[pull] develop from DBCG:develop

.travis.yml

@@ -2,53 +2,44 @@ language: java
 jdk: openjdk11
 os: linux
 dist: xenial
-
 services:
-  - docker
-
+- docker
 cache:
   timeout: 180
   directories:
   - "$HOME/.m2/repository"
-
 install:
-   - mvn install -U -DskipTests=true -Dmaven.javadoc.skip=true -B -V
-
+- ./scripts/install.sh
 script:
-  # master or PRs into master, use the release profile
-  - 'if [[ "$TRAVIS_BRANCH" =~ master* ]]; then mvn test -B -P release; fi'
-  - 'if ! [[ "$TRAVIS_BRANCH" =~ master* ]]; then mvn test -B; fi'
-
-
-## export GPG details
-before_deploy:
-  - 'if [[ "$TRAVIS_BRANCH" =~ master* ]]; then echo $GPG_SECRET_KEYS | base64 --decode | $GPG_EXECUTABLE --import; fi'
-  - 'if [[ "$TRAVIS_BRANCH" =~ master* ]]; then echo $GPG_OWNERTRUST | base64 --decode | $GPG_EXECUTABLE --import-ownertrust; fi'
-  - 'echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin'
-
-# NOTE: tests were already run as part of the script phase
-deploy:
-  # deploy develop as a snapshot
-  - provider: script
-    script: "cp .travis.settings.xml $HOME/.m2/settings.xml && mvn deploy -DskipTests=true && docker build . -t contentgroup/cqf-ruler:develop && docker push contentgroup/cqf-ruler:develop"
-    cleanup: false
-    skip_cleanup: true # This is the current correct option, but is soon to be deprecated by the above.
-    on:
-      branch: develop
-  # deploy master to production
-  - provider: script
-    script: "cp .travis.settings.xml $HOME/.m2/settings.xml && mvn deploy -P release -DskipTests=true  && docker build . -t contentgroup/cqf-ruler && docker push contentgroup/cqf-ruler"
-    cleanup: false
-    skip_cleanup: true # This is the current correct option, but is soon to be deprecated by the above.
-    on:
-      branch: master
-
-# Remove the binaries generated by this build so that the cache isn't invalidated.
-# Probably a better way to do this.
+- ./scripts/test.sh
 before_cache:
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/parent
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/common
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/dstu3
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/r4
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/cqf-ruler-dstu3
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/cqf-ruler-r4
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/parent
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/common
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/dstu3
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/r4
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/cqf-ruler-dstu3
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/cqf-ruler-r4
+after_success:
+- ./scripts/deploy.sh
+deploy:
+  provider: releases
+  api_key:
+    secure: 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
+  file_glob: true
+  file: "target/**/*.jar"
+  skip_cleanup: true
+  name: CQF Ruler $TRAVIS_TAG
+  overwrite: true
+  target_commitish: $TRAVIS_COMMIT
+  on:
+    tags: true
+notifications:
+  slack:
+    - rooms:
+      - secure: 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
+      on_success: always
+      on_failure: never
+    - rooms:
+      - secure: CNBq9ztma598N0CBeQNcvwvx6d+jHnI0B8iWAedqJ+oX+kYwCb4tBRTEwtflB0aQndAzn/5fba0S4tQ1gP9liRWb+RQIeBHVQgopEg7iNXYj6d4NIYBmVxpVq44szQI8T7mQJN/v1DFjXoCRbeMKiA5jN8OCrM4kowF4O15b+9RJ1bxbJULzop5K3WlZQQbsDSdxIuR3CGCmLakvf5G1cqHmHE1xWtXWFrNOSe32bp/Pdv7Vo5jaIeLG1b70G4SUUKk60+cwK9/NH4okewYgU5KlI+q51UW0Io8KEmsoFWV49dJ+1NfINM7uArVS3nNeJViMumR2ba1L1gUjGXj9FkuuIM8OS9FaxSss0IaQ8z+gNekuQLyvrE4020UNGY4/b1B8IueQcs+sucs4juCnvyTGdAEGiT23mVWdurqjT6qFTzYHSbXXd23KlmFoeLs46Iwo4mXwx6pxoUmBbNKpSXs7/irCz0GJHXjJAOb3JXxyBohyimKlfBZu1ZJhLytcsQD9SIVpX5B97SD1xD99BAN3sFgDUtZ91usLc3eSg1jaHmaSimw9PVGcoXHEkxiJYzQVPuZNQtwmRSu0zezAv9DhbkNzZAEBkC+vt1dBWzj9T9An3AwIlyANSb0P2qtC7wreHzvLq5duHA0zKGaMjtAZecnEXpIeuhuJhfximP4=
+      on_success: never
+      on_failure: always

