fix composition instance check in step, add scenario for select instr…

…uction

vehr-integration-tests/src/test/java/com/ethercis/vehr/AqlFeaturesSteps.java

@@ -1,7 +1,9 @@
 package com.ethercis.vehr;
 
+import com.jayway.restassured.path.json.JsonPath;
 import com.jayway.restassured.response.Response;
 import cucumber.api.DataTable;
+import cucumber.api.PendingException;
 import cucumber.api.java.en.And;
 import cucumber.api.java.en.Then;
 import cucumber.api.java.en.When;
@@ -25,6 +27,7 @@
 import static org.junit.Assert.*;
 
 public class AqlFeaturesSteps {
+    private final String SELECT_COMPLETE_INSTRUCTION_AQL = "select_complete_instruction.aql";
     private final String ARCHETYPE_NODE_ID_AND_NAME_PATTERN = "\\[at\\d{4} *, *\\'[\\w\\s]*\\'\\]";
     private final String SELECT_COMPLETE_COMPOSITION_AQL = "select_complete_composition.aql";
     private final String SELECT_DATA_ITEM_NODE_ID_NAME_AQL = "select_data_item_node_id_and_name.aql";
@@ -175,19 +178,43 @@ public void dataItemsWithSameNodeIdShouldHaveDifferentValuesIfTheyHaveDifferentN
     public void aAnAQLQueryThatDescribesAnCompositionUnderAnEHRIsCreated() throws Throwable {
         String fullFilepath = bg.resourcesRootPath + CODE4HEALTH_QUERY_DIR + SELECT_COMPLETE_COMPOSITION_AQL;
         _aqlQuery = readFile(fullFilepath);
-        //set ehr id
-        theQueryContainsEHRIdCriteria();
     }
 
     @Then("^The results should be composition instances$")
     public void theResultsShouldBeCompositionInstances() throws Throwable {
         _aqlResultSet = bg.extractAqlResults(bg.getAqlResponse(_aqlQuery));
         assertTrue(_aqlResultSet.size() > 0);
+
+        _aqlResultSet.forEach(
+            map -> assertArchetypeNodeId(map, "composition", COMPOSITION_ARCH_ID));
     }
 
     private String readFile(String fullFilePath) throws FileNotFoundException {
         return new Scanner(new FileInputStream(fullFilePath))
             .useDelimiter("\\A")
             .next();
     }
+
+    @Then("^The results should be instruction instances$")
+    public void theResultsShouldBeInstructionInstances() throws Throwable {
+        _aqlResultSet = bg.extractAqlResults(bg.getAqlResponse(_aqlQuery));
+        assertTrue(_aqlResultSet.size() > 0);
+
+        _aqlResultSet.forEach(
+            map -> assertArchetypeNodeId(map, "instruction", INSTRUCTION_ARCH_ID));
+    }
+
+    private void assertArchetypeNodeId(Map<String,String> map,
+                                       String nodeAliasInAqlSelectClause,
+                                       String archetypeNodeId){
+        String instructionJson = map.get(nodeAliasInAqlSelectClause);
+        JsonPath path = new JsonPath(instructionJson);
+        String node_id = path.getString("archetype_node_id");
+        assertEquals(node_id, archetypeNodeId);
+    }
+
+    @When("^A an AQL query that describes an instruction under an EHR is created$")
+    public void aAnAQLQueryThatDescribesAnInstructionUnderAnEHRIsCreated() throws Throwable {
+        _aqlQuery = readFile(bg.resourcesRootPath + CODE4HEALTH_QUERY_DIR + SELECT_COMPLETE_INSTRUCTION_AQL);
+    }
 }

