Merge branch 'dev'

Author: eboileau

server/src/scimodom/services/annotation/ensembl.py

@@ -136,6 +136,9 @@ def _get_annotation_paths(
             release=annotation.release,
             fmt=self.FMT,
         )
+        # TODO: AD HOC
+        if annotation.taxa_id in [4932, 6239]:
+            filen = filen.replace(".chr", "")
         url = urljoin(
             specs.ENSEMBL_FTP,
             f"release-{annotation.release}",

server/src/scimodom/utils/specifications.py

@@ -97,11 +97,11 @@
 
 # Assembly/Annotation
 ENSEMBL_FTP = "https://ftp.ensembl.org/pub"
-ENSEMBL_SERVER = "http://rest.ensembl.org"
+# release 110
+ENSEMBL_SERVER = "http://jul2023.rest.ensembl.org"  # "http://rest.ensembl.org"
 ENSEMBL_DATA = "info/data"
 ENSEMBL_ASM = "info/assembly"
-# ENSEMBL_ASM_MAPPING = "assembly_mapping"
-ENSEMBL_ASM_MAPPING = "current_assembly_chain"
+ENSEMBL_ASM_MAPPING = "release-110/assembly_chain"  # "current_assembly_chain"
 
 # GtRNAdb annotation
 GTRNADB_URL = "http://gtrnadb.ucsc.edu/genomes/"

server/tests/unit/services/test_assembly.py

@@ -259,7 +259,7 @@ def test_add_assembly(Session, file_service, setup):
         Session,
         file_service,
         url_to_data={
-            "https://ftp.ensembl.org/pub/current_assembly_chain/homo_sapiens/NCBI36_to_GRCh38.chain.gz": b"foo"
+            "https://ftp.ensembl.org/pub/release-110/assembly_chain/homo_sapiens/NCBI36_to_GRCh38.chain.gz": b"foo"
         },
     )
     assembly_id = service.add_assembly(9606, "NCBI36")
@@ -339,7 +339,7 @@ def test_add_assembly_wrong_url(Session, file_service, setup):
 
 EXPECTED_RELEASE_JSON = """{
 \t"releases": [
-\t\t112
+\t\t110
 \t]
 }"""
 
@@ -351,8 +351,8 @@ def test_prepare_assembly_for_version(Session, file_service, setup):
         Session,
         file_service,
         url_to_result={
-            "http://rest.ensembl.org/info/assembly/homo_sapiens": EXAMPLE_GENE_BUILD_DATA,
-            "http://rest.ensembl.org/info/data": {"releases": [112]},
+            "http://jul2023.rest.ensembl.org/info/assembly/homo_sapiens": EXAMPLE_GENE_BUILD_DATA,
+            "http://jul2023.rest.ensembl.org/info/data": {"releases": [110]},
         },
     )
     service.prepare_assembly_for_version(1)
@@ -403,8 +403,8 @@ def test_prepare_assembly_for_version_build_error(Session, file_service, setup):
         Session,
         file_service,
         url_to_result={
-            "http://rest.ensembl.org/info/assembly/homo_sapiens": NEWEST_EXAMPLE_GENE_BUILD_DATA,
-            "http://rest.ensembl.org/info/data": {"releases": [112]},
+            "http://jul2023.rest.ensembl.org/info/assembly/homo_sapiens": NEWEST_EXAMPLE_GENE_BUILD_DATA,
+            "http://jul2023.rest.ensembl.org/info/data": {"releases": [112]},
         },
     )
     with pytest.raises(AssemblyVersionError) as exc: