protected static async Task PrecalculateAsync(Document document, IndexCreator create, CancellationToken cancellationToken)
{
if (!document.SupportsSyntaxTree)
{
return;
}
using (Logger.LogBlock(FunctionId.SyntaxTreeIndex_Precalculate, cancellationToken))
{
Debug.Assert(document.IsFromPrimaryBranch());
var checksum = await GetChecksumAsync(document, cancellationToken).ConfigureAwait(false);
// Check if we've already created and persisted the index for this document.
if (await PrecalculatedAsync(document, checksum, cancellationToken).ConfigureAwait(false))
{
return;
}
using (Logger.LogBlock(FunctionId.SyntaxTreeIndex_Precalculate_Create, cancellationToken))
{
// If not, create and save the index.
var data = await CreateIndexAsync(document, checksum, create, cancellationToken).ConfigureAwait(false);
await data.SaveAsync(document, cancellationToken).ConfigureAwait(false);
}
}
}
private void btnCreateIndex_Click(object sender, EventArgs e)
{
string sql = "SELECT VerseID, VerseText FROM Verse";
using (SqlCeConnection conn = new SqlCeConnection(ConfigurationManager.ConnectionStrings["ConnectionString"].ConnectionString))
{
conn.Open();
var rdr = new SqlCeCommand(sql, conn).ExecuteReader();
var context = new TextFileAccessContext("Bible", IndexDir, new CultureInfo("en-US"));
var textIndexSaver = new TextIndexSaver <int>(context);
var wordBreaker = new DefaultWordBreaker(new WordBreakingInformationRetriever(context.Directory, context.Culture))
{
DatabasePath = context.Directory
};
var textIndexFiller = new TextIndexFiller <int>(wordBreaker);
var indexCreator = new IndexCreator <int>(textIndexFiller);
var index = indexCreator.CreateIndex(new BibleVersuses(rdr));
textIndexSaver.SaveIndex(index);
rdr.Close();
}
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Before public void setup()
public virtual void Setup()
{
_db = DbRule.GraphDatabaseAPI;
if (WithIndex)
{
using (Org.Neo4j.Graphdb.Transaction tx = _db.beginTx())
{
_db.schema().indexFor(_label).on(Keys[0]).create();
IndexCreator indexCreator = _db.schema().indexFor(_label);
foreach (string key in Keys)
{
indexCreator = indexCreator.On(key);
}
indexCreator.Create();
tx.Success();
}
using (Org.Neo4j.Graphdb.Transaction tx = _db.beginTx())
{
_db.schema().awaitIndexesOnline(5, TimeUnit.MINUTES);
tx.Success();
}
}
}
public void IndexCreation_multiChromosome()
{
var jsonStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var writeStream = new MemoryStream();
using (var indexCreator = new IndexCreator(jsonStream, writeStream))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
var readStream = new MemoryStream(writeStream.ToArray());
readStream.Seek(0, SeekOrigin.Begin);
using (readStream)
{
readBackIndex = new JasixIndex(readStream);
}
Assert.Equal(2268, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(14035925971, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(433156622693, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(439602269527, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
}
public CreateTableBuilder(DbConnection db, IGenerateDDL generator, TableSchema schema)
{
_db = db;
_generator = generator;
_table = schema;
_columns = new ColumnsCreator(Table);
_constraints = new ConstraintsCreator(Table.Constraints);
_indexes = new IndexCreator(Table.Indexes);
}
private static void Main(string[] args)
{
var docFileReader = new DocFileReader("EnglishData");
var indexCreator = new IndexCreator(docFileReader);
var hashInvertedIndex = new HashInvertedIndex(indexCreator.OrganizeDocsAndWords());
var controller = new Controller(new ConsoleView(), new Processor(hashInvertedIndex));
controller.Run();
}
public void SetUp()
{
