feature swap to non javax clinical reasoning (#5463)

* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies * Rev to CR 3.0.0-PRE10 * version bump, pom changes for jakarta conflicts * undo exclusions from other modules * Rework exclusions * Fix type in dependency * new cr version, exclude conflicts in cr and cds-hooks * remove exclusions * pom update * Redo the exclusions * add retrieveSettings config * new CR retrieve settings and config * update config to new enums and parameters * update unit tests and config for new cql and terminology properties * bump CR to 3.0.0-PRE12 * spotless edits, update class path for CR config * missing dependencies * swap for jakarta * moving conflicting dependencies * Fix a couple code review items --------- Co-authored-by: Jonathan Percival <[email protected]>
hapifhir · Nov 22, 2023 · 86ea069 · 86ea069
1 parent 9aa173a
commit 86ea069
Show file tree

Hide file tree

Showing 89 changed files with 13,504 additions and 13,431 deletions.
diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,15 +4,15 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
@@ -257,7 +257,17 @@
  <artifactId>spring-test</artifactId>
  <scope>test</scope>
  </dependency>
-
+ <dependency>
+ <groupId>org.simplejavamail</groupId>
+ <artifactId>simple-java-mail</artifactId>
+ <!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
+ <exclusions>
+ <exclusion>
+ <groupId>com.sun.activation</groupId>
+ <artifactId>jakarta.activation</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
  </dependencies>
 
  <build>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-cli</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/pom.xml b/hapi-fhir-cli/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client-okhttp/pom.xml b/hapi-fhir-client-okhttp/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client/pom.xml b/hapi-fhir-client/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-converter/pom.xml b/hapi-fhir-converter/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-docs/pom.xml b/hapi-fhir-docs/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...resources/ca/uhn/hapi/fhir/changelog/7_0_0/5436-swap-to-non-javax-clinical-reasoning.yaml b/...resources/ca/uhn/hapi/fhir/changelog/7_0_0/5436-swap-to-non-javax-clinical-reasoning.yaml
@@ -0,0 +1,4 @@
+---
+type: add
+issue: 5436
+title: "Moving clinical reasoning to non-javax dependency for alignment with incoming hapi-fhir changes, bumping CR version and updating impacted classes and services"
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml b/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-hfql/pom.xml b/hapi-fhir-jpaserver-hfql/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-ips/pom.xml b/hapi-fhir-jpaserver-ips/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-mdm/pom.xml b/hapi-fhir-jpaserver-mdm/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-model/pom.xml b/hapi-fhir-jpaserver-model/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-searchparam/pom.xml b/hapi-fhir-jpaserver-searchparam/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-subscription/pom.xml b/hapi-fhir-jpaserver-subscription/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-test-dstu2/pom.xml b/hapi-fhir-jpaserver-test-dstu2/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-test-dstu3/pom.xml b/hapi-fhir-jpaserver-test-dstu3/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-test-r4/pom.xml b/hapi-fhir-jpaserver-test-r4/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-test-r4b/pom.xml b/hapi-fhir-jpaserver-test-r4b/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-test-r5/pom.xml b/hapi-fhir-jpaserver-test-r5/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-test-utilities/pom.xml b/hapi-fhir-jpaserver-test-utilities/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
@@ -259,7 +259,6 @@
  </exclusion>
  </exclusions>
  </dependency>
-
  </dependencies>
 
  <build>

diff --git a/hapi-fhir-jpaserver-uhnfhirtest/pom.xml b/hapi-fhir-jpaserver-uhnfhirtest/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-server-cds-hooks/pom.xml b/hapi-fhir-server-cds-hooks/pom.xml
@@ -7,7 +7,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
@@ -38,7 +38,6 @@
  <artifactId>hapi-fhir-storage-cr</artifactId>
  <version>${project.version}</version>
  </dependency>
-
  <dependency>
  <groupId>org.springframework</groupId>
  <artifactId>spring-beans</artifactId>
@@ -77,6 +76,29 @@
  <version>${reflections_version}</version>
  <scope>test</scope>
  </dependency>
+ <dependency>
+ <groupId>org.simplejavamail</groupId>
+ <artifactId>simple-java-mail</artifactId>
+ <!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
+ <exclusions>
+ <exclusion>
+ <groupId>com.sun.activation</groupId>
+ <artifactId>jakarta.activation</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>com.icegreen</groupId>
+ <artifactId>greenmail</artifactId>
+ <scope>compile</scope>
+ <!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
+ <exclusions>
+ <exclusion>
+ <groupId>com.sun.activation</groupId>
+ <artifactId>jakarta.activation</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
  </dependencies>
 
  <build>

diff --git a/hapi-fhir-server-mdm/pom.xml b/hapi-fhir-server-mdm/pom.xml
@@ -7,7 +7,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-server-openapi/pom.xml b/hapi-fhir-server-openapi/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-server/pom.xml b/hapi-fhir-server/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.0-SNAPSHOT</version>
+ <version>6.11.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>