Neha | bdshr-989 | increasing/decreasing the error level for all entr…

…ies in bundle. Decreasing error level for MedicationOrderAction extension.
SharedHealth · Oct 29, 2015 · c26489e · c26489e
1 parent ed0ebfa
commit c26489e
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Showing 7 changed files with 160 additions and 18 deletions.
diff --git a/shr/src/main/java/org/freeshr/validations/FhirResourceValidator.java b/shr/src/main/java/org/freeshr/validations/FhirResourceValidator.java
@@ -19,6 +19,8 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 @Component
 public class FhirResourceValidator {
@@ -27,8 +29,8 @@ public class FhirResourceValidator {
  private TRConceptValidator trConceptValidator;
  private volatile FhirValidator fhirValidator;
  private ShrProfileValidationSupport shrProfileValidationSupport;
- private List<String> resourceFieldErrors = new ArrayList<>();
- private Map<String, String> extensionFieldErrors = new HashMap<>();
+ private List<Pattern> resourceFieldErrors = new ArrayList<>();
+ private Map<Pattern, String> extensionFieldErrors = new HashMap<>();
 
  @Autowired
  public FhirResourceValidator(FhirFeedUtil fhirUtil, TRConceptValidator trConceptValidator, ShrProfileValidationSupport shrProfileValidationSupport) {
@@ -39,12 +41,13 @@ public FhirResourceValidator(FhirFeedUtil fhirUtil, TRConceptValidator trConcept
  }
 
  private void initFieldErrorChecks() {
- this.resourceFieldErrors.add("/f:Bundle/f:entry/f:resource/f:Condition/f:category");
- this.resourceFieldErrors.add("/f:Bundle/f:entry/f:resource/f:Condition/f:code/f:coding");
- this.resourceFieldErrors.add("/f:Bundle/f:entry/f:resource/f:Condition/f:clinicalStatus");
+ this.resourceFieldErrors.add(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:Condition/f:category"));
+ this.resourceFieldErrors.add(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:Condition/f:code/f:coding"));
+ this.resourceFieldErrors.add(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:Condition/f:clinicalStatus"));
 
- this.extensionFieldErrors.put("/f:Bundle/f:entry/f:resource/f:MedicationOrder/f:dosageInstruction/f:timing/f:extension", "https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#TimingScheduledDate");
- this.extensionFieldErrors.put("/f:Bundle/f:entry/f:resource/f:MedicationOrder/f:dosageInstruction/f:extension", "https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#DosageInstructionCustomDosage");
+ this.extensionFieldErrors.put(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:MedicationOrder/f:dosageInstruction(\\[\\d+\\])*/f:timing/f:extension(\\[\\d+\\])*"), "https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#TimingScheduledDate");
+ this.extensionFieldErrors.put(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:MedicationOrder/f:dosageInstruction(\\[\\d+\\])*/f:extension(\\[\\d+\\])*"), "https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#DosageInstructionCustomDosage");
+ this.extensionFieldErrors.put(Pattern.compile("/f:Bundle/f:entry(\\[\\d+\\])*/f:resource/f:MedicationOrder/f:extension(\\[\\d+\\])*"), "https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#MedicationOrderAction");
  }
 
  public FhirValidationResult validate(Bundle bundle) {
@@ -62,8 +65,8 @@ private void checkValidationResult(FhirValidationResult validationResult) {
 
  private void checkForExtensionErrors(FhirValidationResult validationResult) {
  for (SingleValidationMessage validationMessage : validationResult.getMessages()) {
- if (extensionFieldErrors.containsKey(validationMessage.getLocationString())
-  && validationMessage.getMessage().contains(extensionFieldErrors.get(validationMessage.getLocationString()))) {
+ String extensionUrlForLocation = getExtensionForLocationError(validationMessage.getLocationString());
+ if (extensionUrlForLocation != null && validationMessage.getMessage().contains(extensionUrlForLocation)) {
  if (validationMessage.getSeverity().ordinal() >= ResultSeverityEnum.ERROR.ordinal()) {
  validationMessage.setSeverity(ResultSeverityEnum.WARNING);
  }
@@ -73,14 +76,30 @@ private void checkForExtensionErrors(FhirValidationResult validationResult) {
 
  private void checkForConditionErrors(FhirValidationResult validationResult) {
  for (SingleValidationMessage validationMessage : validationResult.getMessages()) {
- if (resourceFieldErrors.contains(validationMessage.getLocationString())) {
+ if (isPossibleResourceFieldError(validationMessage.getLocationString())) {
  if (validationMessage.getSeverity().ordinal() <= ResultSeverityEnum.WARNING.ordinal()) {
  validationMessage.setSeverity(ResultSeverityEnum.ERROR);
  }
  }
  }
  }
 
