Issue 5173 get gateway everything doesnt return all patients

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/UriParamQualifierEnum.java

@@ -48,7 +48,16 @@ public enum UriParamQualifierEnum {
  * Value <code>:below</code>
  * </p>
  */
- BELOW(":below");
+ BELOW(":below"),
+
+ /**
+ * The contains modifier allows clients to indicate that a supplied URI input should be matched
+ * as a case-insensitive and combining-character insensitive match anywhere in the target URI.
+ * <p>
+ * Value <code>:contains</code>
+ * </p>
+ */
+ CONTAINS(":contains");
 
  private static final Map<String, UriParamQualifierEnum> KEY_TO_VALUE;
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlPathTokenizer.java

@@ -19,18 +19,45 @@
  */
 package ca.uhn.fhir.util;
 
-import java.util.StringTokenizer;
+import ca.uhn.fhir.i18n.Msg;
+import org.apache.commons.lang3.ArrayUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class UrlPathTokenizer {
 
- private final StringTokenizer myTok;
+ private String[] tokens;
+ private int curPos;
 
  public UrlPathTokenizer(String theRequestPath) {
- myTok = new StringTokenizer(theRequestPath, "/");
+ if (theRequestPath == null) {
+ theRequestPath = "";
+ }
+ tokens = removeBlanksAndSanitize(theRequestPath.split("/"));
+ curPos = 0;
  }
 
  public boolean hasMoreTokens() {
- return myTok.hasMoreTokens();
+ return curPos < tokens.length;
+ }
+
+ public int countTokens() {
+ return tokens.length;
+ }
+
+ /**
+ * Returns the next token without updating the current position.
+ * Will throw NoSuchElementException if there are no more tokens.
+ */
+ public String peek() {
+ if (!hasMoreTokens()) {
+ throw new NoSuchElementException(Msg.code(2420) + "Attempt to retrieve URL token out of bounds");
+ }
+ return tokens[curPos];
  }
 
  /**
@@ -43,6 +70,22 @@ public boolean hasMoreTokens() {
  * @see UrlUtil#unescape(String)
  */
  public String nextTokenUnescapedAndSanitized() {
- return UrlUtil.sanitizeUrlPart(UrlUtil.unescape(myTok.nextToken()));
+ String token = peek();
+ curPos++;
+ return token;
+ }
+
+ /**
+ * Given an array of Strings, this method will return all the non-blank entries in that
+ * array, after running sanitizeUrlPart() and unescape() on them.
+ */
+ private static String[] removeBlanksAndSanitize(String[] theInput) {
+ List<String> output = new ArrayList<>();
+ for (String s : theInput) {
+ if (!isBlank(s)) {
+ output.add(UrlUtil.sanitizeUrlPart(UrlUtil.unescape(s)));
+ }
+ }
+ return output.toArray(ArrayUtils.EMPTY_STRING_ARRAY);
  }
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java

@@ -40,6 +40,8 @@
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.URLDecoder;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -602,6 +604,39 @@ public static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
  return parameters;
  }
 
+ /**
+ * Creates list of sub URIs candidates for search with :above modifier
+ * Example input: https://[host]/[pathPart1]/[pathPart2]
+ * Example output: https://[host], https://[host]/[pathPart1], https://[host]/[pathPart1]/[pathPart2]
+ *
+ * @param theUri String URI parameter
+ * @return List of URI candidates
+ */
+ public static List<String> getAboveUriCandidates(String theUri) {
+ try {
+ URI uri = new URI(theUri);
+ if (uri.getScheme() == null || uri.getHost() == null) {
+ throwInvalidRequestExceptionForNotValidUri(theUri, null);
+ }
+ } catch (URISyntaxException theCause) {
+ throwInvalidRequestExceptionForNotValidUri(theUri, theCause);
+ }
+
+ List<String> candidates = new ArrayList<>();
+ Path path = Paths.get(theUri);
+ candidates.add(path.toString().replace(":/", ":https://"));
+ while (path.getParent() != null && path.getParent().toString().contains("/")) {
+ candidates.add(path.getParent().toString().replace(":/", ":https://"));
+ path = path.getParent();
+ }
+ return candidates;
+ }
+
+ private static void throwInvalidRequestExceptionForNotValidUri(String theUri, Exception theCause) {
+ throw new InvalidRequestException(
+ Msg.code(2419) + String.format("Provided URI is not valid: %s", theUri), theCause);
+ }
+
  public static class UrlParts {
  private String myParams;
  private String myResourceId;

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>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

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>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

