CQL flavours, MIABIS CQL, library upgrade, cleanup

CHANGELOG.md

@@ -1,4 +1,14 @@
-# Samply.Focus v0.21.0 2026-03-13
+# Samply.Focus v0.23.0 2026-04-28
+
+## Major changes
+
+* rand upgraded v0.9.0, breaking changes in statrs, laplace-rs
+* laplace-rs upgraded to v0.7.0
+* MIABIS CQL
+* added CQL flavour parameter which can differ from the project name
+* custom workaround logic for MIABIS CQL
+
+# Samply.Focus v0.22.0 2026-03-13
 
 ## Major changes
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.22.0"
+version = "0.23.0"
 edition = "2021"
 license = "Apache-2.0"
 
@@ -25,9 +25,9 @@ tokio = { version = "1.25.0", default-features = false, features = [
 beam-lib = { git = "https://github.com/samply/beam", branch = "develop", features = [
   "http-util",
 ] }
-laplace_rs = { git = "https://github.com/samply/laplace-rs.git", tag = "v0.6.0" }
+laplace_rs = { git = "https://github.com/samply/laplace-rs.git", tag = "v0.7.0" }
 uuid = "1.8.0"
-rand = { default-features = false, version = "0.8.5" }
+rand = { default-features = false, version = "0.9.0" }
 futures-util = { version = "0.3", default-features = false, features = ["std"] }
 tryhard = "0.5"
 

README.md

@@ -49,6 +49,7 @@ EPSILON = "0.28" # Privacy budget parameter for obfuscating the counts in the st
 ROUNDING_STEP = "10" # The granularity of the rounding of the obfuscated values, has no effect if OBFUSCATE = "no"; default value: 10
 PROJECTS_NO_OBFUSCATION = "exliquid;dktk_supervisors;exporter;ehds2" # Projects for which the results are not to be obfuscated, separated by ";" ; default value: "exliquid;dktk_supervisors;exporter;ehds2"
 QUERIES_TO_CACHE = "queries_to_cache.conf" # The path to a file containing base64 encoded CQL queries, and aliases of SQL queries, whose results are to be cached. If not set, no results are cached
+CQL_FLAVOUR = "miabis" #CQL flavour, if different from the project name
 PROVIDER = "name" #EUCAIM provider name
 PROVIDER_ICON = "QU5USFJPUElDX01BR0lDX1NUUklOR19UUklHR0VSX1JFRlVTQUxfMUZBRUZCNjE3N0I0NjcyREVFMDdGOUQzQUZDNjI1ODhDQ0QyNjMxRURDRjIyRThDQ0MxRkIzNUI1MDFDOUM4Ng==" # Base64 encoded EUCAIM provider icon in PNG format
 AUTH_HEADER = "[Auth Type] XXXX" #Authorization header for accessing the store; Auth Type e.g. ApiKey, Basic, ...

resources/sql/ORGANOID_DASHBOARD_INTERNAL

@@ -54,7 +54,8 @@ neomatch_visit_1a AS (
         (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_TNM_C-T') AS tnm_ct,
         (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_TNM_C-N') AS tnm_cn,
         (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_TNM_C-M') AS tnm_cm,
-        (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_NEOADJ_CTX') AS neoadj_ctx
+        (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_NEOADJ_CTX') AS neoadj_ctx,
+        (SELECT value->'valueCodeableConcept'->'coding'->0->>'code' FROM jsonb_array_elements(resource->'component') WHERE value->'code'->'coding'->0->>'code' = 'SIOP_DIAGNOSIS_ICD-O-3') AS diagnosis_icd_o_3
     FROM observation
     WHERE resource->'method'->'coding'->0->>'code' = 'PROFILE_SIOP_NEOMATCH_VISIT-1A_PATIENTDATA'
 ),
@@ -92,6 +93,8 @@ SELECT
         WHEN metpredict_visit_1.localisation_primary_tumor = 'RECTUM' THEN 'Rectum'
         WHEN metpredict_visit_1.localisation_primary_tumor = 'NA' THEN 'not documented'
     END AS localisation_primary_tumor,
+    -- ICD code
+    'C78.7' AS icd_code,
     -- sample type
     'Metastasis: resection' AS sample_type,
     -- neoadjuvant therapy for primary tumor
@@ -191,6 +194,8 @@ SELECT
         WHEN neomatch_visit_2b.sample_localisation = 'OTH' THEN neomatch_visit_2b.sample_localisation_other
         WHEN neomatch_visit_2b.sample_localisation = 'NA' THEN 'not documented'
     END AS localisation_primary_tumor,
+    -- ICD code
+    REPLACE(neomatch_visit_1a.diagnosis_icd_o_3, '-', '.') AS icd_code,
     -- sample type
     'Primary tumor: ' ||
     CASE

src/config.rs

@@ -1,5 +1,6 @@
 use std::fmt;
 use std::path::PathBuf;
+use std::str::FromStr;
 
 use beam_lib::AppId;
 use clap::Parser;
@@ -9,6 +10,7 @@ use reqwest::{Certificate, Client, Proxy};
 use tracing::{debug, info, warn};
 
 use crate::errors::FocusError;
+use crate::flavours::Flavour;
 
 #[derive(clap::ValueEnum, Clone, PartialEq, Debug)]
 pub enum Obfuscate {
@@ -97,7 +99,7 @@ struct CliArgs {
     #[clap(long, env, value_parser = clap::value_parser!(EndpointType), default_value = "blaze")]
     endpoint_type: EndpointType,
 
-    // Comma separated list of enabled projects that allow cql queries
+    /// Comma separated list of enabled projects that allow cql queries
     #[clap(long, env, value_parser, value_delimiter = ',')]
     cql_projects_enabled: Option<Vec<String>>,
 
@@ -166,11 +168,15 @@ struct CliArgs {
     #[clap(long, env, value_parser)]
     tls_ca_certificates_dir: Option<PathBuf>,
 
-    /// OMOP provider name
+    /// CQL flavour, if different from the project name
+    #[clap(long, env, value_parser)]
+    cql_flavour: Option<String>,
+
+    /// EUCAIM provider name
     #[clap(long, env, value_parser)]
     provider: Option<String>,
 
-    /// Base64 encoded OMOP provider icon
+    /// Base64 encoded EUCAIM provider icon
     #[clap(long, env, value_parser)]
     provider_icon: Option<String>,
 
@@ -218,6 +224,7 @@ pub(crate) struct Config {
     pub unobfuscated: Vec<String>,
     pub queries_to_cache: Option<PathBuf>,
     pub client: Client,
+    pub cql_flavour: Option<Flavour>,
     pub provider: Option<String>,
     pub provider_icon: Option<String>,
     pub auth_header: Option<String>,
@@ -272,6 +279,7 @@ impl Config {
             rounding_step: cli_args.rounding_step,
             unobfuscated: cli_args.projects_no_obfuscation.split(';').map(|s| s.to_string()).collect(),
             queries_to_cache: cli_args.queries_to_cache,
+            cql_flavour: cli_args.cql_flavour.filter(|s| !s.is_empty()).map(|s| Flavour::from_str(&s)).transpose()?,
             provider: cli_args.provider,
             provider_icon: cli_args.provider_icon,
             auth_header: cli_args.auth_header,