+ private String getExtensionForLocationError(String locationString) {
+ for (Pattern extensionFieldErrorLocationPattern : extensionFieldErrors.keySet()) {
+ Matcher matcher = extensionFieldErrorLocationPattern.matcher(locationString);
+ if (matcher.matches()) return extensionFieldErrors.get(extensionFieldErrorLocationPattern);
+ }
+ return null;
+ }
+
+ private boolean isPossibleResourceFieldError(String locationString) {
+ for (Pattern resourceFieldErrorPattern : resourceFieldErrors) {
+ Matcher matcher = resourceFieldErrorPattern.matcher(locationString);
+ if (matcher.matches()) return true;
+ }
+ return false;
+ }
+
  /**
  * This is required since the InstanceValidator does not raise a severity.error on concept validation failure.
  * InstanceValidator.checkCodeableConcept() line number 225
@@ -98,9 +117,10 @@ private void checkForConceptValidationError(FhirValidationResult validationResul
  }
 
  private static String getTerminologySystem(String message) {
- if (message.contains("Unable to validate code")) {
- String substring = message.substring(message.indexOf("in code system"));
- return StringUtils.remove(StringUtils.removeStart(substring, "in code system"), "\"");
+ Pattern pattern = Pattern.compile("Unable to validate code \"(.*)\" in code system \"(?<TRSERVERURL>.*)\"");
+ Matcher matcher = pattern.matcher(message);
+ if(matcher.matches()) {
+ return matcher.group("TRSERVERURL");
  }
  return "";
  }

diff --git a/shr/src/test/java/org/freeshr/application/fhir/EncounterValidatorIntegrationTest.java b/shr/src/test/java/org/freeshr/application/fhir/EncounterValidatorIntegrationTest.java
@@ -273,13 +273,19 @@ public void shouldRejectEncounterWithInvalidDiagnosisCategoryAndStatusAndSystem(
  FileUtil.asString("xmls/encounters/dstu2/p98001046534_encounter_with_localRefs_invalidCondition.xml"));
  validationContext = new EncounterValidationContext(encounterBundle, new FhirFeedUtil());
  EncounterValidationResponse response = validator.validate(validationContext);
+ assertEquals(6, response.getErrors().size());
  assertFailureInResponse("/f:Bundle/f:entry/f:resource/f:Condition/f:code/f:coding/f:system",
  "@value cannot be empty", false, response);
+ assertFailureInResponse("/f:Bundle/f:entry[3]/f:resource/f:Condition/f:code/f:coding/f:system",
+ "@value cannot be empty", false, response);
  assertFailureInResponse("/f:Bundle/f:entry/f:resource/f:Condition/f:category",
  "None of the codes are in the example value set http://hl7.org/fhir/ValueSet/condition-category", true, response);
+ assertFailureInResponse("/f:Bundle/f:entry[3]/f:resource/f:Condition/f:category",
+ "None of the codes are in the example value set http://hl7.org/fhir/ValueSet/condition-category", true, response);
  assertFailureInResponse("/f:Bundle/f:entry/f:resource/f:Condition/f:clinicalStatus",
  "Coded value wrong is not in value set http://hl7.org/fhir/ValueSet/condition-clinical", true, response);
- assertEquals(3, response.getErrors().size());
+ assertFailureInResponse("/f:Bundle/f:entry[3]/f:resource/f:Condition/f:clinicalStatus",
+ "Coded value wrong is not in value set http://hl7.org/fhir/ValueSet/condition-clinical", true, response);
  }
 
