Merge pull request #1480 from samply/release/v0.24.1

Release v0.24.1

.github/workflows/build.yml

@@ -190,7 +190,7 @@ jobs:
       run: make uberjar
 
     - name: Upload Blaze Uberjar
-      uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4
+      uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
       with:
         name: blaze-uberjar
         path: target/blaze-*-standalone.jar
@@ -206,7 +206,7 @@ jobs:
         outputs: type=docker,dest=/tmp/blaze.tar
 
     - name: Upload Blaze Image
-      uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4
+      uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
       with:
         name: blaze-image
         path: /tmp/blaze.tar
@@ -1527,4 +1527,4 @@ jobs:
     steps:
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@87c3283f01cd6fe19a0ab93a23b2f6fcba5a8e42 # v4
+      uses: actions/deploy-pages@decdde0ac072f6dcbe43649d82d9c635fff5b4e4 # v4

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## v0.24.1
+
+### Notes
+
+Please update from v0.24.0 if you use variable length logical id's.
+
+### Bugfixes
+
+* Fix Error While Reading Non-Existent Resource ([#1475](https://github.com/samply/blaze/issues/1475))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/84?closed=1).
+
 ## v0.24.0
 
 ### Notes

Dockerfile

@@ -8,7 +8,7 @@ RUN apt-get update && apt-get upgrade -y && \
     rm -rf /var/lib/apt/lists/
 
 RUN mkdir -p /app/data && chown 1001:1001 /app/data
-COPY target/blaze-0.24.0-standalone.jar /app/
+COPY target/blaze-0.24.1-standalone.jar /app/
 
 WORKDIR /app
 USER 1001
@@ -19,4 +19,4 @@ ENV INDEX_DB_DIR="/app/data/index"
 ENV TRANSACTION_DB_DIR="/app/data/transaction"
 ENV RESOURCE_DB_DIR="/app/data/resource"
 
-CMD ["java", "-jar",  "blaze-0.24.0-standalone.jar"]
+CMD ["java", "-jar",  "blaze-0.24.1-standalone.jar"]

README.md

@@ -15,7 +15,7 @@ The goal of this project is to provide a FHIR® Store with an internal CQL Evalu
 
 Blaze passes all [Touchstone FHIR 4.0.1 Basic Tests][12] and almost all [CQL Tests][3]. Please refer to the [Conformance](docs/conformance.md) section and report any issues you encounter during evaluation.
 
-Latest release: [v0.24.0][5]
+Latest release: [v0.24.1][5]
 
 ## Quick Start
 
@@ -74,7 +74,7 @@ Unless required by applicable law or agreed to in writing, software distributed
 
 [3]: <https://cql.hl7.org/tests.html>
 [4]: <https://alexanderkiel.gitbook.io/blaze/deployment>
-[5]: <https://github.com/samply/blaze/releases/tag/v0.24.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.24.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

build.clj

@@ -2,7 +2,7 @@
   (:require [clojure.tools.build.api :as b]))
 
 (def lib 'samply/blaze)
-(def version "0.24.0")
+(def version "0.24.1")
 (def class-dir "target/classes")
 (def basis (b/create-basis {:project "deps.edn"}))
 (def uber-file (format "target/%s-%s-standalone.jar" (name lib) version))

docs/.vitepress/config.ts

@@ -27,7 +27,7 @@ export default defineConfig({
         nav: [
             {text: 'Home', link: '/'},
             {
-                text: "v0.24.0",
+                text: "v0.24.1",
                 items: [
                     {
                         text: 'Changelog',

docs/deployment/docker-deployment.md

@@ -27,7 +27,7 @@ Blaze should log something like this:
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:67] - JVM version: 17.0.7
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:68] - Maximum available memory: 1738 MiB
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:69] - Number of available processors: 2
-2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:70] - Successfully started 🔥 Blaze version 0.24.0 in 9.0 seconds
+2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:70] - Successfully started 🔥 Blaze version 0.24.1 in 9.0 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.24.0"
+  "version": "0.24.1"
 }
 ```
 

docs/deployment/manual-deployment.md

@@ -2,12 +2,12 @@
 
 The installation works under Windows, Linux and macOS. The only dependency is an installed OpenJDK 11 or 17 with 17 recommended. Blaze is tested with [Eclipse Temurin][1].
 
-Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.24.0). Look for `blaze-0.24.0-standalone.jar`.
+Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.24.1). Look for `blaze-0.24.1-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.24.0-standalone.jar
+java -jar blaze-0.24.1-standalone.jar
 ```
 