IWindsorContainer container = new WindsorContainer().Install(
new RavenInstaller(Array.Empty <Tenant>(), DocumentStoreMode.InMemory));
Store = container.Resolve <IDocumentStore>();
IndexCreator.CreateIndexes(Store);
Session = Store.OpenSession();
OnSetUp();
}
public void ParsingDeletionJsonLine()
{
const string jsonLine =
"{\"chromosome\":\"chr1\",\"refAllele\":\"GT\",\"position\":2337967,\"altAlleles\":[\"G\"],\"cyt\r\nogeneticBand\":\"1p36.32\",\"variants\":[{\"altAllele\":\"C\",\"refAllele\":\"-\",\"begin\":2337968,\"chromosome\":\"chr1\",\"dbsnp\":[\"rs797044762\"],\"end\":2337967,\"variantType\":\"insertion\",\"vid\":\"1:2337968:2337967:C\",\"regulatoryRegions\":[{\"id\":\"ENSR00001576444\",\"consequence\":[\"regulatory_region_variant\"]}],\"transcripts\":{\"refSeq\":[{\"transcript\":\"XM_005244712.1\",\"bioType\":\"protein_coding\",\"geneId\":\"11079\",\"hgnc\":\"RER1\",\"consequence\":[\"downstream_gene_variant\"],\"proteinId\":\"XP_005244769.1\"},{\"transcript\":\"NM_007033.4\",\"bioType\":\"protein_coding\",\"geneId\":\"11079\",\"hgnc\":\"RER1\",\"consequence\":[\"downstream_gene_variant\"],\"isCanonical\":true,\"proteinId\":\"NP_008964.3\"},{\"transcript\":\"XM_005244713.1\",\"bioType\":\"protein_coding\",\"geneId\":\"11079\",\"hgnc\":\"RER1\",\"consequence\":[\"downstream_gene_variant\"],\"proteinId\":\"XP_005244770.1\"},{\"transcript\":\"NM_002617.3\",\"bioType\":\"protein_coding\",\"aminoAcids\":\"-/X\",\"cDnaPos\":\"936-937\",\"codons\":\"-/G\",\"cdsPos\":\"867-868\",\"exons\":\"5/6\",\"geneId\":\"5192\",\"hgnc\":\"PEX10\",\"consequence\":[\"frameshift_variant\"],\"hgvsc\":\"NM_002617.3:c.867_868insG\",\"hgvsp\":\"NP_002608.1:p.His290AlafsTer49\",\"proteinId\":\"NP_002608.1\",\"proteinPos\":\"289-290\"},{\"transcript\":\"NM_153818.1\",\"bioType\":\"protein_coding\",\"aminoAcids\":\"-/X\",\"cDnaPos\":\"996-997\",\"codons\":\"-/G\",\"cdsPos\":\"927-928\",\"exons\":\"5/6\",\"geneId\":\"5192\",\"hgnc\":\"PEX10\",\"consequence\":[\"frameshift_variant\"],\"hgvsc\":\"NM_153818.1:c.927_928insG\",\"hgvsp\":\"NP_722540.1:p.His310AlafsTer49\",\"isCanonical\":true,\"proteinId\":\"NP_722540.1\",\"proteinPos\":\"309-310\"}]}}]}";
var chrPos = IndexCreator.GetChromPosition(jsonLine);
Assert.Equal("chr1", chrPos.Item1);
Assert.Equal(2337967, chrPos.Item2);
Assert.Equal(2337968, chrPos.Item3);
}
public void ParseJsonBreakEnd()
{
const string jsonLine =
"{\"chromosome\":\"2\",\"refAllele\":\"G\",\"position\":321681,\"quality\":6,\"filters\":[\"PASS\"],\"altAlleles\":[\"G]2:421681]\"],\"cytogeneticBand\":\"2p25.3\",\"oneKg\":[{\"chromosome\":\"2\",\"begin\":314969,\"end\":694521,\"variantType\":\"copy_number_gain\",\"variantFreqAll\":0.0008,\"variantFreqEas\":0.00397,\"id\":\"esv3589600\",\"sampleSize\":2504,\"sampleSizeAfr\":661,\"sampleSizeAmr\":347,\"sampleSizeEas\":504,\"sampleSizeEur\":503,\"sampleSizeSas\":489,\"observedGains\":2}],\"variants\":[{\"altAllele\":\"G]2:421681]\",\"refAllele\":\"G\",\"begin\":321681,\"chromosome\":\"2\",\"end\":321686,\"variantType\":\"translocation_breakend\",\"vid\":\"2:321681:+:2:421681:-\",\"overlappingGenes\":[\"AC079779.6\"]}]}";
var chrPos = IndexCreator.GetChromPosition(jsonLine);
Assert.Equal("2", chrPos.Item1);
Assert.Equal(321681, chrPos.Item2);
Assert.Equal(321681, chrPos.Item3);
}
public void ParseJsonStructuralVariant()
{
const string jsonLine =
"{\"chromosome\":\"chr3\",\"refAllele\":\"A\",\"position\":62431401,\"svEnd\":62431801,\"altAlleles\":[\"<DEL>\"],\"cytogeneticBand\":\"3p14.2\",\"variants\":[{\"altAllele\":\"<DEL>\",\"refAllele\":\"A\",\"begin\":62431402,\"chromosome\":\"chr3\",\"end\":62431801,\"variantType\":\"unknown\",\"vid\":\"3:62431402:62431401\",\"globalAllele\":{\"globalMajorAllele\":\"C\",\"globalMajorAlleleFrequency\":0.9856,\"globalMinorAllele\":\"A\",\"globalMinorAlleleFrequency\":0.01438}}]}";
