method2testcases
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### Question:
UriUtils { static String createEntityAttributeUriPath( ServletUriComponentsBuilder builder, String entityTypeId, Object entityId, String attributeName) { return createEntityAttributeUriComponents(builder, entityTypeId, entityId, attributeName) .getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityAttributeUriPath() { String entityTypeId = "MyEntityTypeId"; String attributeName = "MyAttribute"; String entityId = "MyEntityId"; assertEquals( "/myservlet/api/v2/MyEntityTypeId/MyEntityId/MyAttribute", createEntityAttributeUriPath(uriBuilder, entityTypeId, entityId, attributeName)); }
@Test void testCreateEntityAttributeUriPathEncoding() { String entityTypeId = "/\\?=;*"; String attributeName = "/\\?=;*"; String entityId = "/\\?=;*"; assertEquals( "/myservlet/api/v2/%2F%5C%3F=;*/%2F%5C%3F=;*/%2F%5C%3F=;*", createEntityAttributeUriPath(uriBuilder, entityTypeId, entityId, attributeName)); }
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### Question:
UriUtils { static String createEntitiesUriPath( ServletUriComponentsBuilder builder, String entityTypeId, String idAttributeName, Collection<String> entityIds) { String path = createEntitiesUriComponents(builder, entityTypeId, idAttributeName, entityIds).getPath(); String query = createEntitiesUriQuery(idAttributeName, entityIds); return path + '?' + query; } private UriUtils(); }### Answer:
@Test void testCreateEntitiesUriPath() { String entityTypeId = "MyEntityTypeId"; String idAttributeName = "MyIdAttribute"; Collection<String> entityIds = asList("MyEntityId0", "MyEntityId1"); assertEquals( "/myservlet/api/v2/MyEntityTypeId?q=MyIdAttribute=in=(\"MyEntityId0\",\"MyEntityId1\")", createEntitiesUriPath(uriBuilder, entityTypeId, idAttributeName, entityIds)); }
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### Question:
DataConverter { @Nullable @CheckForNull public static Double toDouble(@Nullable @CheckForNull Object source) { if (source == null) { return null; } if (source instanceof Double) { return (Double) source; } return convert(source, Double.class); } private DataConverter(); static Object convert(Object source, Attribute attr); @Nullable @CheckForNull static String toString(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Integer toInt(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Long toLong(@Nullable @CheckForNull Object source); @SuppressWarnings("java:S2447") // null is a valid return value @Nullable @CheckForNull static Boolean toBoolean(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Double toDouble(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static LocalDate toLocalDate(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Instant toInstant(@Nullable @CheckForNull Object source); static List<String> toList(@Nullable @CheckForNull Object source); static void setConversionService(ConversionService conversionService); }### Answer:
@Test void testToDoubleNull() { assertNull(DataConverter.toDouble(null)); }
@SuppressWarnings("ConstantConditions") @Test void testToDoubleBoolean() { assertEquals(DataConverter.toDouble(1.23), 1.23, 0.01); }
@SuppressWarnings("ConstantConditions") @Test void testToDoubleString() { assertEquals(DataConverter.toDouble("1.23"), 1.23, 0.01); }
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### Question:
AttributeFilterToFetchConverter { public static Fetch createDefaultEntityFetch(EntityType entityType, String languageCode) { boolean hasRefAttr = false; Fetch fetch = new Fetch(); for (Attribute attr : entityType.getAtomicAttributes()) { Fetch subFetch = createDefaultAttributeFetch(attr, languageCode); if (subFetch != null) { hasRefAttr = true; } fetch.field(attr.getName(), subFetch); } return hasRefAttr ? fetch : null; } private AttributeFilterToFetchConverter(); static Fetch convert(
AttributeFilter attrFilter, EntityType entityType, String languageCode); static Fetch createDefaultEntityFetch(EntityType entityType, String languageCode); static Fetch createDefaultAttributeFetch(Attribute attr, String languageCode); }### Answer:
@Test void createDefaultEntityFetchRefs() { Fetch fetch = new Fetch() .field(ID_ATTR_NAME) .field(LABEL_ATTR_NAME) .field( COMPOUND_PART_FILE_ATTR_NAME, new Fetch() .field(FileMetaMetadata.ID) .field(FileMetaMetadata.FILENAME) .field(FileMetaMetadata.URL)) .field(XREF_ATTR_NAME, new Fetch().field(REF_ID_ATTR_NAME).field(REF_LABEL_ATTR_NAME)) .field(COMPOUND_PART_COMPOUND_PART_ATTR_NAME) .field(COMPOUND_PART_COMPOUND_PART_ATTR2_NAME); assertEquals(fetch, createDefaultEntityFetch(entityType, "en")); }
@Test void createDefaultEntityFetchNoRefs() { assertNull(AttributeFilterToFetchConverter.createDefaultEntityFetch(xrefEntityType, "en")); }
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### Question:
AttributeFilterToFetchConverter { public static Fetch createDefaultAttributeFetch(Attribute attr, String languageCode) { Fetch fetch; if (isReferenceType(attr)) { fetch = new Fetch(); EntityType refEntityType = attr.getRefEntity(); String idAttrName = refEntityType.getIdAttribute().getName(); fetch.field(idAttrName); String labelAttrName = refEntityType.getLabelAttribute(languageCode).getName(); if (!labelAttrName.equals(idAttrName)) { fetch.field(labelAttrName); } if (attr.getDataType() == FILE) { fetch.field(FileMetaMetadata.URL); } } else { fetch = null; } return fetch; } private AttributeFilterToFetchConverter(); static Fetch convert(
AttributeFilter attrFilter, EntityType entityType, String languageCode); static Fetch createDefaultEntityFetch(EntityType entityType, String languageCode); static Fetch createDefaultAttributeFetch(Attribute attr, String languageCode); }### Answer:
@Test void createDefaultEntityFetchRefAttr() { Fetch fetch = new Fetch().field(REF_ID_ATTR_NAME).field(REF_LABEL_ATTR_NAME); assertEquals(fetch, createDefaultAttributeFetch(xrefAttr, "en")); }
@Test void createDefaultAttributeFetchNoRefAttr() { assertNull(AttributeFilterToFetchConverter.createDefaultAttributeFetch(labelAttr, "en")); }
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### Question:
DataConverter { @Nullable @CheckForNull public static LocalDate toLocalDate(@Nullable @CheckForNull Object source) { if (source == null) { return null; } if (source instanceof LocalDate) { return (LocalDate) source; } return convert(source, LocalDate.class); } private DataConverter(); static Object convert(Object source, Attribute attr); @Nullable @CheckForNull static String toString(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Integer toInt(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Long toLong(@Nullable @CheckForNull Object source); @SuppressWarnings("java:S2447") // null is a valid return value @Nullable @CheckForNull static Boolean toBoolean(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Double toDouble(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static LocalDate toLocalDate(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Instant toInstant(@Nullable @CheckForNull Object source); static List<String> toList(@Nullable @CheckForNull Object source); static void setConversionService(ConversionService conversionService); }### Answer:
@Test void testToLocalDateNull() { assertNull(DataConverter.toLocalDate(null)); }
@Test void testToLocalDateLocalDate() { LocalDate localDate = LocalDate.now(); assertEquals(localDate, DataConverter.toLocalDate(localDate)); }
@Test void testToLocalDateString() { assertEquals(parse("2015-06-04"), DataConverter.toLocalDate("2015-06-04")); }
@Test void toLocalDate() { assertEquals(parse("2015-06-04"), DataConverter.toLocalDate("2015-06-04")); }
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### Question:
UriUtils { static String createEntityCollectionUriPath(String entityTypeId) { return createEntityCollectionUriComponents(entityTypeId).getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityCollectionUriPath() { String entityTypeId = "MyEntityTypeId"; assertEquals("/myservlet/api/v1/MyEntityTypeId", createEntityCollectionUriPath(entityTypeId)); }
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### Question:
UriUtils { static String createEntityTypeMetadataUriPath(String entityTypeId) { return createEntityTypeMetadataUriComponents(entityTypeId).getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityTypeMetadataUriPath() { String entityTypeId = "MyEntityTypeId"; assertEquals( "/myservlet/api/v1/MyEntityTypeId/meta", createEntityTypeMetadataUriPath(entityTypeId)); }
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### Question:
UriUtils { static String createEntityTypeMetadataAttributeUriPath( String entityTypeId, String attributeName) { return createEntityTypeMetadataAttributeUriComponents(entityTypeId, attributeName).getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityTypeMetadataAttributeUriPath() { String entityTypeId = "MyEntityTypeId"; String attributeName = "MyAttribute"; assertEquals( "/myservlet/api/v1/MyEntityTypeId/meta/MyAttribute", createEntityTypeMetadataAttributeUriPath(entityTypeId, attributeName)); }
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### Question:
UriUtils { static String createEntityUriPath(String entityTypeId, Object entityId) { return createEntityUriComponents(entityTypeId, entityId).getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityUriPath() { String entityTypeId = "MyEntityTypeId"; String entityId = "MyEntityId"; assertEquals( "/myservlet/api/v1/MyEntityTypeId/MyEntityId", createEntityUriPath(entityTypeId, entityId)); }
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### Question:
UriUtils { static String createEntityAttributeUriPath( String entityTypeId, Object entityId, String attributeName) { return createEntityAttributeUriComponents(entityTypeId, entityId, attributeName).getPath(); } private UriUtils(); }### Answer:
@Test void testCreateEntityAttributeUriPath() { String entityTypeId = "MyEntityTypeId"; String attributeName = "MyAttribute"; String entityId = "MyEntityId"; assertEquals( "/myservlet/api/v1/MyEntityTypeId/MyEntityId/MyAttribute", createEntityAttributeUriPath(entityTypeId, entityId, attributeName)); }
@Test void testCreateEntityAttributeUriPathEncoding() { String entityTypeId = "/\\?=;*"; String attributeName = "/\\?=;*"; String entityId = "/\\?=;*"; assertEquals( "/myservlet/api/v1/%2F%5C%3F=;*/%2F%5C%3F=;*/%2F%5C%3F=;*", createEntityAttributeUriPath(entityTypeId, entityId, attributeName)); }
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### Question:
DataConverter { @Nullable @CheckForNull public static Instant toInstant(@Nullable @CheckForNull Object source) { if (source == null) { return null; } if (source instanceof Instant) { return (Instant) source; } return convert(source, Instant.class); } private DataConverter(); static Object convert(Object source, Attribute attr); @Nullable @CheckForNull static String toString(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Integer toInt(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Long toLong(@Nullable @CheckForNull Object source); @SuppressWarnings("java:S2447") // null is a valid return value @Nullable @CheckForNull static Boolean toBoolean(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Double toDouble(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static LocalDate toLocalDate(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Instant toInstant(@Nullable @CheckForNull Object source); static List<String> toList(@Nullable @CheckForNull Object source); static void setConversionService(ConversionService conversionService); }### Answer:
@Test void testToInstantNull() { assertNull(DataConverter.toInstant(null)); }
@Test void testToInstantInstant() { Instant instant = Instant.now(); assertEquals(instant, toInstant(instant)); }
@Test void testToInstantString() { assertEquals(Instant.parse("1986-08-12T06:12:13Z"), toInstant("1986-08-12T06:12:13Z")); }
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### Question:
EntityCollectionResponse { public String getNextHref() { return nextHref; } EntityCollectionResponse(
EntityPager entityPager,
List<Map<String, Object>> items,
String href,
EntityType meta,
UserPermissionEvaluator permissionService,
DataService dataService); String getHref(); EntityTypeResponse getMeta(); int getStart(); int getNum(); long getTotal(); String getPrevHref(); String getNextHref(); List<Map<String, Object>> getItems(); }### Answer:
@Test void getNextHref() { EntityPager pager = new EntityPager(0, 10, 25L, null); EntityCollectionResponse response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertEquals("/test?start=10&num=10", response.getNextHref()); pager = new EntityPager(10, 10, 25L, null); response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertEquals("/test?start=20&num=10", response.getNextHref()); pager = new EntityPager(0, 25, 25L, null); response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertNull(response.getNextHref()); }
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### Question:
EntityCollectionResponse { public String getPrevHref() { return prevHref; } EntityCollectionResponse(
EntityPager entityPager,
List<Map<String, Object>> items,
String href,
EntityType meta,
UserPermissionEvaluator permissionService,
DataService dataService); String getHref(); EntityTypeResponse getMeta(); int getStart(); int getNum(); long getTotal(); String getPrevHref(); String getNextHref(); List<Map<String, Object>> getItems(); }### Answer:
@Test void getPrevHref() { EntityPager pager = new EntityPager(0, 15, 30L, null); EntityCollectionResponse response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertNull(response.getPrevHref()); pager = new EntityPager(15, 15, 30L, null); response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertEquals("/test?start=0&num=15", response.getPrevHref()); pager = new EntityPager(30, 15, 30L, null); response = new EntityCollectionResponse( pager, null, "/test", entityType, permissionService, dataService); assertEquals("/test?start=15&num=15", response.getPrevHref()); }
