From fab5f397a35733cc93b82087a44355049edc9f4b Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Tue, 19 Sep 2023 11:24:19 +0000
Subject: [PATCH 01/22] Fix erroneous warning

---
 Cargo.toml  | 2 +-
 src/beam.rs | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index c07963e..53ebfe1 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.1.0"
+version = "0.1.1"
 edition = "2021"
 license = "Apache-2.0"
 
diff --git a/src/beam.rs b/src/beam.rs
index 8d80e16..8ae080d 100644
--- a/src/beam.rs
+++ b/src/beam.rs
@@ -350,7 +350,7 @@ pub async fn claim_task(task: &BeamTask) -> Result<(), FocusError> {
         .map_err(|e| FocusError::UnableToAnswerTask(e))?;
 
     match resp.status() {
-        StatusCode::NO_CONTENT => {
+        StatusCode::CREATED | StatusCode::NO_CONTENT => {
             info!("Task {} claimed", task.id);
             Ok(())
         },

From 55d5922f45911143f34b306575c952f9455ac4c0 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Tue, 19 Sep 2023 12:10:55 +0000
Subject: [PATCH 02/22] In Beam's TaskResults, use null rather than "unused"
 for empty fields.

---
 src/beam.rs | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/beam.rs b/src/beam.rs
index 8d80e16..2e1bfc9 100644
--- a/src/beam.rs
+++ b/src/beam.rs
@@ -117,8 +117,8 @@ pub struct BeamResult {
     pub to: Vec<AppId>,
     pub task: Uuid,
     pub status: Status,
-    pub metadata: String,
-    pub body: String,
+    pub metadata: Option<String>,
+    pub body: Option<String>,
 }
 
 #[derive(Debug, Serialize, Deserialize, Clone, Eq, PartialEq)]
@@ -137,8 +137,8 @@ impl BeamResult {
             to,
             task,
             status: Status::Claimed,
-            metadata: "unused".to_owned(),
-            body: "unused".to_owned(),
+            metadata: None,
+            body: None,
         }
     }
     pub fn succeeded(from: AppId, to: Vec<AppId>, task: Uuid, body: String) -> Self {
@@ -147,8 +147,8 @@ impl BeamResult {
             to,
             task,
             status: Status::Succeeded,
-            metadata: "unused".to_owned(),
-            body,
+            metadata: None,
+            body: Some(body),
         }
     }
 
@@ -158,8 +158,8 @@ impl BeamResult {
             to,
             task,
             status: Status::PermFailed,
-            metadata: "unused".to_owned(),
-            body,
+            metadata: None,
+            body: Some(body),
         }
     }
 }

From 8b4c208ae362c7bcef98b977731d361d295f46b7 Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Tue, 19 Sep 2023 16:21:46 +0000
Subject: [PATCH 03/22] First version of `focusdev`

---
 .github/workflows/rust.yml |   2 +-
 Dockerfile                 |   3 +-
 Dockerfile.ci              |  15 ----
 dev/docker-compose.yml     | 106 ++++++++++++++++++++++++++++
 dev/focusdev               | 137 +++++++++++++++++++++++++++++++++++++
 dev/pki/pki                | 123 +++++++++++++++++++++++++++++++++
 src/main.rs                |   5 ++
 7 files changed, 374 insertions(+), 17 deletions(-)
 delete mode 100644 Dockerfile.ci
 create mode 100644 dev/docker-compose.yml
 create mode 100755 dev/focusdev
 create mode 100755 dev/pki/pki

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 061f0ff..f6bf92f 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -111,7 +111,7 @@ jobs:
       # Define the build context of your image, typically default '.' will be enough
       # build-context: '.'
       # Define the Dockerfile of your image, typically default './Dockerfile' will be enough
-      build-file: './Dockerfile.ci'
+      build-file: './Dockerfile'
       # NOTE: This doesn't work currently
       # A list of build arguments, passed to the docker build
 #      build-args: |
diff --git a/Dockerfile b/Dockerfile
index 6ec8b1f..e84eb22 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,11 +1,12 @@
 # This assumes binaries are present, see COPY directive.
+ARG IMGNAME=gcr.io/distroless/cc
 
 FROM alpine AS chmodder
 ARG TARGETARCH
 COPY /artifacts/binaries-$TARGETARCH/focus /app/
 RUN chmod +x /app/*
 
-FROM alpine
+FROM ${IMGNAME}
 COPY --from=chmodder /app/* /usr/local/bin/
 ENTRYPOINT [ "/usr/local/bin/focus" ]
 
