Merge pull request #648 from samply/release-v0.16.3

Release v0.16.3

.github/workflows/build.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Setup clj-kondo
       uses: DeLaGuardo/setup-clj-kondo@master
       with:
-        version: '2022.03.04'
+        version: '2022.03.09'
 
     - name: Check out Git repository
       uses: actions/checkout@v3

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.16.3
+
+### Bugfixes
+
+* Trim Values in FHIR Search ([#644](https://github.com/samply/blaze/pull/644))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/33?closed=1).
+
 ## v0.16.2
 
 ### Bugfixes

README.md

@@ -14,7 +14,7 @@ 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: [v0.16.2][5]
+Latest release: [v0.16.3][5]
 
 ## Quick Start
 
@@ -72,7 +72,7 @@ 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/v0.16.2>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.16.3>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

docs/deployment/docker-deployment.md

@@ -27,7 +27,7 @@ Blaze should log something 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 0.16.2 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.16.3 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.16.2"
+  "version": "0.16.3"
 }
 ```
 

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. Blaze is tested with [AdoptOpenJDK][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/v0.16.2). Look for `blaze-0.16.2-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/v0.16.3). Look for `blaze-0.16.3-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.16.2-standalone.jar -m blaze.core
+java -jar blaze-0.16.3-standalone.jar -m blaze.core
 ```
 
 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-0.16.2-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.16.3-standalone.jar -m blaze.core
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.16.2-standalone.jar -m blaze.core
+java -jar blaze-0.16.3-standalone.jar -m blaze.core
 ```
 
 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 0.16.2 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.16.3 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.16.2"
+  "version": "0.16.3"
 }
 ```
 

modules/cassandra/deps.edn

@@ -10,7 +10,7 @@
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   io.netty/netty-handler
-  {:mvn/version "4.1.74.Final"}}
+  {:mvn/version "4.1.75.Final"}}
 
  :aliases
  {:test

modules/db/src/blaze/db/impl/search_param/composite/token_quantity.clj

@@ -43,11 +43,11 @@
         #(case (::spq/category %)
           ::spq/invalid-decimal-value
           (assoc %
-            ::anom/message (spq/invalid-decimal-value-msg code v2))
+            ::anom/message (u/invalid-decimal-value-msg code v2))
           ::spq/unsupported-prefix
           (assoc %
             ::anom/message
-            (spq/unsupported-prefix-msg
+            (u/unsupported-prefix-msg
               code (::spq/unsupported-prefix %)))
           %))))
 

modules/db/src/blaze/db/impl/search_param/date.clj

@@ -176,10 +176,6 @@
   (format "Invalid date-time value `%s` in search parameter `%s`." value code))
 
 
-(defn- unsupported-prefix-msg [code op]
-  (format "Unsupported prefix `%s` in search parameter `%s`." (name op) code))
-
-
 (defn- resource-keys!
   ([context c-hash tid {:keys [op lower-bound upper-bound]}]
    (case op
@@ -221,7 +217,7 @@
           (:le :lt)
           {:op op
            :upper-bound (date-ub date-time-value)}
-          (ba/unsupported (unsupported-prefix-msg code op)))
+          (ba/unsupported (u/unsupported-prefix-msg code op)))
         #(assoc % ::anom/message (invalid-date-time-value-msg code value)))))
 
   (-resource-handles [_ context tid _ value]

modules/db/src/blaze/db/impl/search_param/number.clj

@@ -18,25 +18,6 @@
 (set! *warn-on-reflection* true)
 
 
-
-;; ---- compile-value ---------------------------------------------------------
-
-(defn invalid-decimal-value-msg [code value]
-  (format "Invalid decimal value `%s` in search parameter `%s`." value code))
-
-
-(defn unsupported-prefix-msg [code op]
-  (format "Unsupported prefix `%s` in search parameter `%s`." (name op) code))
-
-
-(defn- eq-value [decimal-value]
-  (let [delta (.movePointLeft 0.5M (.scale ^BigDecimal decimal-value))]
-    {:op :eq
-     :lower-bound (codec/number (- decimal-value delta))
-     :exact-value (codec/number decimal-value)
-     :upper-bound (codec/number (+ decimal-value delta))}))
-
-
 (defmulti index-entries
   "Returns index entries for `value` from a resource."
   {:arglists '([url value])}
@@ -66,16 +47,16 @@
       (if-ok [decimal-value (system/parse-decimal value)]
         (case op
           :eq
-          (eq-value decimal-value)
+          (u/eq-value codec/number decimal-value)
           (:gt :lt :ge :le)
           {:op op :exact-value (codec/number decimal-value)}
           (ba/unsupported
-            (unsupported-prefix-msg code op)
+            (u/unsupported-prefix-msg code op)
             ::category ::unsupported-prefix
             ::unsupported-prefix op))
         #(assoc %
            ::category ::invalid-decimal-value
-           ::anom/message (invalid-decimal-value-msg code value)))))
+           ::anom/message (u/invalid-decimal-value-msg code value)))))
 