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### Question:
EntityPager { public Integer getNextStart() { if (total == null) return this.start + this.num; if (this.start + this.num > this.total - 1) return null; else return this.start + this.num; } EntityPager(int start, int num, Long total, Iterable<Entity> iterable); int getStart(); int getNum(); Long getTotal(); Integer getNextStart(); Integer getPrevStart(); Iterable<Entity> getIterable(); }### Answer:
@Test void getNextStart() { EntityPager pager = new EntityPager(10, 15, null, null); assertEquals(valueOf(25), pager.getNextStart()); pager = new EntityPager(0, 10, 25L, null); assertEquals(valueOf(10), pager.getNextStart()); pager = new EntityPager(10, 10, 25L, null); assertEquals(valueOf(20), pager.getNextStart()); pager = new EntityPager(0, 25, 25L, null); assertNull(pager.getNextStart()); }
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### Question:
EntityPager { public Integer getPrevStart() { if (this.start == 0) return null; else return this.start - this.num >= 0 ? this.start - this.num : 0; } EntityPager(int start, int num, Long total, Iterable<Entity> iterable); int getStart(); int getNum(); Long getTotal(); Integer getNextStart(); Integer getPrevStart(); Iterable<Entity> getIterable(); }### Answer:
@Test void getPrevStart() { EntityPager pager = new EntityPager(10, 15, null, null); assertEquals(valueOf(0), pager.getPrevStart()); pager = new EntityPager(0, 15, 30L, null); assertNull(pager.getPrevStart()); pager = new EntityPager(15, 15, 30L, null); assertEquals(valueOf(0), pager.getPrevStart()); pager = new EntityPager(30, 15, 30L, null); assertEquals(valueOf(15), pager.getPrevStart()); }
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### Question:
ExplainServiceHelper { Set<String> findMatchedWords(Explanation explanation) { Set<String> words = new HashSet<>(); String description = explanation.getDescription(); if (description.startsWith(Options.SUM_OF.toString()) || description.startsWith(Options.PRODUCT_OF.toString())) { if (newArrayList(explanation.getDetails()).stream().allMatch(this::reachLastLevel)) { words.add(extractMatchedWords(explanation.getDetails())); } else { for (Explanation subExplanation : explanation.getDetails()) { words.addAll(findMatchedWords(subExplanation)); } } } else if (description.startsWith(Options.MAX_OF.toString())) { Explanation maxExplanation = newArrayList(explanation.getDetails()).stream() .max( (explanation1, explanation2) -> Float.compare(explanation1.getValue(), explanation2.getValue())) .orElseThrow( () -> new IllegalStateException( "explanation.getDetails() shouldn't return an empty array")); words.addAll(findMatchedWords(maxExplanation)); } else if (description.startsWith(Options.WEIGHT.toString())) { words.add(getMatchedWord(description)); } return words; } }### Answer:
@Test void discoverMatchedQueries() throws JsonSyntaxException, IOException { Explanation explanation = new Gson().fromJson(ResourceUtils.getString("explain_api_example.json"), Explanation.class); Set<String> discoverMatchedQueries = explainServiceHelper.findMatchedWords(explanation); assertEquals(2, discoverMatchedQueries.size()); assertTrue(discoverMatchedQueries.contains("high blood")); assertTrue(discoverMatchedQueries.contains("medic")); }
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### Question:
ExplainServiceHelper { String getMatchedWord(String description) { Matcher matcher = REGEXR_PATTERN.matcher(description); if (matcher.find()) { return matcher.group(1); } throw new MolgenisDataAccessException("Failed to find matched word in : " + description); } }### Answer:
@Test void getMatchedWord() { assertEquals( "blood", explainServiceHelper.getMatchedWord( "weight(label:blood in 20697) [PerFieldSimilarity], result of:")); assertEquals( "blood", explainServiceHelper.getMatchedWord( "weight(label:blood^0.5 in 20697) [PerFieldSimilarity], result of:")); }
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### Question:
SemanticSearchServiceHelper { public String parseBoostQueryString(String queryString, double boost) { return StringUtils.join( removeStopWords(queryString).stream() .map(word -> word + CARET_CHARACTER + boost) .collect(Collectors.toSet()), SPACE_CHAR); } SemanticSearchServiceHelper(
DataService dataService,
OntologyService ontologyService,
TermFrequencyService termFrequencyService); QueryRule createDisMaxQueryRuleForAttribute(
Set<String> searchTerms, Collection<OntologyTerm> ontologyTerms); QueryRule createDisMaxQueryRuleForTerms(List<String> queryTerms); QueryRule createBoostedDisMaxQueryRuleForTerms(
List<String> queryTerms, Double boostValue); QueryRule createShouldQueryRule(String multiOntologyTermIri); List<String> parseOntologyTermQueries(OntologyTerm ontologyTerm); Set<String> getOtLabelAndSynonyms(OntologyTerm ontologyTerm); Map<String, String> collectExpandedQueryMap(
Set<String> queryTerms, Collection<OntologyTerm> ontologyTerms); void collectOntologyTermQueryMap(
Map<String, String> expanedQueryMap, OntologyTerm ontologyTerm); List<String> getAttributeIdentifiers(EntityType sourceEntityType); List<OntologyTerm> findTags(String description, List<String> ontologyIds); String processQueryString(String queryString); String parseBoostQueryString(String queryString, double boost); String escapeCharsExcludingCaretChar(String string); Set<String> removeStopWords(String description); static final int MAX_NUM_TAGS; }### Answer:
@Test void testParseBoostQueryString() { String description = "falling in the ocean!"; String actual = semanticSearchServiceHelper.parseBoostQueryString(description, 0.5); assertEquals("ocean^0.5 falling^0.5", actual); }
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### Question:
SemanticSearchServiceHelper { public String escapeCharsExcludingCaretChar(String string) { return QueryParser.escape(string).replace(ESCAPED_CARET_CHARACTER, CARET_CHARACTER); } SemanticSearchServiceHelper(
DataService dataService,
OntologyService ontologyService,
TermFrequencyService termFrequencyService); QueryRule createDisMaxQueryRuleForAttribute(
Set<String> searchTerms, Collection<OntologyTerm> ontologyTerms); QueryRule createDisMaxQueryRuleForTerms(List<String> queryTerms); QueryRule createBoostedDisMaxQueryRuleForTerms(
List<String> queryTerms, Double boostValue); QueryRule createShouldQueryRule(String multiOntologyTermIri); List<String> parseOntologyTermQueries(OntologyTerm ontologyTerm); Set<String> getOtLabelAndSynonyms(OntologyTerm ontologyTerm); Map<String, String> collectExpandedQueryMap(
Set<String> queryTerms, Collection<OntologyTerm> ontologyTerms); void collectOntologyTermQueryMap(
Map<String, String> expanedQueryMap, OntologyTerm ontologyTerm); List<String> getAttributeIdentifiers(EntityType sourceEntityType); List<OntologyTerm> findTags(String description, List<String> ontologyIds); String processQueryString(String queryString); String parseBoostQueryString(String queryString, double boost); String escapeCharsExcludingCaretChar(String string); Set<String> removeStopWords(String description); static final int MAX_NUM_TAGS; }### Answer:
@Test void testEscapeCharsExcludingCaretChar() { assertEquals( "\\(hypertension^4\\)\\~\\[\\]", semanticSearchServiceHelper.escapeCharsExcludingCaretChar("(hypertension^4)~[]")); assertEquals( "hypertension^4", semanticSearchServiceHelper.escapeCharsExcludingCaretChar("hypertension^4")); }
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### Question:
SemanticSearchServiceImpl implements SemanticSearchService { float distanceFrom(String synonym, Set<String> searchTerms) { String s1 = Stemmer.stemAndJoin(splitIntoTerms(synonym)); String s2 = Stemmer.stemAndJoin(searchTerms); float distance = (float) NGramDistanceAlgorithm.stringMatching(s1, s2) / 100; LOG.debug("Similarity between: {} and {} is {}", s1, s2, distance); return distance; } SemanticSearchServiceImpl(
DataService dataService,
OntologyService ontologyService,
SemanticSearchServiceHelper semanticSearchServiceHelper,
ElasticSearchExplainService elasticSearchExplainService,
OntologyTagService ontologyTagService); Hits<ExplainedAttribute> findAttributes(
EntityType sourceEntityType, Set<String> queryTerms, Collection<OntologyTerm> ontologyTerms); @Override EntityTypeSearchResults findAttributes(
EntityType sourceEntityType, EntityType targetEntityType, Set<String> searchTerms); @Override AttributeSearchResults findAttributes(
EntityType sourceEntityType,
EntityType targetEntityType,
Attribute targetAttribute,
Set<String> searchTerms); Set<String> createLexicalSearchQueryTerms(
Attribute targetAttribute, Set<String> searchTerms); Set<ExplainedQueryString> convertAttributeToExplainedAttribute(
Attribute attribute, Map<String, String> collectExpandedQueryMap, Query<Entity> query); @Override Hits<OntologyTerm> findOntologyTerms(
Attribute attribute, Collection<Ontology> ontologies); }### Answer:
@Test void testDistanceFrom() { assertEquals( semanticSearchService.distanceFrom("Hypertension", ImmutableSet.of("history", "hypertens")), .6923, 0.0001, "String distance should be equal"); assertEquals( semanticSearchService.distanceFrom( "Maternal Hypertension", ImmutableSet.of("history", "hypertens")), .5454, 0.0001, "String distance should be equal"); }
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### Question:
DataConverter { @Nullable @CheckForNull public static String toString(@Nullable @CheckForNull Object source) { if (source == null) { return null; } if (source instanceof String) { return (String) source; } if (source instanceof Iterable<?>) { StringBuilder sb = new StringBuilder(); for (Object obj : (Iterable<?>) source) { if (sb.length() > 0) sb.append(","); sb.append(toString(obj)); } return sb.toString(); } return convert(source, String.class); } private DataConverter(); static Object convert(Object source, Attribute attr); @Nullable @CheckForNull static String toString(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Integer toInt(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Long toLong(@Nullable @CheckForNull Object source); @SuppressWarnings("java:S2447") // null is a valid return value @Nullable @CheckForNull static Boolean toBoolean(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Double toDouble(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static LocalDate toLocalDate(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Instant toInstant(@Nullable @CheckForNull Object source); static List<String> toList(@Nullable @CheckForNull Object source); static void setConversionService(ConversionService conversionService); }### Answer:
@Test void testToStringNull() { assertNull(DataConverter.toString(null)); }
@Test void testToStringString() { assertEquals("abc", DataConverter.toString("abc")); }
@Test void testToStringIterable() { assertEquals("a,b,c", DataConverter.toString(asList("a", "b", "c"))); }
@Test void testToStringInt() { assertEquals("123", DataConverter.toString(123)); }
@Test void toStringIterable() { Iterable<String> iterable = () -> asList("str1", "str2").iterator(); assertEquals("str1,str2", DataConverter.toString(iterable)); }
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### Question:
NGramDistanceAlgorithm { private static double calculateScore( Map<String, Integer> inputStringTokens, Map<String, Integer> ontologyTermTokens) { if (inputStringTokens.size() == 0 || ontologyTermTokens.size() == 0) { return (double) 0; } int totalToken = getTotalNumTokens(inputStringTokens) + getTotalNumTokens(ontologyTermTokens); int numMatchedToken = 0; for (Entry<String, Integer> token : inputStringTokens.entrySet()) { if (ontologyTermTokens.containsKey(token.getKey())) { numMatchedToken += Math.min(token.getValue(), ontologyTermTokens.get(token.getKey())); } } if (totalToken == 0) { return 0; } else { return 2.0 * numMatchedToken / totalToken * 100; } } private NGramDistanceAlgorithm(); static double stringMatching(String queryOne, String queryTwo); static Map<String, Integer> createNGrams(String inputQuery, boolean removeStopWords); static final Set<String> STOPWORDSLIST; }### Answer:
@Test void calculateScore() { assertEquals(100.0, stringMatching("hypertensive", "hypertensive")); assertEquals( NGramDistanceAlgorithm.stringMatching("hypertensive disorder", "hypertensive order"), 72.727, 0.001); assertEquals(0.0, stringMatching("hypertensive", "diabetes")); assertEquals(0.0, stringMatching("", "")); }
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### Question:
Stemmer { public static String replaceIllegalCharacter(String string) { return string.replaceAll(ILLEGAL_REGEX_PATTERN, " ").replaceAll(" +", " ").trim().toLowerCase(); } private Stemmer(); static String cleanStemPhrase(String phrase); static String stem(String word); static String stemAndJoin(Set<String> terms); static String replaceIllegalCharacter(String string); }### Answer:
@Test void replaceIllegalCharacter() { assertEquals("hello world", Stemmer.replaceIllegalCharacter("Hello__world!")); assertEquals("hello world 1234", Stemmer.replaceIllegalCharacter("Hello__world! 1234")); assertEquals("hello 45 world 1234", Stemmer.replaceIllegalCharacter("Hello_#45_world! 1234")); }
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### Question:
Stemmer { public static String cleanStemPhrase(String phrase) { StringBuilder stringBuilder = new StringBuilder(); for (String word : replaceIllegalCharacter(phrase).split(" ")) { String stemmedWord = stem(word); if (StringUtils.isNotEmpty(stemmedWord)) { if (stringBuilder.length() > 0) { stringBuilder.append(' '); } stringBuilder.append(stemmedWord); } } return stringBuilder.toString(); } private Stemmer(); static String cleanStemPhrase(String phrase); static String stem(String word); static String stemAndJoin(Set<String> terms); static String replaceIllegalCharacter(String string); }### Answer:
@Test void stemPhrase() { assertEquals("i like smoke", cleanStemPhrase("i like smoking!")); assertEquals("it not possibl", cleanStemPhrase("it`s not possibilities!")); }
