From 06382009ceffd19f6de712fb96f8609c4337ec19 Mon Sep 17 00:00:00 2001
From: dotasek <david.otasek@smilecdr.com>
Date: Wed, 9 Feb 2022 14:08:24 -0500
Subject: [PATCH 1/7] Bump mockito and bytebuddy versions for Java 17
 compatibility

---
 org.hl7.fhir.validation/pom.xml | 7 +++++++
 pom.xml                         | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/org.hl7.fhir.validation/pom.xml b/org.hl7.fhir.validation/pom.xml
index 1a2f1a09f..c200b03b1 100644
--- a/org.hl7.fhir.validation/pom.xml
+++ b/org.hl7.fhir.validation/pom.xml
@@ -218,6 +218,13 @@
             <scope>test</scope>
         </dependency>
 
+<dependency>
+    <groupId>net.bytebuddy</groupId>
+    <artifactId>byte-buddy</artifactId>
+    <version>1.10.21</version>
+	<scope>test</scope>
+</dependency>
+
         <!-- End to end -->
         <dependency>
             <groupId>org.seleniumhq.selenium</groupId>
diff --git a/pom.xml b/pom.xml
index 3b85795e4..acdfffdd6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-deployable-pom</artifactId>
-        <version>5.1.0</version>
+        <version>5.4.0</version>
     </parent>
 
     <!--
@@ -18,7 +18,7 @@
     <packaging>pom</packaging>
 
     <properties>
-        <hapi_fhir_version>5.1.0</hapi_fhir_version>
+        <hapi_fhir_version>5.4.0</hapi_fhir_version>
         <validator_test_case_version>1.1.88</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>

From e547bb749bb2b578a4ece67c204d1797dbd999d5 Mon Sep 17 00:00:00 2001
From: Grahame Grieve <grahameg@gmail.com>
Date: Thu, 10 Feb 2022 11:17:49 +1100
Subject: [PATCH 2/7] fix OID validation

---
 .../main/java/org/hl7/fhir/utilities/Utilities.java   |  5 +----
 .../src/main/resources/Messages.properties            |  4 ++--
 .../fhir/validation/instance/InstanceValidator.java   |  4 +++-
 ....0_CodeSystem_medcom-messaging-activityCodes.cache | 11 +++++++++++
 4 files changed, 17 insertions(+), 7 deletions(-)
 create mode 100644 org.hl7.fhir.validation/src/test/resources/txCache/4.0.1/http___medcomfhir.dk_fhir_core_1.0_CodeSystem_medcom-messaging-activityCodes.cache

diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
index db22d051a..6f6666817 100644
--- a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
+++ b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
@@ -995,7 +995,6 @@ public class Utilities {
     return s.substring(0, 1).toLowerCase() + s.substring(1);
   }
 
-
   public static int charCount(String s, char c) {
     int res = 0;
     for (char ch : s.toCharArray())
@@ -1004,12 +1003,10 @@ public class Utilities {
     return res;
   }
 
-
   public static boolean isOid(String cc) {
-    return cc.matches(OID_REGEX) && cc.lastIndexOf('.') >= 5;
+    return cc.matches(OID_REGEX);
   }
 
