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New annotations from opencravat #188

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merged 10 commits into from
Dec 11, 2024
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Merged

New annotations from opencravat #188

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3e23ed5
work in progress for new annotations
SeriousHorncat Dec 10, 2024
2215466
wip with fixing the config a bit for gnomad and added the css to make…
SeriousHorncat Dec 10, 2024
55cbc0b
Rendering some of the new linkouts and datasets, with some fixture up…
SeriousHorncat Dec 11, 2024
a389b54
Fixed linting and added gnomad to be added as annotations; even thoug…
SeriousHorncat Dec 11, 2024
537c558
Fixed frontend unit test
SeriousHorncat Dec 11, 2024
a9e37c9
Updated python formatting
SeriousHorncat Dec 11, 2024
315fcfd
pleaaase
SeriousHorncat Dec 11, 2024
40adcce
please again
SeriousHorncat Dec 11, 2024
187c73b
Fixed the last unit test please
SeriousHorncat Dec 11, 2024
1221b24
removed print statement that shouldn't be there
SeriousHorncat Dec 11, 2024
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4 changes: 2 additions & 2 deletions backend/src/core/annotation_unit.py
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Expand Up @@ -100,10 +100,10 @@ def increment_delay_count(self):

def delay_count_exceeds(self):
"""
Checks if the annotation unit has exceeded the delay count within the queue.
Checks if the annotation unit has exceeded the delay count within the queue
Delay count is set as a magic number (10).
"""
if self.dataset['delay_count'] < 10:
if self.dataset['delay_count'] < 15:
return False
return True

Expand Down
27 changes: 27 additions & 0 deletions backend/tests/unit/core/test_annotation_task.py
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Expand Up @@ -47,6 +47,13 @@ def test_extraction_forge_gene_linkout_dataset(forge_annotation_task_gene):
assert extracted_annotations[0]['value'] == 'https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=45614'


def test_extraction_forge_hgvs_variant_without_transcript_version(hgvs_without_transcript_version_annotation_task):
"""Verifies the jq query used to forge create the transcript without a version dataset for a variant"""
forge_annotation = hgvs_without_transcript_version_annotation_task.annotate()
actual_extractions = hgvs_without_transcript_version_annotation_task.extract(forge_annotation)
assert actual_extractions[0]['value'] == "NM_170707:c.745C>T"


def test_annotation_extraction_for_transcript_id_dataset(http_annotation_transcript_id, transcript_annotation_response):
"""Verifying genomic unit extraction for a transcript using the the transcript ID dataset"""
actual_extractions = http_annotation_transcript_id.extract(transcript_annotation_response)
Expand Down Expand Up @@ -250,6 +257,26 @@ def fixture_transcript_id_dataset():
}


@pytest.fixture(name="hgvs_without_transcript_version_annotation_task")
def fixture_hgvs_without_transcript_version(hgvs_variant_genomic_unit):
"""An Annotation Unit to experiment with jq parsing and rebuilding a string in a result."""
annotation_unit = AnnotationUnit(
hgvs_variant_genomic_unit,
{
"data_set": "hgvs_variant_without_transcript_version",
"data_source": "Rosalution",
"annotation_source_type": "forge",
"genomic_unit_type": "hgvs_variant",
"base_string": "{hgvs_variant}",
"attribute":
".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}", # pylint: disable=line-too-long
"versioning_type": "rosalution"
}
)
task = ForgeAnnotationTask(annotation_unit)
return task