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### Question:
Stemmer { public static String stem(String word) { PorterStemmer porterStemmer = new PorterStemmer(); porterStemmer.setCurrent(word); porterStemmer.stem(); return porterStemmer.getCurrent(); } private Stemmer(); static String cleanStemPhrase(String phrase); static String stem(String word); static String stemAndJoin(Set<String> terms); static String replaceIllegalCharacter(String string); }### Answer:
@Test void stem() { assertEquals("us", Stemmer.stem("use")); assertEquals("hypertens", Stemmer.stem("hypertension")); PorterStemmer porterStemmer = new PorterStemmer(); porterStemmer.setCurrent("use"); porterStemmer.stem(); assertEquals("us", porterStemmer.getCurrent()); }
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### Question:
PretendingEntity extends AbstractEntityDecorator { @Override public EntityType getEntityType() { String id = delegate().getEntityType().getId(); if (copiedEntityTypes.containsKey(id)) { return copiedEntityTypes.get(id); } else { return delegate().getEntityType(); } } PretendingEntity(Entity entity, Map<String, EntityType> copiedEntityTypes); @Override EntityType getEntityType(); @Override Entity getEntity(String attributeName); @Override @SuppressWarnings("unchecked") E getEntity(String attributeName, Class<E> clazz); @Override Iterable<Entity> getEntities(String attributeName); @Override @SuppressWarnings("unchecked") Iterable<E> getEntities(String attributeName, Class<E> clazz); }### Answer:
@Test void testPretendingEntityIsNotCopy() { Entity entity = mock(Entity.class); EntityType entityType = mock(EntityType.class); when(entityType.getId()).thenReturn("oldId"); when(entity.getEntityType()).thenReturn(entityType); PretendingEntity pretendingEntity = new PretendingEntity(entity, new HashMap<>()); assertEquals(entityType, pretendingEntity.getEntityType()); }
@Test void testPretendingEntityIsCopy() { Entity entity = mock(Entity.class); EntityType entityType = mock(EntityType.class); when(entityType.getId()).thenReturn("oldId"); EntityType entityTypeCopy = mock(EntityType.class); when(entity.getEntityType()).thenReturn(entityType); Map<String, EntityType> copiedEntityTypes = ImmutableMap.of("oldId", entityTypeCopy); PretendingEntity pretendingEntity = new PretendingEntity(entity, copiedEntityTypes); assertEquals(entityTypeCopy, pretendingEntity.getEntityType()); }
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### Question:
PretendingEntity extends AbstractEntityDecorator { @Override public Entity getEntity(String attributeName) { Entity entity = delegate().getEntity(attributeName); return entity != null ? newPretendingEntity(entity) : null; } PretendingEntity(Entity entity, Map<String, EntityType> copiedEntityTypes); @Override EntityType getEntityType(); @Override Entity getEntity(String attributeName); @Override @SuppressWarnings("unchecked") E getEntity(String attributeName, Class<E> clazz); @Override Iterable<Entity> getEntities(String attributeName); @Override @SuppressWarnings("unchecked") Iterable<E> getEntities(String attributeName, Class<E> clazz); }### Answer:
@Test void testTypedReferenceIsNotFileMeta() { Entity entity = mock(Entity.class); PretendingEntity pretendingEntity = new PretendingEntity(entity, new HashMap<>()); Exception exception = assertThrows( UnsupportedOperationException.class, () -> pretendingEntity.getEntity("ref", Plugin.class)); assertThat(exception.getMessage()).containsPattern("Can't return typed pretending entities"); }
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### Question:
PretendingEntity extends AbstractEntityDecorator { @Override public Iterable<Entity> getEntities(String attributeName) { return stream(delegate().getEntities(attributeName)) .map(this::newPretendingEntity) .collect(toList()); } PretendingEntity(Entity entity, Map<String, EntityType> copiedEntityTypes); @Override EntityType getEntityType(); @Override Entity getEntity(String attributeName); @Override @SuppressWarnings("unchecked") E getEntity(String attributeName, Class<E> clazz); @Override Iterable<Entity> getEntities(String attributeName); @Override @SuppressWarnings("unchecked") Iterable<E> getEntities(String attributeName, Class<E> clazz); }### Answer:
@Test void testTypedMultiReferenceNotFileMeta() { Entity entity = mock(Entity.class); PretendingEntity pretendingEntity = new PretendingEntity(entity, new HashMap<>()); Exception exception = assertThrows( UnsupportedOperationException.class, () -> pretendingEntity.getEntities("ref", Plugin.class)); assertThat(exception.getMessage()).containsPattern("Can't return typed pretending entities"); }
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### Question:
RelationTransformer { static void transformPackage(EntityType entityType, Map<String, Package> newPackages) { if (newPackages.isEmpty()) { return; } Package entityTypePackage = entityType.getPackage(); if (entityTypePackage != null) { String packageId = entityTypePackage.getId(); if (newPackages.containsKey(packageId)) { entityType.setPackage(newPackages.get(packageId)); } } } private RelationTransformer(); }### Answer:
@Test void testTransformPackageEmptyMap() { EntityType entityType = mock(EntityType.class); RelationTransformer.transformPackage(entityType, emptyMap()); verify(entityType, never()).setPackage(any(Package.class)); }
@SuppressWarnings("ConstantConditions") @Test void testTransformPackage() { EntityType entityType = mock(EntityType.class, RETURNS_DEEP_STUBS); when(entityType.getPackage().getId()).thenReturn("oldPackage"); Package newPackage = mock(Package.class); Map<String, Package> newPackages = ImmutableMap.of("oldPackage", newPackage); RelationTransformer.transformPackage(entityType, newPackages); verify(entityType).setPackage(newPackage); }
@SuppressWarnings("ConstantConditions") @Test void testTransformPackageNoChange() { EntityType entityType = mock(EntityType.class, RETURNS_DEEP_STUBS); when(entityType.getPackage().getId()).thenReturn("oldPackage"); Package newPackage = mock(Package.class); Map<String, Package> newPackages = ImmutableMap.of("otherOldPackage", newPackage); RelationTransformer.transformPackage(entityType, newPackages); verify(entityType, never()).setPackage(newPackage); }
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### Question:
RelationTransformer { static void transformExtends(EntityType entityType, Map<String, EntityType> newEntityTypes) { if (newEntityTypes.isEmpty()) { return; } EntityType entityTypeExtends = entityType.getExtends(); if (entityTypeExtends != null) { String extendsId = entityTypeExtends.getId(); if (newEntityTypes.containsKey(extendsId)) { entityType.setExtends(newEntityTypes.get(extendsId)); } } } private RelationTransformer(); }### Answer:
@Test void testTransformExtendsEmptyMap() { EntityType entityType = mock(EntityType.class); RelationTransformer.transformExtends(entityType, emptyMap()); verify(entityType, never()).setExtends(any(EntityType.class)); }
@SuppressWarnings("ConstantConditions") @Test void testTransformExtends() { EntityType entityType = mock(EntityType.class, RETURNS_DEEP_STUBS); when(entityType.getExtends().getId()).thenReturn("oldExtends"); EntityType newExtends = mock(EntityType.class); Map<String, EntityType> newEntityTypes = ImmutableMap.of("oldExtends", newExtends); RelationTransformer.transformExtends(entityType, newEntityTypes); verify(entityType).setExtends(newExtends); }
@SuppressWarnings("ConstantConditions") @Test void testTransformExtendsNoChange() { EntityType entityType = mock(EntityType.class, RETURNS_DEEP_STUBS); when(entityType.getExtends().getId()).thenReturn("oldExtends"); EntityType newExtends = mock(EntityType.class); Map<String, EntityType> newEntityTypes = ImmutableMap.of("otherOldExtends", newExtends); RelationTransformer.transformExtends(entityType, newEntityTypes); verify(entityType, never()).setExtends(newExtends); }
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### Question:
RelationTransformer { static void transformRefEntities(EntityType entityType, Map<String, EntityType> newEntityTypes) { if (newEntityTypes.isEmpty()) { return; } stream(entityType.getAtomicAttributes()) .filter(EntityTypeUtils::isReferenceType) .forEach(attr -> transformRefEntity(attr, newEntityTypes)); } private RelationTransformer(); }### Answer:
@Test void testTransformRefEntitiesEmptyMap() { EntityType entityType = mock(EntityType.class); RelationTransformer.transformRefEntities(entityType, emptyMap()); verify(entityType, never()).getAtomicAttributes(); }
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### Question:
RelationTransformer { private static void transformRefEntity( Attribute attribute, Map<String, EntityType> newEntityTypes) { if (attribute.hasRefEntity()) { String refId = attribute.getRefEntity().getId(); if (newEntityTypes.containsKey(refId)) { attribute.setRefEntity(newEntityTypes.get(refId)); } } } private RelationTransformer(); }### Answer:
@SuppressWarnings("ConstantConditions") @Test void testTransformRefEntity() { EntityType entityType = mock(EntityType.class); Attribute refAttr1 = mock(Attribute.class, RETURNS_DEEP_STUBS); Attribute refAttr2 = mock(Attribute.class, RETURNS_DEEP_STUBS); Attribute normalAttr = mock(Attribute.class); when(refAttr1.getIdentifier()).thenReturn("refAttr1"); when(refAttr1.getDataType()).thenReturn(MREF); when(refAttr1.hasRefEntity()).thenReturn(true); when(refAttr1.getRefEntity().getId()).thenReturn("ref1"); when(refAttr2.getIdentifier()).thenReturn("refAttr2"); when(refAttr2.getDataType()).thenReturn(XREF); when(refAttr2.hasRefEntity()).thenReturn(true); when(refAttr2.getRefEntity().getId()).thenReturn("ref2"); when(normalAttr.getIdentifier()).thenReturn("normalAttr"); when(normalAttr.getDataType()).thenReturn(STRING); EntityType newRef1 = mock(EntityType.class); EntityType newRef3 = mock(EntityType.class); when(entityType.getAtomicAttributes()).thenReturn(asList(refAttr1, refAttr2, normalAttr)); Map<String, EntityType> newEntityTypes = ImmutableMap.of("ref1", newRef1, "ref3", newRef3); RelationTransformer.transformRefEntities(entityType, newEntityTypes); verify(refAttr1).setRefEntity(newRef1); verify(refAttr2, never()).setRefEntity(any(EntityType.class)); verify(normalAttr, never()).setRefEntity(any(EntityType.class)); }
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### Question:
RelationTransformer { static void transformMappedBys(EntityType entityType, Map<String, Attribute> newAttributes) { if (newAttributes.isEmpty()) { return; } stream(entityType.getAtomicAttributes()) .filter(Attribute::isMappedBy) .forEach(attr -> transformMappedBy(attr, newAttributes)); } private RelationTransformer(); }### Answer:
@Test void testTransformMappedBysEmptyMap() { EntityType entityType = mock(EntityType.class); RelationTransformer.transformMappedBys(entityType, emptyMap()); verify(entityType, never()).getAtomicAttributes(); }
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### Question:
LabelGenerator { static String generateUniqueLabel(String label, Set<String> existingLabels) { StringBuilder newLabel = new StringBuilder(label); while (existingLabels.contains(newLabel.toString())) { newLabel.append(POSTFIX); } return newLabel.toString(); } private LabelGenerator(); }### Answer:
@Test void testGenerateLabelAlreadyUnique() { Set<String> existingLabels = newHashSet("labelA", "labelB", "labelC"); String result = LabelGenerator.generateUniqueLabel("labelX", existingLabels); assertEquals("labelX", result); }
@Test void testGenerateUniqueLabel() { Set<String> existingLabels = newHashSet("labelA", "labelB", "labelC"); String result = LabelGenerator.generateUniqueLabel("labelB", existingLabels); assertEquals("labelB (Copy)", result); }
@Test void testGenerateUniqueLabelRecursive() { Set<String> existingLabels = newHashSet("labelA", "labelB", "labelB (Copy)", "labelC"); String result = LabelGenerator.generateUniqueLabel("labelB", existingLabels); assertEquals("labelB (Copy) (Copy)", result); }
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### Question:
EntityTypeMetadataCopier { public EntityType copy(EntityType entityType, CopyState state) { EntityType copy = EntityType.newInstance(entityType, SHALLOW_COPY_ATTRS, attributeFactory); Map<String, Attribute> copiedAttributes = EntityType.deepCopyAttributes(entityType, copy, attributeFactory); state.copiedAttributes().putAll(copiedAttributes); return copy; } EntityTypeMetadataCopier(AttributeFactory attributeFactory); EntityType copy(EntityType entityType, CopyState state); }### Answer:
@Test void testCopy() { EntityType entityType = mock(EntityType.class); EntityType entityTypeMeta = mockEntityTypeMetadata(); when(entityType.getEntityType()).thenReturn(entityTypeMeta); Attribute idAttr = mock(Attribute.class); when(idAttr.getIdentifier()).thenReturn("id"); when(idAttr.getName()).thenReturn("id"); Attribute idAttrCopy = mock(Attribute.class); when(idAttrCopy.getName()).thenReturn("id"); when(idAttrCopy.setEntity(any())).thenReturn(idAttrCopy); when(entityType.getOwnAllAttributes()).thenReturn(singletonList(idAttr)); when(attributeFactory.create()).thenReturn(idAttrCopy); CopyState state = CopyState.create(null, mock(Progress.class)); copier.copy(entityType, state); assertEquals(of("id", idAttrCopy), state.copiedAttributes()); }
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### Question:
ResourceIdentifierUtil { public static List<ResourceIdentifier> getResourcesFromJson(String resourceJson) { Gson gson = new Gson(); List<ResourceIdentifier> resources = newArrayList(); @SuppressWarnings("unchecked") List<Map<String, String>> jsonList = gson.fromJson(resourceJson, List.class); for (Map<String, String> jsonResource : jsonList) { resources.add( ResourceIdentifier.create( ResourceType.valueOf(jsonResource.get("type")), jsonResource.get("id"))); } return resources; } private ResourceIdentifierUtil(); static List<ResourceIdentifier> getResourcesFromJson(String resourceJson); }### Answer:
