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Update graphql queries to work with newly released feature schema
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@susannasiebert
susannasiebert committed Apr 18, 2024
1 parent 65ff07f commit 67b5dc9
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Showing 6 changed files with 110 additions and 56 deletions.
36 changes: 36 additions & 0 deletions .github/workflows/tests.yml
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name: CIViCpy tests

on:
push:
branches: [ master, staging, hotfix ]
pull_request:
types: [opened, synchronize, edited, reopened]
branches: [ master, staging, hotfix]

jobs:
run_tests:
name: "Test CIViCpy in various Python versions"

runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']

steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install Python dependencies
run: |
pip install -e .[test]
- name: List installed packages
run: |
pip list
- name: Run tests
run: pytest --cov civicpy --cov-report term-missing
- name: Coveralls
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: coveralls --service=github
1 change: 0 additions & 1 deletion .gitignore
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Expand Up @@ -104,7 +104,6 @@ ENV/

# data folders
analysis/data/
civicpy/data/

# vcf files
*.vcf
115 changes: 67 additions & 48 deletions civicpy/civic.py
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Expand Up @@ -1215,6 +1215,8 @@ def _get_elements_by_ids(element, id_list=[], allow_cached=True, get_all=False):


def _postprocess_response_element(e, element):
if e is None:
raise Exception("{} not found".format(element.title()))
e['type'] = element
if element == 'assertion':
e['molecular_profile_id'] = e['molecular_profile']['id']
Expand All @@ -1227,7 +1229,10 @@ def _postprocess_response_element(e, element):
elif element == 'variant':
e['gene_id'] = e['gene']['id']
e['entrez_name'] = e['gene']['name']
e['entrez_id'] = e['gene']['entrezId']
#TODO: handle other types of Variants
if e['__typename'] != 'GeneVariant':
raise Exception("Variant type {} not supported yet".format(e['__typename']))
e['entrez_id'] = e['gene']['featureInstance']['entrezId']
build = e['referenceBuild']
if build == 'GRCH37':
build = 'GRCh37'
Expand Down Expand Up @@ -1325,7 +1330,7 @@ def _construct_get_gene_payload():
name
description
entrez_id: entrezId
aliases: geneAliases
aliases: featureAliases
sources {
id
name
Expand Down Expand Up @@ -1367,7 +1372,7 @@ def _construct_get_all_genes_payload():
name
description
entrez_id: entrezId
aliases: geneAliases
aliases: featureAliases
sources {
id
name
Expand Down Expand Up @@ -1485,17 +1490,40 @@ def _construct_get_variant_payload():
return """
query variant($id: Int!) {
variant(id: $id) {
__typename
id
name
allele_registry_id: alleleRegistryId
gene {
... on GeneVariant {
allele_registry_id: alleleRegistryId
clinvar_entries: clinvarIds
hgvs_expressions: hgvsDescriptions
variantBases
referenceBases
referenceBuild
primaryCoordinates {
chromosome
representativeTranscript
start
stop
}
secondaryCoordinates {
chromosome
representativeTranscript
start
stop
}
ensemblVersion
}
gene: feature {
id
name
entrezId
featureInstance {
... on Gene {
entrezId
}
}
}
single_variant_molecular_profile_id: singleVariantMolecularProfileId
clinvar_entries: clinvarIds
hgvs_expressions: hgvsDescriptions
variant_aliases: variantAliases
variant_types: variantTypes {
id
Expand All @@ -1504,47 +1532,54 @@ def _construct_get_variant_payload():
description
url
}
variantBases
referenceBases
referenceBuild
primaryCoordinates {
chromosome
representativeTranscript
start
stop
}
secondaryCoordinates {
chromosome
representativeTranscript
start
stop
}
ensemblVersion
}
}"""


