Merge branch 'release/0.13.0'

.gitignore

@@ -187,10 +187,6 @@ std*
 
 ### VisualStudioCode ###
 .vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
 
 ### VisualStudioCode Patch ###
 # Ignore all local history of files

CHANGELOG.md

@@ -9,11 +9,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-
 ### Changed
 
+### Fixed
+
+## [0.13.0] (beta)
+
+### Added
+- added support for various functions in AQL (aggregation, statistical, string etc.) (see: https://github.com/ehrbase/ehrbase/pull/223/)
+
+### Changed
+- Update of AQL-Query test suite (see: https://github.com/ehrbase/ehrbase/pull/179)
 
 ### Fixed
+- Added validation checking for other_details and ehr_status. (see: https://github.com/ehrbase/ehrbase/pull/207)
+- Supports archetype_node_id and name for EHR_STATUS (see: https://github.com/ehrbase/ehrbase/pull/207)
+- fixes bad canonical encoding for observation/data/origin (see: https://github.com/ehrbase/ehrbase/pull/213)
+- POST without accept header for ehr, composition and contribution endpoints (see: https://github.com/ehrbase/ehrbase/pull/199)
+- force a default timezone if not present for context/start_time and context/end_time if specified (https://github.com/ehrbase/ehrbase/pull/215)
+- Representation of version uid of EHR_STATUS (see: https://github.com/ehrbase/ehrbase/pull/180)
 
 
 ## [0.12.0] (alpha)
@@ -25,8 +39,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Contribution endpoint checks for some invalid input combinations (see: https://github.com/ehrbase/ehrbase/pull/202)
 - Fixes response code on /ehr PUT with invalid ID (see: https://github.com/ehrbase/project_management/issues/163)
 - Fixes STATUS w/ empty subject bug (see: https://github.com/ehrbase/ehrbase/pull/196)
+- Now querying on composition category returns the correct result (composition/category...)
 - Fixes storage of party self inside compositions (see: https://github.com/ehrbase/ehrbase/pull/195)
 - Added support of AQL query in the form of c/composer (see: https://github.com/ehrbase/ehrbase/pull/184)
 - Java error with UTF-8 encoding resolved (see: https://github.com/ehrbase/ehrbase/pull/173)
@@ -74,6 +90,7 @@ Starting with the next release this file will provide a proper overview.
 - Correct resolution of ehr/system_id in AQL (see: https://github.com/ehrbase/ehrbase/pull/102)
 - Detection of duplicate aliases in aql select (see: https://github.com/ehrbase/ehrbase/pull/98)
 
+
 ## [0.10.0] (alpha)
 
 ### Added
@@ -114,7 +131,9 @@ Starting with the next release this file will provide a proper overview.
 - Fixed error regarding DISTINCT operator in AQL (https://github.com/ehrbase/ehrbase/issues/50)
 - Fixed null pointer exceptions that could occur in persistent compositions
 
-[unreleased]: https://github.com/ehrbase/ehrbase/compare/v0.10.0...HEAD
+[unreleased]: https://github.com/ehrbase/ehrbase/compare/v0.13.0...HEAD
+[0.13.0]: https://github.com/ehrbase/ehrbase/compare/v0.12.0...v0.13.0
+[0.12.0]: https://github.com/ehrbase/ehrbase/compare/v0.11.0...v0.12.0
 [0.11.0]: https://github.com/ehrbase/ehrbase/compare/v0.10.0...v0.11.0
 [0.10.0]: https://github.com/ehrbase/ehrbase/compare/v0.9.0...v0.10.0
 [0.9.0]: https://github.com/ehrbase/ehrbase/releases/tag/v0.9.0

README.md

@@ -3,8 +3,8 @@
 EHRbase is an [openEHR](openehr.org) Clinical Data Repository, providing a standard-based backend for interoperable clinical applications. It implements the latest version of the openEHR Reference Model (RM 1.0.4) and version 1.4 of the Archetype Definition Language (ADL). Applications can use the capabilities of EHRbase through the latest version of the [openEHR REST API](https://specifications.openehr.org/releases/ITS-REST/latest/) and model-based queries using the [Archetype Query Language](https://specifications.openehr.org/releases/QUERY/latest/AQL.html).
 