-
   public static boolean equals(String one, String two) {
     if (one == null && two == null)
       return true;
diff --git a/org.hl7.fhir.utilities/src/main/resources/Messages.properties b/org.hl7.fhir.utilities/src/main/resources/Messages.properties
index f8b8cd4c7..222fdb7ce 100644
--- a/org.hl7.fhir.utilities/src/main/resources/Messages.properties
+++ b/org.hl7.fhir.utilities/src/main/resources/Messages.properties
@@ -199,7 +199,7 @@ Type_Specific_Checks_DT_Integer_LT0 = value is less than permitted minimum value
 Type_Specific_Checks_DT_Integer_LT1 = value is less than permitted minimum value of 1
 Type_Specific_Checks_DT_Integer_Valid = The value ''{0}'' is not a valid integer
 Type_Specific_Checks_DT_OID_Start = OIDs must start with urn:oid:
-Type_Specific_Checks_DT_OID_Valid = OIDs must be valid
+Type_Specific_Checks_DT_OID_Valid = OIDs must be valid ({0})
 Type_Specific_Checks_DT_Primitive_Length = value is longer than permitted maximum length of {0}
 Type_Specific_Checks_DT_Primitive_NotEmpty = @value cannot be empty
 Type_Specific_Checks_DT_Primitive_Regex = Element value ''{0}'' does not meet regex ''{1}''
@@ -643,7 +643,7 @@ SD_ED_SHOULD_BIND_WITH_VS = The element {0} has a type that should have a bindin
 SD_ED_BIND_UNKNOWN_VS = The valueSet reference {1} on element {0} could not be resolved
 SD_ED_BIND_NOT_VS = The valueSet reference {1} on element {0} points to something that is not a value set ({2}) 
 SD_ED_BIND_NO_BINDABLE = The element {0} has a binding, but no bindable types are present {1}
-SD_ED_BIND_MULTIPLE_TYPES = The element {0} has a binding, and has multiple types ({1}). The binding will apply to all the types
+SD_ED_BIND_MULTIPLE_TYPES = The element {0} has a binding, and has multiple types subject to bindings ({1}). The binding will apply to all the types
 DISCRIMINATOR_BAD_PATH = Error processing path expression for discriminator: {0} (src = ''{1}'')
 SLICING_CANNOT_BE_EVALUATED = Slicing cannot be evaluated: {0}
 TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE = Canonical URL ''{0}'' does not resolve
diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
index 8101d65cf..4d366ec83 100644
--- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
+++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
@@ -2109,7 +2109,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isValidUUID(url.substring(9)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_UUID_VALID);
       }
       if (url != null && url.startsWith("urn:oid:")) {
-        rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isOid(url.substring(8)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_OID_VALID);
+        String cc = url.substring(8);
+        // OIDs shorter than 5 chars are almost never valid for namespaces, except for the special OID 1.3.88
+        rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isOid(cc) && (cc.lastIndexOf('.') >= 5 || "1.3.88".equals(cc)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_OID_VALID, cc);
       }
 
       if (isCanonicalURLElement(e)) {
diff --git a/org.hl7.fhir.validation/src/test/resources/txCache/4.0.1/http___medcomfhir.dk_fhir_core_1.0_CodeSystem_medcom-messaging-activityCodes.cache b/org.hl7.fhir.validation/src/test/resources/txCache/4.0.1/http___medcomfhir.dk_fhir_core_1.0_CodeSystem_medcom-messaging-activityCodes.cache
new file mode 100644
index 000000000..ffbfe7675
--- /dev/null
+++ b/org.hl7.fhir.validation/src/test/resources/txCache/4.0.1/http___medcomfhir.dk_fhir_core_1.0_CodeSystem_medcom-messaging-activityCodes.cache
@@ -0,0 +1,11 @@
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://medcomfhir.dk/fhir/core/1.0/CodeSystem/medcom-messaging-activityCodes",
+  "code" : "new-message"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
+v: {
+  "severity" : "error",
+  "error" : "The code system 'http://medcomfhir.dk/fhir/core/1.0/CodeSystem/medcom-messaging-activityCodes' is not known (encountered paired with code = 'new-message'); The code provided (http://medcomfhir.dk/fhir/core/1.0/CodeSystem/medcom-messaging-activityCodes#new-message) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4)",
+  "class" : "CODESYSTEM_UNSUPPORTED"
+}
+-------------------------------------------------------------------------------------

From 60cd37eca60e53f3f7e8614b55339dbe428a0b51 Mon Sep 17 00:00:00 2001
From: Grahame Grieve <grahameg@gmail.com>
Date: Thu, 10 Feb 2022 11:18:51 +1100
Subject: [PATCH 3/7] fix semver version for -tag tags

---
 .../main/java/org/hl7/fhir/utilities/VersionUtilities.java | 3 +++
 .../java/org/hl7/fhir/utilities/VersionUtilitiesTest.java  | 7 +++++++
 2 files changed, 10 insertions(+)

diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
index 80042df27..07bc9db92 100644
--- a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
+++ b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
@@ -231,6 +231,9 @@ public class VersionUtilities {
       return false;
     }
     String[] p = version.split("\\.");
+    if (p[2].contains("-")) {
+      p[2] = p[2].substring(0, p[2].indexOf("-"));
+    }
     return Utilities.isInteger(p[0]) && Utilities.isInteger(p[1]) && Utilities.isInteger(p[2]);
   }
 
diff --git a/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/VersionUtilitiesTest.java b/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/VersionUtilitiesTest.java
index 1e8b68694..2ed5cab5b 100644
--- a/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/VersionUtilitiesTest.java
+++ b/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/VersionUtilitiesTest.java
@@ -6,6 +6,13 @@ import static org.junit.jupiter.api.Assertions.*;
 
 public class VersionUtilitiesTest {
 
+  @Test
+  public void isValidSemVer() {
+    assertTrue(VersionUtilities.isSemVer("0.1.1"));
+    assertTrue(VersionUtilities.isSemVer("0.1.1-ballot1"));
+    assertFalse(VersionUtilities.isSemVer("0.1.a"));
+  }
+
   @Test
   public void isThisOrLater_Simple() {
     assertTrue(VersionUtilities.isThisOrLater("0.1", "0.2"));