var chrPos = IndexCreator.GetChromPosition(jsonLine);
Assert.Equal("chr3", chrPos.Item1);
Assert.Equal(62431401, chrPos.Item2);
Assert.Equal(62431801, chrPos.Item3);
}
public static IIndex Provide(string name, DateTime startDate, DateTime endDate, string frequency)
{
var historicalData = ReadDataFromFile.ReadDataSeriesFromFile(
DownloadedFile.ProvideHistoridalDataFile(name, startDate, endDate, frequency));
var currentPrice = new DataPoint(); //currently not available
var listOfStocks = new List <IStock>(); //currently not available
var index = IndexCreator.CreateIndex(name, currentPrice, listOfStocks, historicalData);
return(index);
}
private static void Main(string[] args)
{
var context = new SearchContextFactory().CreateDbContext(args);
var docFileReader = new DocFileReader();
var documentRepository = new DocumentRepository(context);
var indexCreator = new IndexCreator(docFileReader, documentRepository);
indexCreator.OrganizeDocsAndWords("EnglishData");
var controller = new Controller(new ConsoleView(), new Processor(documentRepository));
controller.Run();
}
public CreateTableBuilder(DbConnection db, IGenerateDDL generator, string tableName, IfTableExists option)
{
_db = db;
_generator = generator;
tableName.MustNotBeEmpty();
_table = new TableSchema(tableName);
_columns = new ColumnsCreator(Table);
_constraints = new ConstraintsCreator(Table.Constraints);
_indexes = new IndexCreator(Table.Indexes);
Table.Name = tableName;
Table.CreationOption = option;
}
public FileItemsView()
{
InitializeComponent();
BackButton.Command = BackCommand;
ForwardButton.Command = ForwardCommand;
// Create search index
var searchIndexCreator = new IndexCreator(Dispatcher);
// searchIndexCreator.CreateSearchIndex();
_imageLoader = new ImageLoader(Dispatcher);
Unloaded += EndLoadingImage;
FileItems.Focusable = true;
FileItems.Focus();
InitializeCommand();
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in C#:
//ORIGINAL LINE: void shouldFailWithNonExistentProviderName(IndexCreator creator) throws org.neo4j.internal.kernel.api.exceptions.KernelException
internal virtual void ShouldFailWithNonExistentProviderName(IndexCreator creator)
{
// given
SchemaWrite schemaWrite = SchemaWriteInNewTransaction();
// when
try
{
creator.Create(schemaWrite, forLabel(0, 0), "something-completely-different");
fail("Should have failed");
}
catch (IndexProviderNotFoundException)
{
// then good
}
}
public static void Initialize()
{
ranker = new Ranker.Ranker();
indexer = new Indexer.Indexer();
urlFilter = new UrlFilter();
urlFrontier = new UrlFrontier();
indexCreator = new IndexCreator();
pageRetriever = new PageRetriever();
termContructor = new TermConstructor();
tokenizer = new Tokenizer();
webCrawler = new WebCrawler.WebCrawler();
pageDB = new PageDB();
DPC = new DuplicatePageChecker();
DUC = new DuplicateURLChecker();
pageFetcher = new PageFetcher();
pageParser = new PageParser();
}
private void CreateIndex(params string[] propKeys)
{
using (Transaction tx = Db.beginTx())
{
IndexCreator indexCreator = Db.schema().indexFor(LABEL_ONE);
foreach (string propKey in propKeys)
{
indexCreator = indexCreator.On(propKey);
}
indexCreator.Create();
tx.Success();
}
using (Transaction tx = Db.beginTx())
{
Db.schema().awaitIndexesOnline(1, TimeUnit.MINUTES);
tx.Success();
}
}
public void WhenIIndexThePeople()
{
var people = ScenarioContext.Current.Get<IEnumerable<Person>>();
var mock = new Mock<IWordBreakingInformationRetriever>();
mock.Setup(x => x.GetWordBreakingInformation())
.Returns(new WordBreakingInformation{NoiseWords = new Dictionary<string, string>(),
