher disease"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba_multiple_phase_unknown_1.json"]
+        },
+        "expected": {
+            "GBA": {"warning": "Multiple GBA variants detected; phase is unknown (could be in cis or in trans). Interpret cautiously."}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba_multiple_phase_unknown_2.json"]
+        },
+        "expected": {
+            "GBA": {"warning": "Multiple GBA variants detected; phase is unknown (could be in cis or in trans). Interpret cautiously."}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba_positive_2.json"]
+        },
+        "expected": {
+            "GBA": {"warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_carrier_2.json"]
+        },
+        "expected": {
+            "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>carrier</b>"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_carrier_3.json"]
+        },
+        "expected": {
+            "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>carrier</b>"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["hba_carrier_4.json"]
+        },
+        "expected": {
+            "HBA": {"warning": "Based on HBA Special Caller, this sample is defined as <b>carrier</b>"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["smn_silent_carrier_risk.json"]
+        },
+        "expected": {
+            "SMN": {"warning": "Based on the SMN Caller, this sample has increased risk of being a silent carrier (2+0) for Spinal Muscular Atrophy"},
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["dragen424.targeted.json"]
+        },
+        "expected": {
+            "CYP2D6": {},
+            "CYP2B6": {},
+            "CYP21A2": {},
+            "LPA": {}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files" : ["dummy_gba_affected_nonrecomb_acn2.targeted.json"]
+        },
+        "expected": {
+            "GBA": {"warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["gba.tsv"]
+        },
+        "expected": {
+            "GBA": {"warning": "Based on the GBA Caller, this sample is positive for Gaucher disease"}
+        }
+    },
+    {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["smn.tsv"]
+        },
+        "expected": {
+            "SMN1": {"warning": "Based on the SMN Caller, this sample is positive for Spinal Muscular Atrophy"}
+        }
+    },
+        {
+        "request": {
+            "output_json": "out.json",
+            "input_dir": TEST_DATA_DIR,
+            "output_dir": TEST_DATA_DIR,
+            "input_files": ["TruSightOncology500.CombinedVariantOutput.tsv"]
+        },
+        "expected": {
+            # TODO: Fill in expected output for this file
+        }
+    },
+]
+
+@pytest.mark.parametrize("context", TEST_CONTEXTS)
+def test_parser_in_memory(context: JsonDict) -> None:
+    parser = AdvancedAnalysisParser(context["request"])
+    result = parser.run(return_dict=True)
+    print(json.dumps(result, indent=2, default=str))
+    if result is not None:
+        print(f"[DEBUG] Result keys: {list(result.keys())}")
+        for gene in result:
+            print(f"[DEBUG] {gene} warning: {result[gene].get('warning')}")
+    assert result is not None
+    # Validate all expected fields (not just warning)
+    for gene, expected in context["expected"].items():
+        assert gene in result, f"Missing result for {gene}"
+        for key, value in expected.items():
+            result_value = result[gene].get(key, None)
+            assert result_value == value, f"Mismatch for {gene}.{key}: got {result_value}, expected {value}"
+    

AdvancedAnalysisFileParser/Warnings/CarrierPositiveWarning.py

@@ -0,0 +1,18 @@
+from .IWarning import IWarning
+from ..Models import *
+class CarrierPositiveWarning(IWarning):
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        name = config.get("caller_name") or config.get("name")
+        disease = config.get("disease_name") or config.get("disease")
+        conditions = config.get("conditions",{})
+        for condition in conditions:
+            condition["operator"] = ConditionOperator[condition["operator"]]
+            field_condition = FieldCondition(
+                field= condition.get("field",None),
+                operator=condition.get("operator"),
+                value=condition.get("value"),
+                message=f"Based on the {name}, this sample is <b>Positive</b> for {disease}"
+            )
+            if field_condition.check(data):
+                return field_condition.__str__()
+        return ""