From dadda110d2664e1768d8f649190a6ea5addac6c2 Mon Sep 17 00:00:00 2001
From: Grahame Grieve <grahameg@gmail.com>
Date: Thu, 10 Feb 2022 11:19:52 +1100
Subject: [PATCH 4/7] fix validation of bindings on choice types - only
 consider bindable types

---
 .../type/StructureDefinitionValidator.java        | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
index 8e9b7eced..b623469f9 100644
--- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
+++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
@@ -211,7 +211,10 @@ public class StructureDefinitionValidator extends BaseValidator {
 
   private void validateBinding(List<ValidationMessage> errors, Element binding, NodeStack stack, Set<String> typeCodes, boolean snapshot, String path) {
     rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !snapshot || bindableType(typeCodes) != null, I18nConstants.SD_ED_BIND_NO_BINDABLE, path, typeCodes.toString());
-    hint(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), typeCodes.size() <= 1, I18nConstants.SD_ED_BIND_MULTIPLE_TYPES, path, typeCodes.toString());
+    if (!snapshot) {
+      Set<String> bindables = getListofBindableTypes(typeCodes);    
+      hint(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), bindables.size() <= 1, I18nConstants.SD_ED_BIND_MULTIPLE_TYPES, path, typeCodes.toString());
+    }
     
     if (binding.hasChild("valueSet")) {
       Element valueSet = binding.getNamedChild("valueSet");
@@ -230,6 +233,16 @@ public class StructureDefinitionValidator extends BaseValidator {
     } 
   }
 
+  private Set<String> getListofBindableTypes(Set<String> types) {
+    Set<String> res = new HashSet<>();
+    for (String s : types) {
+      if (Utilities.existsInList(s, "code", "string", "url", "uri", "Coding", "CodeableConcept", "Quantity", "CodeableReference")) {
+        res.add(s);
+      }
+    }
+    return res;
+  }
+
   private boolean serverSupportsValueSet(String ref) {
     ValidationResult vr = context.validateCode(new ValidationOptions().checkValueSetOnly().setVsAsUrl().noClient(), new Coding("http://loinc.org", "5792-7", null), new ValueSet().setUrl(ref));
     return vr.getErrorClass() == null;

From f6d3139461b5b35ea464f842fd5cb5bfcd0c2211 Mon Sep 17 00:00:00 2001
From: dotasek <david.otasek@smilecdr.com>
Date: Thu, 10 Feb 2022 13:44:54 -0500
Subject: [PATCH 5/7] Clean up duplicate entries for httpclient in pom.xml

---
 org.hl7.fhir.dstu3/pom.xml | 5 -----
 org.hl7.fhir.r4/pom.xml    | 7 -------
 org.hl7.fhir.r4b/pom.xml   | 5 -----
 3 files changed, 17 deletions(-)

diff --git a/org.hl7.fhir.dstu3/pom.xml b/org.hl7.fhir.dstu3/pom.xml
index a06aebe48..c373763cf 100644
--- a/org.hl7.fhir.dstu3/pom.xml
+++ b/org.hl7.fhir.dstu3/pom.xml
@@ -52,11 +52,6 @@
         </dependency>
 
         <!-- HTTP Client -->
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpclient</artifactId>
-            <optional>true</optional>
-        </dependency>
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
diff --git a/org.hl7.fhir.r4/pom.xml b/org.hl7.fhir.r4/pom.xml
index 781bafa2d..3e2e58c83 100644
--- a/org.hl7.fhir.r4/pom.xml
+++ b/org.hl7.fhir.r4/pom.xml
@@ -104,13 +104,6 @@
 			<optional>true</optional>
 		</dependency>
 
-		<!-- HTTP Client -->
-		<dependency>
-			<groupId>org.apache.httpcomponents</groupId>
-			<artifactId>httpclient</artifactId>
-			<optional>true</optional>
-		</dependency>
-
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
diff --git a/org.hl7.fhir.r4b/pom.xml b/org.hl7.fhir.r4b/pom.xml
index a9373f2fb..e83fd328a 100644
--- a/org.hl7.fhir.r4b/pom.xml
+++ b/org.hl7.fhir.r4b/pom.xml
@@ -58,11 +58,6 @@
 		</dependency>
 
