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found incorrect/missing assembly_link_type #436
Description
Hi!
I have been playing around with python and the api library generated from (https://www.ncbi.nlm.nih.gov/datasets/docs/v2/openapi3/openapi3.docs.yaml)
and found a missing data typ or incorrect set data value when trying to get genome links. For accession number GCF_003957565.2. I get the following error:
ValidationError: 1 validation error for V2AssemblyLinksReplyAssemblyLink
assembly_link_type
Input should be 'GDV_LINK', 'FTP_LINK', 'ASSEMBLY_PUBMED', 'BLAST_LINK', 'ASSEMBLY_NUCCORE_REFSEQ' or 'ASSEMBLY_NUCCORE_GENBANK' [type=enum,
input_value='ASSEMBLY_NUCCORE', input_type=str]
For further information visit https://errors.pydantic.dev/2.10/v/enum
The assembly_link_type that generate the error is "ASSEMBLY_NUCCORE" which one can see when using curl to fetch the data
curl -X GET "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_003957565.2/links" \
-H 'accept: application/json' Result
{
"assembly_links": [
{
"accession": "GCF_003957565.2",
"assembly_link_type": "BLAST_LINK",
"resource_link": "https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_SPEC=GDH_GCF_003957565.2"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "GDV_LINK",
"resource_link": "https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_003957565.2"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "FTP_LINK",
"resource_link": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/957/565/GCF_003957565.2_bTaeGut1.4.pri"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "ASSEMBLY_PUBMED",
"resource_link": "https://www.ncbi.nlm.nih.gov/nuccore/?from_uid=10005361&linkname=assembly_pubmed"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "ASSEMBLY_NUCCORE",
"resource_link": "https://www.ncbi.nlm.nih.gov/nuccore/?from_uid=10005361&linkname=assembly_nuccore_refseq"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "ASSEMBLY_NUCCORE_REFSEQ",
"resource_link": "https://www.ncbi.nlm.nih.gov/nuccore/?from_uid=10005361&linkname=assembly_nuccore_refseq"
},
{
"accession": "GCF_003957565.2",
"assembly_link_type": "ASSEMBLY_NUCCORE_GENBANK",
"resource_link": "https://www.ncbi.nlm.nih.gov/nuccore/?from_uid=10005361&linkname=assembly_nuccore_insdc"
}
]
}If we look at the yaml definition we can see "ASSEMBLY_NUCCORE" that isn't defined
datasets/datasets.openapi.yaml
Lines 11477 to 11485 in d511fd7
and the generate python code will not have it as a value
class V2AssemblyLinksReplyAssemblyLinkType(str, Enum):
"""
V2AssemblyLinksReplyAssemblyLinkType
"""
"""
allowed enum values
"""
GDV_LINK = 'GDV_LINK'
FTP_LINK = 'FTP_LINK'
ASSEMBLY_PUBMED = 'ASSEMBLY_PUBMED'
BLAST_LINK = 'BLAST_LINK'
ASSEMBLY_NUCCORE_REFSEQ = 'ASSEMBLY_NUCCORE_REFSEQ'
ASSEMBLY_NUCCORE_GENBANK = 'ASSEMBLY_NUCCORE_GENBANK'
@classmethod
def from_json(cls, json_str: str) -> Self:
"""Create an instance of V2AssemblyLinksReplyAssemblyLinkType from a JSON string"""
return cls(json.loads(json_str))
Activity
olearyna commentedon Dec 10, 2024
Hi Smeds,
Thanks for letting us know about this issue. We’ve confirmed the problem and will work on fixing it as soon as we can.
Nuala