@Test void testGetResourcesFromJson() { String json = "[{'id':'idValue1','type':'ENTITY_TYPE_ABSTRACT'},{'id':'idValue2','type':'PACKAGE'}]"; ResourceIdentifier expected1 = ResourceIdentifier.create(ResourceType.ENTITY_TYPE_ABSTRACT, "idValue1"); ResourceIdentifier expected2 = ResourceIdentifier.create(ResourceType.PACKAGE, "idValue2"); List<ResourceIdentifier> expected = newArrayList(expected1, expected2); assertEquals(expected, getResourcesFromJson(json)); }
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### Question:
NavigatorController extends PluginController { @GetMapping("/**") public String init(Model model) { model.addAttribute(KEY_BASE_URL, menuReaderService.findMenuItemPath(ID)); asList("dataexplorer", "metadata-manager", "importwizard") .forEach( pluginId -> model.addAttribute( pluginId.replace('-', '_'), menuReaderService.findMenuItemPath(pluginId))); return "view-navigator"; } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testInit() throws Exception { when(menuReaderService.findMenuItemPath(NavigatorController.ID)).thenReturn("/test/path"); when(localeResolver.resolveLocale(any())).thenReturn(Locale.FRENCH); mockMvc .perform(get(NavigatorController.URI)) .andExpect(status().isOk()) .andExpect(view().name("view-navigator")) .andExpect(model().attribute("baseUrl", "/test/path")); }
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### Question:
NavigatorController extends PluginController { @GetMapping("/search") @ResponseBody public SearchResourcesResponse searchResources(@RequestParam(value = "query") String query) { List<Resource> resources = navigatorService.findResources(query); return SearchResourcesResponse.create(resources); } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testSearchResources() throws Exception { String query = "text"; when(navigatorService.findResources(query)).thenReturn(getMockResources()); String expectedContent = "{\"resources\":[{\"type\":\"PACKAGE\",\"id\":\"myPackageId\",\"label\":\"label\",\"description\":\"description\",\"hidden\":false,\"readonly\":false}]}"; mockMvc .perform(get(NavigatorController.URI + "/search?query=" + query)) .andExpect(status().isOk()) .andExpect(content().string(expectedContent)); }
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### Question:
NavigatorController extends PluginController { @PostMapping("/copy") @ResponseBody public JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest) { return navigatorService.copyResources( copyResourcesRequest.getResources(), copyResourcesRequest.getTargetFolderId()); } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testCopyResources() throws Exception { String targetFolderId = "myFolderId"; List<ResourceIdentifier> resources = getMockResourceIdentifiers(); JobExecution jobExecution = mock(JobExecution.class); EntityType entityType = mock(EntityType.class); when(jobExecution.getEntityType()).thenReturn(entityType); when(navigatorService.copyResources(resources, targetFolderId)).thenReturn(jobExecution); String json = "{\"resources\":[{\"type\":\"PACKAGE\",\"id\":\"myPackageId\",\"label\":\"label\",\"description\":\"description\"}],\"targetFolderId\":\"myFolderId\"}"; mockMvc .perform( post(NavigatorController.URI + "/copy").content(json).contentType(APPLICATION_JSON)) .andExpect(status().isOk()); }
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### Question:
NavigatorController extends PluginController { @PostMapping("/download") @ResponseBody public JobExecution downloadResources( @RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest) { return navigatorService.downloadResources(downloadResourcesRequest.getResources()); } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testDownloadResources() throws Exception { List<ResourceIdentifier> resources = getMockResourceIdentifiers(); JobExecution jobExecution = mock(JobExecution.class); EntityType entityType = mock(EntityType.class); when(jobExecution.getEntityType()).thenReturn(entityType); when(navigatorService.downloadResources(resources)).thenReturn(jobExecution); String json = "{\"resources\":[{\"type\":\"PACKAGE\",\"id\":\"myPackageId\",\"label\":\"label\",\"description\":\"description\"}],\"targetFolderId\":\"myFolderId\"}"; mockMvc .perform( post(NavigatorController.URI + "/download").content(json).contentType(APPLICATION_JSON)) .andExpect(status().isOk()); }
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### Question:
NavigatorController extends PluginController { @PostMapping("/move") @ResponseStatus(OK) public void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest) { navigatorService.moveResources( moveResourcesRequest.getResources(), moveResourcesRequest.getTargetFolderId()); } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testMoveResources() throws Exception { String targetFolderId = "myFolderId"; List<ResourceIdentifier> resources = getMockResourceIdentifiers(); String json = "{\"resources\":[{\"type\":\"PACKAGE\",\"id\":\"myPackageId\",\"label\":\"label\",\"description\":\"description\"}],\"targetFolderId\":\"myFolderId\"}"; mockMvc .perform( post(NavigatorController.URI + "/move").content(json).contentType(APPLICATION_JSON)) .andExpect(status().isOk()); verify(navigatorService).moveResources(resources, targetFolderId); }
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### Question:
NavigatorController extends PluginController { @PutMapping("/update") @ResponseStatus(OK) public void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest) { navigatorService.updateResource(updateResourceRequest.getResource()); } NavigatorController(MenuReaderService menuReaderService, NavigatorService navigatorService); @GetMapping("/**") String init(Model model); @GetMapping("/get") @ResponseBody GetResourcesResponse getResources(
@RequestParam(value = "folderId", required = false) @Nullable @CheckForNull String folderId); @GetMapping("/search") @ResponseBody SearchResourcesResponse searchResources(@RequestParam(value = "query") String query); @PutMapping("/update") @ResponseStatus(OK) void updateResource(@RequestBody @Valid UpdateResourceRequest updateResourceRequest); @PostMapping("/copy") @ResponseBody JobExecution copyResources(@RequestBody @Valid CopyResourcesRequest copyResourcesRequest); @PostMapping("/download") @ResponseBody JobExecution downloadResources(
@RequestBody @Valid DownloadResourcesRequest downloadResourcesRequest); @PostMapping("/move") @ResponseStatus(OK) void moveResources(@RequestBody @Valid MoveResourcesRequest moveResourcesRequest); @DeleteMapping("/delete") @ResponseBody JobExecution deleteResources(
@RequestBody @Valid DeleteResourcesRequest deleteItemsRequest); static final String ID; static final String URI; }### Answer:
@Test void testUpdateResource() throws Exception { String json = "{\"resource\":{\"id\":\"p0\",\"type\":\"PACKAGE\",\"label\":\"label\",\"description\":\"description\"}}"; mockMvc .perform( put(NavigatorController.URI + "/update").content(json).contentType(APPLICATION_JSON)) .andExpect(status().isOk()); verify(navigatorService) .updateResource( Resource.builder() .setType(ResourceType.PACKAGE) .setId("p0") .setLabel("label") .setDescription("description") .build()); }
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### Question:
ResourceDeleteServiceImpl implements ResourceDeleteService { ResourceDeleteServiceImpl(DataService dataService, ContextMessageSource contextMessageSource) { this.dataService = requireNonNull(dataService); this.contextMessageSource = requireNonNull(contextMessageSource); } ResourceDeleteServiceImpl(DataService dataService, ContextMessageSource contextMessageSource); @Override Void delete(List<ResourceIdentifier> resources, Progress progress); }### Answer:
@Test void testResourceDeleteServiceImpl() { assertThrows(NullPointerException.class, () -> new ResourceDeleteServiceImpl(null, null)); }
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### Question:
NavigatorServiceImpl implements NavigatorService { NavigatorServiceImpl( DataService dataService, JobExecutor jobExecutor, ResourceDownloadJobExecutionFactory downloadJobExecutionFactory, ResourceCopyJobExecutionFactory copyJobExecutionFactory, ResourceDeleteJobExecutionFactory resourceDeleteJobExecutionFactory) { this.dataService = requireNonNull(dataService); this.jobExecutor = requireNonNull(jobExecutor); this.downloadJobExecutionFactory = requireNonNull(downloadJobExecutionFactory); this.copyJobExecutionFactory = requireNonNull(copyJobExecutionFactory); this.resourceDeleteJobExecutionFactory = requireNonNull(resourceDeleteJobExecutionFactory); } NavigatorServiceImpl(
DataService dataService,
JobExecutor jobExecutor,
ResourceDownloadJobExecutionFactory downloadJobExecutionFactory,
ResourceCopyJobExecutionFactory copyJobExecutionFactory,
ResourceDeleteJobExecutionFactory resourceDeleteJobExecutionFactory); @Transactional(readOnly = true) @Override @Nullable @CheckForNull Folder getFolder(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> getResources(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> findResources(String query); @Transactional @Override void moveResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution copyResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution downloadResources(List<ResourceIdentifier> resources); @Transactional @Override JobExecution deleteResources(List<ResourceIdentifier> resources); @Transactional @Override void updateResource(Resource resource); }### Answer:
@Test void testNavigatorServiceImpl() { assertThrows( NullPointerException.class, () -> new NavigatorServiceImpl(null, null, null, null, null)); }
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### Question:
FallbackLocaleSupplierImpl implements FallbackLocaleSupplier { FallbackLocaleSupplierImpl(AppSettings appSettings) { this.appSettings = requireNonNull(appSettings); } FallbackLocaleSupplierImpl(AppSettings appSettings); @Override Locale get(); }### Answer:
@Test void testFallbackLocaleSupplierImpl() { assertThrows(NullPointerException.class, () -> new FallbackLocaleSupplierImpl(null)); }
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### Question:
DataConverter { public static List<String> toList(@Nullable @CheckForNull Object source) { List<String> stringList; if (source == null) { stringList = emptyList(); } else if (source instanceof Iterable<?>) { Iterable<?> iterable = (Iterable<?>) source; stringList = stream(iterable).map(DataConverter::toString).collect(Collectors.toList()); } else if (source instanceof String) { String string = (String) source; stringList = ListEscapeUtils.toList(string); } else { stringList = ListEscapeUtils.toList(source.toString()); } return stringList; } private DataConverter(); static Object convert(Object source, Attribute attr); @Nullable @CheckForNull static String toString(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Integer toInt(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Long toLong(@Nullable @CheckForNull Object source); @SuppressWarnings("java:S2447") // null is a valid return value @Nullable @CheckForNull static Boolean toBoolean(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Double toDouble(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static LocalDate toLocalDate(@Nullable @CheckForNull Object source); @Nullable @CheckForNull static Instant toInstant(@Nullable @CheckForNull Object source); static List<String> toList(@Nullable @CheckForNull Object source); static void setConversionService(ConversionService conversionService); }### Answer:
@Test void testToListNull() { assertEquals(emptyList(), toList(null)); }
@Test void testToListIterableString() { String value0 = "0"; String value1 = "1"; assertEquals(asList(value0, value1), toList(asList(value0, value1))); }
@Test void testToListString() { String value = "a,b,c"; assertEquals(asList("a", "b", "c"), toList(value)); }
@Test void testToListOther() { assertEquals(singletonList("0"), toList(0L)); }
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### Question:
NavigatorServiceImpl implements NavigatorService { @Override public JobExecution downloadResources(List<ResourceIdentifier> resources) { if (resources.isEmpty()) { throw new IllegalArgumentException(MESSAGE_EMPTY_RESOURCES); } ResourceDownloadJobExecution jobExecution = downloadJobExecutionFactory.create(); jobExecution.setResources(resources); jobExecutor.submit(jobExecution); return jobExecution; } NavigatorServiceImpl(
DataService dataService,
JobExecutor jobExecutor,
ResourceDownloadJobExecutionFactory downloadJobExecutionFactory,
ResourceCopyJobExecutionFactory copyJobExecutionFactory,
ResourceDeleteJobExecutionFactory resourceDeleteJobExecutionFactory); @Transactional(readOnly = true) @Override @Nullable @CheckForNull Folder getFolder(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> getResources(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> findResources(String query); @Transactional @Override void moveResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution copyResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution downloadResources(List<ResourceIdentifier> resources); @Transactional @Override JobExecution deleteResources(List<ResourceIdentifier> resources); @Transactional @Override void updateResource(Resource resource); }### Answer:
@WithMockUser @Test void testDownloadResources() { ResourceDownloadJobExecution downloadJobExecution = mock(ResourceDownloadJobExecution.class); when(downloadJobExecutionFactory.create()).thenReturn(downloadJobExecution); List<ResourceIdentifier> resources = asList( ResourceIdentifier.builder().setType(ResourceType.PACKAGE).setId("p0").build(), ResourceIdentifier.builder().setType(ResourceType.ENTITY_TYPE).setId("e0").build()); assertEquals(downloadJobExecution, navigatorServiceImpl.downloadResources(resources)); verify(downloadJobExecution).setResources(resources); verify(jobExecutor).submit(downloadJobExecution); }
@WithMockUser @Test void testDownloadResourcesNoResources() { assertThrows( IllegalArgumentException.class, () -> navigatorServiceImpl.downloadResources(emptyList())); }
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### Question:
NavigatorServiceImpl implements NavigatorService { @Transactional @Override public JobExecution deleteResources(List<ResourceIdentifier> resources) { if (resources.isEmpty()) { throw new IllegalArgumentException(MESSAGE_EMPTY_RESOURCES); } ResourceDeleteJobExecution jobExecution = resourceDeleteJobExecutionFactory.create(); jobExecution.setResources(resources); jobExecutor.submit(jobExecution); return jobExecution; } NavigatorServiceImpl(
DataService dataService,
JobExecutor jobExecutor,
ResourceDownloadJobExecutionFactory downloadJobExecutionFactory,
ResourceCopyJobExecutionFactory copyJobExecutionFactory,
ResourceDeleteJobExecutionFactory resourceDeleteJobExecutionFactory); @Transactional(readOnly = true) @Override @Nullable @CheckForNull Folder getFolder(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> getResources(@Nullable @CheckForNull String folderId); @Transactional(readOnly = true) @Override List<Resource> findResources(String query); @Transactional @Override void moveResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution copyResources(
List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetFolderId); @Override JobExecution downloadResources(List<ResourceIdentifier> resources); @Transactional @Override JobExecution deleteResources(List<ResourceIdentifier> resources); @Transactional @Override void updateResource(Resource resource); }### Answer:
@WithMockUser @Test void testDeleteResources() { ResourceDeleteJobExecution deleteJobExecution = mock(ResourceDeleteJobExecution.class); when(deleteJobExecutionFactory.create()).thenReturn(deleteJobExecution); List<ResourceIdentifier> resources = asList( ResourceIdentifier.builder().setType(ResourceType.PACKAGE).setId("p0").build(), ResourceIdentifier.builder().setType(ResourceType.ENTITY_TYPE).setId("e0").build()); assertEquals(deleteJobExecution, navigatorServiceImpl.deleteResources(resources)); verify(deleteJobExecution).setResources(resources); verify(jobExecutor).submit(deleteJobExecution); }
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### Question:
ScriptUtils { public static String generateScript(Script script, Map<String, Object> parameterValues) { StringWriter stringWriter = new StringWriter(); try { Template template = new Template(null, new StringReader(script.getContent()), new Configuration(VERSION)); template.process(parameterValues, stringWriter); } catch (TemplateException | IOException e) { throw new GenerateScriptException( "Error processing parameters for script [" + script.getName() + "]. " + e.getMessage()); } return stringWriter.toString(); } private ScriptUtils(); static String generateScript(Script script, Map<String, Object> parameterValues); static boolean hasScriptVariable(Script script, String variable); static Set<String> getScriptVariables(Script script); }### Answer:
@Test void testGenerateScript() { Script script = mock(Script.class); when(script.getContent()).thenReturn("Hey ${name}"); Map<String, Object> parameterValues = Collections.singletonMap("name", "Piet"); String renderedScript = ScriptUtils.generateScript(script, parameterValues); assertEquals("Hey Piet", renderedScript); }
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### Question:
ScriptUtils { public static boolean hasScriptVariable(Script script, String variable) { return getScriptVariables(script).contains(variable); } private ScriptUtils(); static String generateScript(Script script, Map<String, Object> parameterValues); static boolean hasScriptVariable(Script script, String variable); static Set<String> getScriptVariables(Script script); }### Answer:
@Test void testHasScriptVariableTrue() { Script script = when(mock(Script.class).getContent()).thenReturn("lorum ${x}").getMock(); assertTrue(ScriptUtils.hasScriptVariable(script, "x")); }
@Test void testHasScriptVariableTrueHash() { Script script = when(mock(Script.class).getContent()).thenReturn("lorum ${x.y}").getMock(); assertTrue(ScriptUtils.hasScriptVariable(script, "x")); }
@Test void testHasScriptVariableFalse() { Script script = when(mock(Script.class).getContent()).thenReturn("lorum ${x}").getMock(); assertFalse(ScriptUtils.hasScriptVariable(script, "y")); }
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### Question:
ScriptUtils { public static Set<String> getScriptVariables(Script script) { Set<String> scriptExpressions = new LinkedHashSet<>(); Configuration configuration = new Configuration(VERSION); configuration.setTemplateExceptionHandler( (te, env, out) -> { if (te instanceof InvalidReferenceException) { scriptExpressions.add(te.getBlamedExpressionString()); return; } throw te; }); try { Template template = new Template(null, new StringReader(script.getContent()), configuration); template.process(emptyMap(), new StringWriter()); } catch (TemplateException | IOException e) { throw new GenerateScriptException( "Error processing parameters for script [" + script.getName() + "]. " + e.getMessage()); } return scriptExpressions; } private ScriptUtils(); static String generateScript(Script script, Map<String, Object> parameterValues); static boolean hasScriptVariable(Script script, String variable); static Set<String> getScriptVariables(Script script); }### Answer:
@Test void testGetScriptVariables() { Script script = when(mock(Script.class).getContent()).thenReturn("lorum ${x} ipsum ${y.z}").getMock(); assertEquals(newLinkedHashSet(asList("x", "y")), getScriptVariables(script)); }
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### Question:
PythonScriptRunner implements ScriptRunner { @Override public boolean hasFileOutput(Script script) { return false; } PythonScriptRunner(PythonScriptExecutor pythonScriptExecutor); @Override String getName(); @Override boolean hasFileOutput(Script script); @Override String runScript(Script script, Map<String, Object> parameters); }### Answer:
@Test void testHasFileOutput() { assertFalse(pythonScriptRunner.hasFileOutput(mock(Script.class))); }
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### Question:
PermissionRegistry { public Set<PermissionSet> getPermissions(Permission permission) { return mapping.get(permission); } void addMapping(Permission permission, PermissionSet... permissionSet); Set<PermissionSet> getPermissions(Permission permission); Map<PermissionSet, Set<Permission>> getPermissionSets(); }### Answer:
@Test void testGetPermissions() { assertEquals(of(WRITE, WRITEMETA), permissionRegistry.getPermissions(TestPermission.UPDATE)); }
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### Question:
PermissionRegistry { public Map<PermissionSet, Set<Permission>> getPermissionSets() { return mapping.entries().stream() .collect(groupingBy(Entry::getValue, LinkedHashMap::new, mapping(Entry::getKey, toSet()))); } void addMapping(Permission permission, PermissionSet... permissionSet); Set<PermissionSet> getPermissions(Permission permission); Map<PermissionSet, Set<Permission>> getPermissionSets(); }### Answer:
@Test void testGetPermissionSets() { Map<PermissionSet, Set<Permission>> expected = ImmutableMap.of( WRITEMETA, ImmutableSet.of(TestPermission.READ, TestPermission.UPDATE, TestPermission.DELETE), WRITE, ImmutableSet.of(TestPermission.READ, TestPermission.UPDATE, TestPermission.DELETE), READ, ImmutableSet.of(TestPermission.READ)); assertEquals(expected, permissionRegistry.getPermissionSets()); }
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### Question:
MolgenisPasswordEncoder implements PasswordEncoder { public MolgenisPasswordEncoder(BCryptPasswordEncoder bCryptPasswordEncoder) { if (bCryptPasswordEncoder == null) throw new IllegalArgumentException("BCrypt password encoder is null"); this.bCryptPasswordEncoder = bCryptPasswordEncoder; } MolgenisPasswordEncoder(BCryptPasswordEncoder bCryptPasswordEncoder); @Override String encode(CharSequence rawPassword); @Override boolean matches(CharSequence rawPassword, String encodedPassword); }### Answer:
@Test void MolgenisPasswordEncoder() { assertThrows(IllegalArgumentException.class, () -> new MolgenisPasswordEncoder(null)); }
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### Question:
MolgenisPasswordEncoder implements PasswordEncoder { @Override public String encode(CharSequence rawPassword) { return bCryptPasswordEncoder.encode(rawPassword); } MolgenisPasswordEncoder(BCryptPasswordEncoder bCryptPasswordEncoder); @Override String encode(CharSequence rawPassword); @Override boolean matches(CharSequence rawPassword, String encodedPassword); }### Answer:
@Test void encode() { String password = "password"; String encodedPassword = "encoded-password"; BCryptPasswordEncoder bCryptPasswordEncoder = mock(BCryptPasswordEncoder.class); when(bCryptPasswordEncoder.encode(password)).thenReturn(encodedPassword); assertEquals( encodedPassword, new MolgenisPasswordEncoder(bCryptPasswordEncoder).encode(password)); }
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### Question:
MolgenisPasswordEncoder implements PasswordEncoder { @Override public boolean matches(CharSequence rawPassword, String encodedPassword) { return bCryptPasswordEncoder.matches(rawPassword, encodedPassword); } MolgenisPasswordEncoder(BCryptPasswordEncoder bCryptPasswordEncoder); @Override String encode(CharSequence rawPassword); @Override boolean matches(CharSequence rawPassword, String encodedPassword); }### Answer:
@Test void matches() { String password = "password"; String encodedPassword = "encoded-password"; BCryptPasswordEncoder bCryptPasswordEncoder = mock(BCryptPasswordEncoder.class); when(bCryptPasswordEncoder.matches(password, encodedPassword)).thenReturn(true); assertTrue( new MolgenisPasswordEncoder(bCryptPasswordEncoder).matches(password, encodedPassword)); }
@Test void matches_noMatch() { String password = "password"; String encodedPassword = "encoded-password"; BCryptPasswordEncoder bCryptPasswordEncoder = mock(BCryptPasswordEncoder.class); when(bCryptPasswordEncoder.matches(password, encodedPassword)).thenReturn(true); assertFalse( new MolgenisPasswordEncoder(bCryptPasswordEncoder) .matches("invalid-password", encodedPassword)); }
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### Question:
SecurityUtils { public static @Nullable @CheckForNull String getCurrentUsername() { Authentication authentication = SecurityContextHolder.getContext().getAuthentication(); if (authentication == null) { return null; } return getUsername(authentication); } private SecurityUtils(); static @Nullable @CheckForNull String getCurrentUsername(); static boolean currentUserHasRole(String... roles); static boolean currentUserIsSuOrSystem(); static boolean currentUserIsSu(); static boolean currentUserIsSystem(); static boolean currentUserIsAuthenticated(); static boolean currentUserIsAnonymous(); static final String ANONYMOUS_USERNAME; static final String AUTHORITY_SU; static final String AUTHORITY_ANONYMOUS; static final String AUTHORITY_USER; static final String ROLE_SYSTEM; static final String ROLE_ACL_TAKE_OWNERSHIP; static final String ROLE_ACL_MODIFY_AUDITING; static final String ROLE_ACL_GENERAL_CHANGES; }### Answer:
@Test void getCurrentUsernameSystemPrincipal() { try { SecurityContextHolder.getContext().setAuthentication(SystemSecurityToken.getInstance()); assertNull(SecurityUtils.getCurrentUsername()); } finally { SecurityContextHolder.getContext().setAuthentication(authentication); } }
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### Question:
SecurityUtils { public static boolean currentUserHasRole(String... roles) { if (roles == null || roles.length == 0) return false; Authentication authentication = SecurityContextHolder.getContext().getAuthentication(); if (authentication != null) { Collection<? extends GrantedAuthority> authorities = authentication.getAuthorities(); if (authorities == null) throw new IllegalStateException("No user currently logged in"); for (String role : roles) { for (GrantedAuthority grantedAuthority : authorities) { if (role.equals(grantedAuthority.getAuthority())) return true; } } } return false; } private SecurityUtils(); static @Nullable @CheckForNull String getCurrentUsername(); static boolean currentUserHasRole(String... roles); static boolean currentUserIsSuOrSystem(); static boolean currentUserIsSu(); static boolean currentUserIsSystem(); static boolean currentUserIsAuthenticated(); static boolean currentUserIsAnonymous(); static final String ANONYMOUS_USERNAME; static final String AUTHORITY_SU; static final String AUTHORITY_ANONYMOUS; static final String AUTHORITY_USER; static final String ROLE_SYSTEM; static final String ROLE_ACL_TAKE_OWNERSHIP; static final String ROLE_ACL_MODIFY_AUDITING; static final String ROLE_ACL_GENERAL_CHANGES; }### Answer:
@Test void isUserInRole() { assertTrue(SecurityUtils.currentUserHasRole("authority1")); assertTrue(SecurityUtils.currentUserHasRole("authority2")); assertTrue(SecurityUtils.currentUserHasRole("authority1", "authority2")); assertTrue(SecurityUtils.currentUserHasRole("authority2", "authority1")); assertTrue(SecurityUtils.currentUserHasRole("authority1", "authority3")); }
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### Question:
RunAsSystemAspect { public static void runAsSystem(Runnable runnable) { runAsSystem( () -> { runnable.run(); return null; }); } @SuppressWarnings("java:S00112") // generic exceptions should never be thrown @Around("@annotation(RunAsSystem)") Object aroundAdvice(ProceedingJoinPoint joinPoint); static void runAsSystem(Runnable runnable); static T runAsSystem(RunnableAsSystem<T, X> runnable); }### Answer:
@Test @WithMockUser void testRunAsSystemRunnableAsSystem() { assertTrue(getAuthentication() instanceof UsernamePasswordAuthenticationToken); assertTrue(runAsSystem(this::getAuthentication) instanceof SystemSecurityToken); assertTrue(getAuthentication() instanceof UsernamePasswordAuthenticationToken); }
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### Question:
SystemSecurityToken extends AbstractAuthenticationToken { public static SystemSecurityToken getInstance() { return INSTANCE; } private SystemSecurityToken(); static SystemSecurityToken getInstance(); @Override Object getCredentials(); @Override Object getPrincipal(); @Override boolean isAuthenticated(); }### Answer:
@Test void testGetAuthorities() { ImmutableList<SimpleGrantedAuthority> expectedAuthorities = ImmutableList.of( new SimpleGrantedAuthority("ROLE_SYSTEM"), new SimpleGrantedAuthority("ROLE_ACL_TAKE_OWNERSHIP"), new SimpleGrantedAuthority("ROLE_ACL_MODIFY_AUDITING"), new SimpleGrantedAuthority("ROLE_ACL_GENERAL_CHANGES")); assertEquals(expectedAuthorities, getInstance().getAuthorities()); }
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### Question:
SystemSecurityToken extends AbstractAuthenticationToken { @Override public Object getCredentials() { return null; } private SystemSecurityToken(); static SystemSecurityToken getInstance(); @Override Object getCredentials(); @Override Object getPrincipal(); @Override boolean isAuthenticated(); }### Answer:
@Test void testGetCredentials() { assertNull(SystemSecurityToken.getInstance().getCredentials()); }
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### Question:
SystemSecurityToken extends AbstractAuthenticationToken { @Override public Object getPrincipal() { return SystemPrincipal.getInstance(); } private SystemSecurityToken(); static SystemSecurityToken getInstance(); @Override Object getCredentials(); @Override Object getPrincipal(); @Override boolean isAuthenticated(); }### Answer:
@Test void testGetPrincipal() { assertTrue(SystemSecurityToken.getInstance().getPrincipal() instanceof SystemPrincipal); }
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### Question:
SystemSecurityToken extends AbstractAuthenticationToken { @Override public boolean isAuthenticated() { return true; } private SystemSecurityToken(); static SystemSecurityToken getInstance(); @Override Object getCredentials(); @Override Object getPrincipal(); @Override boolean isAuthenticated(); }### Answer:
@Test void testIsAuthenticated() { assertTrue(SystemSecurityToken.getInstance().isAuthenticated()); }
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### Question:
GroupValueFactory { public GroupValue createGroup( String groupName, String label, @Nullable @CheckForNull String description, boolean publiclyVisible, Collection<String> roleLabels, String packageValueName) { GroupValue.Builder groupBuilder = GroupValue.builder().setName(groupName).setLabel(label).setPublic(publiclyVisible); Optional.ofNullable(description).ifPresent(groupBuilder::setDescription); PackageValue.Builder packageBuilder = PackageValue.builder().setName(packageValueName).setLabel(label); Optional.ofNullable(description).ifPresent(packageBuilder::setDescription); PackageValue rootPackage = packageBuilder.build(); groupBuilder.setRootPackage(rootPackage); ImmutableList.Builder<RoleValue> rolesBuilder = groupBuilder.rolesBuilder(); roleLabels.stream() .map(roleLabel -> createRoleValue(groupName, label, roleLabel)) .forEach(rolesBuilder::add); return groupBuilder.build(); } GroupValue createGroup(
String groupName,
String label,
@Nullable @CheckForNull String description,
boolean publiclyVisible,
Collection<String> roleLabels,
String packageValueName); GroupValue createGroup(
String groupName, String label, Collection<String> roleLabels, String packageValueName); static String createRoleName(String groupName, String roleLabel); }### Answer:
@Test void testCreateGroup() { GroupValue bbmri_eric = groupValueFactory.createGroup( "bbmri_eric", "BBMRI Eric", "The world's largest biobank catalogue", true, ImmutableList.of("Manager", "Editor", "Viewer"), "bbmri_eric"); GroupValue groupValue = getTestGroupValue(); assertEquals(groupValue, bbmri_eric); }
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### Question:
SidUtils { public static Sid createSecurityContextSid() { Sid sid; if (SecurityUtils.currentUserIsSystem()) { sid = createSystemSid(); } else if (SecurityUtils.currentUserIsAnonymous()) { sid = createAnonymousSid(); } else { String username = SecurityUtils.getCurrentUsername(); if (username == null) { throw new NullPointerException("SecurityUtils.getCurrentUsername is null"); } sid = new PrincipalSid(username); } return sid; } private SidUtils(); static Sid createSecurityContextSid(); static Sid createUserSid(String username); static Sid createRoleSid(String rolename); static Sid createAuthoritySid(String authority); static String createRoleAuthority(String roleName); static String getRoleName(String authority); static Sid createAnonymousSid(); static final String ROLE_PREFIX; }### Answer:
@Test void createSecurityContextSidUser() { String principal = "username"; SecurityContextHolder.getContext() .setAuthentication(new UsernamePasswordAuthenticationToken(principal, null)); assertEquals(new PrincipalSid(principal), createSecurityContextSid()); }
@Test void createSecurityContextSidSystem() { SecurityContextHolder.getContext().setAuthentication(SystemSecurityToken.getInstance()); assertEquals(new GrantedAuthoritySid("ROLE_SYSTEM"), createSecurityContextSid()); }
@Test void createSecurityContextSidAnonymous() { SecurityContextHolder.getContext().setAuthentication(null); assertEquals(new GrantedAuthoritySid("ROLE_ANONYMOUS"), createSecurityContextSid()); }
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### Question:
SidUtils { public static Sid createUserSid(String username) { if (username.equals(SecurityUtils.ANONYMOUS_USERNAME)) { return createAnonymousSid(); } else { return new PrincipalSid(username); } } private SidUtils(); static Sid createSecurityContextSid(); static Sid createUserSid(String username); static Sid createRoleSid(String rolename); static Sid createAuthoritySid(String authority); static String createRoleAuthority(String roleName); static String getRoleName(String authority); static Sid createAnonymousSid(); static final String ROLE_PREFIX; }### Answer:
@Test void testCreateSidUser() { Sid sid = SidUtils.createUserSid("username"); assertEquals(new PrincipalSid("username"), sid); }
@Test void testCreateSidUsernameAnonymous() { Sid sid = SidUtils.createUserSid("anonymous"); assertEquals(new GrantedAuthoritySid("ROLE_ANONYMOUS"), sid); }
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### Question:
SidUtils { public static Sid createRoleSid(String rolename) { return createAuthoritySid(createRoleAuthority(rolename)); } private SidUtils(); static Sid createSecurityContextSid(); static Sid createUserSid(String username); static Sid createRoleSid(String rolename); static Sid createAuthoritySid(String authority); static String createRoleAuthority(String roleName); static String getRoleName(String authority); static Sid createAnonymousSid(); static final String ROLE_PREFIX; }### Answer:
@Test void testCreateSidRole() { Sid sid = SidUtils.createRoleSid("NAME"); assertEquals(new GrantedAuthoritySid(new SimpleGrantedAuthority("ROLE_NAME")), sid); }
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### Question:
SidUtils { public static String createRoleAuthority(String roleName) { return ROLE_PREFIX + roleName; } private SidUtils(); static Sid createSecurityContextSid(); static Sid createUserSid(String username); static Sid createRoleSid(String rolename); static Sid createAuthoritySid(String authority); static String createRoleAuthority(String roleName); static String getRoleName(String authority); static Sid createAnonymousSid(); static final String ROLE_PREFIX; }### Answer:
@Test void testCreateRoleAuthority() { assertEquals("ROLE_NAME", createRoleAuthority("NAME")); }
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### Question:
SortaServiceUtil { public static List<Map<String, Object>> getEntityAsMap(Iterable<? extends Entity> entities) { List<Map<String, Object>> docs = new ArrayList<>(); for (Entity entity : entities) { docs.add(getEntityAsMap(entity)); } return docs; } private SortaServiceUtil(); static List<Map<String, Object>> getEntityAsMap(Iterable<? extends Entity> entities); static Map<String, Object> getEntityAsMap(Entity entity); }### Answer:
@Test void testGetEntityAsMap() { HashMap<String, Object> expected = newHashMap(); expected.put(ID, null); expected.put(ONTOLOGY_TERM_IRI, "iri"); expected.put(ONTOLOGY_TERM_NAME, "testTerm"); expected.put( ONTOLOGY_TERM_SYNONYM, singletonList( ImmutableMap.of( OntologyTermSynonymMetadata.ID, "1", ONTOLOGY_TERM_SYNONYM_ATTR, "synonym", SCORE, 10.0, COMBINED_SCORE, 20.0))); expected.put(ONTOLOGY_TERM_DYNAMIC_ANNOTATION, null); expected.put(ONTOLOGY_TERM_NODE_PATH, null); expected.put( ONTOLOGY, ImmutableMap.of( OntologyMetadata.ID, "1", OntologyMetadata.ONTOLOGY_IRI, ONTOLOGY_IRI, OntologyMetadata.ONTOLOGY_NAME, "testOntology")); assertEquals(singletonList(expected), getEntityAsMap(singletonList(term))); }
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### Question:
InformationContentService { public Set<String> createStemmedWordSet(String queryString) { Set<String> uniqueTerms = Sets.newHashSet(queryString.toLowerCase().trim().split(NON_WORD_SEPARATOR)).stream() .filter(term -> !NGramDistanceAlgorithm.STOPWORDSLIST.contains(term)) .map(Stemmer::stem) .filter(StringUtils::isNotBlank) .collect(Collectors.toSet()); return Sets.newHashSet(uniqueTerms); } InformationContentService(DataService dataService); Map<String, Double> redistributedNGramScore(String queryString, String ontologyIri); Set<String> createStemmedWordSet(String queryString); }### Answer:
@Test void createStemmedWordSet() { Set<String> actualStemmedWordSet = informationContentService.createStemmedWordSet("hearing-impairment_eye ball"); Set<String> expectedStemmedWordSet = Sets.newHashSet("hear", "impair", "ey", "ball"); assertEquals(expectedStemmedWordSet.size(), actualStemmedWordSet.size()); assertTrue(expectedStemmedWordSet.containsAll(actualStemmedWordSet)); }
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### Question:
SortaCsvRepository extends AbstractRepository { @Override public Iterator<Entity> iterator() { final AtomicInteger count = new AtomicInteger(0); final Iterator<Entity> iterator = csvRepository.iterator(); return new Iterator<>() { @Override public boolean hasNext() { return iterator.hasNext(); } @Override public Entity next() { Entity entity = iterator.next(); if (isEmpty(entity.getString(ALLOWED_IDENTIFIER))) { DynamicEntity dynamicEntity = new DynamicEntity(getEntityType()); dynamicEntity.set(entity); entity = dynamicEntity; entity.set(ALLOWED_IDENTIFIER, String.valueOf(count.incrementAndGet())); } return entity; } }; } SortaCsvRepository(
File file, EntityTypeFactory entityTypeFactory, AttributeFactory attrMetaFactory); SortaCsvRepository(
String entityTypeId,
String entityLabel,
File uploadedFile,
EntityTypeFactory entityTypeFactory,
AttributeFactory attrMetaFactory); EntityType getEntityType(); @Override Iterator<Entity> iterator(); @Override Set<RepositoryCapability> getCapabilities(); @Override long count(); static final String ALLOWED_IDENTIFIER; }### Answer:
@Test void iterator() throws IOException { FileUtils.writeLines(file, asList("Name", "whisper", "SCREAM")); Iterator<Entity> it = sortaCsvRepository.iterator(); assertAll( () -> assertTrue(it.hasNext()), () -> assertEquals("whisper", it.next().getString("Name")), () -> assertTrue(it.hasNext()), () -> assertEquals("scream", it.next().getString("Name")), () -> assertFalse(it.hasNext())); }
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### Question:
EntityListenerRepositoryDecorator extends AbstractRepositoryDecorator<Entity> { public EntityListenerRepositoryDecorator( Repository<Entity> delegateRepository, EntityListenersService entityListenersService) { super(delegateRepository); requireNonNull(entityListenersService).register(delegate().getName()); this.entityListenersService = entityListenersService; } EntityListenerRepositoryDecorator(
Repository<Entity> delegateRepository, EntityListenersService entityListenersService); @Override void update(Entity entity); @Override void update(Stream<Entity> entities); }### Answer:
@SuppressWarnings("resource") @Test void EntityListenerRepositoryDecorator() { assertThrows( NullPointerException.class, () -> new EntityListenerRepositoryDecorator(null, entityListenersService)); }
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### Question:
MetadataApiJobServiceImpl implements MetadataApiJobService { @Override public MetadataUpsertJobExecution scheduleCreate(EntityType entityType) { return scheduleUpsert(Action.CREATE, entityType); } MetadataApiJobServiceImpl(
MetadataUpsertJobExecutionFactory metadataUpsertJobExecutionFactory,
MetadataDeleteJobExecutionFactory metadataDeleteJobExecutionFactory,
JobExecutor jobExecutor,
EntityTypeSerializer entityTypeSerializer); @Override MetadataUpsertJobExecution scheduleCreate(EntityType entityType); @Override MetadataUpsertJobExecution scheduleUpdate(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(Collection<EntityType> entityTypes); }### Answer:
@Test void testScheduleCreate() { EntityType entityType = mock(EntityType.class); MetadataUpsertJobExecution jobExecution = mock(MetadataUpsertJobExecution.class); when(metadataUpsertJobExecutionFactory.create()).thenReturn(jobExecution); when(entityTypeSerializer.serializeEntityType(entityType)).thenReturn("entity data"); MetadataUpsertJobExecution actualJobExecution = metadataApiJobService.scheduleCreate(entityType); assertAll( () -> assertEquals(jobExecution, actualJobExecution), () -> verify(jobExecution).setEntityTypeData("entity data"), () -> verify(jobExecutor).submit(jobExecution)); }
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### Question:
MetadataApiJobServiceImpl implements MetadataApiJobService { @Override public MetadataUpsertJobExecution scheduleUpdate(EntityType entityType) { return scheduleUpsert(Action.UPDATE, entityType); } MetadataApiJobServiceImpl(
MetadataUpsertJobExecutionFactory metadataUpsertJobExecutionFactory,
MetadataDeleteJobExecutionFactory metadataDeleteJobExecutionFactory,
JobExecutor jobExecutor,
