[Cognitive Services - Health Insights] CADL revision for public previ…

…ew (Azure#22990)

* health insights cadl + generated openapi spec

* fix PR Comments

* change country to countryOrRegion

* split to multiple cadl projects

* update cadl-project.yaml files

* update example with generic contact details

* update samples with generic contacts

* convert cadl to typespec

* update generated openapi spec

* convert cadl to typespec (#4)

* convert cadl to typespec

* update generated openapi spec

* move ClinicalNoteEvidence to common modules

* remove redundant imports

* fix typespec dependencies

* remove dependencies from main.tsp

* using rest

* move imports from service.tsp to its caller

* fix comment - directive error

* remove imports from service.tsp

custom-words.txt

@@ -380,6 +380,7 @@ clientaccesspolicy
 clienterror
 clientgroup
 clientlib
+clinicaltrials
 clipart
 CLIs
 CLOGFILE
@@ -923,6 +924,7 @@ hdinsight
 Headnode
 healthbot
 healthcareapis
+healthinsights
 healthstatus
 hecto
 Heatbeat
@@ -1008,6 +1010,7 @@ integrationaccount
 integrationruntimes
 Intelli
 intervaled
+Interventional
 Intraorg
 intset
 intune
@@ -1495,6 +1498,8 @@ OIDC
 onboarded
 Onboarding
 Onboards
+Onco
+oncophenotype
 ondemand
 onedeploy
 onmachine
@@ -1993,6 +1998,7 @@ snapshotset
 snaptshot
 SNAT
 SNMP
+SNOMED
 Sobol
 softwareplan
 SOHSV
@@ -2231,6 +2237,7 @@ transcriptmoderationresult
 transferkey
 translatortext
 trendingtopics
+trialmatcher
 triggeredwebjobs
 triggerruns
 TSVE

specification/cognitiveservices/HealthInsights/.gitignore

@@ -0,0 +1,5 @@
+#### linux gitignore
+
+# Ignore output files
+tsp-output
+package-lock.json

specification/cognitiveservices/HealthInsights/healthinsights.common/model.common.request.tsp

@@ -0,0 +1,121 @@
+import "./model.common.shared.tsp";
+
+using TypeSpec.Rest;
+
+namespace AzureHealthInsights;
+
+alias Request = {
+  @doc("The list of patients, including their clinical information and data.")
+  patients: PatientRecord[];
+};
+
+alias ModelConfiguration = {
+  @doc("An indication whether the model should produce verbose output.")
+  verbose?: boolean = false;
+
+  @doc("An indication whether the model's output should include evidence for the inferences.")
+  includeEvidence?: boolean = true;
+};
+
+@doc("A patient record, including their clinical information and data.")
+model PatientRecord {
+  @doc("""
+A given identifier for the patient. Has to be unique across all patients in a single request.
+""")
+  @minLength(1)
+  id: string;
+
+  @doc("""
+Patient structured information, including demographics and known structured clinical information.
+""")
+  info?: PatientInfo;
+
+  @doc("Patient unstructured clinical data, given as documents.")
+  data?: PatientDocument[];
+}
+
+@doc("Patient structured information, including demographics and known structured clinical information.")
+model PatientInfo {
+  @doc("The patient's sex.")
+  sex?: PatientInfoSex;
+
+  @doc("The patient's date of birth.")
+  birthDate?: plainDate;
+
+  @doc("Known clinical information for the patient, structured.")
+  clinicalInfo?: ClinicalCodedElement[];
+}
+
+@doc("The patient's sex.")
+enum PatientInfoSex {
+  Female: "female",
+  Male: "male",
+  Unspecified: "unspecified",
+}
+
+@doc("The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document).")
+enum DocumentType {
+  Note: "note",
+  FhirBundle: "fhirBundle",
+  Dicom: "dicom",
+  GenomicSequencing: "genomicSequencing",
+}
+
+@doc("The type of the clinical document.")
+enum ClinicalDocumentType {
+  Consultation: "consultation",
+  DischargeSummary: "dischargeSummary",
+  HistoryAndPhysical: "historyAndPhysical",
+  Procedure: "procedure",
+  Progress: "progress",
+  Imaging: "imaging",
+  Laboratory: "laboratory",
+  Pathology: "pathology",
+}
+
+@doc("""
+The type of the content's source. 
+In case the source type is 'inline', the content is given as a string (for instance, text). 
+In case the source type is 'reference', the content is given as a URI.
+""")
+enum DocumentContentSourceType {
+  Inline: "inline",
+  Reference: "reference",
+}
+
+@doc("A clinical document related to a patient. Document here is in the wide sense - not just a text document (note).")
+model PatientDocument {
+  @doc("The type of the patient document, such as 'note' (text document) or 'fhirBundle' (FHIR JSON document).")
+  type: DocumentType;
+
+  @doc("The type of the clinical document.")
+  clinicalType?: ClinicalDocumentType;
+
+  @doc("A given identifier for the document. Has to be unique across all documents for a single patient.")
+  @minLength(1)
+  id: string;
+
+  @doc("A 2 letter ISO 639-1 representation of the language of the document.")
+  language?: string;
+
+  @doc("The date and time when the document was created.")
+  createdDateTime?: zonedDateTime;
+
+  @doc("The content of the patient document.")
+  content: DocumentContent;
+}
+
+@doc("The content of the patient document.")
+model DocumentContent {
+  @doc("""
+The type of the content's source.
+In case the source type is 'inline', the content is given as a string (for instance, text).
+In case the source type is 'reference', the content is given as a URI.
+""")
+  sourceType: DocumentContentSourceType;
+
+  @doc("""
+The content of the document, given either inline (as a string) or as a reference (URI).
+""")
+  value: string;
+}

specification/cognitiveservices/HealthInsights/healthinsights.common/model.common.response.tsp