Substitutions = new Dictionary<string, string>(),
Whitespace = new List<char>()});
var indexCreator = new IndexCreator<int>(new TextIndexFiller<int>(new DefaultWordBreaker(mock.Object)));
var phrases = people.Select(x => new Phrase<int> {Key = x.Key, Text = x.FirstName + " " + x.LastName});
var index = indexCreator.CreateIndex(phrases);
ScenarioContext.Current.Set(index);
}
private void CreateIndex(params string[] keys)
{
using (Transaction tx = Db.beginTx())
{
IndexCreator indexCreator = Db.schema().indexFor(LABEL);
foreach (string key in keys)
{
indexCreator = indexCreator.On(key);
}
indexCreator.Create();
tx.Success();
}
using (Transaction tx = Db.beginTx())
{
Db.schema().awaitIndexesOnline(10, SECONDS);
tx.Success();
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in C#:
//ORIGINAL LINE: void shouldCreateWithSpecificExistingProviderName(IndexCreator creator) throws org.neo4j.internal.kernel.api.exceptions.KernelException
internal virtual void ShouldCreateWithSpecificExistingProviderName(IndexCreator creator)
{
int labelId = 0;
foreach (GraphDatabaseSettings.SchemaIndex indexSetting in GraphDatabaseSettings.SchemaIndex.values())
{
// given
SchemaWrite schemaWrite = SchemaWriteInNewTransaction();
string provider = indexSetting.providerName();
LabelSchemaDescriptor descriptor = forLabel(labelId++, 0);
creator.Create(schemaWrite, descriptor, provider);
// when
Commit();
// then
assertEquals(provider, IndexingService.getIndexProxy(descriptor).Descriptor.providerDescriptor().name());
}
}
public void TestIndexCreation()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var tempFile = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
using (var indexCreator = new IndexCreator(readStream, FileUtilities.GetCreateStream(tempFile)))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
using (var stream = FileUtilities.GetReadStream(tempFile))
{
readBackIndex = new JasixIndex(stream);
}
Assert.Equal(1591, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(11500956299, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(372100991296, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(377682846863, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
File.Delete(tempFile);
}
public void WhenIIndexThePeople()
{
var people = ScenarioContext.Current.Get <IEnumerable <Person> >();
var mock = new Mock <IWordBreakingInformationRetriever>();
mock.Setup(x => x.GetWordBreakingInformation())
.Returns(new WordBreakingInformation {
NoiseWords = new Dictionary <string, string>(),
Substitutions = new Dictionary <string, string>(),
Whitespace = new List <char>()
});
var indexCreator = new IndexCreator <int>(new TextIndexFiller <int>(new DefaultWordBreaker(mock.Object)));
var phrases = people.Select(x => new Phrase <int> {
Key = x.Key, Text = x.FirstName + " " + x.LastName
});
var index = indexCreator.CreateIndex(phrases);
ScenarioContext.Current.Set(index);
}
private static void Main(string[] args)
{
IConfiguration config = new ConfigurationBuilder().AddJsonFile("appsettings.json").Build();
var directoryPath = config.GetValue <string>("DirectoryPath");
var client = new ElasticClientFactory(config).CreateElasticClient();
var queryCreator = new QueryCreator();
var searcher = new Searcher(client, queryCreator, Index);
var consoleView = new ConsoleView();
var controller = new Controller(consoleView, searcher);
if (!IsIndexExisting(Index, client))
{
var indexCreator = new IndexCreator(client);
indexCreator.CreateIndex(Index);
var fileReader = new DocFileReader();
var docCreator = new DocFactory(fileReader);
var importer = new Importer <Doc>(client);
importer.Import(docCreator.GetAllDocuments(directoryPath), Index);