 ## Release Notes
-##### 2020, March 31
-This release of EHRbase (v0.12.0) adds basic authentication (see details below) and allows to overwrite templates. Besides, there are lots of bug fixes. Please see [EHRbase Documentation](https://ehrbase.readthedocs.io/en/latest/01_release_notes/0120.html) for further details.
+##### 2020, May 14
+This release of EHRbase (v0.13.0) is the first **beta** release. Please see [EHRbase Documentation](https://ehrbase.readthedocs.io/en/latest/) for further details.
 
 
 ## Getting Started

api/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

api/src/main/java/org/ehrbase/api/dto/QueryResultDto.java

@@ -18,16 +18,14 @@
 
 package org.ehrbase.api.dto;
 
-import com.google.common.collect.BiMap;
-import org.apache.commons.collections.BidiMap;
-
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
 public class QueryResultDto {
     private String executedAQL;
     private List<List<String>> explain;
-    private BiMap<String, String> variables;
+    private Map<String, String> variables;
     private List<Map<String, Object>> resultSet;
 
     public List<Map<String, Object>> getResultSet() {
@@ -54,11 +52,27 @@ public void setExplain(List<List<String>> explain) {
         this.explain = explain;
     }
 
-    public BiMap<String, String> getVariables() {
+    public Map<String, String> getVariables() {
         return variables;
     }
 
-    public void setVariables(BiMap<String, String> variables) {
+    public void setVariables(Map<String, String> variables) {
         this.variables = variables;
     }
+
+    public boolean variablesIsEmpty() {
+        return variables.size() == 0;
+    }
+
+    public boolean variablesContainsColumnId(String columnId){
+        return getVariables().containsKey(columnId);
+    }
+
+    public String variablesPath(String columnId){
+        return getVariables().get(columnId);
+    }
+
+    public Iterator<Map.Entry<String, String>> variablesIterator(){
+        return variables.entrySet().iterator();
+    }
 }

api/src/main/java/org/ehrbase/api/service/ValidationService.java

@@ -19,6 +19,7 @@
 package org.ehrbase.api.service;
 
 import com.nedap.archie.rm.composition.Composition;
+import com.nedap.archie.rm.ehr.EhrStatus;
 
 import java.util.UUID;
 
@@ -56,6 +57,14 @@ public interface ValidationService {
      */
     void check(Composition composition) throws Exception;
 
+    /**
+     * initially check if ehrstatus is valid for further processing
+     * @param ehrStatus
+     * @throws IllegalArgumentException
+     */
+    void check(EhrStatus ehrStatus);
+
+
     /**
      * Remove all mappings in the cache
      */

application/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

base/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

base/src/main/resources/db/migration/V21__ehr_status_name_archetype_node_id.sql

@@ -0,0 +1,46 @@
+-- Add support for attribute name and archetype_node_id in ehr_status
+
+-- modify table ehr.status to add the missing attributes
+
+ALTER TABLE ehr.status
+  ADD COLUMN archetype_node_id TEXT NOT NULL DEFAULT 'openEHR-EHR-EHR_STATUS.generic.v1',
+  ADD COLUMN name ehr.dv_coded_text NOT NULL DEFAULT ('EHR Status',NULL,NULL,NULL,NULL)::ehr.dv_coded_text ;
+
+-- modify function to return ehr_status canonical json to support the new attributes
+CREATE OR REPLACE FUNCTION ehr.js_ehr_status(UUID)
+  RETURNS JSON AS
+$$
+DECLARE
+  ehr_uuid ALIAS FOR $1;
+BEGIN
+  RETURN (
+    WITH ehr_status_data AS (
+      SELECT
+        status.other_details as other_details,
+        status.party as subject,
+        status.is_queryable as is_queryable,
+        status.is_modifiable as is_modifiable,
+        status.sys_transaction as time_created,
+        status.name as status_name,
+        status.archetype_node_id as archetype_node_id
+      FROM ehr.status
+      WHERE status.ehr_id = ehr_uuid
+      LIMIT 1
+    )
+    SELECT
+      jsonb_strip_nulls(
+          jsonb_build_object(
+              '_type', 'EHR_STATUS',
+              'archetype_node_id', archetype_node_id,
+              'name', status_name,
+              'subject', ehr.js_party(subject),
+              'is_queryable', is_queryable,
+              'is_modifiable', is_modifiable,
+              'other_details', other_details
+            )
+        )
+    FROM ehr_status_data
+  );
+END
+$$
+  LANGUAGE plpgsql;

