adding tests for creating the input file

tests/test_create_input_data.py

@@ -0,0 +1,166 @@
+import unittest
+from pathlib import Path
+
+from phenopackets import (
+    Diagnosis,
+    Disease,
+    Family,
+    File,
+    GeneDescriptor,
+    GenomicInterpretation,
+    Individual,
+    Interpretation,
+    MetaData,
+    OntologyClass,
+    Pedigree,
+    Phenopacket,
+    PhenotypicFeature,
+    Resource,
+    VariantInterpretation,
+    VariationDescriptor,
+    VcfRecord,
+)
+from pheval.utils.phenopacket_utils import PhenopacketUtil
+
+from pheval_gado.prepare.create_input_data import (
+    get_list_of_phenotypic_features, create_case_id_from_phenopacket,
+    create_entry_for_phenopacket
+)
+
+interpretations = [
+    Interpretation(
+        id="test-subject-1-int",
+        progress_status="SOLVED",
+        diagnosis=Diagnosis(
+            disease=OntologyClass(id="OMIM:219700", label="Cystic Fibrosis"),
+            genomic_interpretations=[
+                GenomicInterpretation(
+                    subject_or_biosample_id="test-subject-1",
+                    interpretation_status=4,
+                    variant_interpretation=VariantInterpretation(
+                        acmg_pathogenicity_classification="NOT_PROVIDED",
+                        therapeutic_actionability="UNKNOWN_ACTIONABILITY",
+                        variation_descriptor=VariationDescriptor(
+                            gene_context=GeneDescriptor(
+                                value_id="ENSG00000102302",
+                                symbol="FGD1",
+                                alternate_ids=[
+                                    "HGNC:3663",
+                                    "ncbigene:2245",
+                                    "ensembl:ENSG00000102302",
+                                    "symbol:FGD1",
+                                ],
+                            ),
+                            vcf_record=VcfRecord(
+                                genome_assembly="GRCh37",
+                                chrom="X",
+                                pos=54492285,
+                                ref="C",
+                                alt="T",
+                            ),
+                            allelic_state=OntologyClass(
+                                id="GENO:0000134",
+                                label="hemizygous",
+                            ),
+                        ),
+                    ),
+                ),
+                GenomicInterpretation(
+                    subject_or_biosample_id="test-subject-1",
+                    interpretation_status=4,
+                    variant_interpretation=VariantInterpretation(
+                        acmg_pathogenicity_classification="NOT_PROVIDED",
+                        therapeutic_actionability="UNKNOWN_ACTIONABILITY",
+                        variation_descriptor=VariationDescriptor(
+                            gene_context=GeneDescriptor(
+                                value_id="ENSG00000176225",
+                                symbol="RTTN",
+                                alternate_ids=[
+                                    "HGNC:18654",
+                                    "ncbigene:25914",
+                                    "ensembl:ENSG00000176225",
+                                    "symbol:RTTN",
+                                ],
+                            ),
+                            vcf_record=VcfRecord(
+                                genome_assembly="GRCh37",
+                                chrom="18",
+                                pos=67691994,
+                                ref="G",
+                                alt="A",
+                            ),
+                            allelic_state=OntologyClass(
+                                id="GENO:0000402", label="compound heterozygous"
+                            ),
+                        ),
+                    ),
+                ),
+            ],
+        ),
+    )
+]
+phenotypic_features_with_excluded = [
+    PhenotypicFeature(type=OntologyClass(id="HP:0000256", label="Macrocephaly")),
+    PhenotypicFeature(type=OntologyClass(id="HP:0002059", label="Cerebral atrophy")),
+    PhenotypicFeature(type=OntologyClass(id="HP:0100309", label="Subdural hemorrhage")),
+    PhenotypicFeature(type=OntologyClass(id="HP:0003150", label="Glutaric aciduria")),
+    PhenotypicFeature(type=OntologyClass(id="HP:0001332", label="Dystonia")),
+    PhenotypicFeature(
+        type=OntologyClass(id="HP:0008494", label="Inferior lens subluxation"), excluded=True
+    ),
+]
+
+diseases = [Disease(term=OntologyClass(id="OMIM:219700", label="Cystic Fibrosis"))]
+
+phenopacket_files = [
+    File(
+        uri="test/path/to/test_1.vcf",
+        file_attributes={"fileFormat": "vcf", "genomeAssembly": "GRCh37"},
+    ),
+    File(
+        uri="test_1.ped",
+        file_attributes={"fileFormat": "PED", "genomeAssembly": "GRCh37"},
+    ),
+]
+phenopacket_metadata = MetaData(
+    created_by="pheval-converter",
+    resources=[
+        Resource(
+            id="hp",
+            name="human phenotype ontology",
+            url="http://purl.obolibrary.org/obo/hp.owl",
+            version="hp/releases/2019-11-08",
+            namespace_prefix="HP",
+            iri_prefix="http://purl.obolibrary.org/obo/HP_",
+        )
+    ],
+    phenopacket_schema_version="2.0",
+)
+
+phenopacket = Phenopacket(
+    id="test-subject",
+    subject=Individual(id="test-subject-1", sex=1),
+    phenotypic_features=phenotypic_features_with_excluded,
+    interpretations=interpretations,
+    diseases=diseases,
+    files=phenopacket_files,
+    meta_data=phenopacket_metadata,
+)
+
+
+class TestGetListOfPhenotypicFeatures(unittest.TestCase):
+    def test_get_list_of_phenotypic_features(self):
+        self.assertEqual(get_list_of_phenotypic_features(PhenopacketUtil(phenopacket)),
+                         ['HP:0000256', 'HP:0002059', 'HP:0100309', 'HP:0003150', 'HP:0001332'])
+
+
+class TestCreateCaseIDFromPhenopacket(unittest.TestCase):
+    def test_create_case_id_from_phenopacket(self):
+        self.assertEqual(create_case_id_from_phenopacket(Path("/path/to/Phenopacket-case-1.json")),
+                         "Phenopacket-case-1")
+
+
+class TestCreateEntryForPhenopacket(unittest.TestCase):
+    def test_create_entry_for_phenopacket(self):
+        self.assertEqual(create_entry_for_phenopacket(Path("/path/to/Phenopacket-case-1.json"), phenopacket),
+                         ['Phenopacket-case-1', 'HP:0000256', 'HP:0002059', 'HP:0100309', 'HP:0003150', 'HP:0001332'])