   (-resource-handles [_ context tid _ value]
     (coll/eduction

modules/db/src/blaze/db/impl/search_param/quantity.clj

@@ -22,25 +22,6 @@
 (set! *warn-on-reflection* true)
 
 
-
-;; ---- compile-value ---------------------------------------------------------
-
-(defn invalid-decimal-value-msg [code value]
-  (format "Invalid decimal value `%s` in search parameter `%s`." value code))
-
-
-(defn unsupported-prefix-msg [code op]
-  (format "Unsupported prefix `%s` in search parameter `%s`." (name op) code))
-
-
-(defn- eq-value [unit decimal-value]
-  (let [delta (.movePointLeft 0.5M (.scale ^BigDecimal decimal-value))]
-    {:op :eq
-     :lower-bound (codec/quantity unit (- decimal-value delta))
-     :exact-value (codec/quantity unit decimal-value)
-     :upper-bound (codec/quantity unit (+ decimal-value delta))}))
-
-
 (defmulti index-entries
   "Returns index entries for `value` from a resource."
   {:arglists '([url value])}
@@ -302,20 +283,20 @@
   p/SearchParam
   (-compile-value [_ _ value]
     (let [[op value-and-unit] (u/separate-op value)
-          [value unit] (str/split value-and-unit #"\|" 2)]
+          [value unit] (str/split value-and-unit #"\s*\|\s*" 2)]
       (if-ok [decimal-value (system/parse-decimal value)]
         (case op
           :eq
-          (eq-value unit decimal-value)
+          (u/eq-value (partial codec/quantity unit) decimal-value)
           (:gt :lt :ge :le)
           {:op op :exact-value (codec/quantity unit decimal-value)}
           (ba/unsupported
-            (unsupported-prefix-msg code op)
+            (u/unsupported-prefix-msg code op)
             ::category ::unsupported-prefix
             ::unsupported-prefix op))
         #(assoc %
            ::category ::invalid-decimal-value
-           ::anom/message (invalid-decimal-value-msg code value)))))
+           ::anom/message (u/invalid-decimal-value-msg code value)))))
 
   (-resource-handles [_ context tid _ value]
     (coll/eduction

modules/db/src/blaze/db/impl/search_param/util.clj

@@ -3,7 +3,8 @@
     [blaze.byte-string :as bs]
     [blaze.db.impl.byte-buffer :as bb]
     [blaze.db.impl.codec :as codec]
-    [blaze.fhir.spec :as fhir-spec])
+    [blaze.fhir.spec :as fhir-spec]
+    [clojure.string :as str])
   (:import
     [clojure.lang IReduceInit Indexed]))
 
@@ -18,9 +19,10 @@
   returns a tuple of operator and value. The default operator :eq is returned if
   no prefix was given."
   [value]
-  (if (re-find #"^(eq|ne|gt|lt|ge|le|sa|eb|ap)" value)
-    [(keyword (subs value 0 2)) (subs value 2)]
-    [:eq value]))
+  (let [value (str/trim value)]
+    (if (re-find #"^(eq|ne|gt|lt|ge|le|sa|eb|ap)" value)
+      [(keyword (subs value 0 2)) (str/trim (subs value 2))]
+      [:eq value])))
 
 
 (defn format-skip-indexing-msg [value url type]
@@ -103,3 +105,19 @@
           (let [id (.substring s (unchecked-inc-int idx))]
             (when (.matches (re-matcher #"[A-Za-z0-9\-\.]{1,64}" id))
               [type id])))))))
+
+
+(defn invalid-decimal-value-msg [code value]
+  (format "Invalid decimal value `%s` in search parameter `%s`." value code))
+
+
+(defn unsupported-prefix-msg [code op]
+  (format "Unsupported prefix `%s` in search parameter `%s`." (name op) code))
+
+
+(defn eq-value [f ^BigDecimal decimal-value]
+  (let [delta (.movePointLeft 0.5M (.scale decimal-value))]
+    {:op :eq
+     :lower-bound (f (.subtract decimal-value delta))
+     :exact-value (f decimal-value)
+     :upper-bound (f (.add decimal-value delta))}))

