Merge pull request #193 from samply/develop

EHDS2, separating explorer API key from auth header CLA, thiserror version bump

.github/workflows/rust.yml

@@ -4,9 +4,6 @@ on:
   push:
   workflow_dispatch:
   pull_request:
-  schedule:
-    # Fetch new base image updates every night at 1am
-    - cron: '0 1 * * *'
 
 jobs:
   build-with-samply:

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Samply.Focus v0.8.0 2024-11-04
 
+## Major changes
+* EHDS2 query support
+
+## Minor changes
+* Separated exporter API key CLA from authorization header CLA
+
+
+# Samply.Focus v0.8.0 2024-11-04
+
 In this release, we are supporting 4 types of SQL queries for Exliquid and Organoids
 
 ## Major changes

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.8.0"
+version = "0.9.0"
 edition = "2021"
 license = "Apache-2.0"
 
@@ -11,12 +11,12 @@ base64 = "0.22.1"
 reqwest = { version = "0.12", default-features = false, features = ["json", "default-tls"] }
 serde = { version = "1.0.152", features = ["serde_derive"] }
 serde_json = "1.0"
-thiserror = "1.0.38"
+thiserror = "2.0.3"
 chrono = "0.4.31"
 indexmap = "2.1.0"
 tokio = { version = "1.25.0", default-features = false, features = ["signal", "rt-multi-thread", "macros"] }
 beam-lib = { git = "https://github.com/samply/beam", branch = "develop", features = ["http-util"] }
-laplace_rs = {git = "https://github.com/samply/laplace-rs.git", tag = "v0.3.0" }
+laplace_rs = {git = "https://github.com/samply/laplace-rs.git", tag = "v0.4.0" }
 uuid = "1.8.0"
 rand = { default-features = false, version = "0.8.5" }
 futures-util = { version = "0.3", default-features = false, features = ["std"] }