@@ -0,0 +1,101 @@
+import "./model.common.shared.tsp";
+
+using TypeSpec.Rest;
+
+namespace AzureHealthInsights;
+
+alias Response = {
+  @doc("A processing job identifier.")
+  @visibility("read")
+  @key
+  @format("uuid")
+  jobId: string;
+
+  @doc("The date and time when the processing job was created.")
+  @visibility("read")
+  createdDateTime: zonedDateTime;
+
+  @doc("The date and time when the processing job is set to expire.")
+  @visibility("read")
+  expirationDateTime: zonedDateTime;
+
+  @doc("The date and time when the processing job was last updated.")
+  @visibility("read")
+  lastUpdateDateTime: zonedDateTime;
+
+  @doc("The status of the processing job.")
+  @visibility("read")
+  status: JobStatus;
+
+  @doc("An array of errors, if any errors occurred during the processing job.")
+  @visibility("read")
+  errors?: Azure.Core.Foundations.Error[];
+};
+
+
+@doc("An inference made by the model regarding a patient.")
+model Inference {
+  @doc("The value of the inference, as relevant for the given inference type.")
+  value: string;
+
+  @doc("The description corresponding to the inference value.")
+  description?: string;
+
+  @doc("Confidence score for this inference.")
+  @minValue(0)
+  @maxValue(1)
+  confidenceScore?: float32;
+}
+
+@doc("A piece of evidence from a clinical note (text document).")
+model ClinicalNoteEvidence {
+  @doc("The identifier of the document containing the evidence.")
+  id: string;
+
+  @doc("The actual text span which is evidence for the inference.")
+  text?: string;
+
+  @doc("The start index of the evidence text span in the document (0 based).")
+  @minValue(0)
+  offset: int32;
+
+  @doc("The length of the evidence text span.")
+  @minValue(1)
+  length: int32;
+}
+
+@doc("A piece of evidence corresponding to an inference.")
+model InferenceEvidence {
+  @doc("A piece of evidence from a clinical note (text document).")
+  patientDataEvidence?: ClinicalNoteEvidence;
+
+  @doc("""
+A piece of clinical information, expressed as a code in a clinical coding
+system.
+""")
+  patientInfoEvidence?: ClinicalCodedElement;
+
+  @doc("A value indicating how important this piece of evidence is for the inference.")
+  @minValue(0)
+  @maxValue(1)
+  importance?: float32;
+}
+
+@doc("A piece of evidence corresponding to a Trial Matcher inference.")
+model TrialMatcherInferenceEvidence {
+  @doc("A piece of evidence from the eligibility criteria text of a clinical trial.")
+  eligibilityCriteriaEvidence?: string;
+  ...InferenceEvidence;
+}
+
+@doc("The status of the processing job.")
+enum JobStatus {
+  NotStarted: "notStarted",
+  Running: "running",
+  Succeeded: "succeeded",
+  Failed: "failed",
+  PartiallyCompleted: "partiallyCompleted",
+}
+
+@doc("The version of the model used for inference, expressed as the model date.")
+scalar ModelVersion extends string;

specification/cognitiveservices/HealthInsights/healthinsights.common/model.common.shared.tsp

@@ -0,0 +1,36 @@
+using TypeSpec.Rest;
+
+namespace AzureHealthInsights;
+
+@doc("""
+A piece of clinical information, expressed as a code in a clinical coding system.
+""")
+model ClinicalCodedElement {
+  @doc("The clinical coding system, e.g. ICD-10, SNOMED-CT, UMLS.")
+  system: string;
+
+  @doc("The code within the given clinical coding system.")
+  code: string;
+
+  @doc("The name of this coded concept in the coding system.")
+  name?: string;
+
+  @doc("A value associated with the code within the given clinical coding system.")
+  value?: string;
+}
+
+@doc("""
+A location given as a combination of city, state and country/region. It could specify a city, a state or a country/region.
+In case a city is specified, either state +country/region or country/region (for countries/regions where there are no states) should be added.
+In case a state is specified (without a city), country/region should be added.
+""")
+model GeographicLocation {
+  @doc("City name.")
+  city?: string;
+
+  @doc("State name.")
+  state?: string;
+
+  @doc("Country/region name.")
+  countryOrRegion: string;
+}

specification/cognitiveservices/HealthInsights/healthinsights.common/primitives.tsp

@@ -0,0 +1,17 @@
+using Azure.Core;
+using TypeSpec.Http;
+namespace AzureHealthInsights;
+
+@doc("Long running RPC operation template")
+op LongRunningRpcOperation<
+    TParams extends object,
+    TResponse extends object,
+    Traits extends object = {}
+  > is RpcOperation<
+    TParams & Traits,
+    Foundations.AcceptedResponse<Traits &
+                                 Foundations.LongRunningStatusLocation &
+                                 Foundations.RetryAfterHeader &
+                                 RepeatabilityResponseHeaders> | TResponse,
+    Traits
+  >;

specification/cognitiveservices/HealthInsights/healthinsights.oncophenotype/client.tsp

@@ -0,0 +1,19 @@
+import "@azure-tools/typespec-client-generator-core";
+import "./route.oncophenotype.tsp";
+
+import "@typespec/rest";
+import "@typespec/http";
+import "@typespec/versioning";
+import "../healthinsights.openapi/service.tsp";
+
+using Azure.ClientGenerator.Core;
+
+namespace ClientForAzureHealthInsights;
+
+@client({
+    name: "CancerProfilingClient",
+    service: AzureHealthInsights
+})
+  interface CancerProfilingClient {
+  InferCancerProfile is AzureHealthInsights.OncoPhenotype.CreateJob;
+}