Merge branch 'release/0.7.0'

# Conflicts:
#	Dockerfile
#	README.md
#	docker-compose.yml
#	docs/index.adoc
#	project.clj

.clj-kondo/config.edn

@@ -0,0 +1,26 @@
+{:lint-as
+ {blaze.elm.compiler/defunop clojure.core/defn
+  blaze.elm.compiler/defbinop clojure.core/defn
+  blaze.elm.compiler/defternop clojure.core/defn
+  blaze.elm.compiler/defnaryop clojure.core/defn
+  blaze.elm.compiler/defaggop clojure.core/defn
+  blaze.elm.compiler/defbinopp clojure.core/defn
+  blaze.elm.compiler/defunopp clojure.core/defn
+  clojure.test.check.properties/for-all clojure.core/let
+  datomic-tools.schema/defunc clojure.core/defn
+  manifold.deferred/loop clojure.core/loop
+  manifold.deferred/let-flow clojure.core/let
+  manifold.deferred/let-flow' clojure.core/let
+  prometheus.alpha/defcounter clojure.core/def
+  prometheus.alpha/defhistogram clojure.core/def}
+
+ :linters
+ {:unused-private-var
+  {:exclude
+   [blaze.datomic.value/string-short-len-code
+    blaze.datomic.value/string-int-len-code
+    blaze.datomic.value/boolean-code]}
+
+  ;; because of macros in modules/cql/src/blaze/elm/compiler.clj
+  :redefined-var
+  {:level :off}}}

.dockerignore

@@ -1,5 +1,7 @@
 *
+!modules
 !resources
 !src
 !Dockerfile
-!project.clj
+!deps.edn
+!pom.xml

.gitignore

@@ -1,11 +1,12 @@
 /target
 /.lein-*
-/.nrepl-port
+.nrepl-port
 /queries
 /generate-docs.sh
 /fill-store.sh
 /load-test.sh
 /start-db.sh
-/cql-test
 /kube*
 /nginx.conf
+.cpcache
+.cache

.travis.yml

@@ -1,9 +1,19 @@
-dist: trusty
-language: clojure
+sudo: true
+language: java
 jdk:
 - openjdk8
-lein: 2.8.1
+- openjdk11
+cache:
+  directories:
+  - $HOME/.m2
+  - $HOME/.cljs
+  - $HOME/.gitlibs
+  - .cpcache
+install:
+- curl -O https://download.clojure.org/install/linux-install-1.10.1.469.sh
+- chmod +x linux-install-1.10.1.469.sh
+- sudo ./linux-install-1.10.1.469.sh
 script:
-- ./fetch-cql-tests.sh
-- lein check
-- lein test
+- make check
+- make lint
+- make test

Dockerfile

@@ -1,14 +1,14 @@
-FROM clojure:lein-2.9.1 as build
+FROM clojure:openjdk-11-tools-deps as build
 
 COPY . /build/
 
 WORKDIR /build
-RUN lein uberjar
+RUN clojure -A:depstar -m hf.depstar.uberjar target/blaze-standalone.jar
 
-FROM openjdk:8u222-jre
+FROM openjdk:11.0.4-jre
 
-COPY --from=build /build/target/blaze-0.6.4-standalone.jar /app/
+COPY --from=build /build/target/blaze-standalone.jar /app/
 
 WORKDIR /app
 
-CMD ["/bin/bash", "-c", "java $JVM_OPTS -jar blaze-0.6.4-standalone.jar"]
+CMD ["/bin/bash", "-c", "java $JVM_OPTS -jar blaze-standalone.jar -m blaze.core"]

