예제 #1
0
  private static Double convertDecimal(Attribute attr, Object value) {
    if (value instanceof Double) {
      return (Double) value;
    }

    if (value == null) {
      return null;
    }

    // try to convert value
    Double doubleValue;
    if (value instanceof String) {
      try {
        doubleValue = Double.valueOf((String) value);
      } catch (NumberFormatException e) {
        throw new MolgenisValidationException(
            new ConstraintViolation(
                format(
                    "Attribute [%s] value [%s] cannot be converter to type [%s]",
                    attr.getName(), value, Double.class.getSimpleName())));
      }
    } else if (value instanceof Number) {
      doubleValue = ((Number) value).doubleValue();
    } else {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
                  attr.getName(),
                  value.getClass().getSimpleName(),
                  String.class.getSimpleName(),
                  Number.class.getSimpleName())));
    }
    return doubleValue;
  }
예제 #2
0
  private static Boolean convertBool(Attribute attr, Object value) {
    if (value instanceof Boolean) {
      return (Boolean) value;
    }

    if (value == null) {
      return null;
    }

    Boolean booleanValue;
    if (value instanceof String) {
      String stringValue = (String) value;
      if (stringValue.equalsIgnoreCase(TRUE.toString())) {
        booleanValue = true;
      } else if (stringValue.equalsIgnoreCase(FALSE.toString())) {
        booleanValue = false;
      } else {
        throw new MolgenisValidationException(
            new ConstraintViolation(
                format(
                    "Attribute [%s] value [%s] cannot be converter to type [%s]",
                    attr.getName(), value, Boolean.class.getSimpleName())));
      }
    } else {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
                  attr.getName(),
                  value.getClass().getSimpleName(),
                  String.class.getSimpleName(),
                  Boolean.class.getSimpleName())));
    }
    return booleanValue;
  }
  @BeforeTest
  public void createEntity() {
    entityType = when(mock(EntityType.class).getName()).thenReturn("Source").getMock();
    Attribute idAttr = when(mock(Attribute.class).getName()).thenReturn("Identifier").getMock();

    when(idAttr.getDataType()).thenReturn(INT);
    Attribute intAttr = when(mock(Attribute.class).getName()).thenReturn("Int").getMock();
    when(intAttr.getDataType()).thenReturn(INT);
    Attribute stringAttr = when(mock(Attribute.class).getName()).thenReturn("String").getMock();
    when(stringAttr.getDataType()).thenReturn(STRING);
    Attribute nonNumericStringAttr =
        when(mock(Attribute.class).getName()).thenReturn("NonNumericString").getMock();
    when(nonNumericStringAttr.getDataType()).thenReturn(STRING);
    Attribute longAttr = when(mock(Attribute.class).getName()).thenReturn("Long").getMock();
    when(longAttr.getDataType()).thenReturn(LONG);
    when(entityType.getIdAttribute()).thenReturn(idAttr);
    when(entityType.getAttribute("Identifier")).thenReturn(idAttr);
    when(entityType.getAttribute("Int")).thenReturn(intAttr);
    when(entityType.getAttribute("String")).thenReturn(stringAttr);
    when(entityType.getAttribute("NonNumericString")).thenReturn(nonNumericStringAttr);
    when(entityType.getAttribute("Long")).thenReturn(longAttr);

    entity = new DynamicEntity(entityType);
    entity.set("Int", 1);
    entity.set("String", "12");
    entity.set("Long", 10L);
    entity.set("NonNumericString", "Hello World!");
  }
예제 #4
0
  private static Integer convertInt(Attribute attr, Object value) {
    if (value instanceof Integer) {
      return (Integer) value;
    }