diff --git a/Dockerfile.ci b/Dockerfile.ci
deleted file mode 100644
index 615ead6..0000000
--- a/Dockerfile.ci
+++ /dev/null
@@ -1,15 +0,0 @@
-# This assumes binaries are present, see COPY directive.
-
-FROM alpine AS chmodder
-ARG TARGETARCH
-COPY /artifacts/binaries-$TARGETARCH/focus /app/
-RUN chmod +x /app/*
-
-FROM gcr.io/distroless/cc
-#ARG COMPONENT
-#ARG TARGETARCH
-#COPY /artifacts/binaries-$TARGETARCH/$COMPONENT /usr/local/bin/
-COPY --from=chmodder /app/* /usr/local/bin/
-#ENTRYPOINT [ "/usr/local/bin/$COMPONENT" ]
-ENTRYPOINT [ "/usr/local/bin/focus" ]
-
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
new file mode 100644
index 0000000..ca2c236
--- /dev/null
+++ b/dev/docker-compose.yml
@@ -0,0 +1,106 @@
+version: "3.7"
+services:
+  vault:
+    image: hashicorp/vault
+    ports:
+      - 127.0.0.1:8200:8200
+    environment:
+      VAULT_DEV_ROOT_TOKEN_ID: ${VAULT_TOKEN}
+      VAULT_DEV_LISTEN_ADDRESS: 0.0.0.0:8200
+    volumes:
+      - ./pki:/pki
+    networks:
+      - default
+  broker:
+    depends_on: [vault]
+    image: samply/beam-broker:develop
+    ports:
+      - 8080:8080
+      - 8090:8090
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PKI_ADDRESS: http://vault:8200
+      no_proxy: vault
+      NO_PROXY: vault
+      PRIVKEY_FILE: /run/secrets/dummy.pem
+      BIND_ADDR: 0.0.0.0:8080
+      MONITORING_API_KEY: ${BROKER_MONITORING_KEY}
+      RUST_LOG: ${RUST_LOG}
+      ALL_PROXY: http://mitmproxy:8080
+    secrets:
+      - pki.secret
+      - dummy.pem
+      - root.crt.pem
+  mitmproxy:
+    image: mitmproxy/mitmproxy
+    stop_signal: SIGKILL
+    command: mitmweb --web-host 0.0.0.0 --web-port 9090
+    ports:
+      - 9090:9090
+  proxy1:
+    depends_on: [broker]
+    image: samply/beam-proxy:develop
+    ports:
+      - 8081:8081
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PROXY_ID: ${PROXY1_ID}
+      APP_app1_KEY: ${APP_KEY}
+      APP_app2_KEY: ${APP_KEY}
+      PRIVKEY_FILE: /run/secrets/proxy1.pem
+      BIND_ADDR: 0.0.0.0:8081
+      RUST_LOG: ${RUST_LOG}
+      ALL_PROXY: http://mitmproxy:8080
+    secrets:
+      - proxy1.pem
+      - root.crt.pem
+  proxy2:
+    depends_on: [broker]
+    image: samply/beam-proxy:develop
+    ports:
+      - 8082:8082
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PROXY_ID: ${PROXY2_ID}
+      APP_app1_KEY: ${APP_KEY}
+      APP_app2_KEY: ${APP_KEY}
+      PRIVKEY_FILE: /run/secrets/proxy2.pem
+      BIND_ADDR: 0.0.0.0:8082
+      RUST_LOG: ${RUST_LOG}
+      ALL_PROXY: http://mitmproxy:8080
+    secrets:
+      - proxy2.pem
+      - root.crt.pem
+  focus:
+    depends_on:
+      - proxy1
+      - blaze
+    build:
+      context: ../
+      dockerfile: Dockerfile
+    image: samply/focus:${TAG}
+    environment:
+      API_KEY: ${APP_KEY}
+      BEAM_APP_ID_LONG: app1.${PROXY1_ID}
+      BLAZE_URL: "http://blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://proxy1:8081
+      RETRY_COUNT: 30
+      OBFUSCATE: "no"
+  blaze:
+    image: samply/blaze
+    volumes:
+      - "blaze-data:/app/data"
+secrets:
+  pki.secret:
+    file: ./pki/pki.secret
+  proxy1.pem:
+    file: ./pki/${PROXY1_ID_SHORT}.priv.pem
+  proxy2.pem:
+    file: ./pki/${PROXY2_ID_SHORT}.priv.pem
+  dummy.pem:
+    file: ./pki/dummy.priv.pem
+  root.crt.pem:
+    file: ./pki/root.crt.pem
+
+volumes:
+  blaze-data:
diff --git a/dev/focusdev b/dev/focusdev
new file mode 100755
index 0000000..4de2109
--- /dev/null
+++ b/dev/focusdev
@@ -0,0 +1,137 @@
+#!/bin/bash -e
+
+# https://stackoverflow.com/questions/59895/
+SOURCE=${BASH_SOURCE[0]}
+while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+  SOURCE=$(readlink "$SOURCE")
+  [[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+SD=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+
+cd $SD
+
+export PROXY1_ID=${PROXY1_ID:-proxy1.broker}
+export PROXY2_ID=${PROXY2_ID:-proxy2.broker}
+export PROXY1_ID_SHORT=$(echo $PROXY1_ID | cut -d '.' -f 1)
+export PROXY2_ID_SHORT=$(echo $PROXY2_ID | cut -d '.' -f 1)
+export BROKER_ID=$(echo $PROXY1_ID | cut -d '.' -f 2-)
+export BROKER_URL=http://broker:8080
+export APP1_ID_SHORT=app1
+export APP2_ID_SHORT=app2
+export APP1_P1=${APP1_ID_SHORT}.$PROXY1_ID
+export APP2_P1=${APP2_ID_SHORT}.$PROXY1_ID
+export APP1_P2=${APP1_ID_SHORT}.$PROXY2_ID
+export APP2_P2=${APP2_ID_SHORT}.$PROXY2_ID
+export APP_KEY=App1Secret
+export BROKER_MONITORING_KEY=SuperSecretKey
+export RUST_LOG=${RUST_LOG:-info}
+
+export VAULT_TOKEN=$(echo "ABCDEFGHIJ" | md5sum | head -c 20; echo;)
+
+export P1="http://localhost:8081" # for scripts
+export P2="http://localhost:8082" # for scripts
+
+export ARCH=$(docker version --format "{{.Server.Arch}}")
+
+function image_for_docker() {
+     # Pick the correct Ubuntu version for the Docker image,
+     # so the locally-built rust binary works regarding libssl
+     if [[ "$(pkg-config --modversion libssl)" =~ ^3.* ]]; then
+          echo "ubuntu:latest" # Use libssl3
+     else
+          echo -n "" # Don't change (uses libssl1.1)
+     fi
+}
+
+export IMGNAME="$(image_for_docker)"
+
+function check_prereqs() {
+     set +e
+     if [[ "$(curl --version)" != *" libcurl/"* ]]; then
+          echo "curl not found -- please install curl >= 7.7.0 and put into PATH."
+          exit 1
+     fi
+     if [[ "$(jq --version)" != *"jq-"* ]]; then
+          echo "jq not found -- please install and put into PATH."
+          exit 1
+     fi
+     if [[ "$(rsync --version)" != *"rsync  version"* ]]; then
+          echo "rsync not found -- please install and put into PATH."
+          exit 1
+     fi
+     set -e
+}
+
+function build() {
+    BUILD_DOCKER=0
+    BACK=$(pwd)
+    cd $SD/..
+    FOCUS=./target/debug/focus
+    if [ ! -x ./artifacts/binaries-$ARCH ]; then
+        echo "Binaries missing -- building ..."
+        BUILD="$(cargo build $@ --message-format=json)"
+        echo "Will rebuild docker image since binaries had not been there."
+        mkdir -p artifacts/binaries-$ARCH
+        rsync "$FOCUS" artifacts/binaries-$ARCH/
+        BUILD_DOCKER=1
+    elif [ -z "$(docker images -q samply/focus:$TAG)" ]; then
+        echo "Will rebuild docker image since it is missing."
+        BUILD_DOCKER=1
+    elif [ -x ./target ]; then
+        echo "Checking for changed Rust source code ..."
+        BUILD="$(cargo build $@ --message-format=json)"
+        if echo $BUILD | jq 'select(.fresh==false)' | grep -q 'fresh'; then
+            echo "Will rebuild docker image due to changes in rust binaries."
+            rsync "$FOCUS" artifacts/binaries-$ARCH/
+            BUILD_DOCKER=1
+        fi
+    fi
+    if [ $BUILD_DOCKER -eq 1 ]; then
+        build_docker
+    else
+        echo "Not rebuilding docker image since nothing has changed."
+    fi
+    cd $BACK
+}
+
+function build_docker() {
+    BACK2=$(pwd)
+    cd $SD
+    if [ -z "$IMGNAME" ]; then
+        docker-compose build --build-arg TARGETARCH=$ARCH
+    else
+        docker-compose build --build-arg TARGETARCH=$ARCH --build-arg IMGNAME=$IMGNAME
+    fi
+    cd $BACK2
+}
+
+function start {
+    echo "$VAULT_TOKEN" > pki/pki.secret
+    pki/pki setup
+    build $@
+    docker compose up --no-build --no-recreate -d
+    docker compose logs focus -f
+}
+
+check_prereqs
+
+export TAG=${TAG:-localbuild}
+
+case "$1" in
+    build)
+        shift
+        build $@
+        ;;
+    start)
+        shift
+        start $@
+        ;;
+    restart)
+        docker compose build --build-arg TARGETARCH=$ARCH --build-arg IMGNAME=$IMGNAME focus
+        docker compose up --no-deps --no-build focus
+        ;;
+    *)
+        echo "Usage: $0 build|start"
+        ;;
+esac
diff --git a/dev/pki/pki b/dev/pki/pki
new file mode 100755
index 0000000..cd8643f
--- /dev/null
+++ b/dev/pki/pki
@@ -0,0 +1,123 @@
+#!/bin/bash -e
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+#ME="$(basename "$(test -L "$0" && readlink "$0" || echo "$0")")"
+
+[ -z "$PROXY1_ID" ] && ( echo "PROXY1_ID not set!"; exit 1)
+[ -z "$PROXY2_ID" ] && ( echo "PROXY2_ID not set!"; exit 1)
+
+cd $SCRIPT_DIR
+export PROXY1_ID_SHORT=$(echo $PROXY1_ID | cut -d '.' -f 1)
+export PROXY2_ID_SHORT=$(echo $PROXY2_ID | cut -d '.' -f 1)
+export BROKER_ID=$(echo $PROXY1_ID | cut -d '.' -f 2-)
+export VAULT_ADDR=http://127.0.0.1:8200
+
+function start() {
+    docker-compose up -d --no-build vault
+}
+
+function clean() {
+    rm -vf *.pem *.json
+    docker-compose down
+}
+
+function create_root_ca() {
+    vault secrets enable pki
+    vault secrets tune -max-lease-ttl=87600h pki
+    vault write -field=certificate pki/root/generate/internal \
+        common_name="Broker-Root" \
+        issuer_name="root-2022" \
+        ttl=87600h > dktk_root_2022_ca.crt.pem
+    vault write pki/roles/2022-servers_root allow_any_name=true
+    cp dktk_root_2022_ca.crt.pem root.crt.pem
+}
+
+function create_intermediate_ca() {
+    vault secrets enable -path=samply_pki pki
+    vault secrets tune -max-lease-ttl=43800h samply_pki
+    vault write -format=json samply_pki/intermediate/generate/internal \
+        common_name="$BROKER_ID Intermediate Authority" \
+        issuer_name="$BROKER_ID-intermediate" \
+        | jq -r '.data.csr' > pki_hd_intermediate.csr.pem
+    vault write -format=json pki/root/sign-intermediate \
+        issuer_ref="root-2022" \
+        csr=@pki_hd_intermediate.csr.pem \
+        format=pem_bundle ttl="43800h" \
+        | jq -r '.data.certificate' > hd_intermediate.crt.pem
+    vault write samply_pki/intermediate/set-signed certificate=@hd_intermediate.crt.pem
+    vault write samply_pki/roles/hd-dot-dktk-dot-com \
+        issuer_ref="$(vault read -field=default samply_pki/config/issuers)" \
+        allowed_domains="$BROKER_ID" \
+        allow_subdomains=true \
+        allow_glob_domains=true \
+        max_ttl="720h"
+}
+
+function request_proxy() {
+    application="${1:-app1}"
+    ttl="${2:-24h}"
+    cn="${application}.$BROKER_ID"
+    request "$application" "$cn" "$ttl" 
+}
+
+function request() {
+    application=$1
+    cn=$2
+    ttl=$3
+    data="{\"common_name\": \"$cn\", \"ttl\": \"$ttl\"}"
+    echo $data
+    echo "Creating Certificate for domain $cn"
+    curl --header "X-Vault-Token: $VAULT_TOKEN" \
+        --request POST \
+        --data "$data" \
+        --no-progress-meter \
+    $VAULT_ADDR/v1/samply_pki/issue/hd-dot-dktk-dot-com | jq > ${application}.json
+    cat ${application}.json | jq -r .data.certificate > ${application}.crt.pem
+    cat ${application}.json | jq -r .data.ca_chain[] > ${application}.chain.pem
+    cat ${application}.json | jq -r .data.private_key > ${application}.priv.pem
+    echo "Success: PEM files stored to ${application}*.pem"
+}
+
+function setup() {
+    clean
+    touch ${PROXY1_ID_SHORT}.priv.pem # see https://github.com/docker/compose/issues/8305
+    touch ${PROXY2_ID_SHORT}.priv.pem # see https://github.com/docker/compose/issues/8305
+    # touch test0.priv.pem # see https://github.com/docker/compose/issues/8305
+    # touch test1.priv.pem # see https://github.com/docker/compose/issues/8305
+    # touch root.crt.pem # see https://github.com/docker/compose/issues/8304
+    start
+    while ! [ "$(curl -s $VAULT_ADDR/v1/sys/health | jq -r .sealed)" == "false" ]; do echo "Waiting ..."; sleep 0.1; done
+    docker compose exec -T vault sh -c "https_proxy=$http_proxy apk add --no-cache bash curl jq"
+    docker compose exec -T vault sh -c "VAULT_TOKEN=$VAULT_TOKEN http_proxy= HTTP_PROXY= PROXY1_ID=$PROXY1_ID PROXY2_ID=$PROXY2_ID /pki/pki init"
+    docker compose exec -T vault sh -c "VAULT_TOKEN=$VAULT_TOKEN http_proxy= HTTP_PROXY= PROXY1_ID=$PROXY1_ID PROXY2_ID=$PROXY2_ID /pki/pki request_proxy $PROXY1_ID_SHORT" "1y"
+    docker compose exec -T vault sh -c "VAULT_TOKEN=$VAULT_TOKEN http_proxy= HTTP_PROXY= PROXY1_ID=$PROXY1_ID PROXY2_ID=$PROXY2_ID /pki/pki request_proxy $PROXY2_ID_SHORT" "1y"
+    docker compose exec -T vault sh -c "VAULT_TOKEN=$VAULT_TOKEN http_proxy= HTTP_PROXY= PROXY1_ID=$PROXY1_ID PROXY2_ID=$PROXY2_ID /pki/pki request_proxy dummy" "1y"
+}
+
+function init() {
+    echo "Creating Root CA"
+    create_root_ca
+
+    echo "Creating Intermediate HD CA"
+    create_intermediate_ca
+
+    echo "Successfully completed 'init'."
+}
+
+case "$1" in
+    clean)
+        clean
+        ;;
+    setup)
+        setup
+        ;;
+    init)
+        init
+        ;;
+    request_proxy)
+        request_proxy $2 $3
+        ;;
+    *)
+        echo "Usage: $0 setup|clean|init"
+        ;;
+esac
diff --git a/src/main.rs b/src/main.rs
index 21873f3..e8e1063 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -59,6 +59,11 @@ pub async fn main() -> ExitCode {
 }
 
 async fn main_loop() -> ExitCode {
+    warn!("asdfasdfafd");
+    warn!("asdfasdfafd");
+    warn!("asdfasdfafd");
+    warn!("asdfasdfafd");
+    warn!("asdfasdfafd");
     let mut obf_cache: ObfCache = ObfCache {
         cache: HashMap::new(),
     };