 		<!-- HTTP Client -->
-		<dependency>
-			<groupId>org.apache.httpcomponents</groupId>
-			<artifactId>httpclient</artifactId>
-			<optional>true</optional>
-		</dependency>
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>

From 1905035d7b2880a61174174da032001e80a165c3 Mon Sep 17 00:00:00 2001
From: dotasek <david.otasek@smilecdr.com>
Date: Thu, 10 Feb 2022 13:45:45 -0500
Subject: [PATCH 6/7] Move bytebuddy to managed dependency

---
 org.hl7.fhir.validation/pom.xml | 19 ++++++-------------
 pom.xml                         |  7 +++++++
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/org.hl7.fhir.validation/pom.xml b/org.hl7.fhir.validation/pom.xml
index c200b03b1..9f12a881b 100644
--- a/org.hl7.fhir.validation/pom.xml
+++ b/org.hl7.fhir.validation/pom.xml
@@ -217,14 +217,12 @@
             <version>${junit_jupiter_version}</version>
             <scope>test</scope>
         </dependency>
-
-<dependency>
-    <groupId>net.bytebuddy</groupId>
-    <artifactId>byte-buddy</artifactId>
-    <version>1.10.21</version>
-	<scope>test</scope>
-</dependency>
-
+        <dependency>
+            <groupId>net.bytebuddy</groupId>
+            <artifactId>byte-buddy</artifactId>
+            <optional>true</optional>
+            <scope>test</scope>
+        </dependency>
         <!-- End to end -->
         <dependency>
             <groupId>org.seleniumhq.selenium</groupId>
@@ -252,11 +250,6 @@
                 <goals>
                     <goal>test</goal>
                 </goals>
-                <configuration>
-                    <excludes combine.children="override">
-                        <exclude>org/hl7/fhir/validation/cli/services/ValidationServiceTest.java</exclude>
-                    </excludes>
-                </configuration>
                 </execution>
                 </executions>
             </plugin>
diff --git a/pom.xml b/pom.xml
index acdfffdd6..ffb18644c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -27,6 +27,7 @@
         <jacoco_version>0.8.7</jacoco_version>
         <info_cqframework_version>1.5.1</info_cqframework_version>
         <lombok_version>1.18.22</lombok_version>
+        <byte_buddy_version>1.10.21</byte_buddy_version>
     </properties>
 
     <name>HL7 Core Artifacts</name>
@@ -139,6 +140,12 @@
                 <version>${junit_jupiter_version}</version>
                 <scope>test</scope>
             </dependency>
+            <dependency>
+                <groupId>net.bytebuddy</groupId>
+                <artifactId>byte-buddy</artifactId>
+                <version>${byte_buddy_version}</version>
+                <scope>test</scope>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

From 37c1e7e72002d8cacdc7fbfec24fd171c02489d4 Mon Sep 17 00:00:00 2001
From: dotasek <david.otasek@smilecdr.com>
Date: Thu, 10 Feb 2022 13:48:00 -0500
Subject: [PATCH 7/7] Fix validation.cli jar build

Removes any signature files that could cause the module to become invalid

Also bumps exec-maven plugin
---
 org.hl7.fhir.validation.cli/pom.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/org.hl7.fhir.validation.cli/pom.xml b/org.hl7.fhir.validation.cli/pom.xml
index 437e5ed46..85e5a66fc 100644
--- a/org.hl7.fhir.validation.cli/pom.xml
+++ b/org.hl7.fhir.validation.cli/pom.xml
@@ -76,7 +76,7 @@
                             <goal>unpack-dependencies</goal>
                         </goals>
                         <configuration>
-                            <excludes>**/module-info.class</excludes>
+                            <excludes>**/module-info.class,META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</excludes>
                             <outputDirectory>${project.build.directory}/classes</outputDirectory>
                             <overWriteReleases>false</overWriteReleases>
                             <overWriteSnapshots>true</overWriteSnapshots>
@@ -121,7 +121,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
-                <version>1.2.1</version>
+                <version>1.6.0</version>
                 <executions>
                     <execution>
                         <id>default-cli</id>
@@ -134,7 +134,7 @@
                             <workingDirectory>/tmp</workingDirectory>
                             <arguments>
                                 <argument>-jar</argument>
-                                <argument>${basedir}/target/org.hl7.fhir.validation.cli-${project.version}.jar</argument>
+                                <argument>${project.basedir}/target/org.hl7.fhir.validation.cli-${project.version}.jar</argument>
                             </arguments>
                         </configuration>
                     </execution>