    if (value == null) {
      return null;
    }

    // try to convert value
    Integer integerValue;
    if (value instanceof String) {
      try {
        integerValue = Integer.valueOf((String) value);
      } catch (NumberFormatException e) {
        throw new MolgenisValidationException(
            new ConstraintViolation(
                format(
                    "Attribute [%s] value [%s] cannot be converter to type [%s]",
                    attr.getName(), value, Integer.class.getSimpleName())));
      }
    } else if (value instanceof Number) {
      integerValue = ((Number) value).intValue();
    } else {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
                  attr.getName(),
                  value.getClass().getSimpleName(),
                  String.class.getSimpleName(),
                  Number.class.getSimpleName())));
    }
    return integerValue;
  }
 @Test
 public void testStringEvaluatorLookupAttributeAndConvertFromIntToLong() {
   Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#POS").getMock();
   when(amd.getDataType()).thenReturn(LONG);
   when(amd.getExpression()).thenReturn("Int");
   assertEquals(new StringExpressionEvaluator(amd, entityType).evaluate(entity), 1L);
 }
예제 #6
0
  private static String convertEnum(Attribute attr, Object value) {
    if (value == null) {
      return null;
    }

    String stringValue;
    if (value instanceof String) {
      stringValue = (String) value;
    } else if (value instanceof Enum) {
      stringValue = value.toString();
    } else {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
                  attr.getName(),
                  value.getClass().getSimpleName(),
                  String.class.getSimpleName(),
                  Enum.class.getSimpleName())));
    }

    if (!attr.getEnumOptions().contains(stringValue)) {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value [%s] is not a valid enum option",
                  attr.getName(), stringValue)));
    }

    return stringValue;
  }
예제 #7
0
  private static Date convertDate(Attribute attr, Object value) {
    if (value instanceof Date) {
      return (Date) value;
    }

    if (value == null) {
      return null;
    }

    // try to convert value
    Date dateValue;
    if (value instanceof String) {
      String paramStrValue = (String) value;
      try {
        dateValue = getDateFormat().parse(paramStrValue);
      } catch (ParseException e) {
        throw new MolgenisValidationException(
            new ConstraintViolation(
                format(
                    "Attribute [%s] value [%s] does not match date format [%s]",
                    attr.getName(),
                    paramStrValue,
                    MolgenisDateFormat.getDateFormat().toPattern())));
      }
    } else {
      throw new MolgenisValidationException(
          new ConstraintViolation(
              format(
                  "Attribute [%s] value is of type [%s] instead of [%s]",
                  attr.getName(), value.getClass().getSimpleName(), String.class.getSimpleName())));
    }
    return dateValue;
  }
예제 #8
0
 @Override
 public void setIdValue(Object id) {
   Attribute idAttr = entityType.getIdAttribute();
   if (idAttr == null) {
     throw new IllegalArgumentException(
         format("Entity [%s] doesn't have an id attribute", entityType.getName()));
   }
   set(idAttr.getName(), id);
 }
 @Test(
     expectedExceptions = ConversionFailedException.class,
     expectedExceptionsMessageRegExp =
         "Failed to convert from type \\[java.lang.String\\] to type \\[java.lang.Long\\] for value 'Hello World!'; nested exception is java.lang.NumberFormatException: For input string: \"HelloWorld!\"")
 public void testStringEvaluatorLookupAttributeAndConvertFromNonNumericStringToLongFails() {
   Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#POS").getMock();
   when(amd.getDataType()).thenReturn(LONG);
   when(amd.getExpression()).thenReturn("NonNumericString");
   new StringExpressionEvaluator(amd, entityType).evaluate(entity);
 }
 @Test
 public void testStringEvaluatorConstructorChecksIfAttributeHasExpression() {
   Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
   when(amd.getDataType()).thenReturn(STRING);
   try {
     new StringExpressionEvaluator(amd, entityType);
     fail("Expected NPE");
   } catch (NullPointerException expected) {
     assertEquals(expected.getMessage(), "Attribute has no expression.");
   }
 }
예제 #11
0
 private Object toQueryRuleValue(Object queryRuleValue, Attribute attr) {
   Object value;
   AttributeType attrType = attr.getDataType();
   switch (attrType) {
     case BOOL:
       value = convertBool(attr, queryRuleValue);
       break;
     case EMAIL:
     case HTML:
     case HYPERLINK:
     case SCRIPT:
     case STRING:
     case TEXT:
       value = convertString(attr, queryRuleValue);
       break;
     case ENUM:
       value = convertEnum(attr, queryRuleValue);
       break;
     case CATEGORICAL:
     case XREF:
     case CATEGORICAL_MREF:
     case MREF:
     case ONE_TO_MANY:
       value = convertRef(attr, queryRuleValue);
       break;
     case DATE:
       value = convertDate(attr, queryRuleValue);
       break;
     case DATE_TIME:
       value = convertDateTime(attr, queryRuleValue);
       break;
     case DECIMAL:
       value = convertDecimal(attr, queryRuleValue);
       break;
     case FILE:
       value = convertFile(attr, queryRuleValue);
       break;
     case INT:
       value = convertInt(attr, queryRuleValue);
       break;
     case LONG:
       value = convertLong(attr, queryRuleValue);
       break;
     case COMPOUND:
       throw new MolgenisValidationException(
           new ConstraintViolation(
               format(
                   "Attribute [%s] type [%s] is not allowed",
                   attr.getName(), attrType.toString())));
     default:
       throw new RuntimeException(format("Unknown attribute type [%s]", attrType.toString()));
   }
   return value;
 }
 @Test
 public void testStringEvaluatorConstructorChecksIfExpressionIsMap() {
   Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
   when(amd.getDataType()).thenReturn(STRING);
   when(amd.getExpression()).thenReturn("{}");
   try {
     new StringExpressionEvaluator(amd, entityType);
     fail("expected illegal state exception");
   } catch (JsonSyntaxException expected) {
   }
 }
예제 #13
0
  private Entity convertRef(Attribute attr, Object value) {
    if (value instanceof Entity) {
      return (Entity) value;
    }