From 2dab0629d40eb8382e9f1f94513dc82138a39105 Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 07:46:52 +0000
Subject: [PATCH 04/22] Rebuild fsource on `focusdev restart` if needed

---
 dev/focusdev | 5 +++--
 dev/pki/pki  | 3 ---
 src/main.rs  | 5 -----
 3 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/dev/focusdev b/dev/focusdev
index 4de2109..4e8ed23 100755
--- a/dev/focusdev
+++ b/dev/focusdev
@@ -128,10 +128,11 @@ case "$1" in
         start $@
         ;;
     restart)
-        docker compose build --build-arg TARGETARCH=$ARCH --build-arg IMGNAME=$IMGNAME focus
+        shift
+        build $@
         docker compose up --no-deps --no-build focus
         ;;
     *)
-        echo "Usage: $0 build|start"
+        echo "Usage: $0 build|start|restart"
         ;;
 esac
diff --git a/dev/pki/pki b/dev/pki/pki
index cd8643f..da98242 100755
--- a/dev/pki/pki
+++ b/dev/pki/pki
@@ -82,9 +82,6 @@ function setup() {
     clean
     touch ${PROXY1_ID_SHORT}.priv.pem # see https://github.com/docker/compose/issues/8305
     touch ${PROXY2_ID_SHORT}.priv.pem # see https://github.com/docker/compose/issues/8305
-    # touch test0.priv.pem # see https://github.com/docker/compose/issues/8305
-    # touch test1.priv.pem # see https://github.com/docker/compose/issues/8305
-    # touch root.crt.pem # see https://github.com/docker/compose/issues/8304
     start
     while ! [ "$(curl -s $VAULT_ADDR/v1/sys/health | jq -r .sealed)" == "false" ]; do echo "Waiting ..."; sleep 0.1; done
     docker compose exec -T vault sh -c "https_proxy=$http_proxy apk add --no-cache bash curl jq"
diff --git a/src/main.rs b/src/main.rs
index e8e1063..21873f3 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -59,11 +59,6 @@ pub async fn main() -> ExitCode {
 }
 
 async fn main_loop() -> ExitCode {
-    warn!("asdfasdfafd");
-    warn!("asdfasdfafd");
-    warn!("asdfasdfafd");
-    warn!("asdfasdfafd");
-    warn!("asdfasdfafd");
     let mut obf_cache: ObfCache = ObfCache {
         cache: HashMap::new(),
     };

From 9ee0ee760f1c4a7fac91a0aa359873af0f11c675 Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 08:39:58 +0000
Subject: [PATCH 05/22] Upgrade distoless to debian 12

This allows droping the extra logic to link against a diffrent libssl
version
---
 Dockerfile   |  2 +-
 dev/focusdev | 20 ++------------------
 2 files changed, 3 insertions(+), 19 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e84eb22..db66d8e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
 # This assumes binaries are present, see COPY directive.
-ARG IMGNAME=gcr.io/distroless/cc
+ARG IMGNAME=gcr.io/distroless/cc-debian12
 
 FROM alpine AS chmodder
 ARG TARGETARCH
diff --git a/dev/focusdev b/dev/focusdev
index 4e8ed23..3cdb756 100755
--- a/dev/focusdev
+++ b/dev/focusdev
@@ -34,18 +34,6 @@ export P2="http://localhost:8082" # for scripts
 
 export ARCH=$(docker version --format "{{.Server.Arch}}")
 
-function image_for_docker() {
-     # Pick the correct Ubuntu version for the Docker image,
-     # so the locally-built rust binary works regarding libssl
-     if [[ "$(pkg-config --modversion libssl)" =~ ^3.* ]]; then
-          echo "ubuntu:latest" # Use libssl3
-     else
-          echo -n "" # Don't change (uses libssl1.1)
-     fi
-}
-
-export IMGNAME="$(image_for_docker)"
-
 function check_prereqs() {
      set +e
      if [[ "$(curl --version)" != *" libcurl/"* ]]; then
@@ -67,7 +55,7 @@ function build() {
     BUILD_DOCKER=0
     BACK=$(pwd)
     cd $SD/..
-    FOCUS=./target/debug/focus
+    FOCUS=./target/release/focus
     if [ ! -x ./artifacts/binaries-$ARCH ]; then
         echo "Binaries missing -- building ..."
         BUILD="$(cargo build $@ --message-format=json)"
@@ -98,11 +86,7 @@ function build() {
 function build_docker() {
     BACK2=$(pwd)
     cd $SD
-    if [ -z "$IMGNAME" ]; then
-        docker-compose build --build-arg TARGETARCH=$ARCH
-    else
-        docker-compose build --build-arg TARGETARCH=$ARCH --build-arg IMGNAME=$IMGNAME
-    fi
+    docker-compose build --build-arg TARGETARCH=$ARCH
     cd $BACK2
 }
 

From c37d8c3303cb0ced5bcf08e03e6f6560eea784cf Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 08:42:42 +0000
Subject: [PATCH 06/22] Update CI images to link against libssl 3

---
 .github/workflows/rust.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index f6bf92f..75e3a66 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -22,7 +22,7 @@ jobs:
 
   build-rust:
     name: Build (Rust)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     strategy:
       matrix:
@@ -86,7 +86,7 @@ jobs:
   test:
     name: Run tests
     needs: [ build-rust ]
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
   
     steps:
       - uses: actions/checkout@v3

From 295ec33faeda291814ebc3edbcc62fa5656f96e8 Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 12:48:04 +0000
Subject: [PATCH 07/22] Use fix version to build rust

---
 .github/workflows/rust.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 75e3a66..b27b78c 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -22,7 +22,7 @@ jobs:
 
   build-rust:
     name: Build (Rust)
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -86,7 +86,7 @@ jobs:
   test:
     name: Run tests
     needs: [ build-rust ]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
   
     steps:
       - uses: actions/checkout@v3

From ffd285f93971466198fd398b6774b70d64ec717e Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 13:10:16 +0000
Subject: [PATCH 08/22] Add `focusdev stop`

---
 dev/focusdev | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/dev/focusdev b/dev/focusdev
index 3cdb756..6b88851 100755
--- a/dev/focusdev
+++ b/dev/focusdev
@@ -116,7 +116,10 @@ case "$1" in
         build $@
         docker compose up --no-deps --no-build focus
         ;;
+    stop)
+        docker compose down
+        ;;
     *)
-        echo "Usage: $0 build|start|restart"
+        echo "Usage: $0 build|start|restart|stop"
         ;;
 esac

From 2c73c9da91968703d60d51882c6198798e710e37 Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 20 Sep 2023 13:14:59 +0000
Subject: [PATCH 09/22] Remove `IMGNAME` build arg

---
 Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index db66d8e..dc15b04 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,12 +1,10 @@
 # This assumes binaries are present, see COPY directive.
-ARG IMGNAME=gcr.io/distroless/cc-debian12
-
 FROM alpine AS chmodder
 ARG TARGETARCH
 COPY /artifacts/binaries-$TARGETARCH/focus /app/
 RUN chmod +x /app/*
 
-FROM ${IMGNAME}
+FROM gcr.io/distroless/cc-debian12
 COPY --from=chmodder /app/* /usr/local/bin/
 ENTRYPOINT [ "/usr/local/bin/focus" ]
 

From f7638c76d115c6535cd238690498092b1e1d5aeb Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Mon, 25 Sep 2023 12:39:01 +0000
Subject: [PATCH 10/22] Fix compiler errors

---
 src/beam.rs | 10 +++++-----
 src/main.rs | 19 ++++++++-----------
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/src/beam.rs b/src/beam.rs
index 2e1bfc9..e9eda1a 100644
--- a/src/beam.rs
+++ b/src/beam.rs
@@ -141,25 +141,25 @@ impl BeamResult {
             body: None,
         }
     }
-    pub fn succeeded(from: AppId, to: Vec<AppId>, task: Uuid, body: String) -> Self {
+    pub fn succeeded(from: AppId, to: Vec<AppId>, task: Uuid, body: Option<String>) -> Self {
         Self {
             from,
             to,
             task,
             status: Status::Succeeded,
             metadata: None,
-            body: Some(body),
+            body,
         }
     }
 
-    pub fn perm_failed(from: AppId, to: Vec<AppId>, task: Uuid, body: String) -> Self {
+    pub fn perm_failed(from: AppId, to: Vec<AppId>, task: Uuid, body: Option<String>) -> Self {
         Self {
             from,
             to,
             task,
             status: Status::PermFailed,
             metadata: None,
-            body: Some(body),
+            body,
         }
     }
 }
@@ -279,7 +279,7 @@ pub async fn answer_task(task: &BeamTask, result: &BeamResult) -> Result<(), Foc
 pub async fn fail_task(task: &BeamTask, body: impl Into<String>) -> Result<(), FocusError> {
     let body = body.into();
     warn!("Reporting failed task with id {}: {}", task.id, body);
-    let result = BeamResult::perm_failed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id, body);
+    let result = BeamResult::perm_failed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id, Some(body));
     let url = format!(
         "{}v1/tasks/{}/results/{}",
         CONFIG.beam_proxy_url, task.id, CONFIG.beam_app_id_long
diff --git a/src/main.rs b/src/main.rs
index 21873f3..8004aad 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -228,7 +228,7 @@ async fn run_query(
             CONFIG.beam_app_id_long.clone(),
             vec![task.from.clone()],
             task.id,
-            format!("Can't run inqueries with language {}", query.lang),
+            Some(format!("Can't run inquiries with language {}", query.lang)),
         ));
     }
 }
@@ -239,13 +239,6 @@ async fn run_cql_query(
     obf_cache: &mut ObfCache,
     report_cache: &mut ReportCache,
 ) -> Result<BeamResult, FocusError> {
-    let mut err = beam::BeamResult::perm_failed(
-        CONFIG.beam_app_id_long.clone(),
-        vec![task.to_owned().from],
-        task.to_owned().id,
-        String::new(),
-    );
-
     let encoded_query =
         query.lib["content"][0]["data"]
             .as_str()
@@ -302,8 +295,12 @@ async fn run_cql_query(
     };
 
     let result = beam_result(task.to_owned(), cql_result_new).unwrap_or_else(|e| {
-        err.body = e.to_string();
-        return err;
+        beam::BeamResult::perm_failed(
+            CONFIG.beam_app_id_long.clone(),
+            vec![task.to_owned().from],
+            task.to_owned().id,
+            Some(e.to_string())
+        )
     });
 