Makefile

@@ -0,0 +1,54 @@
+VERSION = "0.7.0"
+
+check:
+	clojure -A:check
+
+lint:
+	clojure -A:clj-kondo --lint modules
+	clojure -A:clj-kondo --lint src
+
+modules/cql/cql-test:
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlAggregateFunctionsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlArithmeticFunctionsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlComparisonOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlConditionalOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlDateTimeOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlErrorsAndMessagingOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlIntervalOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlListOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlLogicalOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlNullologicalOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlStringOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlTypeOperatorsTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/CqlTypesTest.xml
+	wget -P modules/cql/cql-test -q https://raw.githubusercontent.com/HL7/cql/v1.4-ballot/tests/cql/ValueLiteralsAndSelectors.xml
+
+test-cql: modules/cql/cql-test
+	cd modules/cql;	clojure -A:test --profile :ci
+
+test-datomic:
+	cd modules/datomic;	clojure -A:test --profile :ci
+
+test-interaction:
+	cd modules/interaction;	clojure -A:test --profile :ci
+
+test-openid-auth:
+	cd modules/openid-auth;	clojure -A:test --profile :ci
+
+test-operations-measure-evaluate-measure:
+	cd modules/operations/measure-evaluate-measure;	clojure -A:test --profile :ci
+
+test-rest-api:
+	cd modules/rest-api;	clojure -A:test --profile :ci
+
+test-rest-util:
+	cd modules/rest-util;	clojure -A:test --profile :ci
+
+test: test-cql test-datomic test-interaction test-openid-auth test-operations-measure-evaluate-measure test-rest-api test-rest-util
+	clojure -A:test --profile :ci
+
+uberjar:
+	clojure -A:depstar -m hf.depstar.uberjar target/blaze-${VERSION}-standalone.jar
+
+
+.PHONY: check test-cql test-datomic test-interaction test-openid-auth test-operations-measure-evaluate-measure test-rest-api test-rest-util test uberjar

README.md

@@ -14,7 +14,7 @@ The goal of this project is to provide a FHIR® Store with an internal CQL Evalu
 
 The project is currently under active development. Essentially all official [CQL Tests][3] pass. Please report any issues you encounter during evaluation.
 
-Latest release: [v0.6.4][5]
+Latest release: [v0.7.0][5]
 
 ## Quick Start
 
@@ -23,14 +23,14 @@ In order to run Blaze with an in-memory, volatile database, just execute the fol
 ### Docker
 
 ```bash
-docker run -p 8080:8080 liferesearch/blaze:0.6.4
+docker run -p 8080:8080 liferesearch/blaze:0.7.0
 ```
 
 ### Java
 
 ```bash
-wget https://github.com/life-research/blaze/releases/download/v0.6.4/blaze-0.6.4-standalone.jar
-java -jar blaze-0.6.4-standalone.jar
+wget https://github.com/samply/blaze/releases/download/v0.7.0/blaze-0.7.0-standalone.jar
+java -jar blaze-0.7.0-standalone.jar
 ```
 
 Logging output should appear which prints the most important settings and system parameters like Java version and available memory.
@@ -47,13 +47,16 @@ In-deep deployment options of Blaze are described in the [Deployment Section][4]
 
 ## License
 
-Copyright © 2019 LIFE Research Center (Alexander Kiel)
+Copyright 2019 The Samply Development Community
 
-Distributed under the Eclipse Public License either version 1.0 or (at
-your option) any later version.
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
 
 [1]: <https://github.com/life-research/life-fhir-gen>
 [2]: <http://cql-runner.dataphoria.org/>
 [3]: <https://cql.hl7.org/tests.html>
 [4]: <https://alexanderkiel.gitbook.io/blaze/deployment>
-[5]: <https://github.com/life-research/blaze/releases/tag/v0.6.4>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.7.0>