    if (value == null) {
      return null;
    }

    // try to convert value
    Object idValue = toQueryRuleValue(value, attr.getRefEntity().getIdAttribute());
    return entityManager.getReference(attr.getRefEntity(), idValue);
  }
 Entity getDefaultSettings() {
   Entity defaultSettingsEntity = new DynamicEntity(this);
   for (Attribute attr : this.getAtomicAttributes()) {
     // default values are stored/retrieved as strings, so we convert them to the required type
     // here.
     String defaultValue = attr.getDefaultValue();
     if (defaultValue != null) {
       Object typedDefaultValue = getTypedValue(defaultValue, attr, entityManager);
       defaultSettingsEntity.set(attr.getName(), typedDefaultValue);
     }
   }
   return defaultSettingsEntity;
 }
 @Test
 public void testStringEvaluatorConstructorChecksIfAttributeMentionsExistingAttribute() {
   Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
   when(amd.getDataType()).thenReturn(STRING);
   when(amd.getExpression()).thenReturn("bogus");
   try {
     new StringExpressionEvaluator(amd, entityType);
     fail("expected illegal argument exception");
   } catch (IllegalArgumentException expected) {
     assertEquals(
         expected.getMessage(),
         "Expression for attribute '#CHROM' references non-existant attribute 'bogus'.");
   }
 }
  @Test
  public void testGenerateRules() {
    EntityType targetRefEntityType = createCategoricalRefEntityType("HOP_HYPERTENSION");
    Entity targetEntity1 =
        new DynamicEntity(
            targetRefEntityType, of("code", 0, "label", "Never had high blood pressure "));
    Entity targetEntity2 =
        new DynamicEntity(
            targetRefEntityType, of("code", 1, "label", "Ever had high blood pressure "));
    Entity targetEntity3 =
        new DynamicEntity(targetRefEntityType, of("code", 9, "label", "Missing"));
    Mockito.when(dataService.findAll(targetRefEntityType.getName()))
        .thenReturn(Stream.of(targetEntity1, targetEntity2, targetEntity3));
    targetAttribute =
        attrMetaFactory.create().setName("History of Hypertension").setDataType(CATEGORICAL);
    targetAttribute.setRefEntity(targetRefEntityType);