def _construct_get_all_variants_payload():
return """
query variants($after: String) {
variants(after: $after) {
variants(after: $after, category: GENE) {
totalCount
pageInfo {
hasNextPage
endCursor
}
nodes {
__typename
id
name
allele_registry_id: alleleRegistryId
gene {
id
name
entrezId
... on GeneVariant {
allele_registry_id: alleleRegistryId
clinvar_entries: clinvarIds
hgvs_expressions: hgvsDescriptions
variantBases
referenceBases
referenceBuild
primaryCoordinates {
chromosome
representativeTranscript
start
stop
}
secondaryCoordinates {
chromosome
representativeTranscript
start
stop
}
ensemblVersion
}
gene: feature {
id
name
featureInstance {
... on Gene {
entrezId
}
}
}
single_variant_molecular_profile_id: singleVariantMolecularProfileId
clinvar_entries: clinvarIds
hgvs_expressions: hgvsDescriptions
variant_aliases: variantAliases
variant_types: variantTypes {
id
Expand All @@ -1553,22 +1588,6 @@ def _construct_get_all_variants_payload():
description
url
}
variantBases
referenceBases
referenceBuild
primaryCoordinates {
chromosome
representativeTranscript
start
stop
}
secondaryCoordinates {
chromosome
representativeTranscript
start
stop
}
ensemblVersion
}
}
}"""
Expand Down
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10 changes: 5 additions & 5 deletions civicpy/tests/test_civic.py
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Expand Up @@ -173,9 +173,9 @@ def test_get_accepted_only(self):
assert len(mps) >= 1333

def test_get_by_id(self):
mp = civic.get_molecular_profile_by_id(6353)
mp = civic.get_molecular_profile_by_id(12)
assert mp.type == 'molecular_profile'
assert mp.id == 6353
assert mp.id == 12

class TestVariantGroups(object):

Expand Down Expand Up @@ -335,7 +335,7 @@ def test_bulk_any_search_variants(self):
CoordinateQuery('7', 140453136, 140453137, 'TT')
]
search_results = civic.bulk_search_variants_by_coordinates(sorted_queries, search_mode='any')
assert len(search_results[sorted_queries[0]]) == 20
assert len(search_results[sorted_queries[0]]) == 19
assert len(search_results[sorted_queries[1]]) >= 19

def test_bulk_exact_search_variants(self):
Expand Down Expand Up @@ -366,8 +366,8 @@ def test_bulk_re_search_variants(self):
CoordinateQuery('7', 140453136, 140453137)
]
search_results = civic.bulk_search_variants_by_coordinates(sorted_queries, search_mode='record_encompassing')
assert len(search_results[sorted_queries[0]]) == 20
assert len(search_results[sorted_queries[1]]) == 17
assert len(search_results[sorted_queries[0]]) == 19
assert len(search_results[sorted_queries[1]]) == 16

def test_build38_exact_search_variants(self, v600e):
query = CoordinateQuery('7', 140753336, 140753336, 'T', 'A', 'GRCh38')
Expand Down
4 changes: 2 additions & 2 deletions civicpy/tests/test_exports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ def test_addrecord_from_gene(self, vcf_writer):
assert len(vcf_writer.variant_records) <= len(gene.variants)

def test_addrecord_from_evidence(self, vcf_writer):
evidence = civic._get_element_by_id('evidence', 373)
evidence = civic._get_element_by_id('evidence', 12)
vcf_writer.addrecord(evidence)
assert len(vcf_writer.variant_records) == 1
assert list(vcf_writer.variant_records)[0].id == evidence.molecular_profile.variants[0].id
Expand All @@ -106,7 +106,7 @@ def test_addrecord_from_assertion(self, vcf_writer):
assert list(vcf_writer.variant_records)[0].id == assertion.molecular_profile.variants[0].id

def test_add_record_from_molecular_profile(self, vcf_writer):
mp = civic._get_element_by_id('molecular_profile', 6353)
mp = civic._get_element_by_id('molecular_profile', 12)
vcf_writer.addrecord(mp)
assert len(vcf_writer.variant_records) == 1
assert list(vcf_writer.variant_records)[0].id == mp.variants[0].id
Expand Down

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