modules/db/test/blaze/db/impl/search_param/number_test.clj

@@ -8,6 +8,7 @@
     [blaze.db.impl.search-param :as search-param]
     [blaze.db.impl.search-param-spec]
     [blaze.db.impl.search-param.number :as spn]
+    [blaze.db.impl.search-param.util-spec]
     [blaze.db.search-param-registry :as sr]
     [blaze.fhir-path :as fhir-path]
     [blaze.fhir.hash :as hash]

modules/db/test/blaze/db/impl/search_param/quantity_spec.clj

@@ -5,6 +5,7 @@
     [blaze.db.impl.index.search-param-value-resource-spec]
     [blaze.db.impl.search-param.quantity :as spq]
     [blaze.db.impl.search-param.quantity.spec]
+    [blaze.db.impl.search-param.util-spec]
     [blaze.db.spec]
     [blaze.fhir.spec.type.system-spec]
     [clojure.spec.alpha :as s]))

modules/db/test/blaze/db/impl/search_param/quantity_test.clj

@@ -102,6 +102,9 @@
 
         "23.4" (codec/quantity nil 23.35M) (codec/quantity nil 23.45M)
         "23.0|kg/m2" (codec/quantity "kg/m2" 22.95M) (codec/quantity "kg/m2" 23.05M)
+        ;; with white space between value and unit
+        "23.0| kg/m2" (codec/quantity "kg/m2" 22.95M) (codec/quantity "kg/m2" 23.05M)
+        "23.0 | kg/m2" (codec/quantity "kg/m2" 22.95M) (codec/quantity "kg/m2" 23.05M)
         "0.1" (codec/quantity nil 0.05M) (codec/quantity nil 0.15M)
         "0" (codec/quantity nil -0.5M) (codec/quantity nil 0.5M)
         "0.0" (codec/quantity nil -0.05M) (codec/quantity nil 0.05M)))
@@ -113,8 +116,14 @@
             :op := op
             :exact-value := exact-value)
 
-          (str (name op) "23") (codec/quantity nil 23M)
-          (str (name op) "0.1") (codec/quantity nil 0.1M))))
+          (str (name op) "23.4") (codec/quantity nil 23.4M)
+          (str (name op) "23.0|kg/m2") (codec/quantity "kg/m2" 23.0M)
+          ;; with white space between value and unit
+          (str (name op) "23.0| kg/m2") (codec/quantity "kg/m2" 23.0M)
+          (str (name op) "23.0 | kg/m2") (codec/quantity "kg/m2" 23.0M)
+          (str (name op) "0.1") (codec/quantity nil 0.1M)
+          ;; with white space between op and value
+          (str (name op) " 1") (codec/quantity nil 1M))))
 
     (testing "invalid decimal value"
       (given (search-param/compile-values

modules/db/test/blaze/db/impl/search_param/util_spec.clj

@@ -11,5 +11,15 @@
     [clojure.spec.alpha :as s]))
 
 
+(s/fdef u/separate-op
+  :args (s/cat :value string?)
+  :ret (s/tuple keyword? string?))
+
+
 (s/fdef u/resource-handle-mapper
   :args (s/cat :context :blaze.db.impl.batch-db/context :tid :blaze.db/tid))
+
+
+(s/fdef u/eq-value
+  :args (s/cat :f ifn? :decimal-value decimal?)
+  :ret map?)

modules/db/test/blaze/db/impl/search_param/util_test.clj

@@ -1,6 +1,7 @@
 (ns blaze.db.impl.search-param.util-test
   (:require
     [blaze.db.impl.search-param.util :as util]
+    [blaze.db.impl.search-param.util-spec]
     [clojure.spec.test.alpha :as st]
     [clojure.test :as test :refer [are deftest is]]
     [taoensso.timbre :as log]))
@@ -22,7 +23,11 @@
 (deftest separate-op-test
   (are [value tuple] (= tuple (util/separate-op value))
     "1" [:eq "1"]
+    " 1" [:eq "1"]
+    "1 " [:eq "1"]
+    " 1 " [:eq "1"]
     "eq1" [:eq "1"]
+    "eq 1" [:eq "1"]
     "ne1" [:ne "1"]
     "fo1" [:eq "fo1"]
     "1ne" [:eq "1ne"]))

modules/interaction/src/blaze/interaction/util.clj

@@ -24,7 +24,11 @@
     []
     (comp
       (remove remove-query-param?)
-      (mapcat (fn [[k v]] (mapv #(into [k] (str/split % #",")) (fhir-util/to-seq v)))))
+      (mapcat
+        (fn [[k v]]
+          (map
+            #(into [k] (map str/trim) (str/split % #","))
+            (fhir-util/to-seq v)))))
     query-params))