README.md

@@ -51,7 +51,8 @@ PROJECTS_NO_OBFUSCATION = "exliquid;dktk_supervisors;exporter;ehds2" # Projects
 QUERIES_TO_CACHE = "queries_to_cache.conf" # The path to a file containing base64 encoded queries whose results are to be cached. If not set, no results are cached
 PROVIDER = "name" #EUCAIM provider name
 PROVIDER_ICON = "iVBORw0KGgoAAAANSUhEUgAAAAEAAAABAQMAAAAl21bKAAAAA1BMVEUAAACnej3aAAAAAXRSTlMAQObYZgAAAApJREFUCNdjYAAAAAIAAeIhvDMAAAAASUVORK5CYII=" # Base64 encoded EUCAIM provider icon
-AUTH_HEADER = "ApiKey XXXX" #Authorization header
+AUTH_HEADER = "[Auth Type] XXXX" #Authorization header for accessing the store; Auth Type e.g. ApiKey, Basic, ...
+EXPORTER_API_KEY = "XXXX" # Value of header x-api-key for accessing the Exporter application
 ```
 
 In order to use Postgres querying, a Docker image built with the feature "dktk" needs to be used and this optional variable set:

resources/cql/DKTK_STRAT_GENETIC_VARIANT

@@ -0,0 +1,5 @@
+define GeneticVariantCount:
+if InInitialPopulation then [Observation: Code '69548-6' from loinc] else {} as List <Observation>
+
+define GeneticVariantCode:
+First (from [Observation: Code '69548-6' from loinc] O return O.component.where(code.coding contains Code '48018-6' from loinc).value.coding.code.first())

resources/cql/EHDS2_IN_INITIAL_POPULATION

@@ -0,0 +1 @@
+define InInitialPopulation:

resources/cql/EHDS2_OBSERVATION

@@ -0,0 +1,125 @@
+define ObservationList:
+    if InInitialPopulation then [Observation] else {} as List<Observation>
+
+// Return the value in the given system for the given Observation
+define function ObservationValueCode(observation FHIR.Observation, system_var String):
+    (observation.value as CodeableConcept).coding.where(system = system_var).code.first()
+
+// Check to see if there are any Observation resources with the
+// given system/value pair.
+define function ExistsObservationValueCode(system_var String, code_var String):
+    exists from [Observation] O
+        where ObservationValueCode(O, system_var) = code_var
+
+// Return the value associated with the extension with the given URL for the given Observation
+define function BaseObservationExtensionValue(observation FHIR.Observation, url_var String):
+    observation.extension.where(url = url_var).value
+
+// Return the value of the Observation extension with the given URL
+define function ObservationExtensionValue(observation FHIR.Observation, url_var String):
+    SensibleString(BaseObservationExtensionValue(observation, url_var))
+
+define function ExistsObservationExtensionValue(url_var String, value_var String):
+    exists from [Observation] O
+        where ObservationExtensionValue(O, url_var) = value_var
+
+// Return the pathogen type for the given Observation
+define function PathogenCode(observation FHIR.Observation):
+    ObservationValueCode(observation, 'https://ecdc.amr/pathogen-codes')
+
+// Check to see if there are any Observation resources with the
+// given pathogen type.
+define function ExistsPathogenCode(code_var String):
+    ExistsObservationValueCode('https://ecdc.amr/pathogen-codes', code_var)
+
+// Return the antibiotic type for the given Observation
+define function AntibioticCode(observation FHIR.Observation):
+    ObservationValueCode(observation, 'https://ecdc.amr/antibiotic-codes')
+
+// Check to see if there are any Observation resources with the
+// given antibiotic type.
+define function ExistsAntibioticCode(code_var String):
+    ExistsObservationValueCode('https://ecdc.amr/antibiotic-codes', code_var)
+
+// Return the resistance type for the given Observation
+define function SirCode(observation FHIR.Observation):
+    ObservationValueCode(observation, 'https://ecdc.amr/sir-codes')
+
+// Check to see if there are any Observation resources with the
+// given resistance type.
+define function ExistsSirCode(code_var String):
+    ExistsObservationValueCode('https://ecdc.amr/sir-codes', code_var)
+
+// Return the data source for the given Observation
+define function DataSource(observation FHIR.Observation):
+    ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationDataSource')
+
+// Check to see if there are any Observation resources with the
+// given data source.
+define function ExistsDataSource(value_var String):
+    ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationDataSource', value_var)
+
+// Return the isolate ID for the given Observation
+define function IsolateId(observation FHIR.Observation):
+    ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationIsolateId')
+
+// Check to see if there are any Observation resources with the
+// given isolate ID.
+define function ExistsIsolateId(value_var String):
+    ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationIsolateId', value_var)
+
+// Return the patient type for the given Observation
+define function PatientType(observation FHIR.Observation):
+    ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationPatientType')
+
+// Check to see if there are any Observation resources with the
+// given patient type.
+define function ExistsPatientType(value_var String):
+    ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationPatientType', value_var)
+
+// Return the reference guidelines SIR for the given Observation
+define function ReferenceGuidelinesSir(observation FHIR.Observation):
+    ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationReferenceGuidelinesSIR')
+
+// Check to see if there are any Observation resources with the
+// given reference guidelines SIR.
+define function ExistsReferenceGuidelinesSir(value_var String):