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>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.15-SNAPSHOT</version>
+ <version>6.8.0-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5095-add-support-for-source-search-parameter-modifiers.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 5095
+title: "Added support for :above, :below, :contains and :missing _source search parameter modifiers."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5117-fix-no-match-mdm-score-included-in-total-score.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5117
+title: "Previously, all MDM field scores, including `NO_MATCH`es, were included in the final total MDM score. This has 
+now been fixed so that only `MATCH`ed fields are included in the total MDM score."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5119-consent-removing-all-resources-suppresses-next-link-in-bundle.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5119
+jira: SMILE-7090
+title: "Previously, when the consent service would remove all resources to be returned, the response bundle would
+ not provide the previous/next link(s). This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5126-hfj_res_ver_prov-might-cause-migration-error-on-db-that-automatically-indexes-the-primary-key.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5126
+title: "Previously, updating from Hapi-fhir 6.6.0 to 6.8.0 would cause migration error, it is now fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5150--delete-expunge-over-10k-resources-deletes-only-10k.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5150
+title: "When running a $delete-expunge with over 10,000 resources, only the first 10,000 resources were deleted.
+ This is now fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5155-expunge-operation-on-codesystem-may-return-500.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5155
+title: "Previously, requesting an $expunge operation on CodeSystem resources while CS batch deletion is underway would return HTTP 500.
+ This has been fixed to return HTTP 412 (precondition failed)."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5158-add-support-for-subscription-matching-of-source-search-parameter-modifiers.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 5158
+title: "Added support for Subscription matching of ':above', ':below', ':contains' and ':missing' '_source' search parameter modifiers."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5167-fix-jdbc-deps.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5167
+title: "Fixed a dependency in the HSQL JDBC driver referencing a non-bundled class (javax.ServletOutputStream)"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5173-gateway-everything-doesnt-return-all-patients.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5173
+title: "Fix gateway `$everything` operation to respect server configured default and maximum page sizes."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5182-fix-removing-tags-does-not-trigger-subscription.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5182
+jira: SMILE-6857
+title: "Previously, removing tags in a resource update with proper headers and versioning flag would not trigger a 
+new subscription. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5183-us-core-ig-ingestion-fails-value-set-version-id-conflict.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5183
+title: "The latest US Core IG includes two ValueSets with different contents, but the same FHIR Id and OID via two different included IGs (i.e. `2.16.840.1.113762.1.4.1010.9` via us.cdc.phinvads and us.nlm.vsac). Ingesting these duplicates in US Core failed with a 500 error. This has been resolved by logging the error and allowing the rest of the ingestion to proceed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/hfql/hfql.md

@@ -14,8 +14,8 @@ A simple example query is shown below:
 
 ```sql
 SELECT
- name.family as family, 
- name.given as given, 
+ name[0].family as family, 
+ name[0].given[0] as given, 
  birthDate,
  identifier.where(system='https://hl7.org/fhir/sid/us-ssn').value as SSN
 FROM

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_details.md

@@ -22,10 +22,7 @@ Below are some simplifying principles HAPI MDM follows to reduce complexity and
 
 1. The only source resources in the system that do not have a MATCH link are those that have the 'NO-MDM' tag or those that have POSSIBLE_MATCH links pending review.
 
-1. The HAPI MDM rules define a single identifier system that holds the external enterprise id ("EID"). If a source resource has an external EID, then the Golden Resource it links to always has the same EID. If a source resource has no EID when it arrives, a unique UUID will be assigned as that source resource's EID.
-
-1. A Golden Resource can have both an internal EID (auto-created by HAPI), and an external EID (provided by an 
-external system).
+1. The HAPI MDM rules define a single identifier system that holds the external enterprise id ("EID"). If a source resource has an external EID, then the Golden Resource it links to always has the same EID.
 
 1. Two different Golden Resources cannot have the same EID.
 
@@ -85,7 +82,7 @@ possible that hundreds of John Doe's could be linked to the same Golden Resource
 
 When a new source resource is compared with all other resources of the same type in the repository, there are four possible outcomes:
 
-* CASE 1: No MATCH and no POSSIBLE_MATCH outcomes -> a new Golden Resource is created and linked to that source resource as MATCH. If the incoming resource has an EID, it is copied to the Golden Resource. Otherwise a new UUID is generated and used as the internal EID.
+* CASE 1: No MATCH and no POSSIBLE_MATCH outcomes -> a new Golden Resource is created and linked to that source resource as MATCH. If the incoming resource has an EID, it is copied to the Golden Resource.
 
 * CASE 2: All of the MATCH source resources are already linked to the same Golden Resource -> a new Link is created between the new source resource and that Golden Resource and is set to MATCH.
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_eid.md

@@ -1,8 +1,9 @@
 # MDM Enterprise Identifiers
 
-An Enterprise Identifier (EID) is a unique identifier that can be attached to source resources. Each implementation is expected to use exactly one EID system for incoming resources, defined in the MDM Rules file. If a source resource with a valid EID is submitted, that EID will be copied over to the Golden Resource that was matched. In the case that the incoming source resource had no EID assigned, an internal EID will be created for it. There are thus two classes of EID:
- * Internal EIDs, created by HAPI-MDM, and 
- * External EIDs, provided by the submitted resources.
+An Enterprise Identifier (EID) is a unique identifier that can be attached to source resources.
+Each implementation is expected to use exactly one EID system for incoming resources,
+defined in the MDM Rules file.
+If a source resource with a valid EID is submitted, that EID will be copied over to the Golden Resource that was matched.
 
 ## MDM EID Settings