Merge pull request #20 from DBCG/develop

Proposed Release 1.3.0
DBCG · Sep 30, 2020 · 116c48a · 116c48a
2 parents 4229226 + 8936fff
commit 116c48a
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diff --git a/.travis.yml b/.travis.yml
@@ -2,44 +2,43 @@ language: java
 jdk: openjdk11
 os: linux
 dist: xenial
-
 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 ! [[ "$TRAVIS_BRANCH" =~ master* ]]; then mvn test -B; fi'
-
-
-## export GPG details
+- if [[ "$TRAVIS_BRANCH" =~ master* ]]; then mvn test -B -P release; fi
+- if ! [[ "$TRAVIS_BRANCH" =~ master* ]]; then mvn test -B; fi
 before_deploy:
-  - 'if [[ "$TRAVIS_BRANCH" =~ master* ]]; then echo $GPG_SECRET_KEYS | base64 --decode | $GPG_EXECUTABLE --import; fi'
-  - 'if [[ "$TRAVIS_BRANCH" =~ master* ]]; then echo $GPG_OWNERTRUST | base64 --decode | $GPG_EXECUTABLE --import-ownertrust; fi'
-
-# NOTE: tests were already run as part of the script phase
+- if [[ "$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
 deploy:
-  # deploy develop as a snapshot
-  - provider: script
-    script: "cp .travis.settings.xml $HOME/.m2/settings.xml && mvn deploy -DskipTests=true"
-    cleanup: false
-    skip_cleanup: true # this is the current correct option, 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"
-    cleanup: false
-    skip_cleanup: true # this is the current correct option, 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.
+- provider: script
+  script: cp .travis.settings.xml $HOME/.m2/settings.xml && mvn deploy -DskipTests=true
+  cleanup: false
+  skip_cleanup: true
+  on:
+    branch: develop
+- provider: script
+  script: cp .travis.settings.xml $HOME/.m2/settings.xml && mvn deploy -P release
+    -DskipTests=true
+  cleanup: false
+  skip_cleanup: true
+  on:
+    branch: master
 before_cache:
-      - rm -rf $HOME/.m2/repository/org/opencds/cqf/cds
+- rm -rf $HOME/.m2/repository/org/opencds/cqf/cds
+notifications:
+  slack:
+    - rooms:
+      - secure: ECKEk6sCGWP0IdlKx8cW7JMuD5Z9UsrpIa+gcHFyYHTly0ExTAaGAFFbFI3h1hnLdVqlUDhP5F65VXurEJ430Z9nF9Eb5oy+2Evhur5S0jWiHwak8Yf7MAkhf3waAWPtft4I0imMmMHgBSMI9R9VLjCiyhhS90OQpN7giDK0uo6AovijN+UelkZUNMH+6mQS9c1q5BXqoFU90hCCX5VUPPGXAXW535ZadNTd3b284MFVmLxik+p+hg+FxjI5utAA5o5f9uxxAtEBkDgM9vxyDRKKi4rMvNG12YZ/e20RiFJwPcsUA4uuaWqAJP8J9OHRTfrbGbFUDCTaSUp8CZcS/ydoaZBb0BYhF33U19aqYTovdcKzoCmWs5csoEHeFqjKYKyBc6dZcj3sZ1C2HOoz+Hb7uqRAAfi0N+kxTR2j/h1eAPS/28np1Uh1nSuVNx1h3OwCms0fDBNANRcpXOhfI01aV7Zx0HSu4fO9Gek6fJ4mB6eK47cO0H8O9F6px1WtPvaEoCXPoaCCO5QLI+OM/WX+Vj+iYE+3Z/FBBwcTgVrrHc5GFW5SPttr01qKGjkee5VBUkPTL9zr2tvavZYzJ9V25gvCta5ZXDGyLjfW7HoB6dOh9sDpQTzMUnb2AiYKLztEaotQwJRX6Se8ASHpkzbkwMszzmpta2qR1uvsrhE=
+      on_success: always
+      on_failure: never
+    - rooms:
+      - secure: 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
+      on_success: never
+      on_failure: always
diff --git a/pom.xml b/pom.xml
@@ -9,15 +9,16 @@
 