EntityTypeSerializer entityTypeSerializer); @Override MetadataUpsertJobExecution scheduleCreate(EntityType entityType); @Override MetadataUpsertJobExecution scheduleUpdate(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(Collection<EntityType> entityTypes); }### Answer:
@Test void testScheduleUpdate() { EntityType entityType = mock(EntityType.class); MetadataUpsertJobExecution jobExecution = mock(MetadataUpsertJobExecution.class); when(metadataUpsertJobExecutionFactory.create()).thenReturn(jobExecution); when(entityTypeSerializer.serializeEntityType(entityType)).thenReturn("entity data"); MetadataUpsertJobExecution actualJobExecution = metadataApiJobService.scheduleUpdate(entityType); assertAll( () -> assertEquals(jobExecution, actualJobExecution), () -> verify(jobExecution).setAction(Action.UPDATE), () -> verify(jobExecution).setEntityTypeData("entity data"), () -> verify(jobExecutor).submit(jobExecution)); }
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### Question:
MetadataApiJobServiceImpl implements MetadataApiJobService { @Override public MetadataDeleteJobExecution scheduleDelete(EntityType entityType) { return scheduleDelete(singletonList(entityType.getId())); } MetadataApiJobServiceImpl(
MetadataUpsertJobExecutionFactory metadataUpsertJobExecutionFactory,
MetadataDeleteJobExecutionFactory metadataDeleteJobExecutionFactory,
JobExecutor jobExecutor,
EntityTypeSerializer entityTypeSerializer); @Override MetadataUpsertJobExecution scheduleCreate(EntityType entityType); @Override MetadataUpsertJobExecution scheduleUpdate(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(EntityType entityType); @Override MetadataDeleteJobExecution scheduleDelete(Collection<EntityType> entityTypes); }### Answer:
@Test void testScheduleDelete() { EntityType entityType = mock(EntityType.class); when(entityType.getId()).thenReturn("entity1"); MetadataDeleteJobExecution jobExecution = mock(MetadataDeleteJobExecution.class); when(metadataDeleteJobExecutionFactory.create()).thenReturn(jobExecution); MetadataDeleteJobExecution actualJobExecution = metadataApiJobService.scheduleDelete(entityType); assertAll( () -> assertEquals(jobExecution, actualJobExecution), () -> verify(jobExecution).setIds(singletonList("entity1")), () -> verify(jobExecutor).submit(jobExecution)); }
@Test void testScheduleDeleteCollection() { EntityType entityType1 = mock(EntityType.class); when(entityType1.getId()).thenReturn("entity1"); EntityType entityType2 = mock(EntityType.class); when(entityType2.getId()).thenReturn("entity2"); MetadataDeleteJobExecution jobExecution = mock(MetadataDeleteJobExecution.class); when(metadataDeleteJobExecutionFactory.create()).thenReturn(jobExecution); MetadataDeleteJobExecution actualJobExecution = metadataApiJobService.scheduleDelete(asList(entityType1, entityType2)); assertAll( () -> assertEquals(jobExecution, actualJobExecution), () -> verify(jobExecution).setIds(asList("entity1", "entity2")), () -> verify(jobExecutor).submit(jobExecution)); }
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### Question:
MetadataApiServiceImpl implements MetadataApiService { MetadataApiServiceImpl( MetaDataService metadataService, QueryMapper queryMapperV3, SortMapper sortMapper, MetadataApiJobService metadataApiJobService) { this.metadataService = requireNonNull(metadataService); this.queryMapper = requireNonNull(queryMapperV3); this.sortMapper = requireNonNull(sortMapper); this.metadataApiJobService = requireNonNull(metadataApiJobService); } MetadataApiServiceImpl(
MetaDataService metadataService,
QueryMapper queryMapperV3,
SortMapper sortMapper,
MetadataApiJobService metadataApiJobService); EntityTypes findEntityTypes(
@Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override EntityType findEntityType(String identifier); @Override Attributes findAttributes(
String entityTypeId, @Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override Attribute findAttribute(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributesAsync(String entityTypeId, Query query); @Override void createEntityType(EntityType entityType); @Override MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType); @Override MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId); @Override MetadataDeleteJobExecution deleteEntityTypesAsync(Query query); }### Answer:
@Test void testMetadataApiServiceImpl() { assertThrows( NullPointerException.class, () -> new MetadataApiServiceImpl(null, null, null, metadataApiJobService)); }
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### Question:
MetadataApiServiceImpl implements MetadataApiService { @Override public void createEntityType(EntityType entityType) { metadataService.addEntityType(entityType); } MetadataApiServiceImpl(
MetaDataService metadataService,
QueryMapper queryMapperV3,
SortMapper sortMapper,
MetadataApiJobService metadataApiJobService); EntityTypes findEntityTypes(
@Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override EntityType findEntityType(String identifier); @Override Attributes findAttributes(
String entityTypeId, @Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override Attribute findAttribute(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributesAsync(String entityTypeId, Query query); @Override void createEntityType(EntityType entityType); @Override MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType); @Override MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId); @Override MetadataDeleteJobExecution deleteEntityTypesAsync(Query query); }### Answer:
@Test void testCreateEntityType() { EntityType entityType = mock(EntityType.class); metadataApiService.createEntityType(entityType); verify(metadataService).addEntityType(entityType); }
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### Question:
MetadataApiServiceImpl implements MetadataApiService { @Override public MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType) { return metadataApiJobService.scheduleUpdate(entityType); } MetadataApiServiceImpl(
MetaDataService metadataService,
QueryMapper queryMapperV3,
SortMapper sortMapper,
MetadataApiJobService metadataApiJobService); EntityTypes findEntityTypes(
@Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override EntityType findEntityType(String identifier); @Override Attributes findAttributes(
String entityTypeId, @Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override Attribute findAttribute(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributesAsync(String entityTypeId, Query query); @Override void createEntityType(EntityType entityType); @Override MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType); @Override MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId); @Override MetadataDeleteJobExecution deleteEntityTypesAsync(Query query); }### Answer:
@Test void testUpdateEntityTypeAsync() { EntityType entityType = mock(EntityType.class); MetadataUpsertJobExecution metadataUpsertJobExecution = mock(MetadataUpsertJobExecution.class); when(metadataApiJobService.scheduleUpdate(entityType)).thenReturn(metadataUpsertJobExecution); assertEquals(metadataUpsertJobExecution, metadataApiService.updateEntityTypeAsync(entityType)); }
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### Question:
MetadataApiServiceImpl implements MetadataApiService { @Override public MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId) { EntityType entityType = findEntityType(entityTypeId); Attribute attribute = entityType.getOwnAttributeById(attributeId); entityType.removeAttribute(attribute); return metadataApiJobService.scheduleUpdate(entityType); } MetadataApiServiceImpl(
MetaDataService metadataService,
QueryMapper queryMapperV3,
SortMapper sortMapper,
MetadataApiJobService metadataApiJobService); EntityTypes findEntityTypes(
@Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override EntityType findEntityType(String identifier); @Override Attributes findAttributes(
String entityTypeId, @Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override Attribute findAttribute(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributesAsync(String entityTypeId, Query query); @Override void createEntityType(EntityType entityType); @Override MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType); @Override MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId); @Override MetadataDeleteJobExecution deleteEntityTypesAsync(Query query); }### Answer:
@Test void testDeleteAttribute() { String entityTypeId = "entityTypeId"; EntityType entityType = mock(EntityType.class); when(metadataService.getEntityType(entityTypeId)).thenReturn(Optional.of(entityType)); String attributeId = "attr1"; Attribute attr = mock(Attribute.class); when(entityType.getOwnAttributeById(attributeId)).thenReturn(attr); metadataApiService.deleteAttributeAsync(entityTypeId, attributeId); assertAll( () -> verify(entityType).removeAttribute(attr), () -> verify(metadataApiJobService).scheduleUpdate(entityType)); }
@Test void testDeleteAttributeUnknownEntityType() { String entityTypeId = "unknown"; assertThrows( UnknownEntityTypeException.class, () -> metadataApiService.deleteAttributeAsync(entityTypeId, "attr1")); }
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### Question:
FallbackLocaleSupplierImpl implements FallbackLocaleSupplier { @Override public Locale get() { String languageCode = appSettings.getLanguageCode(); return Locale.forLanguageTag(languageCode); } FallbackLocaleSupplierImpl(AppSettings appSettings); @Override Locale get(); }### Answer:
@Test void testGet() { String languageCode = "nl"; when(appSettings.getLanguageCode()).thenReturn(languageCode); assertEquals(forLanguageTag("nl"), fallbackLocaleSupplierImpl.get()); }
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### Question:
MetadataApiServiceImpl implements MetadataApiService { @Override public MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId) { EntityType entityType = findEntityType(entityTypeId); return metadataApiJobService.scheduleDelete(entityType); } MetadataApiServiceImpl(
MetaDataService metadataService,
QueryMapper queryMapperV3,
SortMapper sortMapper,
MetadataApiJobService metadataApiJobService); EntityTypes findEntityTypes(
@Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override EntityType findEntityType(String identifier); @Override Attributes findAttributes(
String entityTypeId, @Nullable @CheckForNull Query query, Sort sort, int size, int number); @Override Attribute findAttribute(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributeAsync(String entityTypeId, String attributeId); @Override MetadataUpsertJobExecution deleteAttributesAsync(String entityTypeId, Query query); @Override void createEntityType(EntityType entityType); @Override MetadataUpsertJobExecution updateEntityTypeAsync(EntityType entityType); @Override MetadataDeleteJobExecution deleteEntityTypeAsync(String entityTypeId); @Override MetadataDeleteJobExecution deleteEntityTypesAsync(Query query); }### Answer:
@Test void testDeleteEntityType() { String entityTypeId = "MyEntityTypeId"; EntityType entityType = mock(EntityType.class); when(metadataService.getEntityType(entityTypeId)).thenReturn(Optional.of(entityType)); metadataApiService.deleteEntityTypeAsync(entityTypeId); verify(metadataApiJobService).scheduleDelete(entityType); }
@Test void testDeleteEntityTypeUnknownEntityType() { String entityTypeId = "unknown"; assertThrows( UnknownEntityTypeException.class, () -> metadataApiService.deleteEntityTypeAsync(entityTypeId)); }
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### Question:
EntityTypeSerializerImpl implements EntityTypeSerializer { @Override public String serializeEntityType(EntityType entityType) { SerializableEntityType serializableEntityType = toSerializableEntityType(entityType); return gson.toJson(serializableEntityType); } EntityTypeSerializerImpl(
DataService dataService,
EntityTypeFactory entityTypeFactory,
AttributeFactory attributeFactory); @Override String serializeEntityType(EntityType entityType); @Override EntityType deserializeEntityType(String serializedEntityType); }### Answer:
@Test void serializeEntityType() { EntityType entityType = mock(EntityType.class); when(entityType.getId()).thenReturn("MyEntityTypeId"); when(entityType.getLabel()).thenReturn("My Entity Type"); doReturn("My Entity Type (en)").when(entityType).getString(EntityTypeMetadata.LABEL + "En"); when(entityType.getBackend()).thenReturn("PostgreSQL"); String serializedEntityType = "{\"id\":\"MyEntityTypeId\",\"label\":\"My Entity Type\",\"labelI18n\":{\"en\":\"My Entity Type (en)\"},\"descriptionI18n\":{},\"attributes\":[],\"abstract0\":false,\"tagIds\":[],\"backend\":\"PostgreSQL\",\"indexingDepth\":0}"; String actualSerializedEntityType = entityTypeSerializerImpl.serializeEntityType(entityType); assertTrue(new IsEqualJson(serializedEntityType).matches(actualSerializedEntityType)); }
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### Question:
MetadataUtils { public static <E extends Entity> ImmutableMap<String, String> getI18n( E entity, String attributeName) { Builder<String, String> builder = ImmutableMap.builder(); getLanguageCodes() .forEach( languageCode -> { String value = entity.getString(getI18nAttributeName(attributeName, languageCode)); if (value != null) { builder.put(languageCode, value); } }); return builder.build(); } private MetadataUtils(); static ImmutableMap<String, String> getI18n(
E entity, String attributeName); }### Answer:
@Test void getI18n() { EntityType entityType = mock(EntityType.class); when(entityType.getString("labelEn")).thenReturn("English"); when(entityType.getString("labelNl")).thenReturn("Dutch"); assertEquals( ImmutableMap.of("en", "English", "nl", "Dutch"), MetadataUtils.getI18n(entityType, "label")); }
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### Question:
SettingsController extends PluginController { @GetMapping("/**") public String init(Model model) { model.addAttribute(KEY_BASE_URL, menuReaderService.findMenuItemPath(ID)); return VIEW_TEMPLATE; } SettingsController(MenuReaderService menuReaderService); @GetMapping("/**") String init(Model model); static final String ID; static final String URI; static final String VIEW_TEMPLATE; }### Answer:
@Test public void testInit() throws Exception { mockMvc .perform(get(SettingsController.URI)) .andExpect(status().isOk()) .andExpect(view().name(SettingsController.VIEW_TEMPLATE)) .andExpect(model().attribute("baseUrl", "/test/path")); }
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### Question:
ApiController { String getApiId() { return apiId; } ApiController(String apiId, Integer apiVersion); }### Answer:
@Test void testGetApiId() { String apiId = "myapi"; ApiController apiController = new ApiController(apiId, 1) {}; assertEquals(apiId, apiController.getApiId()); }
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### Question:
ApiController { int getApiVersion() { return apiVersion; } ApiController(String apiId, Integer apiVersion); }### Answer:
@Test void testGetApiVersion() { int apiVersion = 2; ApiController apiController = new ApiController("myapi", apiVersion) {}; assertEquals(apiVersion, apiController.getApiVersion()); }
@Test void testGetApiVersionEmpty() { int apiVersion = 2; ApiController apiController = new ApiController("", apiVersion) {}; assertEquals(apiVersion, apiController.getApiVersion()); }
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### Question:
RootApiController extends ApiController { @ApiOperation( value = "Get the current version and build date of the application.", response = OptionsResponse.class) @RequestMapping(method = OPTIONS) public OptionsResponse getVersion() throws ParseException { Instant date; if (molgenisBuildDate.equals("${maven.build.timestamp}")) { date = now().toInstant(); } else { date = new SimpleDateFormat(VERSION_DATE_FORMAT).parse(molgenisBuildDate).toInstant(); } AppVersionResponse appVersionResponse = AppVersionResponse.create(molgenisVersion, date); return OptionsResponse.create(appVersionResponse); } RootApiController(
@Value("${molgenis.version:@null}") String molgenisVersion,
@Value("${molgenis.build.date:@null}") String molgenisBuildDate); @ApiOperation( value = "Get the current version and build date of the application.", response = OptionsResponse.class) @RequestMapping(method = OPTIONS) OptionsResponse getVersion(); static final String VERSION_DATE_FORMAT; }### Answer:
@Test void testGetVersion() throws Exception { MvcResult result = mockMvc .perform(options("/api").contentType(APPLICATION_JSON_UTF8)) .andExpect(status().isOk()) .andReturn(); String actual = result.getResponse().getContentAsString(); String expected = "{\"app\":{\"version\":\"versionString\",\"buildDate\":{\"seconds\":1558434720,\"nanos\":0}}}"; assertEquals(expected, actual); }
|
### Question:
PageUtils { public static PageResponse getPageResponse(int pageSize, int offset, int total) { int newNumber = offset / pageSize; return PageResponse.create(pageSize, total, newNumber); } private PageUtils(); static PageResponse getPageResponse(int pageSize, int offset, int total); static int getTotalPages(int pageSize, int totalElements); static final String PAGE_QUERY_PARAMETER_NAME; }### Answer:
@Test void getPageResponse() { PageResponse pageResponse = PageResponse.builder() .setSize(10) .setNumber(0) .setTotalPages(9) .setTotalElements(90) .build(); assertEquals(pageResponse, PageUtils.getPageResponse(10, 0, 90)); }
@Test void getPageResponseTotalPagesRounding() { PageResponse pageResponse = PageResponse.builder() .setSize(10) .setNumber(0) .setTotalPages(9) .setTotalElements(89) .build(); assertEquals(pageResponse, PageUtils.getPageResponse(10, 0, 89)); }
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### Question:
PageUtils { public static int getTotalPages(int pageSize, int totalElements) { return pageSize > 0 ? (int) Math.ceil(totalElements / (double) pageSize) : 0; } private PageUtils(); static PageResponse getPageResponse(int pageSize, int offset, int total); static int getTotalPages(int pageSize, int totalElements); static final String PAGE_QUERY_PARAMETER_NAME; }### Answer:
@Test void testGetTotalPages() { assertEquals(2, PageUtils.getTotalPages(5, 10)); }
@Test void testGetTotalPagesBelow() { assertEquals(2, PageUtils.getTotalPages(5, 9)); }
@Test void testGetTotalPagesAbove() { assertEquals(3, PageUtils.getTotalPages(5, 11)); }
@Test void testGetTotalPagesZeroPageSize() { assertEquals(0, PageUtils.getTotalPages(0, 10)); }
|
### Question:
MolgenisServletUriComponentsBuilder extends ServletUriComponentsBuilder { @SuppressWarnings("RedundantCast") public static ServletUriComponentsBuilder fromCurrentRequestDecodedQuery() { ServletUriComponentsBuilder builder = ServletUriComponentsBuilder.fromCurrentRequest(); Map<String, String[]> params = getCurrentRequest().getParameterMap(); for (Entry<String, String[]> param : params.entrySet()) { builder.replaceQueryParam(param.getKey(), (Object[]) param.getValue()); } return builder; } @SuppressWarnings("RedundantCast") static ServletUriComponentsBuilder fromCurrentRequestDecodedQuery(); }### Answer:
@Test void testFromCurrentRequestDecodedQueryNoWithoutQuery() { when(request.getRequestURI()).thenReturn("/api/data/EntityType"); when(request.getScheme()).thenReturn("http"); when(request.getServerName()).thenReturn("localhost"); when(request.getServerPort()).thenReturn(80); assertEquals( "http: MolgenisServletUriComponentsBuilder.fromCurrentRequestDecodedQuery().build().toUriString()); }
@Test void testFromCurrentRequestDecodedQueryWithQuery() { Map<String, String[]> params = new HashMap<>(); params.put("query", new String[] {"a==b,c=in=('d e','f g','h i')&j==k"}); params.put("page", new String[] {"1"}); params.put("attr", new String[] {"#CHROM,POS,REF,ALT"}); when(request.getRequestURI()).thenReturn("/api/data/EntityType"); when(request.getScheme()).thenReturn("http"); when(request.getServerName()).thenReturn("localhost"); when(request.getServerPort()).thenReturn(80); when(request.getParameterMap()).thenReturn(params); assertEquals( "http: MolgenisServletUriComponentsBuilder.fromCurrentRequestDecodedQuery().build().toUriString()); }
|
### Question:
SortConverter implements Converter<String, Sort> { @Override public Sort convert(String source) { try { return new SortParser(source).parse(); } catch (ParseException e) { throw new SortParseException(e); } } @Override Sort convert(String source); }### Answer:
@Test void testConvert() { assertEquals(create("item"), sortConverter.convert("item")); }
@Test void testConvertParseException() { assertThrows(SortParseException.class, () -> sortConverter.convert("-")); }
|
### Question:
SelectionConverter implements Converter<String, Selection> { @Override public Selection convert(String source) { if (source.isEmpty()) { return Selection.FULL_SELECTION; } try { return new SelectionParser(source).parse(); } catch (ParseException e) { throw new SelectionParseException(e); } } @Override Selection convert(String source); }### Answer:
@Test void testConvert() { assertEquals(new Selection(singletonMap("item", null)), selectionConverter.convert("item")); }
@Test void testConvertEmptySelection() { assertEquals(FULL_SELECTION, selectionConverter.convert("")); }
@Test void testConvertParseException() { assertThrows(SelectionParseException.class, () -> selectionConverter.convert("item,")); }
|
### Question:
QueryConverter implements Converter<String, Query> { @Override public Query convert(@Nonnull String source) { Node node; try { node = rsqlParser.parse(source); } catch (RSQLParserException e) { Throwable cause = e.getCause(); if (cause instanceof UnknownOperatorException) { String operator = ((UnknownOperatorException) cause).getOperator(); throw new UnknownQueryOperatorException(operator); } else { throw new QueryParseException(e); } } return node.accept(rsqlVisitor); } QueryConverter(RSQLParser rsqlParser, QueryRsqlVisitor rsqlVisitor); @Override Query convert(@Nonnull String source); }### Answer:
@Test void testCreateQuery() { String rsqlQuery = "item==value"; ComparisonNode node = new ComparisonNode(new ComparisonOperator("=="), "item", singletonList("value")); Query query = Query.builder().setItem("item").setOperator(Operator.EQUALS).build(); when(node.accept(rsqlVisitor)).thenReturn(query); assertEquals(query, queryConverter.convert(rsqlQuery)); verify(rsqlVisitor).visit(node, null); }
@Test void testCreateQueryParseException() { String rsqlQuery = "illegalQuery"; assertThrows(QueryParseException.class, () -> queryConverter.convert(rsqlQuery)); }
@Test void testCreateQueryUnknownQueryOperatorException() { String rsqlQuery = "item=illegalOperator=value"; Exception exception = assertThrows(UnknownQueryOperatorException.class, () -> queryConverter.convert(rsqlQuery)); assertThat(exception.getMessage()).containsPattern("operator:=illegalOperator="); }
|
### Question:
EntityListenersService { void register(String repoFullName) { lock.writeLock().lock(); try { if (!entityListenersByRepo.containsKey(requireNonNull(repoFullName))) { entityListenersByRepo.put(repoFullName, HashMultimap.create()); } } finally { lock.writeLock().unlock(); } } void addEntityListener(String repoFullName, EntityListener entityListener); boolean removeEntityListener(String repoFullName, EntityListener entityListener); }### Answer:
@Test void registerNullPointer() { assertThrows(NullPointerException.class, () -> entityListenersService.register(null)); }
@Test void registerTest() { String repoFullName = "EntityRepo"; entityListenersService.register(repoFullName); EntityListener entityListener1 = Mockito.when(Mockito.mock(EntityListener.class).getEntityId()).thenReturn(1).getMock(); EntityListener entityListener2 = Mockito.when(Mockito.mock(EntityListener.class).getEntityId()).thenReturn(2).getMock(); entityListenersService.addEntityListener(repoFullName, entityListener1); entityListenersService.addEntityListener(repoFullName, entityListener2); assertFalse(entityListenersService.isEmpty(repoFullName)); entityListenersService.register(repoFullName); assertFalse(entityListenersService.isEmpty(repoFullName)); entityListenersService.removeEntityListener(repoFullName, entityListener1); entityListenersService.removeEntityListener(repoFullName, entityListener2); assertTrue(entityListenersService.isEmpty(repoFullName)); }
|
### Question:
GenomeBrowserAttributesFactory extends AbstractSystemEntityFactory<
GenomeBrowserAttributes, GenomeBrowserAttributesMetadata, String> { public GenomeBrowserAttributes create( String id, boolean isDefault, int order, String pos, String chr, String ref, String alt, String stop) { GenomeBrowserAttributes gba = super.create(id); gba.setPos(pos); gba.setChrom(chr); gba.setRef(ref); gba.setAlt(alt); gba.setDefault(isDefault); gba.setOrder(order); gba.setStop(stop); return gba; } GenomeBrowserAttributesFactory(
GenomeBrowserAttributesMetadata myEntityMeta, EntityPopulator entityPopulator); GenomeBrowserAttributes create(
String id,
boolean isDefault,
int order,
String pos,
String chr,
String ref,
String alt,
String stop); }### Answer:
@Override @Test public void testCreate() { super.testCreate(factory, GenomeBrowserAttributes.class); }
|
### Question:
SecurityUiController extends PluginController { @GetMapping("/**") public String init(Model model) { model.addAttribute(KEY_BASE_URL, menuReaderService.findMenuItemPath(ID)); return VIEW_TEMPLATE; } SecurityUiController(MenuReaderService menuReaderService); @GetMapping("/**") String init(Model model); static final String ID; static final String URI; }### Answer:
@Test public void testInit() throws Exception { mockMvc .perform(get(SecurityUiController.URI)) .andExpect(status().isOk()) .andExpect(view().name(SecurityUiController.VIEW_TEMPLATE)) .andExpect(model().attribute("baseUrl", MENU_PATH_SECURITY_UI)); }
|
### Question:
ExcelUtils { static String toValue(Cell cell) { return toValue(cell, null); } private ExcelUtils(); static void renameSheet(String newSheetname, File file, int index); static int getNumberOfSheets(File file); static boolean isExcelFile(String filename); }### Answer:
@Test void testToValueNumericLong() throws Exception { Cell cell = mock(Cell.class); when(cell.getCellTypeEnum()).thenReturn(NUMERIC); when(cell.getNumericCellValue()).thenReturn(1.2342151234E10); assertEquals("12342151234", toValue(cell)); }
@Test void testToValueFormulaNumericLong() throws Exception { CellValue cellValue = new CellValue(1.2342151234E10); Cell cell = mock(Cell.class); FormulaEvaluator formulaEvaluator = mock(FormulaEvaluator.class); when(formulaEvaluator.evaluate(cell)).thenReturn(cellValue); CreationHelper creationHelper = mock(CreationHelper.class); when(creationHelper.createFormulaEvaluator()).thenReturn(formulaEvaluator); Workbook workbook = mock(Workbook.class); when(workbook.getCreationHelper()).thenReturn(creationHelper); Sheet sheet = mock(Sheet.class); when(sheet.getWorkbook()).thenReturn(workbook); when(cell.getCellTypeEnum()).thenReturn(FORMULA); when(cell.getSheet()).thenReturn(sheet); when(cell.getNumericCellValue()).thenReturn(1.2342151234E10); assertEquals("12342151234", toValue(cell)); }
|
### Question:
ExcelUtils { public static void renameSheet(String newSheetname, File file, int index) { try (FileInputStream fis = new FileInputStream(file); Workbook workbook = WorkbookFactory.create(fis)) { workbook.setSheetName(index, newSheetname); workbook.write(new FileOutputStream(file)); } catch (Exception e) { throw new MolgenisDataException(e); } } private ExcelUtils(); static void renameSheet(String newSheetname, File file, int index); static int getNumberOfSheets(File file); static boolean isExcelFile(String filename); }### Answer:
@Test void renameSheetTest() throws IOException, InvalidFormatException { File file = ResourceUtils.getFile(getClass(), "/test.xls"); File temp = File.createTempFile("unittest_", ".xls"); FileUtils.copyFile(file, temp); ExcelUtils.renameSheet("unittest", temp, 0); Workbook workbook = WorkbookFactory.create(new FileInputStream(temp)); assertEquals("unittest", workbook.getSheetAt(0).getSheetName()); }
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