AdvancedAnalysisFileParser/Warnings/ConditionWarning.py

@@ -0,0 +1,20 @@
+from .IWarning import IWarning
+from ..Models import JsonDict, FieldCondition, ConditionOperator
+
+class ConditionWarning(IWarning):
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        # config["conditions"] is expected to be a list of FieldCondition-like dicts
+        msgs = []
+        for cond_dict in config.get("conditions", []):
+            cond_dict["operator"] = ConditionOperator[cond_dict["operator"]]
+            cond = FieldCondition(**cond_dict)
+            if isinstance(data, dict):
+                if cond_dict.get("field") in data:
+                    data = data[cond_dict["field"]]
+            warning = cond.__str__()
+            if warning in msgs:
+                continue
+            if cond.check(data):
+                msgs.append(warning)
+                print(f"Warning triggered by condition: {warning}")
+        return ". ".join(msgs)

AdvancedAnalysisFileParser/Warnings/GbaWarning.py

@@ -0,0 +1,50 @@
+from .IWarning import IWarning
+from ..Models import JsonDict
+
+class GbaWarning(IWarning):
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        name = config.get("caller_name") or config.get("name") or "GBA Caller"
+        disease = config.get("disease_name") or config.get("disease") or "Gaucher disease"
+
+        rec_list = [x for x in (data.get("recombinantHaplotypes") or []) if x]
+        rec_count = len(rec_list)
+
+        nonrec = []
+        for v in data.get("variants", []) or []:
+            # treat strings as nonrecombinant variants without copy number (defaults to 1 for counting phase-unknown conditions)
+            if isinstance(v, dict) or isinstance(v, str):
+                nonrec.append(v)
+
+        # Helper counts
+        def allele_copy(v):
+            if isinstance(v, dict):
+                ac = (
+                    v.get("alleleCopyNumber")
+                    or v.get("allele_copy_number")
+                    or v.get("altCopyNumber")
+                )
+                return ac if isinstance(ac, (int, float)) else 0
+            # if variant represented as string, assume copy number 1 for phase-unknown heuristics
+            if isinstance(v, str):
+                return 1
+            return 0
+
+        any_nonrec_ge2 = any(allele_copy(v) >= 2 for v in nonrec)
+        nonrec_eq1 = [v for v in nonrec if allele_copy(v) == 1]
+        nonrec_eq1_count = len(nonrec_eq1)
+
+        # Positive: evidence of two affected alleles
+        if rec_count >= 2 or any_nonrec_ge2:
+            return f"Based on the {name}, this sample is positive for {disease}"
+
+        # Phase unknown: mixed findings
+        if (rec_count == 1 and nonrec_eq1_count >= 1) or (rec_count == 0 and nonrec_eq1_count >= 2):
+            return (
+                "Multiple GBA variants detected; phase is unknown (could be in cis or in trans). Interpret cautiously."
+            )
+
+        # Carrier: exactly one affected allele
+        if (rec_count == 1 and nonrec_eq1_count == 0 and not any_nonrec_ge2) or (rec_count == 0 and nonrec_eq1_count == 1):
+            return f"Based on the {name}, this sample is carrier for {disease}"
+
+        return ""

AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py

@@ -0,0 +1,22 @@
+from .IWarning import IWarning
+from ..Models import JsonDict
+class GenotypeWarning(IWarning):
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        name = config.get("caller_name") or config.get("name")
+        genotype_key = config.get("genotype_data_key", "genotype")
+        sample = data.get(genotype_key)
+        mapping = config.get("phenotypeGenotypeMapping") or config.get("phenotype_genotype_mapping") or {}
+        warning = ""
+        # Support both old and new mapping formats
+        if mapping:
+            if all(isinstance(v, str) for v in mapping.values()):
+                # Old format: genotype→phenotype
+                if sample in mapping:
+                    warning = f"Based on {name}, this sample is defined as <b>{mapping[sample]}</b>"
+            elif all(isinstance(v, list) for v in mapping.values()):
+                # New format: phenotype→[genotypes]
+                for phenotype, genotypes in mapping.items():
+                    if sample in genotypes:
+                        warning = f"Based on {name}, this sample is defined as <b>{phenotype}</b>"
+                        break
+        return warning

AdvancedAnalysisFileParser/Warnings/IWarning.py

@@ -0,0 +1,7 @@
+from abc import ABC, abstractmethod
+from ..Models import JsonDict
+
+class IWarning(ABC):
+    @abstractmethod
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        pass