    EntityType sourceRefEntityType = createCategoricalRefEntityType("High_blood_pressure_ref");
    Entity sourceEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "yes"));
    Entity sourceEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "no"));
    Entity sourceEntity3 =
        new DynamicEntity(targetRefEntityType, of("code", 3, "label", "I do not know"));
    Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
        .thenReturn(Stream.of(sourceEntity1, sourceEntity2, sourceEntity3));

    sourceAttribute =
        attrMetaFactory.create().setName("High_blood_pressure").setDataType(CATEGORICAL);
    sourceAttribute.setRefEntity(sourceRefEntityType);

    String generatedAlgorithm =
        categoryAlgorithmGenerator.generate(
            targetAttribute, singletonList(sourceAttribute), targetEntityType, sourceEntityType);

    String expectedAlgorithm =
        "$('High_blood_pressure').map({\"1\":\"1\",\"2\":\"0\",\"3\":\"9\"}, null, null).value();";

    Assert.assertEquals(generatedAlgorithm, expectedAlgorithm);
  }
예제 #17
0
 private FileMeta convertFile(Attribute attr, Object paramValue) {
   Entity entity = convertRef(attr, paramValue);
   if (entity == null) {
     return null;
   }
   if (!(entity instanceof FileMeta)) {
     throw new MolgenisValidationException(
         new ConstraintViolation(
             format(
                 "Attribute [%s] value is of type [%s] instead of [%s]",
                 attr.getName(),
                 entity.getClass().getSimpleName(),
                 FileMeta.class.getSimpleName())));
   }
   return (FileMeta) entity;
 }
  @BeforeMethod
  public void init() {
    dataService = Mockito.mock(DataService.class);

    categoryAlgorithmGenerator = new OneToOneCategoryAlgorithmGenerator(dataService);

    EntityType targetRefEntityType = createCategoricalRefEntityType("POTATO_REF");
    Entity targetEntity1 =
        new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Almost daily + daily"));
    Entity targetEntity2 =
        new DynamicEntity(targetRefEntityType, of("code", 2, "label", "Several times a week"));
    Entity targetEntity3 =
        new DynamicEntity(targetRefEntityType, of("code", 3, "label", "About once a week"));
    Entity targetEntity4 =
        new DynamicEntity(
            targetRefEntityType, of("code", 4, "label", "Never + fewer than once a week"));
    Entity targetEntity5 =
        new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));

    targetAttribute =
        attrMetaFactory
            .create()
            .setName("Current Consumption Frequency of Potatoes")
            .setDataType(CATEGORICAL);
    targetAttribute.setRefEntity(targetRefEntityType);

    Mockito.when(dataService.findAll(targetRefEntityType.getName()))
        .thenReturn(
            Stream.of(targetEntity1, targetEntity2, targetEntity3, targetEntity4, targetEntity5));

    targetEntityType = entityTypeFactory.create("target");
    targetEntityType.addAttribute(targetAttribute);

    EntityType sourceRefEntityType = createCategoricalRefEntityType("LifeLines_POTATO_REF");
    Entity sourceEntity1 =
        new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Not this month"));
    Entity sourceEntity2 =
        new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1 day per month"));
    Entity sourceEntity3 =
        new DynamicEntity(targetRefEntityType, of("code", 3, "label", "2-3 days per month"));
    Entity sourceEntity4 =
        new DynamicEntity(targetRefEntityType, of("code", 4, "label", "1 day per week"));
    Entity sourceEntity5 =
        new DynamicEntity(targetRefEntityType, of("code", 5, "label", "2-3 days per week"));
    Entity sourceEntity6 =
        new DynamicEntity(targetRefEntityType, of("code", 6, "label", "4-5 days per week"));
    Entity sourceEntity7 =
        new DynamicEntity(targetRefEntityType, of("code", 7, "label", "6-7 days per week"));
    Entity sourceEntity8 =
        new DynamicEntity(targetRefEntityType, of("code", 8, "label", "9 days per week"));