     Ok(result)
@@ -356,6 +353,6 @@ fn beam_result(
         CONFIG.beam_app_id_long.clone(),
         vec![task.from],
         task.id,
-        data,
+        Some(data)
     ));
 }

From 72ace792802b4c95045aed1fddfa429c4de1eb3d Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Mon, 25 Sep 2023 12:46:02 +0000
Subject: [PATCH 11/22] Reformat query.lang

---
 src/main.rs | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/src/main.rs b/src/main.rs
index 21873f3..173ea72 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -220,16 +220,19 @@ async fn run_query(
 ) -> Result<BeamResult, FocusError> {
     debug!("Run");
 
-    if query.lang == "cql" {
-        // TODO: Change query.lang to an enum
-        return Ok(run_cql_query(task, query, obf_cache, report_cache).await)?;
-    } else {
-        return Ok(beam::BeamResult::perm_failed(
-            CONFIG.beam_app_id_long.clone(),
-            vec![task.from.clone()],
-            task.id,
-            format!("Can't run inqueries with language {}", query.lang),
-        ));
+    match query.lang.as_str() {
+        "cql" => {
+            // TODO: Change query.lang to an enum
+            Ok(run_cql_query(task, query, obf_cache, report_cache).await)?
+        },
+        unsupported_lang => {
+            Ok(beam::BeamResult::perm_failed(
+                CONFIG.beam_app_id_long.clone(),
+                vec![task.from.clone()],
+                task.id,
+                format!("Can't run queries with language {unsupported_lang}"),
+            ))
+        }
     }
 }
 

From d322b1bb10428adbc72796fb0a0685e538c3dcff Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Mon, 25 Sep 2023 12:51:49 +0000
Subject: [PATCH 12/22] Allow to build docker image manually for branches

---
 .github/workflows/rust.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index b27b78c..661954d 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -2,6 +2,7 @@ name: Build with rust and docker
 
 on:
   push:
+  workflow_dispatch:
   pull_request:
   schedule:
     # Fetch new base image updates every night at 1am
@@ -98,7 +99,7 @@ jobs:
 
   docker-focus:
     needs: [ build-rust, pre-check, test ]
-    if: github.ref_protected == true
+    if: github.ref_protected == true || github.event_name == 'workflow_dispatch'
     
     # This workflow defines how a maven package is built, tested and published.
     # Visit: https://github.com/samply/github-workflows/blob/develop/.github/workflows/docker-ci.yml, for more information

From 51d1aa78fdae66cdf3bad77ac82f397be87f07d6 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Mon, 25 Sep 2023 12:52:53 +0000
Subject: [PATCH 13/22] Be explicit about Ubuntu image usage

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 661954d..6acbc50 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -15,7 +15,7 @@ env:
 jobs:
   pre-check:
     name: Security, License Check
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/checkout@v3

From 1078f5c7849610129fa1b1615e5d52f0e9a13a98 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Mon, 25 Sep 2023 12:58:44 +0000
Subject: [PATCH 14/22] Build and run tests faster

---
 .github/workflows/rust.yml | 32 ++++++++++++++++++++++++++------
 1 file changed, 26 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 6acbc50..bebe260 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -71,18 +71,34 @@ jobs:
         with:
           key: ${{ matrix.arch }}-${{ env.PROFILE }}
           prefix-key: "v1-rust" # Increase to invalidate old caches.
-      - name: Build (${{ matrix.arch }})
+      - name: Build (cross to ${{ matrix.arch }})
+        if: env.is_cross == 'true'
         uses: actions-rs/cargo@v1
         with:
           use-cross: ${{ env.is_cross }}
           command: build
-          args: --target ${{ env.rustarch }} ${{ env.profilestr }}
-      - name: Upload Artifact
+          args: --target ${{ env.rustarch }} ${{ matrix.features && format('--features {0}', matrix.features) }} ${{ env.profilestr }}
+      - name: Build (native)
+        if: env.is_cross == 'false'
+        run: |
+          BINS=$(cargo build --tests --bins --message-format=json --target ${{ env.rustarch }} ${{ matrix.features && format('--features {0}', matrix.features) }} ${{ env.profilestr }} | jq -r 'select(.profile.test == true) | .executable | select(. != null)')
+          mkdir -p testbinaries/
+          for testbin in $BINS; do
+            mv -v $testbin testbinaries/
+          done
+      - name: Upload (bins)
         uses: actions/upload-artifact@v3
         with:
           name: binaries-${{ matrix.arch }}
           path: |
             target/${{ env.rustarch }}/${{ env.PROFILE }}/focus
+      - name: Upload (test, native only)
+        if: matrix.arch == 'amd64'
+        uses: actions/upload-artifact@v3
+        with:
+          name: testbinaries-${{ matrix.arch }}
+          path: |
+            testbinaries/*
 
   test:
     name: Run tests
@@ -93,9 +109,13 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/download-artifact@v3
         with:
-          name: binaries-amd64
-          path: artifacts/binaries-amd64/
-      - run: cargo test
+          name: testbinaries-amd64
+          path: testbinaries/
+      - run: |
+          for testbin in testbinaries/*; do
+            chmod +x $testbin
+            $testbin
+          done
 
   docker-focus:
     needs: [ build-rust, pre-check, test ]

From 095ba851a4063f66117e3a08ecc7905784463526 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Wed, 27 Sep 2023 08:34:40 +0000
Subject: [PATCH 15/22] Add build hint to Dockerfile

---
 Dockerfile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index dc15b04..24f078a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,10 @@
-# This assumes binaries are present, see COPY directive.
+# This Dockerfile is infused with magic to speedup the build.
+# In particular, it requires built binaries to be present (see COPY directive).
+#
+# tl;dr: To make this build work, run
+#   ./dev/focusdev build
+# and find your freshly built images tagged with the `localbuild` tag.
+
 FROM alpine AS chmodder
 ARG TARGETARCH
 COPY /artifacts/binaries-$TARGETARCH/focus /app/

From 993a0bdcf256afc220715e92eb48f32c706734b3 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Wed, 27 Sep 2023 08:35:05 +0000
Subject: [PATCH 16/22] Add build hint to Dockerfile

---
 Dockerfile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index dc15b04..24f078a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,10 @@
-# This assumes binaries are present, see COPY directive.
+# This Dockerfile is infused with magic to speedup the build.
+# In particular, it requires built binaries to be present (see COPY directive).
+#
+# tl;dr: To make this build work, run
+#   ./dev/focusdev build
+# and find your freshly built images tagged with the `localbuild` tag.
+
 FROM alpine AS chmodder
 ARG TARGETARCH
 COPY /artifacts/binaries-$TARGETARCH/focus /app/

From 223acf671b76e4db0752478329768d55a1c3bcf6 Mon Sep 17 00:00:00 2001
From: Torben Brenner <t.brenner@dkfz-heidelberg.de>
Date: Tue, 25 Jul 2023 17:51:52 +0200
Subject: [PATCH 17/22] fix: search for age at primary diagnosis

---
 src/util.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/util.rs b/src/util.rs
index 3ce4574..5996a7d 100644
--- a/src/util.rs
+++ b/src/util.rs
@@ -103,7 +103,7 @@ pub(crate) fn replace_cql(decoded_library: impl Into<String>) -> String {
             ("EXLIQUID_CQL", "define ExliquidSpecimen:\n  from [Specimen] S\n  where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'\ndefine retrieveCondition:\n First(from [Condition] C\n  return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis:\n  if (retrieveCondition is null) then 'unknown' else retrieveCondition\ndefine function SampleType(specimen FHIR.Specimen):\n  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
             ("EXLIQUID_ALIQUOTS_CQL", "define Aliquot: [Specimen] S where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id    define retrieveCondition:   First(from [Condition] C   return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())    define Diagnosis:   if (retrieveCondition is null) then 'unknown' else retrieveCondition define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
             ("DKTK_STRAT_GENDER_STRATIFIER", "define Gender:\nif (Patient.gender is null) then 'unknown' else Patient.gender"),
-            ("DKTK_STRAT_AGE_STRATIFIER", "define AgeClass:\nif (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)"),
+            ("DKTK_STRAT_AGE_STRATIFIER", "define PrimaryDiagnosis:\nFirst(\nfrom [Condition] C\nwhere C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()\nsort by date from onset asc)\n\ndefine AgeClass:\nif (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)"),
             ("DKTK_STRAT_DECEASED_STRATIFIER", "define PatientDeceased:\nFirst (from [Observation: Code '75186-7' from loinc] O return O.value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/VitalstatusCS').code.first())\ndefine Deceased:\nif (PatientDeceased is null) then 'unbekannt' else PatientDeceased"),
             ("DKTK_STRAT_DIAGNOSIS_STRATIFIER", "define Diagnosis:\nif InInitialPopulation then [Condition] else {} as List<Condition>\n\ndefine function DiagnosisCode(condition FHIR.Condition):\ncondition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()"),
             ("DKTK_STRAT_SPECIMEN_STRATIFIER", "define Specimen:\nif InInitialPopulation then [Specimen] else {} as List<Specimen>\n\ndefine function SampleType(specimen FHIR.Specimen):\nspecimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),

From fc510bc16eb7af61c1cc13751ec5e6c02f27782b Mon Sep 17 00:00:00 2001
From: Jan <59206115+Threated@users.noreply.github.com>
Date: Thu, 28 Sep 2023 12:52:25 +0200
Subject: [PATCH 18/22] Use beam-lib for beam interactions (#44)