     <properties>
         <version.major>1</version.major>
-        <version.minor>1</version.minor>
+        <version.minor>3</version.minor>
         <version.patch>0</version.patch>
         <!-- NOTE: Building under the release profile automatically drops the -SNAPSHOT extension -->
         <revision>${version.major}.${version.minor}.${version.patch}-SNAPSHOT</revision>
 
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
-        <cql-engine.version>1.4.0</cql-engine.version>
+        <cql-engine.version>1.5.0</cql-engine.version>
+        <cql-evaluator-execution.version>1.0.0</cql-evaluator-execution.version>
     </properties>
 
     <name>cds-hooks</name>
@@ -59,6 +60,12 @@
     </repositories>
 
     <dependencies>
+        <dependency>
+            <groupId>org.opencds.cqf.cql</groupId>
+            <artifactId>evaluator.execution</artifactId>
+            <version>${cql-evaluator-execution.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>org.opencds.cqf.cql</groupId>
             <artifactId>engine</artifactId>
@@ -82,6 +89,12 @@
                 </exclusion>
             </exclusions>
         </dependency>
+
+      <dependency>
+        <groupId>com.google.code.gson</groupId>
+        <artifactId>gson</artifactId>
+        <version>2.8.5</version>
+      </dependency>
     </dependencies>
 
     <distributionManagement>

diff --git a/scripts/install.sh b/scripts/install.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mvn install -U -DskipTests=true -Dmaven.javadoc.skip=true -B -V
diff --git a/src/main/java/org/opencds/cqf/cds/discovery/DiscoveryResolutionR4.java b/src/main/java/org/opencds/cqf/cds/discovery/DiscoveryResolutionR4.java
@@ -10,12 +10,26 @@
 public class DiscoveryResolutionR4 {
 
     private final String PATIENT_ID_CONTEXT = "{{context.patientId}}";
-    private final int URI_MAX_LENGTH = 8000;
+    private final int DEFAULT_MAX_URI_LENGTH = 8000;
+    private int maxUriLength;
 
     private IGenericClient client;
 
     public DiscoveryResolutionR4(IGenericClient client) {
         this.client = client;
+        this.maxUriLength = DEFAULT_MAX_URI_LENGTH;
+    }
+
+    public int getMaxUriLength() {
+        return this.maxUriLength;
+    }
+
+    public void setMaxUriLength(int maxUriLength) {
+        if (maxUriLength <= 0) {
+            throw new IllegalArgumentException("maxUriLength must be >0");
+        }
+
+        this.maxUriLength = maxUriLength;
     }
 
     public PlanDefinition resolvePlanDefinition(Bundle.BundleEntryComponent component) {
@@ -115,10 +129,10 @@ private StringBuilder getCodesStringBuilder(List<String> ret, StringBuilder code
         String codeToken = system + "|" + code;
         int postAppendLength = codes.length() + codeToken.length();
 
-        if (codes.length() > 0 && postAppendLength < URI_MAX_LENGTH) {
+        if (codes.length() > 0 && postAppendLength < this.maxUriLength) {
             codes.append(",");
         }
-        else if (postAppendLength > URI_MAX_LENGTH) {
+        else if (postAppendLength > this.maxUriLength) {
             ret.add(codes.toString());
             codes = new StringBuilder();
         }
@@ -128,7 +142,7 @@ else if (postAppendLength > URI_MAX_LENGTH) {
 
     public List<String> createRequestUrl(DataRequirement dataRequirement) {
         if (!isPatientCompartment(dataRequirement.getType())) return null;
-        String patientRelatedResource = dataRequirement.getType() + "?" + getPatientSearchParam(dataRequirement.getType()) + "=" + PATIENT_ID_CONTEXT;
+        String patientRelatedResource = dataRequirement.getType() + "?" + getPatientSearchParam(dataRequirement.getType()) + "=Patient/" + PATIENT_ID_CONTEXT;
         List<String> ret = new ArrayList<>();
         if (dataRequirement.hasCodeFilter()) {
             for (DataRequirement.DataRequirementCodeFilterComponent codeFilterComponent : dataRequirement.getCodeFilter()) {