vehr-integration-tests/src/test/resources/features/code4health/Aql.feature

@@ -120,3 +120,16 @@ Feature: Support for openEHR Archetype Query Language
     And Composition archetype id criteria
     And Composition name criteria using WHERE clause
     Then The results should be composition instances
+
+  Scenario: Select instruction
+  A composition with an instruction is queried. The composition sits under the EHR.
+  AQL query specifies EHR id, Composition archetype node id and instruction archetype node id.
+  The query uses WHERE clause to add Composition name as an extra criteria. The SELECT clause
+  selects the complete instruction instance
+
+    When A an AQL query that describes an instruction under an EHR is created
+    And The query contains EHR id criteria
+    And Composition archetype id criteria
+    And Composition name criteria using WHERE clause
+    And Instruction archetype id criteria
+    Then The results should be instruction instances

vehr-integration-tests/src/test/resources/test_data/code4health/queries/population-composition-evaluation.aql

@@ -0,0 +1,35 @@
+select 
+e/ehr_id/value as ehrId,
+ e/ehr_status/subject/external_ref/id/value as subjectId,
+ e/ehr_status/subject/external_ref/namespace as subjectNamespace,
+
+ a/context/start_time/value as compositionStartTime,
+ a/uid/value as compositionId,
+ a/composer/name as composerName,
+ a/composer/external_ref/id/value as composerId,
+ a/composer/external_ref/namespace as composerNamespace,
+
+ b_a/uid/value as entryId,
+ b_a/protocol[at0042]/items[at0062]/value/value as AssertedDate,
+ b_a/data[at0001]/items[at0002] as Causative_agent,
+ b_a/data[at0001]/items[at0063]/value/defining_code/code_string as Status_code,
+ b_a/data[at0001]/items[at0101]/value/defining_code/code_string as Criticality_code,
+ b_a/data[at0001]/items[at0120]/value/defining_code/code_string as Category_code,
+ b_a/data[at0001]/items[at0117]/value/value as Onset_of_last_reaction,
+ b_a/data[at0001]/items[at0058]/value/defining_code/code_string as Reaction_mechanism_code,
+ b_a/data[at0001]/items[at0006]/value/value as Comment,
+ b_a/data[at0001]/items[at0009]/items[at0010] as Specific_substance,
+ b_a/data[at0001]/items[at0009]/items[at0021]/value/defining_code/code_string as Certainty_code,
+ b_a/data[at0001]/items[at0009]/items[at0011] as Manifestation,
+ b_a/data[at0001]/items[at0009]/items[at0012]/value/value as Reaction_description,
+ b_a/data[at0001]/items[at0009]/items[at0027]/value/value as Onset_of_reaction,
+ b_a/data[at0001]/items[at0009]/items[at0089]/value/defining_code/code_string as Severity_code,
+ b_a/data[at0001]/items[at0009]/items[at0106] as Route_of_exposure,
+ b_a/data[at0001]/items[at0009]/items[at0032]/value/value as Adverse_reaction_risk_Comment 
+
+ from EHR e 
+ 	contains COMPOSITION a[openEHR-EHR-COMPOSITION.adverse_reaction_list.v1] 
+
+ 	contains EVALUATION b_a[openEHR-EHR-EVALUATION.adverse_reaction_risk.v1] 
+
+ 	where a/name/value='Adverse reaction list'

vehr-integration-tests/src/test/resources/test_data/code4health/queries/select_complete_composition.aql

@@ -1,5 +1,5 @@
 SELECT
-	a
+	a composition
  FROM
  	EHR e [ehr_id/value = '{{ehrId}}']
  		CONTAINS COMPOSITION a[{{compositionArchetypeIdId}}]

vehr-integration-tests/src/test/resources/test_data/code4health/queries/select_complete_instruction.aql

@@ -0,0 +1,10 @@
+SELECT
+	b_a as instruction
+ FROM
+ 	EHR e [ehr_id/value = '{{ehrId}}']
+
+ 		CONTAINS COMPOSITION a[{{compositionArchetypeIdId}}]
+
+ 			CONTAINS INSTRUCTION b_a[{{instructionArchetypeId}}]
+WHERE
+	a/name/value='{{compositionName}}'