 Blaze will run with an in-memory, volatile database for testing and demo purposes.
@@ -17,14 +17,14 @@ Blaze can be run with durable storage by setting the environment variables `STOR
 Under Linux/macOS:
 
 ```sh
-STORAGE=standalone java -jar blaze-0.24.0-standalone.jar
+STORAGE=standalone java -jar blaze-0.24.1-standalone.jar
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.24.0-standalone.jar
+java -jar blaze-0.24.1-standalone.jar
 ```
 
 This will create three directories called `index`, `transaction` and `resource` inside the current working directory, one for each database part used.
@@ -42,7 +42,7 @@ The output should look like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.24.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.24.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.24.0"
+  "version": "0.24.1"
 }
 ```
 

modules/db/src/blaze/db/impl/index/resource_as_of.clj

@@ -315,24 +315,29 @@
     (bb/flip! target-buf)
     (kv/seek-buffer! iter target-buf)
     (when (kv/valid? iter)
+      ;; it's important to clear key-buf before reading, because otherwise
+      ;; the limit could be to small
+      (bb/clear! key-buf)
       (kv/key! iter key-buf)
       ;; we have to check that we are still on target, because otherwise we
-      ;; would find the next resource
-      ;; focus target buffer on tid and id
-      (bb/rewind! target-buf)
-      (bb/set-limit! target-buf tid-id-size)
-      ;; focus key buffer on tid and id
-      (bb/set-limit! key-buf tid-id-size)
-      (when (= target-buf key-buf)
-        ;; focus key buffer on t
-        (bb/set-limit! key-buf key-size)
-        (let [value-buf (bb/allocate value-size)]
-          (kv/value! iter value-buf)
-          (rh/resource-handle!
-           tid
-           (codec/id-string id)
-           (codec/descending-long (bb/get-long! key-buf tid-id-size))
-           value-buf))))))
+      ;; would find the next resource. First the length of the found key has
+      ;; to equal our key size
+      (when (= key-size (bb/limit key-buf))
+        ;; focus target buffer on tid and id
+        (bb/rewind! target-buf)
+        (bb/set-limit! target-buf tid-id-size)
+        ;; focus key buffer on tid and id
+        (bb/set-limit! key-buf tid-id-size)
+        (when (= target-buf key-buf)
+          ;; focus key buffer on t
+          (bb/set-limit! key-buf key-size)
+          (let [value-buf (bb/allocate value-size)]
+            (kv/value! iter value-buf)
+            (rh/resource-handle!
+             tid
+             (codec/id-string id)
+             (codec/descending-long (bb/get-long! key-buf tid-id-size))
+             value-buf)))))))
 
 (defn resource-handle
   "Returns the resource handle with `tid` and `id` at `t` in `snapshot` when

modules/db/test/blaze/db/api_test.clj

@@ -28,6 +28,7 @@
    [blaze.log]
    [blaze.module.test-util :refer [with-system]]
    [blaze.test-util :as tu :refer [satisfies-prop]]
+   [clojure.spec.alpha :as s]
    [clojure.spec.test.alpha :as st]
    [clojure.test :as test :refer [are deftest is testing]]
    [clojure.test.check.generators :as gen]
@@ -550,12 +551,12 @@
             [:subject :reference] := "Patient/0"
             [meta :blaze.db/op] := :create)))))
 
-  (testing "creating 100 transactions in parallel"
+  (testing "creating 1000 transactions in parallel"
     (with-system [{:blaze.db/keys [node]} slow-resource-store-system]
       (let [db-futures
             (mapv
              #(d/transact node [[:create {:fhir/type :fhir/Patient :id (str %)}]])
-             (range 100))]
+             (range 1000))]
 
         (testing "wait for all transactions finishing"
           @(ac/all-of db-futures))
@@ -568,7 +569,7 @@
                 true?
                 (map
                  #(= % (d/type-total (d/as-of db %) "Patient"))
-                 (range 100))))))))))
+                 (range 1000))))))))))
 
