Split into Modules

.dockerignore

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

.gitignore

@@ -1,11 +1,11 @@
 /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

.travis.yml

@@ -1,9 +1,18 @@
-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 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-0.7.0-alpha3-standalone.jar /app/
+COPY --from=build /build/target/blaze-standalone.jar /app/
 
 WORKDIR /app
 
-CMD ["/bin/bash", "-c", "java $JVM_OPTS -jar blaze-0.7.0-alpha3-standalone.jar"]
+CMD ["/bin/bash", "-c", "java $JVM_OPTS -jar blaze-standalone.jar -m blaze.core"]

Makefile

@@ -0,0 +1,50 @@
+VERSION = "0.7.0-alpha5"
+
+check:
+	clojure -A:check
+
+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: [v0.7.0-alpha2][5]
+Latest release: [v0.7.0-alpha5][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:0.7.0-alpha3
+docker run -p 8080:8080 liferesearch/blaze:0.7.0-alpha5
 ```
 
 ### Java
 
 ```bash
-wget https://github.com/life-research/blaze/releases/download/v0.7.0-alpha2/blaze-0.7.0-alpha3-standalone.jar
-java -jar blaze-0.7.0-alpha3-standalone.jar
+wget https://github.com/life-research/blaze/releases/download/v0.7.0-alpha5/blaze-0.7.0-alpha5-standalone.jar
+java -jar blaze-0.7.0-alpha5-standalone.jar
 ```
 
 Logging output should appear which prints the most important settings and system parameters like Java version and available memory.
@@ -56,4 +56,4 @@ your option) any later version.
 [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/v0.7.0-alpha2>
+[5]: <https://github.com/life-research/blaze/releases/tag/v0.7.0-alpha5>

deps.edn

@@ -0,0 +1,119 @@
+{: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"}
+
+  phrase
+  {:mvn/version "0.3-alpha3"}
+
+  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"]}}}

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))
+  )
+