Update to work with features

.github/workflows/tests.yml

@@ -0,0 +1,36 @@
+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

.gitignore

@@ -104,7 +104,6 @@ ENV/
 
 # data folders
 analysis/data/
-civicpy/data/
 
 # vcf files
 *.vcf

civicpy/civic.py

@@ -1223,6 +1223,8 @@ 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']
@@ -1235,7 +1237,10 @@ 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'
@@ -1333,7 +1338,7 @@ def _construct_get_gene_payload():
                 name
                 description
                 entrez_id: entrezId
-                aliases: geneAliases
+                aliases: featureAliases
                 sources {
                     id
                     name
@@ -1375,7 +1380,7 @@ def _construct_get_all_genes_payload():
                 name
                 description
                 entrez_id: entrezId
-                aliases: geneAliases
+                aliases: featureAliases
                 sources {
                     id
                     name
@@ -1421,7 +1426,7 @@ def _construct_get_molecular_profile_payload():
                     ... on MolecularProfileTextSegment {
                         text
                     }
-                    ... on Gene {
+                    ... on Feature {
                         id
                         name
                     }
@@ -1482,7 +1487,7 @@ def _construct_get_all_molecular_profiles_payload():
                     ... on MolecularProfileTextSegment {
                         text
                     }
-                    ... on Gene {
+                    ... on Feature {
                         id
                         name
                     }
@@ -1523,17 +1528,40 @@ 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
@@ -1542,47 +1570,54 @@ 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
@@ -1591,22 +1626,6 @@ def _construct_get_all_variants_payload():
                         description
                         url
                     }
-                    variantBases
-                    referenceBases
-                    referenceBuild
-                    primaryCoordinates {
-                        chromosome
-                        representativeTranscript
-                        start
-                        stop
-                    }
-                    secondaryCoordinates {
-                        chromosome
-                        representativeTranscript
-                        start
-                        stop
-                    }
-                    ensemblVersion
                 }
             }
         }"""
@@ -2200,7 +2219,7 @@ def search_variants_by_coordinates(coordinate_query, search_mode='any'):
         start_ct_idx = start_idx[:right_idx].index
         left_idx = stop_idx.searchsorted(start)
         stop_ct_idx = stop_idx[left_idx:].index
-        match_idx = chr_ct_idx & start_ct_idx & stop_ct_idx
+        match_idx = list(set(chr_ct_idx) & set(start_ct_idx) & set(stop_ct_idx))
         m_df = ct.loc[match_idx, ]
         if search_mode == 'any':
             var_digests = m_df.v_hash.to_list()

civicpy/tests/test_civic.py

@@ -173,13 +173,17 @@ def test_get_accepted_only(self):
         assert len(mps) >= 1333
 
     def test_get_by_id(self):
-        # Complex MP
+        mp = civic.get_molecular_profile_by_id(12)
+        assert mp.type == 'molecular_profile'
+        assert mp.id == 12
+
+    def test_get_by_id_complex_mp(self):
         mp = civic.get_molecular_profile_by_id(4432)
         assert mp.type == 'molecular_profile'
         mp_parsed_name = mp.parsed_name
         assert len(mp_parsed_name) == 5
         egfr_gene = mp_parsed_name[0]
-        assert egfr_gene.type == "gene"
+        assert egfr_gene.type == "feature"
         assert egfr_gene.id == 19
         assert egfr_gene.name == "EGFR"
         variant0 = mp_parsed_name[1]
@@ -197,7 +201,6 @@ def test_get_by_id(self):
         assert variant1.name == "Exon 19 Deletion"
         assert variant1.deprecated is False
 
-
 class TestVariantGroups(object):
 
     def test_get_all(self):
@@ -356,7 +359,7 @@ 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):
@@ -387,8 +390,8 @@ 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')

civicpy/tests/test_exports.py

@@ -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
@@ -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

setup.py

@@ -31,11 +31,11 @@
     ],
     extras_require={
         'test': [
-            'pytest==4.1.0',
-            'pytest-cov==2.9.0',
-            'attrs==18.2.0',
-            'python-coveralls',
-            'coverage<5.0',
+            'pytest==6.2.5',
+            'pytest-cov==5.0.0',
+            'attrs==22.1.0',
+            'coveralls',
+            'coverage<7.4.4',
         ],
         'docs': [
             'sphinx',