Dockerfile

@@ -1,20 +1,20 @@
 FROM jetty:9-jre11
 
 USER jetty:jetty
+
+# Default database directory
 RUN mkdir -p /var/lib/jetty/target
-COPY ./cqf-ruler-dstu3/target/cqf-ruler-dstu3.war /var/lib/jetty/webapps/cqf-ruler-dstu3.war
-COPY ./cqf-ruler-r4/target/cqf-ruler-r4.war /var/lib/jetty/webapps/cqf-ruler-r4.war
+
+#Default config directory
+RUN mkdir -p /var/lib/jetty/webapps/config
+
+COPY --chown=jetty:jetty ./cqf-ruler-dstu3/target/cqf-ruler-dstu3.war /var/lib/jetty/webapps/cqf-ruler-dstu3.war
+COPY --chown=jetty:jetty ./cqf-ruler-r4/target/cqf-ruler-r4.war /var/lib/jetty/webapps/cqf-ruler-r4.war
 EXPOSE 8080
 
 ENV SERVER_ADDRESS_DSTU3="http://localhost:8080/cqf-ruler-dstu3/fhir"
 ENV SERVER_ADDRESS_R4="http://localhost:8080/cqf-ruler-r4/fhir"
-# TODO: Handle these. We probably want some convention to map between the ENV variables and the hapi.properties
-# ENV SERVER_BASE="/cqf-ruler/baseDstu3"
-# ENV HIBERNATE_DIALECT="hibernate.dialect=ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect"
-# ENV DATASOURCE_DRIVER="org.apache.derby.jdbc.EmbeddedDriver"
-# ENV DATASOURCE_URL="jdbc:derby:directory:target/jpaserver_derby_files;create=true"
-# ENV DATASOURCE_URL= DATASOURCE_USERNAME=
-ENV JAVA_OPTIONS="-Dhapi.properties.DSTU3=/var/lib/jetty/webapps/dstu3.properties -Dhapi.properties.R4=/var/lib/jetty/webapps/r4.properties"
+ENV JAVA_OPTIONS=""
 
 COPY --chown=jetty:jetty ./scripts/docker-entrypoint-override.sh /docker-entrypoint-override.sh
 ENTRYPOINT [ "/docker-entrypoint-override.sh" ]

README.md

@@ -1,36 +1,107 @@
 # cqf-ruler
 
-The CQF Ruler is an implementation of FHIR's [Clinical Reasoning Module](
+[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.opencds.cqf/cqf-ruler-r4/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.opencds.cqf/cqf-ruler-r4) [![Build Status](https://www.travis-ci.com/DBCG/cqf-ruler.svg?branch=master)](https://www.travis-ci.com/DBCG/cqf-ruler) [![docker image](https://img.shields.io/docker/v/contentgroup/cqf-ruler/latest?style=flat&color=brightgreen&label=docker%20image)](https://hub.docker.com/r/contentgroup/cqf-ruler/tags) [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://chat.fhir.org/#narrow/stream/179220-cql)
+
+The CQF Ruler is a set of plugins for the [HAPI FHIR Server](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) that provides an implementation of FHIR's [Clinical Reasoning Module](
 http://hl7.org/fhir/clinicalreasoning-module.html) and serves as a
-knowledge artifact repository and clinical decision support service.
+knowledge artifact repository and a [cds-hooks](https://cds-hooks.org/) compatible clinical decision support service. It does this via integrating a number of other CQL-related projects, which are listed below.
 