* Use `beam_lib` for beam interactions

---------

Co-authored-by: janskiba <jan.skiba@dkfz-heidelberg.de>
Co-authored-by: Tobias Kussel <tobias.kussel@dkfz-heidelberg.de>
---
 Cargo.toml               |   8 +-
 src/beam.rs              | 360 ++++++---------------------------------
 src/blaze.rs             |  15 +-
 src/config.rs            |  14 +-
 src/errors.rs            |  10 +-
 src/graceful_shutdown.rs |   4 +-
 src/main.rs              |  48 +++---
 src/util.rs              |   2 +-
 8 files changed, 97 insertions(+), 364 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 53ebfe1..0b9e32f 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,12 +9,12 @@ license = "Apache-2.0"
 [dependencies]
 base64 = { version = "0.21.0", default_features = false }
 http = "0.2"
-reqwest = { version = "0.11.14", default_features = false, features = ["json", "default-tls"] }
+reqwest = { version = "0.11", default_features = false, features = ["json", "default-tls"] }
 serde = { version = "1.0.152", features = ["serde_derive"] }
-serde_json = "1.0.91"
+serde_json = "1.0"
 thiserror = "1.0.38"
 tokio = { version = "1.25.0", default_features = false, features = ["signal", "rt-multi-thread", "macros"] }
-uuid = { version = "1.3.0", default_features = false, features = ["serde"]}
+beam-lib = { git = "https://github.com/samply/beam", branch = "develop", features = ["http-util"] }
 laplace_rs = {version = "0.2.0", git = "https://github.com/samply/laplace-rs.git", branch = "main" }
 
 # Logging
@@ -22,7 +22,7 @@ tracing = { version = "0.1.37", default_features = false }
 tracing-subscriber = { version = "0.3.11", default_features = false, features = ["env-filter", "fmt"] }
 
 # Global variables
-static_init = "1.0.2"
+once_cell = "1.18"
 
 # Command Line Interface
 clap = { version = "4.0", default_features = false, features = ["std", "env", "derive"] }
diff --git a/src/beam.rs b/src/beam.rs
index 2bb0d26..4558dca 100644
--- a/src/beam.rs
+++ b/src/beam.rs
@@ -1,164 +1,45 @@
-use std::{fmt::Display};
+use std::time::Duration;
 
-use http::{HeaderValue, StatusCode};
-use reqwest::header::{HeaderMap, AUTHORIZATION};
-use serde::{de, Deserializer, Deserialize, Serialize, Serializer};
-use tracing::{debug, warn, info};
-use uuid::Uuid;
+use beam_lib::{TaskResult, BeamClient, BlockingOptions, MsgId, TaskRequest};
+use once_cell::sync::Lazy;
+use serde::{de::DeserializeOwned, Serialize};
+use tracing::{debug, warn};
 
 use crate::{config::CONFIG, errors::FocusError};
 
-type BrokerId = String;
+pub mod beam_result {
+    use beam_lib::{AppId, TaskResult, WorkStatus, MsgId};
+    use serde::Serialize;
+    use serde_json::Value;
 
-#[derive(Clone, Debug, Serialize, Deserialize, PartialEq, Eq)]
-pub struct ProxyId {
-    proxy: String,
-    broker: BrokerId,
-}
-
-#[derive(Clone, Debug, PartialEq, Eq)]
-pub struct AppId {
-    app: String,
-    rest: ProxyId,
-}
-
-impl ProxyId {
-    pub fn get_proxy_id(&self) -> String {
-        format!("{}.{}", &self.proxy, &self.broker)
-    }
-    pub fn get_broker_id(&self) -> String {
-        self.broker.clone()
-    }
-    pub fn new(full: String) -> Result<Self, FocusError> {
-        let mut components: Vec<String> = full.split(".").map(|x| x.to_string()).collect();
-        let rest = components.split_off(1).join(".");
-        Ok(ProxyId { 
-            proxy: components
-                .first()
-                .cloned()
-                .ok_or_else(|| FocusError::InvalidBeamId(format!("Invalid ProxyId: {}", full)))?,
-            broker: rest,
-        })
-    }
-}
-
-impl AppId {
-    pub fn get_app_id(&self) -> String {
-        format!("{}.{}", &self.app, &self.rest.get_proxy_id())
-    }
-    pub fn get_proxy_id(&self) -> String {
-        self.rest.get_proxy_id()
-    }
-    pub fn new(full: String) -> Result<Self, FocusError> {
-        let mut components: Vec<String> = full.split(".").map(|x| x.to_string()).collect();
-        let rest = components.split_off(1).join(".");
-        Ok(AppId {
-            app: components
-                .first()
-                .cloned()
-                .ok_or_else(|| FocusError::InvalidBeamId(format!("Invalid ProxyId: {}", full)))?,
-            rest: ProxyId::new(rest)?,
-        })
-    }
-}
-impl Display for ProxyId {
-    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        write!(f, "{}.{}", self.proxy, self.broker)
-    }
-}
-impl Display for AppId {
-    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        write!(f, "{}.{}", self.app, self.rest)
-    }
-}
-
-impl<'de> serde::Deserialize<'de> for AppId {
-    fn deserialize<D: Deserializer<'de>>(d: D) -> Result<Self, D::Error> {
-        let s = String::deserialize(d)?;
-        AppId::new(s).map_err(de::Error::custom)
-    }
-}
-
-impl Serialize for AppId {
-    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
-        where S: Serializer,
-              {
-                  let mut state = String::serialize(&self.to_string(), serializer)?;
-                  Ok(state)
-              }
-}
-
-#[derive(Serialize, Deserialize, Debug, Clone)]
-pub struct BeamTask {
-    pub id: Uuid,
-    pub from: AppId,
-    pub to: Vec<AppId>,
-    pub metadata: String,
-    pub body: String,
-    pub ttl: String,
-    pub failure_strategy: FailureStrategy,
-}
-
-#[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(rename_all = "lowercase")]
-pub enum FailureStrategy {
-    Retry(Retry),
-}
-
-#[derive(Serialize, Deserialize, Debug, Default, Clone)]
-pub struct Retry {
-    pub backoff_millisecs: usize,
-    pub max_tries: usize,
-}
-
-#[derive(Debug, Serialize, Deserialize, Clone)]
-pub struct BeamResult {
-    pub from: AppId,
-    pub to: Vec<AppId>,
-    pub task: Uuid,
-    pub status: Status,
-    pub metadata: Option<String>,
-    pub body: Option<String>,
-}
-
-#[derive(Debug, Serialize, Deserialize, Clone, Eq, PartialEq)]
-#[serde(rename_all = "lowercase")]
-pub enum Status {
-    Claimed,
-    Succeeded,
-    TempFailed,
-    PermFailed,
-}
-
-impl BeamResult {
-    pub fn claimed(from: AppId, to: Vec<AppId>, task: Uuid) -> Self {
-        Self {
+    pub fn claimed(from: AppId, to: Vec<AppId>, task_id: MsgId) -> TaskResult<()> {
+        TaskResult {
             from,
             to,
-            task,
-            status: Status::Claimed,
-            metadata: None,
-            body: None,
+            task: task_id,
+            status: WorkStatus::Claimed,
+            metadata: Value::Null,
+            body: (),
         }
     }
-    pub fn succeeded(from: AppId, to: Vec<AppId>, task: Uuid, body: Option<String>) -> Self {
-        Self {
+    pub fn succeeded<T: Serialize>(from: AppId, to: Vec<AppId>, task_id: MsgId, body: T) -> TaskResult<T> {
+        TaskResult {
             from,
             to,
-            task,
-            status: Status::Succeeded,
-            metadata: None,
+            task: task_id,
+            status: WorkStatus::Succeeded,
+            metadata: Value::Null,
             body,
         }
     }
 
-    pub fn perm_failed(from: AppId, to: Vec<AppId>, task: Uuid, body: Option<String>) -> Self {
-        Self {
+    pub fn perm_failed<T: Serialize>(from: AppId, to: Vec<AppId>, task_id: MsgId, body: T) -> TaskResult<T> {
+        TaskResult {
             from,
             to,
-            task,
-            status: Status::PermFailed,
-            metadata: None,
+            task: task_id,
+            status: WorkStatus::PermFailed,
+            metadata: Value::Null,
             body,
         }
     }
@@ -186,185 +67,42 @@ pub async fn check_availability() -> bool {
     false
 }
 
-pub async fn retrieve_tasks() -> Result<Vec<BeamTask>, FocusError> {
-    debug!("Retrieving tasks...");
-
-    let mut headers = HeaderMap::new();
-    headers.insert(
-        AUTHORIZATION,
-        HeaderValue::from_str(&format!("ApiKey {} {}", CONFIG.beam_app_id_long, CONFIG.api_key))
-            .map_err(|e| {
-                FocusError::ConfigurationError(format!(
-                    "Cannot assemble authorization header: {}",
-                    e
-                ))
-            })?,
-    );
-
-    let url = format!(
-        "{}v1/tasks?filter=todo&wait_count=1&wait_time=10s",
-        CONFIG.beam_proxy_url
-    );
-    let resp = CONFIG.client
-        .get(&url)
-        .headers(headers)
-        .send()
-        .await
-        .map_err(|e| FocusError::UnableToRetrieveTasksHttp(e))?;
+static BEAM_CLIENT: Lazy<BeamClient> = Lazy::new(|| BeamClient::new(
+    &CONFIG.beam_app_id_long,
+    &CONFIG.api_key,
+    CONFIG.beam_proxy_url.to_string().parse().expect("Uri always converts to url")
+));
 
-    let tasks = match resp.status() {
-        StatusCode::OK | StatusCode::PARTIAL_CONTENT => {
-            resp
-                .json::<Vec<BeamTask>>()
-                .await
-                .map_err(|e| FocusError::UnableToParseTasks(e))?
-        }
-        code => {
-            return Err(FocusError::UnableToRetrieveTasksOther(format!("Got status code {code}")));
-        }
+pub async fn retrieve_tasks<T: DeserializeOwned>() -> Result<Vec<TaskRequest<T>>, FocusError> {
+    debug!("Retrieving tasks...");
+    let block = BlockingOptions {
+        wait_time: Some(Duration::from_secs(10)),
+        wait_count: Some(1)
     };
-    Ok(tasks)
+    BEAM_CLIENT.poll_pending_tasks(&block)
+        .await
+        .map_err(FocusError::UnableToRetrieveTasksHttp)
 }
 