+    ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationReferenceGuidelinesSIR', value_var)
+
+// Return the reporting country for the given Observation
+define function ReportingCountry(observation FHIR.Observation):
+    ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationReportingCountry')
+
+// Check to see if there are any Observation resources with the
+// given reporting country.
+define function ExistsReportingCountry(value_var String):
+    ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationReportingCountry', value_var)
+
+// Return the year from the date used for statistics
+define function YearDateUsedForStatistics(observation FHIR.Observation):
+    year from observation.issued
+
+// Return the month from the date used for statistics
+define function MonthDateUsedForStatistics(observation FHIR.Observation):
+    month from observation.issued
+
+// Return the year-month from the date used for statistics
+define function YearMonthDateUsedForStatistics(observation FHIR.Observation):
+    ToString(YearDateUsedForStatistics(observation)) + '-' + ToString(MonthDateUsedForStatistics(observation))
+
+// Return the the date valid from
+define function DateValidFrom(observation FHIR.Observation):
+    ToDate(observation.effective as dateTime)
+
+// Return the year from the date valid from
+define function YearDateValidFrom(observation FHIR.Observation):
+    year from DateValidFrom(observation)
+
+// Return the month from the date valid from
+define function MonthDateValidFrom(observation FHIR.Observation):
+    month from DateValidFrom(observation)
+
+// Return the year-month from the date valid from
+define function YearMonthDateValidFrom(observation FHIR.Observation):
+    ToString(YearDateValidFrom(observation)) + '-' + ToString(MonthDateValidFrom(observation))
+

resources/cql/EHDS2_PATIENT

@@ -0,0 +1,30 @@
+// Return the value of the Patient extension with the given URL.
+// Return "Unknown" if not available or empty.
+define function PatientExtensionValue(url_var String):
+    SensibleString(Patient.extension.where(url = url_var).value)
+
+// Return gender of patient
+define Gender:
+    SensibleString(Patient.gender)
+
+// Return age of patient, as an integer
+define AgeInYears:
+    ToInteger(PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientAge'))
+
+// Round patient age to the nearest multiple of 10 (i/p for a histogram).
+// Return result as a string
+define AgeClass:
+    ToString((AgeInYears div 10) * 10)
+
+// Return ID of hospital associated with patient
+define HospitalId:
+    PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientHospitalId')
+
+// Return hospital unit type associated with patient
+define HospitalUnitType:
+    PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientHospitalUnitType')
+
+// Return laboratory code associated with patient
+define LaboratoryCode:
+    PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientLaboratoryCode')
+

resources/cql/EHDS2_SPECIMEN

@@ -0,0 +1,13 @@
+define SpecimenList:
+    if InInitialPopulation then [Specimen] else {} as List<Specimen>
+
+// Return the isolate ID for the given Specimen
+define function SpecimenIsolateId(specimen FHIR.Specimen):
+    SensibleString(specimen.id)
+
+// Check to see if there are any Specimen resources with the
+// given isolate ID.
+define function ExistsSpecimenIsolateId(id_var String):
+    exists from [Specimen] S
+        where SpecimenIsolateId(S) = id_var
+

resources/cql/EHDS2_UTIL

@@ -0,0 +1,7 @@
+// Return "val" if the supplied string value is sensible.
+// Return "Unknown" if null or empty.
+define function SensibleString(val String):
+    if (val is null or val = '' or val = '-')
+    then 'Unkown'
+    else val
+

src/config.rs

@@ -158,10 +158,15 @@ struct CliArgs {
     #[clap(long, env, value_parser)]
     provider_icon: Option<String>,
 
+    // TODO - refactor to include multiple authorization headers for multiple stores / applications at the same time
     /// Authorization header
     #[clap(long, env, value_parser)]
     auth_header: Option<String>,
 
+    /// Exporter API key
+    #[clap(long, env, value_parser)]
+    exporter_api_key: Option<String>,
+
     /// Postgres connection string
     #[cfg(feature = "query-sql")]
     #[clap(long, env, value_parser)]
@@ -198,6 +203,7 @@ pub(crate) struct Config {
     pub provider: Option<String>,
     pub provider_icon: Option<String>,
     pub auth_header: Option<String>,
+    pub exporter_api_key: Option<String>,
     #[cfg(feature = "query-sql")]
     pub postgres_connection_string: Option<String>,
     #[cfg(feature = "query-sql")]
@@ -243,6 +249,7 @@ impl Config {
             provider: cli_args.provider,
             provider_icon: cli_args.provider_icon,
             auth_header: cli_args.auth_header,
+            exporter_api_key: cli_args.exporter_api_key,
             #[cfg(feature = "query-sql")]
             postgres_connection_string: cli_args.postgres_connection_string,
             #[cfg(feature = "query-sql")]

src/exporter.rs

@@ -42,10 +42,10 @@ pub async fn post_exporter_query(body: &String, task_type: TaskType) -> Result<S
 
     let mut headers = HeaderMap::new();
 
-    if let Some(auth_header_value) = CONFIG.auth_header.clone() {
+    if let Some(api_key) = CONFIG.exporter_api_key.clone() {
         headers.insert(
             "x-api-key",
-            HeaderValue::from_str(auth_header_value.as_str())
+            HeaderValue::from_str(api_key.as_str())
                 .map_err(FocusError::InvalidHeaderValue)?,
         );
     }