-## Usage 
+## Usage
 
- - `mvn jetty:run -am --projects cqf-ruler-dstu3`
-   - Starts embedded Jetty server accessible at base URL `http://localhost:8080/cqf-ruler-dstu3/`
+### Docker
 
-For R4 use `mvn jetty:run -am --projects cqf-ruler-r4`
+The easiest way to get started with the cqf-ruler is to pull and run the docker image
 
- - `mvn package -DskipTests=false`
-   - Builds the project war file (cqf-ruler-dstu3.war and cqf-ruler-r4.war in the projects' target directory) 
-   - Runs the test suite (tests are skipped by default)
-
-Visit the [wiki](https://github.com/DBCG/cqf-ruler/wiki) for more documentation.
+```bash
+docker pull contentgroup/cqf-ruler
+docker run -p 8080:8080 contentgroup/cqf-ruler
+```
+
+This will make the cqf-ruler available on `http://localhost:8080/cqf-ruler-r4`
 
-## Dependencies
+Other options for deployment are listed on the [wiki](https://github.com/DBCG/cqf-ruler/wiki) for more documentation.
 
-Before the instructions in the above "Usage" section will work, you need to
-install several primary dependencies.
+## Development
 
-### Java
+### Dependencies
+
+#### Java
 
 Go to [http://www.oracle.com/technetwork/java/javase/downloads/](
 http://www.oracle.com/technetwork/java/javase/downloads/) and download the
 latest (version 11 or higher) JDK for your platform, and install it.
 
-### Apache Maven 3.5.3
+#### Apache Maven 3.5.3
 
 Go to [https://maven.apache.org](https://maven.apache.org), visit the main
 "Download" page, and under "Files" download the 3.5.3 binary.  Then unpack that archive file and follow the installation
 instructions in its README.txt.  The end result of this should be that the
 binary "mvn" is now in your path.
+
+### Build
+
+`mvn package`
+
+Builds the project war file (cqf-ruler-dstu3.war and cqf-ruler-r4.war in the projects' target directory)
+
+Visit the [wiki](https://github.com/DBCG/cqf-ruler/wiki) for more documentation.
+
+### Run
+
+To run the cqf-ruler directory from this project use:
+
+#### DSTU3
+
+`mvn jetty:run -am --projects cqf-ruler-dstu3`
+
+The cqf-ruler will be available at `http://localhost:8080/cqf-ruler-dstu3/`
+
+#### R4
+
+`mvn jetty:run -am --projects cqf-ruler-r4`
+
+The cqf-ruler will be available at `http://localhost:8080/cqf-ruler-r4/`
+
+## Commit Policy
+
+All new development takes place on `<feature>` branches off `master`. Once feature development on the branch is complete, the feature branch is submitted to `master` as a PR. The PR is reviewed by maintainers and regression testing by the CI build occurs.
+
+Changes to the `master` branch must be done through an approved PR. Delete branches after merging to keep the repository clean.
+
+Merges to `master` trigger a deployment to the Maven Snapshots repositories. Once ready for a release, the `master` branch is updated with the correct version number and is tagged. Tags trigger a full release to Maven Central and a corresponding release to Github. Releases SHALL NOT have a SNAPSHOT version, nor any SNAPSHOT dependencies.
+
+## Getting Help
+
+Additional documentation is on the [wiki](https://github.com/DBCG/cqf-ruler/wiki).
+
+Bugs and feature requests can be filed with [Github Issues](https://github.com/cqframework/cqf-ruler/issues).
+
+The implementers are active on the official FHIR [Zulip chat for CQL](https://chat.fhir.org/#narrow/stream/179220-cql).
+
+Inquires for commercial support can be directed to [[email protected]]([email protected]).
+
+## Related Projects
+
+[Clinical Quality Language](https://github.com/cqframework/clinical_quality_language) - Tooling in support of the CQL specification, including the CQL verifier/translator used in this project.
+
+[CQL Evaluator](https://github.com/DBCG/cql-evaluator) - Provides the CQL execution environment used by the cqf-ruler.
+
+[CQF Tooling](https://github.com/cqframework/cqf-tooling) - Provides several operations that the cqf-ruler exposes are services, such as $refresh-generated content.
+
+[CQL Support for Atom](https://atom.io/packages/language-cql) - Open source CQL IDE with syntax highlighting, linting, and local CQL evaluation.
+
+## License
+
+Copyright 2019+ Dynamic Content Group, LLC (dba Alphora)
+
+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](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.