diff --git a/src/main/java/org/opencds/cqf/cds/discovery/DiscoveryResolutionStu3.java b/src/main/java/org/opencds/cqf/cds/discovery/DiscoveryResolutionStu3.java
@@ -9,12 +9,26 @@
 public class DiscoveryResolutionStu3 {
 
     private final String PATIENT_ID_CONTEXT = "{{context.patientId}}";
-    private final int URI_MAX_LENGTH = 8000;
+    private final int DEFAULT_MAX_URI_LENGTH = 8000;
+    private int maxUriLength;
 
     private IGenericClient client;
 
     public DiscoveryResolutionStu3(IGenericClient client) {
         this.client = client;
+        this.maxUriLength = DEFAULT_MAX_URI_LENGTH;
+    }
+
+    public int getMaxUriLength() {
+        return this.maxUriLength;
+    }
+
+    public void setMaxUriLength(int maxUriLength) {
+        if (maxUriLength <= 0) {
+            throw new IllegalArgumentException("maxUriLength must be >0");
+        }
+
+        this.maxUriLength = maxUriLength;
     }
 
     public PlanDefinition resolvePlanDefinition(Bundle.BundleEntryComponent component) {
@@ -114,10 +128,10 @@ private StringBuilder getCodesStringBuilder(List<String> ret, StringBuilder code
         String codeToken = system + "|" + code;
         int postAppendLength = codes.length() + codeToken.length();
 
-        if (codes.length() > 0 && postAppendLength < URI_MAX_LENGTH) {
+        if (codes.length() > 0 && postAppendLength < this.maxUriLength) {
             codes.append(",");
         }
-        else if (postAppendLength > URI_MAX_LENGTH) {
+        else if (postAppendLength > this.maxUriLength) {
             ret.add(codes.toString());
             codes = new StringBuilder();
         }
@@ -127,7 +141,7 @@ else if (postAppendLength > URI_MAX_LENGTH) {
 
     public List<String> createRequestUrl(DataRequirement dataRequirement) {
         if (!isPatientCompartment(dataRequirement.getType())) return null;
-        String patientRelatedResource = dataRequirement.getType() + "?" + getPatientSearchParam(dataRequirement.getType()) + "=" + PATIENT_ID_CONTEXT;
+        String patientRelatedResource = dataRequirement.getType() + "?" + getPatientSearchParam(dataRequirement.getType()) + "=Patient/" + PATIENT_ID_CONTEXT;
         List<String> ret = new ArrayList<>();
         if (dataRequirement.hasCodeFilter()) {
             for (DataRequirement.DataRequirementCodeFilterComponent codeFilterComponent : dataRequirement.getCodeFilter()) {

diff --git a/src/main/java/org/opencds/cqf/cds/evaluation/EvaluationContext.java b/src/main/java/org/opencds/cqf/cds/evaluation/EvaluationContext.java
@@ -4,6 +4,7 @@
 import java.util.List;
 
 import org.opencds.cqf.cds.hooks.Hook;
+import org.opencds.cqf.cds.providers.ProviderConfiguration;
 import org.opencds.cqf.cds.exceptions.NotImplementedException;
 
 import org.cqframework.cql.elm.execution.Library;
@@ -45,8 +46,10 @@ public abstract class EvaluationContext<T extends IBaseResource> {
 
     private IGenericClient client;
 
+    private ProviderConfiguration providerConfiguration;
+
     public EvaluationContext(Hook hook, FhirVersionEnum fhirVersion, IGenericClient fhirClient, Context context,
-            Library library, T planDefinition) {
+            Library library, T planDefinition, ProviderConfiguration providerConfiguration) {
 
         // How to determine if it's a local server?
         // Local Server url?
@@ -62,6 +65,8 @@ public EvaluationContext(Hook hook, FhirVersionEnum fhirVersion, IGenericClient
 
         this.client = fhirClient;
 
+        this.providerConfiguration = providerConfiguration;
+
         context.registerDataProvider("http://hl7.org/fhir", getDataProvider());
     }
 