@pytest.fixture(name="hgvs_variant_annotation_unit")
def fixture_hgvs_variant_annotation_unit(hgvs_variant_genomic_unit, transcript_id_dataset):
"""
Expand Down
2 changes: 1 addition & 1 deletion backend/tests/unit/core/test_annotation_unit.py
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Expand Up @@ -64,5 +64,5 @@ def fixture_annotation_unit_lmna_has_dependencies(annotation_unit_lmna):
@pytest.fixture(name="annotation_unit_lmna_exceeded_delay_count")
def fixture_annotation_unit_lmna_with_annotated_dependency(annotation_unit_lmna):
"""Returns the annotation unit for the genomic unit LMNA and the dataset Clingen gene url"""
annotation_unit_lmna.dataset['delay_count'] = 10
annotation_unit_lmna.dataset['delay_count'] = 20
return annotation_unit_lmna
161 changes: 134 additions & 27 deletions etc/fixtures/initial-seed/annotations-config.json
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@@ -1,24 +1,37 @@
[
{
"data_set": "hgvs_variant_without_transcript_version",
"data_source": "Rosalution",
"annotation_source_type": "forge",
"genomic_unit_type": "hgvs_variant",
"base_string": "{hgvs_variant}",
"attribute": ".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}",
"versioning_type": "rosalution"
},
{
"data_set": "transcript_id",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { transcript_id: .transcript_id }",
"dependencies": ["hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
},
{
"data_set": "HPO_NCBI_GENE_ID",
"data_source": "HPO",
"genomic_unit_type": "gene",
"data_set": "ensembl_vep_vcf_string",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"url": "https://ontology.jax.org/api/network/search/GENE?q={gene}&page=0&limit=10",
"attribute": "{ \"HPO_NCBI_GENE_ID\": .results[] | select( .name == \"{gene}\") | .id }",
"versioning_type": "date"
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;vcf_string=1;",
"attribute": ".[] | {\"ensembl_vep_vcf_string\": .vcf_string} ",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
{
"data_set": "Ensembl Gene Id",
Expand Down Expand Up @@ -48,8 +61,9 @@
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"attribute": ".[] | select(.colocated_variants != null) | .colocated_variants[] | select(.var_synonyms != null) | .var_synonyms | select( .ClinVar != null ) | select(.ClinVar != []) | .ClinVar[] | select(contains(\"VCV\")) | sub(\"VCV0+\"; \"\") | {\"ClinVar_Variantion_Id\": . } ",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;clinvar=1;",
"versioning_type": "rosalution"
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;clinvar=1;",
"versioning_type": "rosalution",
"dependencies": ["hgvs_variant_without_transcript_version"]
},
{
"data_set": "OMIM_gene_search_url",
Expand Down Expand Up @@ -214,6 +228,44 @@
"dependencies": ["Ensembl Gene Id"],
"versioning_type": "rosalution"
},
{
"data_set": "gnomAD_variant_url",
"data_source": "Rosalution",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "forge",
"base_string": "https://gnomad.broadinstitute.org/variant/{ensembl_vep_vcf_string}?dataset=gnomad_r4",
"attribute": "{ \"gnomAD_variant_url\": .gnomAD_variant_url }",
"dependencies": ["ensembl_vep_vcf_string"],
"versioning_type": "rosalution"
},
{
"data_set": "gnomAD4",
"data_source": "OpenCravat",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"base_string": "https://run.opencravat.org/submit/annotate?{opencravat_search_variant_vcf_string}&annotators=gnomad4",
"attribute": "{ \"gnomad4\": .gnomad4 }",
"dependencies": ["opencravat_search_variant_vcf_string"],
"versioning_type": "date"
},
{
"data_set": "COSMIC_gene_url",
"data_source": "Rosalution",
"genomic_unit_type": "gene",
"annotation_source_type": "forge",
"base_string": "https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln={gene}",
"attribute": "{ \"COSMIC_gene_url\": .COSMIC_gene_url }",
"versioning_type": "rosalution"
},
{
"data_set": "HPO_NCBI_GENE_ID",
"data_source": "HPO",
"genomic_unit_type": "gene",
"annotation_source_type": "http",
"url": "https://ontology.jax.org/api/network/search/GENE?q={gene}&page=0&limit=10",
"attribute": "{ \"HPO_NCBI_GENE_ID\": .results[] | select( .name == \"{gene}\") | .id }",
"versioning_type": "date"
},
{
"data_set": "OMIM",
"data_source": "HPO",
Expand Down Expand Up @@ -384,9 +436,10 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { polyphen_prediction: .polyphen_prediction, transcript_id: .transcript_id }",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
Expand All @@ -396,9 +449,10 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { polyphen_score: .polyphen_score, transcript_id: .transcript_id }",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
Expand All @@ -408,9 +462,10 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { sift_prediction: .sift_prediction, transcript_id: .transcript_id }",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
Expand All @@ -420,9 +475,11 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { sift_score: .sift_score, transcript_id: .transcript_id }",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],