  @Test
@@ -325,7 +331,7 @@ public void shouldRejectInvalidRelationshipTypeInFamilyMemberHistory() throws Ex
  assertFalse(response.isSuccessful());
  assertEquals(1, response.getErrors().size());
  assertFailureInResponse("/f:Bundle/f:entry/f:resource/f:FamilyMemberHistory/f:relationship",
- "Unable to validate code \"FT\" in code system \"http://localhost:9997/openmrs/ws/rest/v1/tr/vs/Relationship-Type\"", true, response);
+ "Unable to validate code \"INVALID\" in code system \"http://localhost:9997/openmrs/ws/rest/v1/tr/vs/Relationship-Type\"", true, response);
  }
 
  @Test
@@ -343,7 +349,6 @@ public void shouldValidateMedicationOrderWithCustomDosageExtension() throws Exce
  FileUtil.asString("xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_custom_dosage.xml"));
  validationContext = new EncounterValidationContext(encounterBundle, new FhirFeedUtil());
  EncounterValidationResponse response = validator.validate(validationContext);
- debugEncounterValidationResponse(response);
  assertTrue(response.isSuccessful());
  }
 

diff --git a/...counters/dstu2/p98001046534_encounter_with_family_member_history_relationship_invalid.xml b/...counters/dstu2/p98001046534_encounter_with_family_member_history_relationship_invalid.xml
@@ -92,7 +92,7 @@
  <relationship>
  <coding>
  <system value="http://localhost:9997/openmrs/ws/rest/v1/tr/vs/Relationship-Type"/>
- <code value="FT"/>
+ <code value="INVALID"/>
  <display value="father"/>
  </coding>
  </relationship>

diff --git a/...esources/xmls/encounters/dstu2/p98001046534_encounter_with_localRefs_invalidCondition.xml b/...esources/xmls/encounters/dstu2/p98001046534_encounter_with_localRefs_invalidCondition.xml
@@ -39,6 +39,12 @@
  <display value="Encounter"/>
  </entry>
  </section>
+ <section>
+ <entry>
+ <reference value="urn:uuid:04e9f319-980c-4ff1-9942-bcb5e2b5243b"/>
+ <display value="Diagnosis"/>
+ </entry>
+ </section>
  <section>
  <entry>
  <reference value="urn:uuid:04e9f317-680c-4ff1-9942-bcb5e2b5243b"/>
@@ -76,6 +82,44 @@
  </Encounter>
  </resource>
  </entry>
+ <entry>
+ <fullUrl value="urn:uuid:04e9f319-980c-4ff1-9942-bcb5e2b5243b"/>
+ <resource>
+ <Condition xmlns="http://hl7.org/fhir">
+ <id value="04e9f319-980c-4ff1-9942-bcb5e2b5243b"/>
+ <identifier>
+ <value value="urn:uuid:04e9f319-980c-4ff1-9942-bcb5e2b5243b"/>
+ </identifier>
+ <patient>
+ <reference value="http://localhost:9997/api/default/patients/98001046534"/>
+ <display value="98001046534"/>
+ </patient>
+ <encounter>
+ <reference value="urn:uuid:dd4d51ac-d4b6-42e4-8b50-fa88af41a3e3"/>
+ </encounter>
+ <asserter>
+ <reference value="http://localhost:9997/providers/19.json"/>
+ </asserter>
+ <dateRecorded value="2015-09-04"/>
+ <code>
+ <coding>
+ <system value=""/>
+ <code value="A90"/>
+ <display value="Dengue Fever"/>
+ </coding>
+ </code>
+ <category>
+ <coding>
+ <system value="http://hl7.org/fhir/condition-category"/>
+ <code value="invalid"/>
+ <display value="invalid-category"/>
+ </coding>
+ </category>
+ <clinicalStatus value="wrong"/>
+ <verificationStatus value="provisional"/>
+ </Condition>
+ </resource>
+ </entry>
  <entry>
  <fullUrl value="urn:uuid:04e9f317-680c-4ff1-9942-bcb5e2b5243b"/>
  <resource>

diff --git a/...rces/xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_custom_dosage.xml b/...rces/xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_custom_dosage.xml
@@ -81,6 +81,10 @@
  <resource>
  <MedicationOrder xmlns="http://hl7.org/fhir">
  <id value="e461943b-7ad6-4b41-9730-70b8fc452f45"/>
+ <extension
+ url="https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#MedicationOrderAction">
+ <valueString value="NEW"/>
+ </extension>
  <identifier>
  <value value="urn:uuid:e461943b-7ad6-4b41-9730-70b8fc452f45"/>
  </identifier>