-pub async fn answer_task(task: &BeamTask, result: &BeamResult) -> Result<(), FocusError> {
-    let task_id = task.id.to_string();
+pub async fn answer_task<T: Serialize>(task_id: MsgId, result: &TaskResult<T>) -> Result<bool, FocusError> {
     debug!("Answer task with id: {task_id}");
-    let result_task = result.task;
-    let url = format!(
-        "{}v1/tasks/{}/results/{}",
-        CONFIG.beam_proxy_url, &result_task, CONFIG.beam_app_id_long
-    );
-
-    let mut headers = HeaderMap::new();
-    headers.insert(
-        AUTHORIZATION,
-        HeaderValue::from_str(&format!("ApiKey {} {}", CONFIG.beam_app_id_long, CONFIG.api_key))
-            .map_err(|e| {
-                FocusError::ConfigurationError(format!(
-                    "Cannot assemble authorization header: {}",
-                    e
-                ))
-            })?,
-    );
-
-    let resp = CONFIG.client
-        .put(&url)
-        .headers(headers)
-        .json(&result)
-        .send()
+    BEAM_CLIENT.put_result(result, &task_id)
         .await
-        .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-
-    let status_code = resp.status();
-    let status_text = status_code.as_str();
-    debug!("{status_text}");
-
-    match status_code {
-        StatusCode::CREATED | StatusCode::NO_CONTENT => Ok(()),
-        StatusCode::BAD_REQUEST => {
-            let msg = resp
-                .text()
-                .await
-                .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-            warn!("Error while answering the task with id: {msg}");
-            Ok(()) // return error
-        }
-        _ => {
-            warn!("Unexpected status code: {}", resp.status());
-            Ok(()) //return error
-        }
-    }
+        .map_err(FocusError::UnableToAnswerTask)
 }
 
-pub async fn fail_task(task: &BeamTask, body: impl Into<String>) -> Result<(), FocusError> {
+pub async fn fail_task<T>(task: &TaskRequest<T>, body: impl Into<String>) -> Result<bool, FocusError> {
     let body = body.into();
     warn!("Reporting failed task with id {}: {}", task.id, body);
-    let result = BeamResult::perm_failed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id, Some(body));
-    let url = format!(
-        "{}v1/tasks/{}/results/{}",
-        CONFIG.beam_proxy_url, task.id, CONFIG.beam_app_id_long
-    );
-
-    let mut headers = HeaderMap::new();
-    headers.insert(
-        AUTHORIZATION,
-        HeaderValue::from_str(&format!("ApiKey {} {}", CONFIG.beam_app_id_long, CONFIG.api_key))
-            .map_err(|e| {
-                FocusError::ConfigurationError(format!(
-                    "Cannot assemble authorization header: {}",
-                    e
-                ))
-            })?,
-    );
-
-    let resp = CONFIG.client
-        .put(&url)
-        .headers(headers)
-        .json(&result)
-        .send()
+    let result = beam_result::perm_failed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id, body);
+    BEAM_CLIENT.put_result(&result, &task.id)
         .await
-        .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-
-    match resp.status() {
-        StatusCode::CREATED | StatusCode::NO_CONTENT => Ok(()),
-        StatusCode::BAD_REQUEST => {
-            let msg = resp
-                .text()
-                .await
-                .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-            warn!("Error while reporting the failed task with id {}: {msg}", task.id);
-            Ok(()) // return error
-        }
-        _ => {
-            warn!("Unexpected status code: {}", resp.status());
-            Ok(()) //return error
-        }
-    }
+        .map_err(FocusError::UnableToAnswerTask)
 }
 
-pub async fn claim_task(task: &BeamTask) -> Result<(), FocusError> {
-    let result = BeamResult::claimed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id);
-    let url = format!(
-        "{}v1/tasks/{}/results/{}",
-        CONFIG.beam_proxy_url, task.id, CONFIG.beam_app_id_long
-    );
-
-    let mut headers = HeaderMap::new();
-    headers.insert(
-        AUTHORIZATION,
-        HeaderValue::from_str(&format!("ApiKey {} {}", CONFIG.beam_app_id_long, CONFIG.api_key))
-            .map_err(|e| {
-                FocusError::ConfigurationError(format!(
-                    "Cannot assemble authorization header: {}",
-                    e
-                ))
-            })?,
-    );
-
-    let resp = CONFIG.client
-        .put(&url)
-        .headers(headers)
-        .json(&result)
-        .send()
+pub async fn claim_task<T>(task: &TaskRequest<T>) -> Result<bool, FocusError> {
+    let result = beam_result::claimed(CONFIG.beam_app_id_long.clone(), vec![task.from.clone()], task.id);
+    BEAM_CLIENT.put_result(&result, &task.id)
         .await
-        .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-
-    match resp.status() {
-        StatusCode::CREATED | StatusCode::NO_CONTENT => {
-            info!("Task {} claimed", task.id);
-            Ok(())
-        },
-        StatusCode::BAD_REQUEST => {
-            let msg = resp
-                .text()
-                .await
-                .map_err(|e| FocusError::UnableToAnswerTask(e))?;
-            warn!("Error while reporting the claimed task with id {}: {msg}", task.id);
-            Ok(()) // return error
-        }
-        _ => {
-            warn!("Unexpected status code: {}", resp.status());
-            Ok(()) //return error
-        }
-    }
+        .map_err(FocusError::UnableToAnswerTask)
 }
diff --git a/src/blaze.rs b/src/blaze.rs
index 9785609..72a69fd 100644
--- a/src/blaze.rs
+++ b/src/blaze.rs
@@ -80,12 +80,11 @@ pub async fn post_measure(measure: String) -> Result<(), FocusError> {
 
 pub async fn evaluate_measure(url: String) -> Result<String, FocusError> {
     debug!("Evaluating the Measure with canonical URL: {}", url);
-    let mut text: String = String::new();
     let resp = CONFIG.client
         .get(format!(
-        "{}Measure/$evaluate-measure?measure={}&periodStart=2000&periodEnd=2030",
-        CONFIG.blaze_url,
-        url
+            "{}Measure/$evaluate-measure?measure={}&periodStart=2000&periodEnd=2030",
+            CONFIG.blaze_url,
+            url
         ))
         .send()
         .await
@@ -96,19 +95,17 @@ pub async fn evaluate_measure(url: String) -> Result<String, FocusError> {
             "Successfully evaluated the Measure with canonical URL: {}",
             url
         );
-        text = resp
+        resp
             .text()
             .await
-            .map_err(|e| FocusError::MeasureEvaluationErrorReqwest(e))?;
+            .map_err(|e| FocusError::MeasureEvaluationErrorReqwest(e))
     } else {
         warn!(
             "Error while evaluating the Measure with canonical URL `{}`: {:?}",
             url, resp
         );
-        return Err(FocusError::MeasureEvaluationErrorBlaze(format!( "Error while evaluating the Measure with canonical URL `{}`: {:?}", url, resp)));
+        Err(FocusError::MeasureEvaluationErrorBlaze(format!( "Error while evaluating the Measure with canonical URL `{}`: {:?}", url, resp)))
     }
-
-    Ok(text)
 }
 
 pub async fn run_cql_query(library: &Value, measure: &Value) -> Result<String, FocusError> {
diff --git a/src/config.rs b/src/config.rs
index a775391..85f7c58 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -1,12 +1,14 @@
 use std::path::PathBuf;
 
+use beam_lib::AppId;
 use clap::Parser;
 use http::{HeaderValue, Uri};
+use once_cell::sync::Lazy;
 use reqwest::{Certificate, Client, Proxy};
-use static_init::dynamic;
 use tracing::{debug, info, warn};
 
-use crate::{beam::AppId, errors::FocusError};
+use crate::errors::FocusError;
+
 
 #[derive(clap::ValueEnum, Clone, Debug)]
 pub enum Obfuscate {
@@ -14,15 +16,13 @@ pub enum Obfuscate {
     Yes,
 }
 
-
-#[dynamic(lazy)]
-pub(crate) static CONFIG: Config = {
+pub(crate) static CONFIG: Lazy<Config> = Lazy::new(|| {
     debug!("Loading config");
     Config::load().unwrap_or_else(|e| {
         eprintln!("Unable to start as there was an error reading the config:\n{}\n\nTerminating -- please double-check your startup parameters with --help and refer to the documentation.", e);
         std::process::exit(1);
     })
-};
+});
 
 const CLAP_FOOTER: &str = "For proxy support, environment variables HTTP_PROXY, HTTPS_PROXY, ALL_PROXY and NO_PROXY (and their lower-case variants) are supported. Usually, you want to set HTTP_PROXY *and* HTTPS_PROXY or set ALL_PROXY if both values are the same.\n\nFor updates and detailed usage instructions, visit https://github.com/samply/focus";
 
@@ -129,7 +129,7 @@ impl Config {
         let client = prepare_reqwest_client(&tls_ca_certificates)?;
         let config = Config {
             beam_proxy_url: cli_args.beam_proxy_url,
-            beam_app_id_long: AppId::new(cli_args.beam_app_id_long)?,
+            beam_app_id_long: AppId::new_unchecked(cli_args.beam_app_id_long),
             api_key: cli_args.api_key,
             retry_count: cli_args.retry_count,
             blaze_url: cli_args.blaze_url,
diff --git a/src/errors.rs b/src/errors.rs
index 26bfb5a..6bd6757 100644
--- a/src/errors.rs
+++ b/src/errors.rs
@@ -13,13 +13,9 @@ pub enum FocusError {
     #[error("CQL query error")]
     CQLQueryError(),
     #[error("Unable to retrieve tasks from Beam: {0}")]
-    UnableToRetrieveTasksHttp(reqwest::Error),
-    #[error("Unable to retrieve tasks from Beam: {0}")]
-    UnableToRetrieveTasksOther(String),
-    #[error("Unable to parse tasks from Beam")]
-    UnableToParseTasks(reqwest::Error),
+    UnableToRetrieveTasksHttp(beam_lib::BeamError),
     #[error("Unable to answer task")]
-    UnableToAnswerTask(reqwest::Error),
+    UnableToAnswerTask(beam_lib::BeamError),
     #[error("Unable to set proxy settings")]
     InvalidProxyConfig(reqwest::Error),
     #[error("Decode error")]
@@ -28,8 +24,6 @@ pub enum FocusError {
     ConfigurationError(String),
     #[error("Cannot open file")]
     FileOpeningError(String),
-    #[error("Invalid BeamID")]
-    InvalidBeamId(String),
     #[error("Parsing error")]
     ParsingError(String),
     #[error("CQL tempered with")]
diff --git a/src/graceful_shutdown.rs b/src/graceful_shutdown.rs
index 8775a38..18cc534 100644
--- a/src/graceful_shutdown.rs
+++ b/src/graceful_shutdown.rs
@@ -1,10 +1,8 @@
-use std::time::Duration;
-
-use tokio::signal::unix::{signal,SignalKind};
 use tracing::info;
 