base/src/main/resources/db/migration/V22__js_concept.sql

@@ -0,0 +1,20 @@
+-- concept as json
+CREATE OR REPLACE FUNCTION ehr.js_concept(UUID)
+  RETURNS JSON AS
+$$
+DECLARE
+  concept_id ALIAS FOR $1;
+BEGIN
+
+  IF (concept_id IS NULL) THEN
+    RETURN NULL;
+  END IF;
+
+  RETURN (
+    SELECT ehr.js_dv_coded_text(description, ehr.js_code_phrase(conceptid :: TEXT, 'openehr'))
+    FROM ehr.concept
+    WHERE id = concept_id AND language = 'en'
+  );
+END
+$$
+  LANGUAGE plpgsql;

base/src/main/resources/db/migration/V23__ehr_status_history_fix.sql

@@ -0,0 +1,3 @@
+ALTER TABLE ehr.status_history
+  ADD COLUMN archetype_node_id TEXT NOT NULL DEFAULT 'openEHR-EHR-EHR_STATUS.generic.v1',
+  ADD COLUMN name ehr.dv_coded_text NOT NULL DEFAULT ('EHR Status',NULL,NULL,NULL,NULL)::ehr.dv_coded_text;

base/src/main/resources/db/migration/V24__typed_element_value.sql

@@ -0,0 +1,53 @@
+-- convert to lower snake case
+CREATE OR REPLACE FUNCTION ehr.camel_to_snake(literal TEXT)
+  RETURNS TEXT AS
+$$
+DECLARE
+  out_literal TEXT := '';
+  literal_size INT;
+  char_at TEXT;
+  ndx INT;
+BEGIN
+  literal_size := length(literal);
+  if (literal_size = 0) then
+    return literal;
+  end if;
+  ndx = 1;
+  while ndx <= literal_size loop
+    char_at := substr(literal, ndx , 1);
+    if (char_at ~ '[A-Z]') then
+      if (ndx > 1 AND substr(literal, ndx - 1, 1) <> '<') then
+        out_literal = out_literal || '_';
+      end if;
+      out_literal = out_literal || lower(char_at);
+    else
+      out_literal = out_literal || char_at;
+    end if;
+    ndx := ndx + 1;
+  end loop;
+  out_literal := replace(replace(replace(out_literal, 'u_r_i', 'uri'), 'i_d', 'id'), 'i_s_m', 'ism');
+  return out_literal;
+END
+$$
+  LANGUAGE plpgsql;
+
+-- add the _type into an element value block
+CREATE OR REPLACE FUNCTION ehr.js_typed_element_value(JSONB)
+  RETURNS JSONB AS
+$$
+DECLARE
+  element_value ALIAS FOR $1;
+BEGIN
+  RETURN (
+    SELECT
+      jsonb_strip_nulls(
+            (element_value #>>'{/value}')::jsonb ||
+            jsonb_build_object(
+                '_type',
+                upper(ehr.camel_to_snake(element_value #>>'{/$CLASS$}'))
+              )
+        )
+  );
+END
+$$
+  LANGUAGE plpgsql;

jooq-pq/pom.xml

@@ -21,7 +21,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

opt/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

pom.xml

@@ -20,7 +20,7 @@
     <packaging>pom</packaging>
     <groupId>org.ehrbase.openehr</groupId>
     <artifactId>server</artifactId>
-    <version>0.12.0</version>
+    <version>0.13.0</version>
 
     <name>${project.groupId}:${project.artifactId}</name>
     <description>EHRbase is a Free, Libre, Open Source openEHR Clinical Data Repository</description>

rest-ehr-scape/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

rest-openehr/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <artifactId>server</artifactId>
         <groupId>org.ehrbase.openehr</groupId>
-        <version>0.12.0</version>
+        <version>0.13.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>