@@ -98,8 +103,6 @@ public Library getLibrary() {
     private DataProvider getDataProvider() {
         if (remoteProvider == null) {
             ModelResolver resolver;
-
-            // TODO: Need to factor out all the SearchParamRegistry stuff.
             TerminologyProvider terminologyProvider;
             switch (fhirVersion) {
                 case DSTU2:
@@ -123,6 +126,11 @@ private DataProvider getDataProvider() {
             RestFhirRetrieveProvider provider = new RestFhirRetrieveProvider(
                     new SearchParameterResolver(this.fhirContext), this.getHookFhirClient());
             provider.setTerminologyProvider(terminologyProvider);
+            provider.setExpandValueSets(true);
+
+            provider.setExpandValueSets(this.providerConfiguration.getExpandValueSets());
+            provider.setMaxCodesPerQuery(this.providerConfiguration.getMaxCodesPerQuery());
+            provider.setSearchStyle(this.providerConfiguration.getSearchStyle());
 
             this.remoteProvider = new CompositeDataProvider(resolver, provider);
         }
@@ -185,6 +193,10 @@ public IGenericClient getHookFhirClient() {
         return client;
     }
 
+    public ProviderConfiguration getProviderConfiguration() {
+        return this.providerConfiguration;
+    }
+
     // NOTE: This is an operation defined in the cqf-ruler
     abstract List<Object> applyCqlToResources(List<Object> resources);
 }
diff --git a/src/main/java/org/opencds/cqf/cds/evaluation/R4EvaluationContext.java b/src/main/java/org/opencds/cqf/cds/evaluation/R4EvaluationContext.java
@@ -4,6 +4,7 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 
 import org.opencds.cqf.cds.hooks.Hook;
+import org.opencds.cqf.cds.providers.ProviderConfiguration;
 import org.cqframework.cql.elm.execution.Library;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Parameters;
@@ -12,18 +13,23 @@
 import org.opencds.cqf.cql.engine.execution.Context;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
 public class R4EvaluationContext extends EvaluationContext<PlanDefinition> {
 
     public R4EvaluationContext(Hook hook, FhirVersionEnum fhirVersion, IGenericClient fhirClient,
-            TerminologyProvider terminologyProvider, Context context, Library library, PlanDefinition planDefinition) {
-        super(hook, fhirVersion, fhirClient, context, library, planDefinition);
+            TerminologyProvider terminologyProvider, Context context, Library library, PlanDefinition planDefinition, ProviderConfiguration providerConfiguration) {
+        super(hook, fhirVersion, fhirClient, context, library, planDefinition, providerConfiguration);
     }
 
     @Override
     List<Object> applyCqlToResources(List<Object> resources) {
+        if (resources == null || resources.isEmpty()) {
+            return new ArrayList<>();
+        }
+
         Bundle bundle = new Bundle();
         for (Object res : resources) {
             bundle.addEntry(new Bundle.BundleEntryComponent().setResource((Resource) res));

diff --git a/src/main/java/org/opencds/cqf/cds/evaluation/Stu3EvaluationContext.java b/src/main/java/org/opencds/cqf/cds/evaluation/Stu3EvaluationContext.java
@@ -4,6 +4,7 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 
 import org.opencds.cqf.cds.hooks.Hook;
+import org.opencds.cqf.cds.providers.ProviderConfiguration;
 import org.cqframework.cql.elm.execution.Library;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Parameters;
@@ -12,18 +13,23 @@
 import org.opencds.cqf.cql.engine.execution.Context;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
 public class Stu3EvaluationContext extends EvaluationContext<PlanDefinition> {
 
     public Stu3EvaluationContext(Hook hook, FhirVersionEnum fhirVersion, IGenericClient fhirClient,
-            TerminologyProvider terminologyProvider, Context context, Library library, PlanDefinition planDefinition) {
-        super(hook, fhirVersion, fhirClient, context, library, planDefinition);
+            TerminologyProvider terminologyProvider, Context context, Library library, PlanDefinition planDefinition, ProviderConfiguration providerConfiguration) {
+        super(hook, fhirVersion, fhirClient, context, library, planDefinition, providerConfiguration);
     }
 
     @Override
     List<Object> applyCqlToResources(List<Object> resources) {
+        if (resources == null || resources.isEmpty()) {
+            return new ArrayList<>();
+        }
+
         Bundle bundle = new Bundle();
         for (Object res : resources) {
             bundle.addEntry(new Bundle.BundleEntryComponent().setResource((Resource) res));