 #[cfg(unix)]
 pub async fn wait_for_signal() {
+    use tokio::signal::unix::{signal,SignalKind};
     let mut sigterm = signal(SignalKind::terminate())
         .expect("Unable to register shutdown handler; are you running a Unix-based OS?");
     let mut sigint = signal(SignalKind::interrupt())
diff --git a/src/main.rs b/src/main.rs
index f224bd7..4fb9990 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -12,7 +12,7 @@ use std::time::{SystemTime, UNIX_EPOCH};
 use std::{process::exit, time::Duration};
 
 use base64::{engine::general_purpose, Engine as _};
-use beam::{BeamResult, BeamTask};
+use beam_lib::{TaskRequest, TaskResult};
 use blaze::Query;
 use serde_json::from_slice;
 
@@ -30,6 +30,8 @@ mod graceful_shutdown;
 type SearchQuery = String;
 type Report = String;
 type Created = std::time::SystemTime; //epoch
+type BeamTask = TaskRequest<String>;
+type BeamResult = TaskResult<String>;
 
 #[derive(Debug, Clone)]
 struct ReportCache {
@@ -178,7 +180,7 @@ async fn process_tasks(
             let comm_result = if let Some(ref err_msg) = error_msg {
                 beam::fail_task(&task, err_msg).await
             } else {
-                beam::answer_task(&task, res.unwrap()).await
+                beam::answer_task(task.id, res.unwrap()).await
             };
             match comm_result {
                 Ok(_) => break,
@@ -220,19 +222,16 @@ async fn run_query(
 ) -> Result<BeamResult, FocusError> {
     debug!("Run");
 
-    match query.lang.as_str() {
-        "cql" => {
-            // TODO: Change query.lang to an enum
-            Ok(run_cql_query(task, query, obf_cache, report_cache).await)?
-        },
-        unsupported_lang => {
-            Ok(beam::BeamResult::perm_failed(
-                CONFIG.beam_app_id_long.clone(),
-                vec![task.from.clone()],
-                task.id,
-                Some(format!("Can't run queries with language {unsupported_lang}")),
-            ))
-        }
+    if query.lang == "cql" {
+        // TODO: Change query.lang to an enum
+        return Ok(run_cql_query(task, query, obf_cache, report_cache).await)?;
+    } else {
+        return Ok(beam::beam_result::perm_failed(
+            CONFIG.beam_app_id_long.clone(),
+            vec![task.from.clone()],
+            task.id,
+            format!("Can't run inqueries with language {}", query.lang),
+        ));
     }
 }
 
@@ -242,6 +241,13 @@ async fn run_cql_query(
     obf_cache: &mut ObfCache,
     report_cache: &mut ReportCache,
 ) -> Result<BeamResult, FocusError> {
+    let mut err = beam::beam_result::perm_failed(
+        CONFIG.beam_app_id_long.clone(),
+        vec![task.to_owned().from],
+        task.to_owned().id,
+        String::new(),
+    );
+
     let encoded_query =
         query.lib["content"][0]["data"]
             .as_str()
@@ -298,11 +304,11 @@ async fn run_cql_query(
     };
 
     let result = beam_result(task.to_owned(), cql_result_new).unwrap_or_else(|e| {
-        beam::BeamResult::perm_failed(
+        beam::beam_result::perm_failed(
             CONFIG.beam_app_id_long.clone(),
             vec![task.to_owned().from],
             task.to_owned().id,
-            Some(e.to_string())
+            e.to_string()
         )
     });
 
@@ -348,14 +354,14 @@ fn replace_cql_library(mut query: Query) -> Result<Query, FocusError> {
 }
 
 fn beam_result(
-    task: beam::BeamTask,
+    task: BeamTask,
     measure_report: String,
-) -> Result<beam::BeamResult, FocusError> {
+) -> Result<BeamResult, FocusError> {
     let data = general_purpose::STANDARD.encode(measure_report.as_bytes());
-    return Ok(beam::BeamResult::succeeded(
+    return Ok(beam::beam_result::succeeded(
         CONFIG.beam_app_id_long.clone(),
         vec![task.from],
         task.id,
-        Some(data)
+        data
     ));
 }
diff --git a/src/util.rs b/src/util.rs
index 3ce4574..aafc585 100644
--- a/src/util.rs
+++ b/src/util.rs
@@ -6,7 +6,7 @@ use rand::thread_rng;
 use serde::{Deserialize, Serialize};
 use serde_json::{json, Value};
 use std::collections::HashMap;
-use tracing::{debug, info, warn};
+use tracing::warn;
 
 #[derive(Debug, Deserialize, Serialize)]
 struct Period {

From 47480f10763c34436ba0ffac480cb3430f457500 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Sat, 30 Sep 2023 12:21:58 +0000
Subject: [PATCH 19/22] Speedup build by minimizing files to be used in docker
 build context

---
 .dockerignore | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..37ad7ed
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,2 @@
+*
+!artifacts/

From 763d72e23acd53e1e41455fe4bed48ecfb73febd Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Mon, 2 Oct 2023 11:05:21 +0200
Subject: [PATCH 20/22] fix: add inital statement to exliquid selection

---
 src/util.rs | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/util.rs b/src/util.rs
index aafc585..866b723 100644
--- a/src/util.rs
+++ b/src/util.rs
@@ -100,8 +100,8 @@ pub(crate) fn replace_cql(decoded_library: impl Into<String>) -> String {
             ("BBMRI_STRAT_AGE_STRATIFIER", "define AgeClass:\n     (AgeInYears() div 10) * 10"),
             ("BBMRI_STRAT_DEF_SPECIMEN", "define Specimen:"),
             ("BBMRI_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:"),
-            ("EXLIQUID_CQL", "define ExliquidSpecimen:\n  from [Specimen] S\n  where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'\ndefine retrieveCondition:\n First(from [Condition] C\n  return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis:\n  if (retrieveCondition is null) then 'unknown' else retrieveCondition\ndefine function SampleType(specimen FHIR.Specimen):\n  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
-            ("EXLIQUID_ALIQUOTS_CQL", "define Aliquot: [Specimen] S where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id    define retrieveCondition:   First(from [Condition] C   return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())    define Diagnosis:   if (retrieveCondition is null) then 'unknown' else retrieveCondition define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
+            ("EXLIQUID_CQL", "define ExliquidSpecimen:\nif InInitialPopulation then [Specimen] S\n where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'\ndefine retrieveCondition:\n First(from [Condition] C\n  return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis:\n  if (retrieveCondition is null) then 'unknown' else retrieveCondition\ndefine function SampleType(specimen FHIR.Specimen):\n  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
+            ("EXLIQUID_ALIQUOTS_CQL", "define Aliquot:\nif InInitialPopulation then [Specimen] S\n where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id    define retrieveCondition:   First(from [Condition] C   return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())    define Diagnosis:   if (retrieveCondition is null) then 'unknown' else retrieveCondition define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
             ("DKTK_STRAT_GENDER_STRATIFIER", "define Gender:\nif (Patient.gender is null) then 'unknown' else Patient.gender"),
             ("DKTK_STRAT_AGE_STRATIFIER", "define AgeClass:\nif (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)"),
             ("DKTK_STRAT_DECEASED_STRATIFIER", "define PatientDeceased:\nFirst (from [Observation: Code '75186-7' from loinc] O return O.value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/VitalstatusCS').code.first())\ndefine Deceased:\nif (PatientDeceased is null) then 'unbekannt' else PatientDeceased"),
@@ -112,8 +112,8 @@ pub(crate) fn replace_cql(decoded_library: impl Into<String>) -> String {
             ("DKTK_STRAT_MEDICATION_STRATIFIER", "define MedicationStatement:\nif InInitialPopulation then [MedicationStatement] else {} as List <MedicationStatement>"),
             ("DKTK_STRAT_ENCOUNTER_STRATIFIER", "define Encounter:\nif InInitialPopulation then [Encounter] else {} as List<Encounter>\n\ndefine function Departments(encounter FHIR.Encounter):\nencounter.identifier.where(system = 'http://dktk.dkfz.de/fhir/sid/hki-department').value.first()"),
             ("DKTK_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:"),
-            ("EXLIQUID_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:\n   exists ExliquidSpecimen\n"),        
-            ("EXLIQUID_STRAT_W_ALIQUOTS", "define InInitialPopulation: exists ExliquidSpecimenWithAliquot")
+            ("EXLIQUID_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:\n   exists ExliquidSpecimen and \n"),        
+            ("EXLIQUID_STRAT_W_ALIQUOTS", "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n")
         ].into();
 
     let mut decoded_library = decoded_library.into();
@@ -414,19 +414,19 @@ mod test {
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "EXLIQUID_CQL";
-        let expected_result = "define ExliquidSpecimen:\n  from [Specimen] S\n  where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'\ndefine retrieveCondition:\n First(from [Condition] C\n  return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis:\n  if (retrieveCondition is null) then 'unknown' else retrieveCondition\ndefine function SampleType(specimen FHIR.Specimen):\n  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()\n";
+        let expected_result = "define ExliquidSpecimen:\nif InInitialPopulation then [Specimen] S\n where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'\ndefine retrieveCondition:\n First(from [Condition] C\n  return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis:\n  if (retrieveCondition is null) then 'unknown' else retrieveCondition\ndefine function SampleType(specimen FHIR.Specimen):\n  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "EXLIQUID_ALIQUOTS_CQL";
-        let expected_result = "define Aliquot: [Specimen] S where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id    define retrieveCondition:   First(from [Condition] C   return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())    define Diagnosis:   if (retrieveCondition is null) then 'unknown' else retrieveCondition define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()\n";
+        let expected_result = "define Aliquot:\nif InInitialPopulation then [Specimen] S\n where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id    define retrieveCondition:   First(from [Condition] C   return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())    define Diagnosis:   if (retrieveCondition is null) then 'unknown' else retrieveCondition define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "EXLIQUID_STRAT_DEF_IN_INITIAL_POPULATION";
-        let expected_result = "define InInitialPopulation:\n   exists ExliquidSpecimen\n\n";
+        let expected_result = "define InInitialPopulation:\n   exists ExliquidSpecimen and \n\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "EXLIQUID_STRAT_W_ALIQUOTS";
-        let expected_result = "define InInitialPopulation: exists ExliquidSpecimenWithAliquot\n";
+        let expected_result = "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "INVALID_KEY";