}
controller.Run();
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Test public void shouldReturnIndexRuleForLabelAndVeryManyPropertiesComposite()
public virtual void ShouldReturnIndexRuleForLabelAndVeryManyPropertiesComposite()
{
string[] props = "abcdefghijklmnopqrstuvwxyzABCDEFGHJILKMNOPQRSTUVWXYZ".Split("\\B", true);
CreateSchema(Db =>
{
IndexCreator indexCreator = Db.schema().indexFor(Label.label(LABEL1));
foreach (string prop in props)
{
indexCreator = indexCreator.on(prop);
}
indexCreator.create();
});
StoreIndexDescriptor rule = _storage.indexGetForSchema(TestIndexDescriptorFactory.forLabel(LabelId(LABEL1), java.util.props.Select(this.propId).ToArray()));
assertNotNull(rule);
assertTrue(SchemaDescriptorPredicates.hasLabel(rule, LabelId(LABEL1)));
foreach (string prop in props)
{
assertTrue(SchemaDescriptorPredicates.hasProperty(rule, PropId(prop)));
}
assertEquals(IndexDescriptor.Type.GENERAL, rule.Type());
}
public override Task Handle(HandlerContext <Command> context)
{
IndexCreator.CreateIndexes(CompositionRoot.DocumentStore);
User admin = CompositionRoot.DocumentSession.Load <User>(User.AdminId);
if (admin == null)
{
admin = new("", "", context.Payload.Email, context.Payload.Password)
{
Id = User.AdminId
};
admin.Initialize(t => context.PublishMessage(t));
admin.Activate();
CompositionRoot.DocumentSession.Store(admin);
}
else
{
admin.SetEmail(context.Payload.Email);
admin.SetPassword(context.Payload.Password);
admin.Activate();
}
return(Task.CompletedTask);
}
private IHttpActionResult Handle(InitializeIndexesMessage message)
{
IndexCreator.CreateIndexes(DocumentStore);
User admin = DocumentSession.Load <User>(Models.User.AdminId);
if (admin == null)
{
admin = new User("", "", message.Email, message.Password)
{
Id = Models.User.AdminId
};
admin.Initialize(PublishMessage);
admin.Activate();
DocumentSession.Store(admin);
}
else
{
admin.SetEmail(message.Email);
admin.SetPassword(message.Password);
admin.Activate();
}
return(Ok());
}
public ActionResult ResetIndexesConfirmed()
{
IndexCreator.ResetIndexes(CompositionRoot.DocumentStore, CompositionRoot.EventStore);
return(RedirectToAction("Raven"));
}
public IndexCreatorTests()
{
_docFileReader = Substitute.For <IFileReader>();
_sut = new IndexCreator(_docFileReader);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in C#:
//ORIGINAL LINE: private java.util.stream.Stream<BuiltInProcedures.SchemaIndexInfo> createIndex(String indexSpecification, String providerName, String statusMessage, IndexCreator indexCreator) throws org.neo4j.internal.kernel.api.exceptions.ProcedureException
private Stream <BuiltInProcedures.SchemaIndexInfo> CreateIndex(string indexSpecification, string providerName, string statusMessage, IndexCreator indexCreator)
{
AssertProviderNameNotNull(providerName);
IndexSpecifier index = IndexSpecifier.ByPattern(indexSpecification);
int labelId = GetOrCreateLabelId(index.Label());
int[] propertyKeyIds = GetOrCreatePropertyIds(index.Properties());
try
{
SchemaWrite schemaWrite = _ktx.schemaWrite();
LabelSchemaDescriptor labelSchemaDescriptor = SchemaDescriptorFactory.forLabel(labelId, propertyKeyIds);
indexCreator(schemaWrite, labelSchemaDescriptor, providerName);
return(Stream.of(new BuiltInProcedures.SchemaIndexInfo(indexSpecification, providerName, statusMessage)));
}
catch (Exception e) when(e is InvalidTransactionTypeKernelException || e is SchemaKernelException)
{
throw new ProcedureException(e.status(), e, e.Message);
}
}
public IndexCreatorTest()
{
_docFileReader = Substitute.For <IFileReader>();
_documentRepository = new DocumentRepositoryForTest();
_sut = new IndexCreator(_docFileReader, _documentRepository);
}