    sourceAttribute = attrMetaFactory.create().setName("MESHED_POTATO").setDataType(CATEGORICAL);
    sourceAttribute.setLabel(
        "How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
    sourceAttribute.setRefEntity(sourceRefEntityType);

    Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
        .thenReturn(
            Stream.of(
                sourceEntity1,
                sourceEntity2,
                sourceEntity3,
                sourceEntity4,
                sourceEntity5,
                sourceEntity6,
                sourceEntity7,
                sourceEntity8));

    sourceEntityType = entityTypeFactory.create("source");
    sourceEntityType.addAttributes(Lists.newArrayList(sourceAttribute));
  }
예제 #19
0
 @Override
 public Object getIdValue() {
   // abstract entities might not have an id attribute
   Attribute idAttr = entityType.getIdAttribute();
   return idAttr != null ? get(idAttr.getName()) : null;
 }
예제 #20
0
 @Override
 public Object getLabelValue() {
   // abstract entities might not have an label attribute
   Attribute labelAttr = entityType.getLabelAttribute();
   return labelAttr != null ? get(labelAttr.getName()) : null;
 }
예제 #21
0
  /**
   * Validate is value is of the type defined by the attribute data type.
   *
   * @param attrName attribute name
   * @param value value (must be of the type defined by the attribute data type.)
   */
  protected void validateValueType(String attrName, Object value) {
    if (value == null) {
      return;
    }

    Attribute attr = entityType.getAttribute(attrName);
    if (attr == null) {
      throw new UnknownAttributeException(format("Unknown attribute [%s]", attrName));
    }

    AttributeType dataType = attr.getDataType();
    switch (dataType) {
      case BOOL:
        if (!(value instanceof Boolean)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Boolean.class.getSimpleName(),
                  attrName));
        }
        break;
      case CATEGORICAL:
        // expected type is FileMeta. validation is not possible because molgenis-data does not
        // depend on molgenis-file
      case FILE:
      case XREF:
        if (!(value instanceof Entity)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Entity.class.getSimpleName(),
                  attrName));
        }
        break;
      case CATEGORICAL_MREF:
      case MREF:
      case ONE_TO_MANY:
        if (!(value instanceof Iterable)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Iterable.class.getSimpleName(),
                  attrName));
        }
        break;
      case COMPOUND:
        throw new IllegalArgumentException(
            format("Unexpected data type [%s] for attribute: [%s]", dataType.toString(), attrName));
      case DATE:
      case DATE_TIME:
        if (!(value instanceof java.util.Date)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  java.util.Date.class.getSimpleName(),
                  attrName));
        }
        break;
      case DECIMAL:
        if (!(value instanceof Double)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Double.class.getSimpleName(),
                  attrName));
        }
        break;
      case EMAIL:
      case ENUM:
      case HTML:
      case HYPERLINK:
      case SCRIPT:
      case STRING:
      case TEXT:
        if (!(value instanceof String)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  String.class.getSimpleName(),
                  attrName));
        }
        break;
      case INT:
        if (!(value instanceof Integer)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Integer.class.getSimpleName(),
                  attrName));
        }
        break;
      case LONG:
        if (!(value instanceof Long)) {
          throw new MolgenisDataException(
              format(
                  "Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
                  value.toString(),
                  value.getClass().getSimpleName(),
                  Long.class.getSimpleName(),
                  attrName));
        }
        break;
      default:
        throw new RuntimeException(format("Unknown data type [%s]", dataType.toString()));
    }
  }