   (testing "with failing resource storage"
     (testing "on put"
@@ -631,6 +632,12 @@
 
       (is (d/resource-handle? (d/resource-handle (d/db node) "Patient" "0")))))
 
+  (testing "doesn't find a resource handle mit prefix of it's id"
+    (with-system-data [{:blaze.db/keys [node]} config]
+      [[[:create {:fhir/type :fhir/Patient :id "00"}]]]
+
+      (is (nil? (d/resource-handle (d/db node) "Patient" "0")))))
+
   (testing "a node contains a resource after a create transaction"
     (with-system-data [{:blaze.db/keys [node]} config]
       [[[:create {:fhir/type :fhir/Patient :id "0"}]]]
@@ -943,9 +950,21 @@
           count := 1
           [0 :fhir/type] := :fhir/Patient
           [0 :id] := "0")
-        (is (= 1 (count-type-query node "Patient" [["active" "true"]]))))))
+        (is (= 1 (count-type-query node "Patient" [["active" "true"]])))))
+
+    (testing "works with variable length ids"
+      (with-system-data [{:blaze.db/keys [node]} config]
+        [[[:put {:fhir/type :fhir/Patient :id "1" :active true}]
+          [:put {:fhir/type :fhir/Patient :id "10" :active true}]]]
 
-  (testing "search by id"
+        (given (pull-type-query node "Patient" [["active" "true"]])
+          count := 2
+          [0 :fhir/type] := :fhir/Patient
+          [0 :id] := "1"
+          [1 :fhir/type] := :fhir/Patient
+          [1 :id] := "10"))))
+
+  (testing "search by _id"
     (with-system-data [{:blaze.db/keys [node]} config]
       [[[:put {:fhir/type :fhir/Patient :id "0" :active true}]
         [:put {:fhir/type :fhir/Patient :id "1" :active false}]
@@ -999,8 +1018,8 @@
 
   (testing "sorting by _id"
     (with-system-data [{:blaze.db/keys [node]} config]
-      [[[:put {:fhir/type :fhir/Patient :id "0" :active true}]
-        [:put {:fhir/type :fhir/Patient :id "1" :active false}]]]
+      [[[:put {:fhir/type :fhir/Patient :id "0"}]
+        [:put {:fhir/type :fhir/Patient :id "1"}]]]
 
       (testing "ascending"
         (given (pull-type-query node "Patient" [[:sort "_id" :asc]])
@@ -1019,7 +1038,15 @@
       (testing "descending"
         (given (d/type-query (d/db node) "Patient" [[:sort "_id" :desc]])
           ::anom/category := ::anom/unsupported
-          ::anom/message := "Unsupported sort direction `desc` for search param `_id`."))))
+          ::anom/message := "Unsupported sort direction `desc` for search param `_id`.")))
+
+    (testing "random id's"
+      (satisfies-prop 100
+        (prop/for-all [ids (gen/set (s/gen :blaze.resource/id) {:min-elements 1})]
+          (with-system-data [{:blaze.db/keys [node]} config]
+            [(mapv #(vector :create {:fhir/type :fhir/Patient :id %}) ids)]
+
+            (= (sort ids) (mapv :id (pull-type-query node "Patient" [[:sort "_id" :asc]]))))))))
 
   (testing "a node with two patients in two transactions"
     (with-system-data [{:blaze.db/keys [node]} config]

modules/frontend/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "blaze-frontend",
-	"version": "0.24.0",
+	"version": "0.24.1",
 	"private": true,
 	"scripts": {
 		"dev": "vite dev",

modules/kv/src/blaze/db/kv.clj

@@ -92,8 +92,8 @@
 (defn key!
   "Puts the key of current entry of `iter` in `buf`.
 
-  Uses the position of `buf` and sets the limit of `buf` according to the key
-  size.
+  Uses the position and limit of `buf` and sets the limit of `buf` according to
+  the key size. Note: doesn't read bytes over the limit!
 
   Returns the size of the actual key. If the key is greater than the length of
   `buf`, then it indicates that the size of the `buf` is insufficient and a

src/blaze/system.clj

@@ -92,9 +92,9 @@
     (into {} (map (fn [[k v]] [k (resolvef k v)])) (ig/find-derived config key))))
 
 (def ^:private root-config
-  {:blaze/version "0.24.0"
+  {:blaze/version "0.24.1"
 
-   :blaze/release-date "2024-02-06"
+   :blaze/release-date "2024-02-07"
 
    :blaze/clock {}