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onconova.terminology.resolver

resolve_canonical_url module-attribute

CanonicalUrlResolver

resolve(canonical_url)

Resolve a canonical URL to a URL that can be used to download the corresponding ValueSet or CodeSystem resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
Source code in onconova/terminology/resolver.py 
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def resolve(self, canonical_url: str) -> str:
    """Resolve a canonical URL to a URL that can be used to download the
    corresponding ValueSet or CodeSystem resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
    """
    # Validate the input canonical_url
    if not urllib.parse.urlparse(canonical_url).scheme:  # type: ignore
        raise ValueError("Invalid URL: " + canonical_url)

    url_resolvers = {
        "loinc.org": self.resolve_LOINC_endpoint,
        "hl7.org": self.resolve_HL7_endpoint,
        "vsac.nlm.nih.gov": self.resolve_VSAC_endpoint,
        "cts.nlm.nih.gov": self.resolve_CTS_endpoint,
        "simplifier.net/onconova": self.resolve_Simplifier_endpoint,
    }

    for url_domain, resolver in url_resolvers.items():
        if url_domain in canonical_url:
            return resolver(canonical_url)
    raise KeyError(f"Unknown resource requested in canonical URL: {canonical_url}")

resolve_CTS_endpoint(canonical_url)

Resolve a CTS canonical URL to a URL that can be used to download the corresponding ValueSet or CodeSystem resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
Source code in onconova/terminology/resolver.py 
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def resolve_CTS_endpoint(self, canonical_url: str) -> str:
    """Resolve a CTS canonical URL to a URL that can be used to download the
    corresponding ValueSet or CodeSystem resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
    """
    return f"{canonical_url}/$expand?_format=json"

resolve_HL7_endpoint(canonical_url)

Resolve a HL7 canonical URL to a URL that can be used to download the corresponding ValueSet or CodeSystem resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
Source code in onconova/terminology/resolver.py 
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def resolve_HL7_endpoint(self, canonical_url: str) -> str:
    """Resolve a HL7 canonical URL to a URL that can be used to download the
    corresponding ValueSet or CodeSystem resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet or CodeSystem resource.
    """
    RELEASE_VERSIONS = {
        "http://hl7.org/fhir/us/core": "STU5.0.1",
        "http://hl7.org/fhir/us/vitals": "STU1",
        "http://hl7.org/fhir/us/mcode": "STU3",
        "http://hl7.org/fhir/uv/genomics-reporting": "STU2",
        "http://hl7.org/fhir/": "R4B",
        "http://terminology.hl7.org/": "",
    }
    for domain in RELEASE_VERSIONS:
        if canonical_url.startswith(domain):
            version = RELEASE_VERSIONS[domain]
            if "http://terminology.hl7.org/" in canonical_url:
                canonical_url = canonical_url.replace(
                    "http://terminology.hl7.org/CodeSystem/",
                    "https://hl7.org/fhir/codesystem-",
                )
                canonical_url = canonical_url.replace(
                    "http://terminology.hl7.org/ValueSet/",
                    "https://hl7.org/fhir/valueset-",
                )
            if "ValueSet" in canonical_url:
                return (
                    canonical_url.replace("/ValueSet/", f"/{version}/ValueSet-")
                    + ".json"
                )
            elif "CodeSystem" in canonical_url:
                return (
                    canonical_url.replace("/CodeSystem/", f"/{version}/CodeSystem-")
                    + ".json"
                )
            else:
                return (
                    canonical_url.replace(
                        "http://hl7.org/fhir/",
                        f"http://hl7.org/fhir/{version}/codesystem-",
                    )
                    + ".json"
                )
    else:
        raise KeyError(
            f"Unknown FHIR/HL7 resource requested in canonical URL: {canonical_url}"
        )

resolve_LOINC_endpoint(canonical_url)

Resolve a LOINC canonical URL to a URL that can be used to download the corresponding ValueSet resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet resource.
Source code in onconova/terminology/resolver.py 
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def resolve_LOINC_endpoint(self, canonical_url: str) -> str:
    """Resolve a LOINC canonical URL to a URL that can be used to download the
    corresponding ValueSet resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet resource.
    """
    valueset_name = (
        canonical_url.replace("http://", "https://")
        .replace("https://loinc.org/", "")
        .replace("/", "")
    )
    return f"http://fhir.loinc.org/ValueSet/$expand?url=http://loinc.org/vs/{valueset_name}&_format=json"

resolve_Simplifier_endpoint(canonical_url)

Resolve a Simplifier canonical URL to a URL that can be used to download the corresponding ValueSet resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet resource.
Source code in onconova/terminology/resolver.py 
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def resolve_Simplifier_endpoint(self, canonical_url: str) -> str:
    """Resolve a Simplifier canonical URL to a URL that can be used to download the
    corresponding ValueSet resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet resource.
    """
    valueset_name = (
        canonical_url.replace("https://simplifier.net/onconova", "")
        .replace(
            "ValueSets/",
            "",
        )
        .replace(
            "CodeSystems/",
            "",
        )
    )
    return f"https://simplifier.net/onconova/{valueset_name}/$download?format=json"

resolve_VSAC_endpoint(canonical_url)

Resolve a VSAC canonical URL to a URL that can be used to download the corresponding ValueSet resource.

Parameters:

Name Type Description Default

canonical_url

str

The canonical URL to resolve.

 required

Returns:

Type Description
str

The URL that can be used to download the corresponding ValueSet resource.
Source code in onconova/terminology/resolver.py 
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def resolve_VSAC_endpoint(self, canonical_url: str) -> str:
    """Resolve a VSAC canonical URL to a URL that can be used to download the
    corresponding ValueSet resource.

    Args:
        canonical_url (str): The canonical URL to resolve.

    Returns:
        (str): The URL that can be used to download the corresponding ValueSet resource.
    """
    valueset_name = canonical_url.replace(
        "https://vsac.nlm.nih.gov/valueset/", ""
    ).split("/")[0]
    return f"https://cts.nlm.nih.gov/fhir/res/ValueSet/{valueset_name}/$expand?_format=json"
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