AdvancedAnalysisFileParser/Warnings/SmnWarning.py

@@ -0,0 +1,29 @@
+from .IWarning import IWarning
+from ..Models import JsonDict
+
+class SmnWarning(IWarning):
+    def format(self, config: JsonDict, data: JsonDict) -> str:
+        name = config.get("caller_name") or config.get("name") or "SMN Caller"
+        disease = config.get("disease_name") or config.get("disease") or "Spinal Muscular Atrophy"
+        smn1_cn = data.get("smn1CopyNumber")
+        # Positive if smn1CopyNumber == 0
+        if isinstance(smn1_cn, (int, float)) and smn1_cn == 0:
+            return f"Based on the {name}, this sample is positive for {disease}"
+        # Carrier if smn1CopyNumber == 1
+        if isinstance(smn1_cn, (int, float)) and smn1_cn == 1:
+            return f"Based on the {name}, this sample is carrier for {disease}"
+        # Silent carrier risk if smn1CopyNumber == 2 and specific variant has alleleCopyNumber >= threshold
+        if isinstance(smn1_cn, (int, float)) and smn1_cn == 2:
+            for v in data.get("variants", []) or []:
+                # variants may be strings or dicts with keys like 'alleleId', 'hgvs', 'name', 'variantName', 'id'
+                if isinstance(v, str):
+                    vid = v
+                    ac = 1  # presence implies >=1 when encoded as string only
+                elif isinstance(v, dict):
+                    vid = v.get("alleleId") or v.get("hgvs") or v.get("name") or v.get("variantName") or v.get("id") or ""
+                    ac = (v.get("alleleCopyNumber") or v.get("allele_copy_number") or v.get("altCopyNumber"))
+                else:
+                    continue
+                if vid != "" and isinstance(ac, (int, float)) and ac >= 1:
+                    return (f"Based on the {name}, this sample has increased risk of being a silent carrier (2+0) for {disease}")
+        return ""

AdvancedAnalysisFileParser/Warnings/WarningFactory.py

@@ -0,0 +1,31 @@
+from typing import Dict, Optional
+from .IWarning import IWarning
+from .CarrierPositiveWarning import CarrierPositiveWarning
+from .GenotypeWarning import GenotypeWarning
+from .ConditionWarning import ConditionWarning
+from .SmnWarning import SmnWarning
+from .GbaWarning import GbaWarning
+class WarningFactory:
+    @staticmethod
+    def get_formatter(wtype: Optional[Dict]) -> IWarning:
+        if wtype is None:
+            raise ValueError("Warning type cannot be None")
+        warning_type = None
+        if isinstance(wtype, Dict) and "type" in wtype:
+            warning_type = wtype["type"]
+        if warning_type == None or warning_type == "":
+            raise ValueError("Warning type cannot be empty")
+        if warning_type == "condition":
+            return ConditionWarning()
+        if warning_type == "carrier_positive":
+            return CarrierPositiveWarning()
+        if warning_type == "genotype":
+            return GenotypeWarning()
+        if warning_type == "smn":
+            return SmnWarning()
+        if warning_type == "gba":
+            return GbaWarning()
+        if not isinstance(wtype, Dict):
+            raise TypeError(f"Warning type must be a dict, got {type(wtype).__name__}")
+        # If the warning type is not found, raise an error
+        raise ValueError(f"Unknown warning type: {warning_type}")

AdvancedAnalysisFileParser/Warnings/__init__.py

@@ -0,0 +1,7 @@
+from .IWarning import IWarning
+from .WarningFactory import WarningFactory
+
+__all__ = [
+    "IWarning",
+    "WarningFactory",
+]

AdvancedAnalysisFileParser/__init__.py

@@ -0,0 +1,18 @@
+from .AdvancedAnalysisParser import AdvancedAnalysisParser
+from .Models import JsonDict, FieldCondition, ConditionOperator, FieldWarningConfig, SectionConfig
+from .Warnings import IWarning, WarningFactory
+from .Parsers import IAdvancedAnalysisFileParser, AdvancedAnalysisFileParserFactory
+from .AdvancedAnalysisConstants import AdvancedAnalysisConstants
+__all__ = [
+    "AdvancedAnalysisParser",
+    "JsonDict",
+    "FieldCondition",
+    "ConditionOperator",
+    "FieldWarningConfig",
+    "SectionConfig",
+    "IWarning",
+    "WarningFactory",
+    "IAdvancedAnalysisFileParser",
+    "AdvancedAnalysisFileParserFactory",
+    "AdvancedAnalysisConstants"
+]