From b9d5aeb2c952079184c73900d73b6817af70d488 Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Mon, 2 Oct 2023 11:16:41 +0200
Subject: [PATCH 21/22] fix: corrected env_vars namming

---
 README.md | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index c9bd160..b1329e2 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ To run a standalone Focus, you need at least one running [Samply.Beam.Proxy](htt
 You can compile and run this application via Cargo, however, we encourage the usage of the pre-compiled [docker images](https://hub.docker.com/r/samply/focus):
 
 ```bash
-docker run --rm -e BEAM_BASE_URL=http://localhost:8081 -e BLAZE_BASE_URL=http://localhost:8089/fhir -e PROXY_ID=proxy1.broker -e API_KEY=App1Secret -e BEAM_APP_ID_LONG=app1.broker.example.com samply/focus:latest
+docker run --rm -e BEAM_PROXY_URL=http://localhost:8081 -e BLAZE_URL=http://localhost:8089/fhir -e PROXY_ID=proxy1.broker -e API_KEY=App1Secret -e BEAM_APP_ID_LONG=app1.broker.example.com samply/focus:latest
 ```
 
 ## Configuration
@@ -24,8 +24,8 @@ docker run --rm -e BEAM_BASE_URL=http://localhost:8081 -e BLAZE_BASE_URL=http://
 The following environment variables are mandatory for the usage of Focus. If compiling and running Focus yourself, they are provided as command line options as well. See `focus  --help` for details.
 
 ```bash
-BEAM_BASE_URL = "http://localhost:8081" 
-BLAZE_BASE_URL = "http://localhost:8089/fhir"
+BEAM_PROXY_URL = "http://localhost:8081" 
+BLAZE_URL = "http://localhost:8089/fhir"
 PROXY_ID = "proxy1.broker"
 API_KEY = "App1Secret"
 BEAM_APP_ID_LONG = "app1.broker.example.com"
@@ -36,16 +36,16 @@ BEAM_APP_ID_LONG = "app1.broker.example.com"
 ```bash
 RETRY_COUNT = "32" # The maximum number of retries for beam and blaze healthchecks, default value: 32
 OBFUSCATE = "yes" # Should the results be obfuscated - the "master switch", allowed values: "yes", "no", default value: "yes"
-OBFUSCATE-BELOW-10 = "1" # The mode of obfuscating values below 10: 0 - return zero, 1 - return ten, 2 - obfuscate using Laplace distribution and rounding, has no effect if OBFUSCATE = "no", default value: 1
-DELTA-PATIENT = "1." # Sensitivity parameter for obfuscating the counts in the Patient stratifier, has no effect if OBFUSCATE = "no", default value: 1
-DELTA-SPECIMEN = "20." # Sensitivity parameter for obfuscating the counts in the Specimen stratifier, has no effect if OBFUSCATE = "no", default value: 20
-DELTA-DIAGNOSIS = "3." # Sensitivity parameter for obfuscating the counts in the Diagnosis stratifier, has no effect if OBFUSCATE = "no", default value: 3
+OBFUSCATE_BELOW_10_MODE = "1" # The mode of obfuscating values below 10: 0 - return zero, 1 - return ten, 2 - obfuscate using Laplace distribution and rounding, has no effect if OBFUSCATE = "no", default value: 1
+DELTA_PATIENT = "1." # Sensitivity parameter for obfuscating the counts in the Patient stratifier, has no effect if OBFUSCATE = "no", default value: 1
+DELTA_SPECIMEN = "20." # Sensitivity parameter for obfuscating the counts in the Specimen stratifier, has no effect if OBFUSCATE = "no", default value: 20
+DELTA_DIAGNOSIS = "3." # Sensitivity parameter for obfuscating the counts in the Diagnosis stratifier, has no effect if OBFUSCATE = "no", default value: 3
 EPSILON = "0.1" # Privacy budget parameter for obfuscating the counts in the stratifiers, has no effect if OBFUSCATE = "no", default value: 0.1
-ROUNDING-STEP = "10" # The granularity of the rounding of the obfuscated values, has no effect if OBFUSCATE = "no", default value: 10
+ROUNDING_STEP = "10" # The granularity of the rounding of the obfuscated values, has no effect if OBFUSCATE = "no", default value: 10
 QUERIES_TO_CACHE_FILE_PATH = "resources/bbmri" # The path to the file containing BASE64 encoded queries whose results are to be cached, if not set, no results are cached
 ```
 
-Obfuscating zero counts is by default switched off. To enable obfuscating zero counts, set the env. variable `OBFUSCATE-ZERO`. 
+Obfuscating zero counts is by default switched off. To enable obfuscating zero counts, set the env. variable `OBFUSCATE_ZERO`. 
 
 Optionally, you can provide the `TLS_CA_CERTIFICATES_DIR` environment variable to add additional trusted certificates, e.g., if you have a TLS-terminating proxy server in place. The application respects the `HTTP_PROXY`, `HTTPS_PROXY`, `ALL_PROXY`, `NO_PROXY`, and their respective lowercase equivalents.
 

From 9d515fb93af4f76d46093d77de1532e8fa15338f Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Wed, 4 Oct 2023 14:51:00 +0000
Subject: [PATCH 22/22] Use new  api

---
 src/beam.rs | 21 +++++++++++----------
 src/main.rs |  2 +-
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/beam.rs b/src/beam.rs
index 4558dca..de17cec 100644
--- a/src/beam.rs
+++ b/src/beam.rs
@@ -1,6 +1,6 @@
 use std::time::Duration;
 
-use beam_lib::{TaskResult, BeamClient, BlockingOptions, MsgId, TaskRequest};
+use beam_lib::{TaskResult, BeamClient, BlockingOptions, MsgId, TaskRequest, RawString};
 use once_cell::sync::Lazy;
 use serde::{de::DeserializeOwned, Serialize};
 use tracing::{debug, warn};
@@ -8,9 +8,9 @@ use tracing::{debug, warn};
 use crate::{config::CONFIG, errors::FocusError};
 
 pub mod beam_result {
-    use beam_lib::{AppId, TaskResult, WorkStatus, MsgId};
-    use serde::Serialize;
+    use super::*;
     use serde_json::Value;
+    use beam_lib::{WorkStatus, AppId};
 
     pub fn claimed(from: AppId, to: Vec<AppId>, task_id: MsgId) -> TaskResult<()> {
         TaskResult {
@@ -22,25 +22,25 @@ pub mod beam_result {
             body: (),
         }
     }
-    pub fn succeeded<T: Serialize>(from: AppId, to: Vec<AppId>, task_id: MsgId, body: T) -> TaskResult<T> {
+    pub fn succeeded(from: AppId, to: Vec<AppId>, task_id: MsgId, body: String) -> TaskResult<RawString> {
         TaskResult {
             from,
             to,
             task: task_id,
             status: WorkStatus::Succeeded,
             metadata: Value::Null,
-            body,
+            body: body.into(),
         }
     }
 
-    pub fn perm_failed<T: Serialize>(from: AppId, to: Vec<AppId>, task_id: MsgId, body: T) -> TaskResult<T> {
+    pub fn perm_failed(from: AppId, to: Vec<AppId>, task_id: MsgId, body: String) -> TaskResult<RawString> {
         TaskResult {
             from,
             to,
             task: task_id,
             status: WorkStatus::PermFailed,
             metadata: Value::Null,
-            body,
+            body: body.into(),
         }
     }
 }
@@ -73,18 +73,19 @@ static BEAM_CLIENT: Lazy<BeamClient> = Lazy::new(|| BeamClient::new(
     CONFIG.beam_proxy_url.to_string().parse().expect("Uri always converts to url")
 ));
 
-pub async fn retrieve_tasks<T: DeserializeOwned>() -> Result<Vec<TaskRequest<T>>, FocusError> {
+pub async fn retrieve_tasks() -> Result<Vec<TaskRequest<String>>, FocusError> {
     debug!("Retrieving tasks...");
     let block = BlockingOptions {
         wait_time: Some(Duration::from_secs(10)),
         wait_count: Some(1)
     };
-    BEAM_CLIENT.poll_pending_tasks(&block)
+    BEAM_CLIENT.poll_pending_tasks::<RawString>(&block)
         .await
+        .map(|v| v.into_iter().map(|TaskRequest { id, body, from, to, metadata, ttl, failure_strategy }| TaskRequest { body: body.into_string(), id, from, to, metadata, ttl, failure_strategy }).collect())
         .map_err(FocusError::UnableToRetrieveTasksHttp)
 }
 
-pub async fn answer_task<T: Serialize>(task_id: MsgId, result: &TaskResult<T>) -> Result<bool, FocusError> {
+pub async fn answer_task<T: Serialize + 'static>(task_id: MsgId, result: &TaskResult<T>) -> Result<bool, FocusError> {
     debug!("Answer task with id: {task_id}");
     BEAM_CLIENT.put_result(result, &task_id)
         .await
diff --git a/src/main.rs b/src/main.rs
index 4fb9990..3bf175c 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -31,7 +31,7 @@ type SearchQuery = String;
 type Report = String;
 type Created = std::time::SystemTime; //epoch
 type BeamTask = TaskRequest<String>;
-type BeamResult = TaskResult<String>;
+type BeamResult = TaskResult<beam_lib::RawString>;
 
 #[derive(Debug, Clone)]
 struct ReportCache {