common/pom.xml

@@ -9,4 +9,5 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>common</artifactId>
+    <name>cqf-ruler-common</name>
 </project>

common/src/main/java/org/opencds/cqf/common/config/FhirServerConfig.java

@@ -4,18 +4,24 @@
 import java.sql.Driver;
 
 import org.apache.commons.dbcp2.BasicDataSource;
+import org.opencds.cqf.cds.providers.ProviderConfiguration;
+import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 
 @Configuration
 @EnableTransactionManagement
+@ComponentScan(basePackages = "org.opencds.cqf.common")
 public class FhirServerConfig {
 
     private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfig.class);
@@ -28,6 +34,9 @@ public class FhirServerConfig {
     private Boolean allowOverrideDefaultSearchParams = HapiProperties.getAllowOverrideDefaultSearchParams();
     private String emailFrom = HapiProperties.getEmailFrom();
 
+    private Boolean enforceReferentialIntegrityOnWrite = HapiProperties.getEnforceReferentialIntegrityOnWrite();
+    private Boolean enforceReferentialIntegrityOnDelete = HapiProperties.getEnforceReferentialIntegrityOnDelete();
+
     public FhirServerConfig() {
         ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
         ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
@@ -36,6 +45,10 @@ public FhirServerConfig() {
         ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
         ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny")
                 + " overriding default search params");
+        ourLog.info("Server configured to " + (this.enforceReferentialIntegrityOnDelete ? "enforce" : "ignore")
+                + " referential integrity on delete");
+        ourLog.info("Server configured to " + (this.enforceReferentialIntegrityOnDelete ? "enforce" : "ignore")
+                + " referential integrity on write");
     }
 
     /**
@@ -51,6 +64,8 @@ public DaoConfig daoConfig() {
         retVal.setExpungeEnabled(this.expungeEnabled);
         retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
         retVal.setEmailFromAddress(this.emailFrom);
+        retVal.setEnforceReferentialIntegrityOnDelete(this.enforceReferentialIntegrityOnDelete);
+        retVal.setEnforceReferentialIntegrityOnWrite(this.enforceReferentialIntegrityOnWrite);
 
         Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
         retVal.setFetchSizeDefaultMaximum(maxFetchSize);
@@ -75,15 +90,6 @@ public ModelConfig modelConfig() {
         return modelConfig;
     }
 
-    /**
-     * The following bean configures the database connection. The 'url' property
-     * value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates
-     * that the server should save resources in a directory called
-     * "jpaserver_derby_files".
-     *
-     * A URL to a remote database could also be placed here, along with login
-     * credentials and other properties supported by BasicDataSource.
-     */
     @Bean(destroyMethod = "close")
     public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException,
             InvocationTargetException, InstantiationException {
@@ -118,4 +124,23 @@ public LoggingInterceptor loggingInterceptor() {
     public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
         return new ResponseHighlighterInterceptor();
     }
+
+    @Bean
+	public PartitionSettings partitionSettings() {
+		return new PartitionSettings();
+    }
+
+    @Bean()
+    public ProviderConfiguration providerConfiguration() {
+        return new ProviderConfiguration(
+                HapiProperties.getCdsHooksFhirServerExpandValueSets(),
+                HapiProperties.getCdsHooksFhirServerMaxCodesPerQuery(),
+                HapiProperties.getCdsHooksFhirServerSearchStyleEnum(),
+                HapiProperties.getCdsHooksPreFetchMaxUriLength());
+    }
+
+    @Bean()
+    public SearchParameterResolver searchParameterResolver(FhirContext fhirContext) {
+        return new SearchParameterResolver(fhirContext);
+    }
 }