deps.edn

@@ -0,0 +1,123 @@
+{:paths ["src" "resources"]
+
+ :deps
+ {blaze/datomic
+  {:local/root "modules/datomic"}
+
+  blaze/extern-terminology-service
+  {:local/root "modules/extern-terminology-service"}
+
+  blaze/interaction
+  {:local/root "modules/interaction"}
+
+  blaze.operation/measure-evaluate-measure
+  {:local/root "modules/operations/measure-evaluate-measure"}
+
+  blaze/openid-auth
+  {:local/root "modules/openid-auth"}
+
+  blaze/rest-api
+  {:local/root "modules/rest-api"}
+
+  blaze/structure-definition
+  {:local/root "modules/structure-definition"}
+
+  blaze/thread-pool-executor-collector
+  {:local/root "modules/thread-pool-executor-collector"}
+
+  com.cognitect/anomalies
+  {:mvn/version "0.1.12"}
+
+  com.datomic/datomic-free
+  {:mvn/version "0.9.5697"
+   :exclusions
+   [io.netty/netty-all]}
+
+  com.h2database/h2
+  {:mvn/version "1.4.199"}
+
+  com.taoensso/timbre
+  {:mvn/version "4.10.0"}
+
+  integrant
+  {:git/url "https://github.com/alexanderkiel/integrant.git"
+   :sha "c673b85130e553feec6d4c5d2d1ec773a49c929c"}
+
+  io.netty/netty-codec-http
+  {:mvn/version "4.1.39.Final"}
+
+  io.netty/netty-handler-proxy
+  {:mvn/version "4.1.39.Final"}
+
+  io.netty/netty-resolver-dns
+  {:mvn/version "4.1.39.Final"}
+
+  io.netty/netty-transport-native-epoll$linux-x86_64
+  {:mvn/version "4.1.39.Final"}
+
+  io.prometheus/simpleclient_hotspot
+  {:mvn/version "0.6.0"}
+
+  org.clojars.akiel/datomic-spec
+  {:mvn/version "0.5.2"}
+
+  org.clojars.akiel/datomic-tools
+  {:mvn/version "0.4"}
+
+  org.clojars.akiel/spec-coerce
+  {:mvn/version "0.4.0"}
+
+  org.clojure/clojure
+  {:mvn/version "1.10.1"}
+
+  org.clojure/tools.reader
+  {:mvn/version "1.3.2"}
+
+  prom-metrics
+  {:mvn/version "0.5-alpha2"}}
+
+ :aliases
+ {:depstar
+  {:extra-deps
+   {seancorfield/depstar
+    {:mvn/version "0.3.3"}}}
+
+  :check
+  {:extra-deps
+   {athos/clj-check
+    {:git/url "https://github.com/athos/clj-check.git"
+     :sha "b48d4e7000586529f81c1e29069b503b57259514"}}
+   :main-opts
+   ["-m" "clj-check.check"]}
+
+  :test
+  {:extra-paths ["dev" "test"]
+
+   :extra-deps
+   {criterium
+    {:mvn/version "0.4.5"}
+
+    lambdaisland/kaocha
+    {:mvn/version "0.0-554"}
+
+    org.clojars.akiel/iota
+    {:mvn/version "0.1"}
+
+    org.clojure/data.xml
+    {:mvn/version "0.0.8"}
+
+    org.clojure/test.check
+    {:mvn/version "0.10.0"}
+
+    org.clojure/tools.namespace
+    {:mvn/version "0.3.1"}}
+
+   :main-opts
+   ["-m" "kaocha.runner"]}
+
+  :clj-kondo
+  {:extra-deps
+   {clj-kondo
+    {:mvn/version "2019.11.03"}}
+
+   :main-opts ["-m" "clj-kondo.main"]}}}

dev/blaze/dev.clj

@@ -0,0 +1,40 @@
+(ns blaze.dev
+  (:require
+    [blaze.spec]
+    [blaze.system :as system]
+    [clojure.repl :refer [pst]]
+    [clojure.spec.test.alpha :as st]
+    [clojure.tools.namespace.repl :refer [refresh]]
+    [datomic-spec.test :as dst]))
+
+
+;; Spec Instrumentation
+(st/instrument)
+(dst/instrument)
+
+
+(defonce system nil)
+
+
+(defn init []
+  (alter-var-root #'system (constantly (system/init! (System/getenv))))
+  nil)
+
+
+(defn reset []
+  (some-> system system/shutdown!)
+  (refresh :after `init))
+
+
+;; Init Development
+(comment
+  (init)
+  (pst)
+  )
+
+
+;; Reset after making changes
+(comment
+  (reset)
+  (st/unstrument)
+  )

dev/blaze/dev/datomic.clj

@@ -0,0 +1,29 @@
+(ns blaze.dev.datomic
+  (:require
+    [blaze.datomic.util :as datomic-util]
+    [blaze.dev :refer [system]]
+    [datomic.api :as d]))
+
+
+(defn count-resources [db type]
+  (d/q '[:find (count ?e) . :in $ ?id :where [?e ?id]] db (datomic-util/resource-id-attr type)))
+
+
+(comment
+  (def conn (::conn system))
+  (def db (d/db conn))
+  (def hdb (d/history db))
+
+  (count-resources (d/db conn) "Coding")
+  (count-resources (d/db conn) "Organization")
+  (count-resources (d/db conn) "Patient")
+  (count-resources (d/db conn) "Specimen")
+  (count-resources (d/db conn) "Observation")
+
+  (d/pull (d/db conn) '[*] 1262239348687945)
+  (d/entity (d/db conn) [:Patient/id "0"])
+  (d/q '[:find (pull ?e [*]) :where [?e :code/id]] (d/db conn))
+
+  (d/pull (d/db conn) '[*] (d/t->tx 1197))
+  )
+