"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
Expand All @@ -432,20 +489,57 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { consequence_terms: .consequence_terms, transcript_id: .transcript_id }",
"dependencies": ["hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
{
"data_set": "CADD",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;CADD=1;refseq=1;",
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;",
"attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { CADD: .cadd_phred }",
"dependencies": ["transcript"],
"dependencies": ["transcript","hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
{
"data_set": "alphamissense_pathogenicity",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
"attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_pathogenicity }",
"dependencies": ["transcript","hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
{
"data_set": "alphamissense_classification",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
"attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_class }",
"dependencies": ["transcript","hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
{
"data_set": "revel",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
"attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { revel: .revel }",
"dependencies": ["transcript","hgvs_variant_without_transcript_version"],
"versioning_type": "rest",
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
Expand All @@ -456,9 +550,10 @@
"genomic_unit_type": "hgvs_variant",
"transcript": true,
"annotation_source_type": "http",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
"url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
"attribute": ".[].transcript_consequences[] | { impact: .impact, transcript_id: .transcript_id }",
"versioning_type": "rest",
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
},
Expand Down Expand Up @@ -538,6 +633,18 @@
"version_url": "https://www.alliancegenome.org/api/releaseInfo",
"version_attribute": ".releaseVersion"
},
{
"data_set": "C-Elegens_Worm_Base_url",
"data_source": "Alliance Genome",
"annotation_source_type": "http",
"genomic_unit_type": "gene",
"url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}",
"attribute": "{ \"C-Elegens_Worm_Base_url\": .modCrossRefCompleteUrl }",
"dependencies": ["C-Elegens Gene Identifier"],
"versioning_type": "rest",
"version_url": "https://www.alliancegenome.org/api/releaseInfo",
"version_attribute": ".releaseVersion"
},
{
"data_set": "C-Elegens_Alliance_Genome_url",
"data_source": "Rosalution",
Expand All @@ -549,15 +656,15 @@
"versioning_type": "rosalution"
},
{
"data_set": "C-Elegens_Worm_Base_url",
"data_source": "Alliance Genome",
"data_set": "opencravat_search_variant_vcf_string",
"data_source": "Ensembl",
"genomic_unit_type": "hgvs_variant",
"annotation_source_type": "http",
"genomic_unit_type": "gene",
"url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}",
"attribute": "{ \"C-Elegens_Worm_Base_url\": .modCrossRefCompleteUrl }",
"dependencies": ["C-Elegens Gene Identifier"],
"url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;vcf_string=1;",
"attribute": ".[] | .vcf_string | split(\"-\") | \"chrom=chr\" + .[0] + \"&pos=\" + .[1] + \"&ref_base=\" + .[2] + \"&alt_base=\" + .[3] | {\"opencravat_search_variant_vcf_string\": . }",
"versioning_type": "rest",
"version_url": "https://www.alliancegenome.org/api/releaseInfo",
"version_attribute": ".releaseVersion"
"dependencies": ["hgvs_variant_without_transcript_version"],
"version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
"version_attribute": ".releases[]"
}
]
46 changes: 46 additions & 0 deletions etc/fixtures/initial-seed/genomic-units.json
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Expand Up @@ -457,6 +457,34 @@
}
]
},
{
"alphamissense_classification": [
{
"data_source": "Ensembl",
"version": 112,
"value": "ambiguous"
}
]
},
{
"alphamissense_pathogenicity": [
{
"data_source": "Ensembl",
"version": 112,
"value": 0.5303
}
]
},
{
"alphamissense": [{
"data_source": "Ensembl",
"version": 112,
"value": {
"am_class": "ambiguous",
"am_pathogenicity": "0.5303"
}
}]
},
{
"ClinVar_variant_url": [
{
Expand All @@ -465,6 +493,24 @@
"value": "https://www.ncbi.nlm.nih.gov/clinvar/variation/581244"
}
]
},
{
"ensembl_vep_vcf_string": [
{
"data_source": "Rosalution",
"version": "rosalution-manifest-00",
"value": "X-151404916-G-T"
}
]
},
{
"gnomAD_variant_url": [
{
"data_source": "Rosalution",
"version": "rosalution-manifest-00",
"value": "https://gnomad.broadinstitute.org/variant/X-151404916-G-T?dataset=gnomad_r4"
}
]
}
]
},
Expand Down
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