diff --git a/...xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_invalid_medication.xml b/...xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_invalid_medication.xml
@@ -81,6 +81,10 @@
  <resource>
  <MedicationOrder xmlns="http://hl7.org/fhir">
  <id value="e461943b-7ad6-4b41-9730-70b8fc452f45"/>
+ <extension
+ url="https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#MedicationOrderAction">
+ <valueString value="NEW"/>
+ </extension>
  <identifier>
  <value value="urn:uuid:e461943b-7ad6-4b41-9730-70b8fc452f45"/>
  </identifier>

diff --git a/...ces/xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_scheduled_date.xml b/...ces/xmls/encounters/dstu2/p98001046534_encounter_with_medication_order_scheduled_date.xml
@@ -39,6 +39,12 @@
  <display value="Encounter"/>
  </entry>
  </section>
+ <section>
+ <entry>
+ <reference value="urn:uuid:3461943b-7ad6-4b41-9730-70b83c332f43"/>
+ <display value="Medication Order"/>
+ </entry>
+ </section>
  <section>
  <entry>
  <reference value="urn:uuid:e461943b-7ad6-4b41-9730-70b8fc452f45"/>
@@ -76,11 +82,70 @@
  </Encounter>
  </resource>
  </entry>
+ <entry>
+ <fullUrl value="urn:uuid:3461943b-7ad6-4b41-9730-70b83c332f43"/>
+ <resource>
+ <MedicationOrder xmlns="http://hl7.org/fhir">
+ <id value="3461943b-7ad6-4b41-9730-70b83c332f43"/>
+ <identifier>
+ <value value="urn:uuid:3461943b-7ad6-4b41-9730-70b83c332f43"/>
+ </identifier>
+ <dateWritten value="2015-09-22T17:09:54.000+05:30"/>
+ <status value="active"/>
+ <patient>
+ <reference value="http://localhost:9997/api/default/patients/98001046534"/>
+ <display value="98001046534"/>
+ </patient>
+ <prescriber>
+ <reference value="http://localhost:9997/providers/19.json"/>
+ </prescriber>
+ <encounter>
+ <reference value="urn:uuid:34ba3e1c-55c0-434d-b74b-b1bfe6472d4c"/>
+ </encounter>
+ <medicationCodeableConcept>
+ <coding>
+ <system value="http://localhost:9997/openmrs/ws/rest/v1/tr/drugs/23d7e743-75bd-4a25-8f34-bd849bd50394"/>
+ <code value="23d7e743-75bd-4a25-8f34-bd849bd50394"/>
+ <display value="Paracetamol"/>
+ </coding>
+ </medicationCodeableConcept>
+ <dosageInstruction>
+ <timing>
+ <repeat>
+ <boundsQuantity>
+ <value value="3"/>
+ <system value="http://unitsofmeasure.org"/>
+ <code value="d"/>
+ </boundsQuantity>
+ <frequency value="2"/>
+ <period value="7"/>
+ <periodUnits value="h"/>
+ </repeat>
+ </timing>
+ <asNeededBoolean value="false"/>
+ <doseQuantity>
+ <value value="1"/>
+ <unit value="mg"/>
+ </doseQuantity>
+ </dosageInstruction>
+ <dispenseRequest>
+ <quantity>
+ <value value="192.0"/>
+ <unit value="mg"/>
+ </quantity>
+ </dispenseRequest>
+ </MedicationOrder>
+ </resource>
+ </entry>
  <entry>
  <fullUrl value="urn:uuid:e461943b-7ad6-4b41-9730-70b8fc452f45"/>
  <resource>
  <MedicationOrder xmlns="http://hl7.org/fhir">
  <id value="e461943b-7ad6-4b41-9730-70b8fc452f45"/>
+ <extension
+ url="https://sharedhealth.atlassian.net/wiki/display/docs/fhir-extensions#MedicationOrderAction">
+ <valueString value="NEW"/>
+ </extension>
  <identifier>
  <value value="urn:uuid:e461943b-7ad6-4b41-9730-70b8fc452f45"/>
  </identifier>
@@ -121,7 +186,7 @@
  </timing>
  <asNeededBoolean value="false"/>
  <doseQuantity>
- <value value="10"/>
+ <value value="1"/>
  <unit value="Pill"/>
  </doseQuantity>
  </dosageInstruction>