A B C D E F G H I L M N O P R S T U V X
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- addChange(BioModelsChange) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChangeSet
- addChange(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- addChange(PmrChange) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChangeSet
- addChange(PmrChange) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Adds a change to the changeSet and creates one if necessary.
- addModel(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- addParent(String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Adds a parent to this model with the same fileId.
- addParent(String, String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Adds a parent to this model.
- addVersion(Date, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo.FileVersionInfo
- App - Class in de.unirostock.sems.ModelCrawler
B
- BioModelRelease - Class in de.unirostock.sems.ModelCrawler.databases.BioModelsDb
- BioModelRelease(String, String, Date) - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- BioModelRelease(String, String, Date, File) - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- BioModelsChange - Class in de.unirostock.sems.ModelCrawler.databases.BioModelsDb
- BioModelsChange(URL, String, String, Date, Date) - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- BioModelsChangeSet - Class in de.unirostock.sems.ModelCrawler.databases.BioModelsDb
- BioModelsChangeSet(URL, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChangeSet
- BioModelsDb - Class in de.unirostock.sems.ModelCrawler.databases.BioModelsDb
- BioModelsDb() - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
-
Default empty constructor
- BMDB - Static variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase.DatabaseTypes
C
- calcXmlHash(File) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- calcXmlHash(File, String) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- call() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- call() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
Starts the process of crawling for this specific Database.
- call() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- call() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb.ExposureTransformJob
- Change - Class in de.unirostock.sems.ModelCrawler.databases.Interface
- Change(URL, String, String, Date, Date) - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- changes - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- ChangeSet - Class in de.unirostock.sems.ModelCrawler.databases.Interface
- ChangeSet(String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- ChangeSet(URL, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- changeSetMap - Variable in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- changeSetMap - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- classifier - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- close() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- close() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
Cleans up the working directory
- close() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- close() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- close() - Method in class de.unirostock.sems.ModelCrawler.storage.ModelStorage
-
Closes the connector and cleans things up
- closeConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- closeConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- closeConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- collectionEndpoint - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- compareTo(BioModelRelease) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- compareTo(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- config - Variable in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- config - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- config - Variable in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- Config - Class in de.unirostock.sems.ModelCrawler
- Config.WorkingMode - Enum in de.unirostock.sems.ModelCrawler
- ConfigurationException - Exception in de.unirostock.sems.ModelCrawler.exceptions
- ConfigurationException() - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.ConfigurationException
- ConfigurationException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.ConfigurationException
- ConfigurationException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.ConfigurationException
- ConfigurationException(String, Throwable, boolean, boolean) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.ConfigurationException
- ConfigurationException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.ConfigurationException
- connect() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- connect() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- connect() - Method in class de.unirostock.sems.ModelCrawler.storage.ModelStorage
-
Connects to the storage destination, is supposed to be called before every other operation.
- Constants - Class in de.unirostock.sems.ModelCrawler
- Constants() - Constructor for class de.unirostock.sems.ModelCrawler.Constants
- CRAWLED_DATE - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- CrawledModelRecord - Class in de.unirostock.sems.ModelCrawler.helper
- CrawledModelRecord(CrawledModel) - Constructor for class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Creates a new CrawledModelRecord based on a simple CrawledModel Dataholder.
- CrawledModelRecord(String, String, String, Map<String, List<String>>, Map<String, String>, String) - Constructor for class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
- CrawledModelRecord(String, String, String, Map<String, List<String>>, Map<String, String>, String, Date, Date) - Constructor for class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
- CrawledModelRecord(String, String, Date, Date) - Constructor for class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
- CrawlerAPI - Class in de.unirostock.sems.ModelCrawler
- CrawlerAPI(String[]) - Constructor for class de.unirostock.sems.ModelCrawler.CrawlerAPI
- createTempDir() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
creates a new and empty temporary directory and sets the class variable.
D
- DatabaseTypes() - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase.DatabaseTypes
- DATE_FORMAT - Static variable in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
- de.unirostock.sems.ModelCrawler - package de.unirostock.sems.ModelCrawler
- de.unirostock.sems.ModelCrawler.databases.BioModelsDb - package de.unirostock.sems.ModelCrawler.databases.BioModelsDb
- de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions - package de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions
- de.unirostock.sems.ModelCrawler.databases.Interface - package de.unirostock.sems.ModelCrawler.databases.Interface
- de.unirostock.sems.ModelCrawler.databases.Interface.exceptions - package de.unirostock.sems.ModelCrawler.databases.Interface.exceptions
- de.unirostock.sems.ModelCrawler.databases.PMR2 - package de.unirostock.sems.ModelCrawler.databases.PMR2
- de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions - package de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions
- de.unirostock.sems.ModelCrawler.exceptions - package de.unirostock.sems.ModelCrawler.exceptions
- de.unirostock.sems.ModelCrawler.helper - package de.unirostock.sems.ModelCrawler.helper
- de.unirostock.sems.ModelCrawler.storage - package de.unirostock.sems.ModelCrawler.storage
- DEFAULT_TEMP_PREFIX - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- defaultConfig() - Static method in class de.unirostock.sems.ModelCrawler.Config
-
Loads some default config parameters.
- detectRelevantVersions(Git, List<RelevantFile>) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- disconnect() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
E
- enabled - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- equals(Object) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- ExposureTransformJob(URL) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb.ExposureTransformJob
- extendDataholder(CrawledModel) - Static method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
- ExtractException - Exception in de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions
- ExtractException() - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.ExtractException
- ExtractException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.ExtractException
- ExtractException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.ExtractException
- ExtractException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.ExtractException
F
- FILE - Static variable in class de.unirostock.sems.ModelCrawler.storage.ModelStorage.Types
- FILE_NAME - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- FILE_PATH - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- FileBasedStorage - Class in de.unirostock.sems.ModelCrawler.storage
- FileBasedStorage() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- FileBasedStorage.VersionInfo - Class in de.unirostock.sems.ModelCrawler.storage
- FileBasedStorage.VersionInfo.FileVersionInfo - Class in de.unirostock.sems.ModelCrawler.storage
- fileExtensionBlacklist - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- fileId - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- fileName - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- filePath - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- FileStorage - Class in de.unirostock.sems.ModelCrawler.storage
- FileStorage() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FileStorage
- FileVersionInfo() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo.FileVersionInfo
- FTP - Static variable in class de.unirostock.sems.ModelCrawler.storage.ModelStorage.Types
- FTP_DEFAULT_PORT - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- FtpConnectionException - Exception in de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions
- FtpConnectionException() - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.FtpConnectionException
- FtpConnectionException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.FtpConnectionException
- FtpConnectionException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.FtpConnectionException
- FtpConnectionException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.BioModelsDb.exceptions.FtpConnectionException
- FtpStorage - Class in de.unirostock.sems.ModelCrawler.storage
- FtpStorage() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FtpStorage
G
- generateFileId(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Generate file id.
- generateFileId(URL, String) - Static method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getApp(String[]) - Static method in class de.unirostock.sems.ModelCrawler.App
- getArchivFile() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getBaseDir() - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- getChangeCrawledDate(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getChangeFileName(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getChangeFilePath(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getChangeRepositoryUrl(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getChanges() - Method in class de.unirostock.sems.ModelCrawler.App
- getChanges() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- getChangeSet() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Return the changeSet or null, if no one was setted and no change added.
- getChangesPerRelease() - Method in class de.unirostock.sems.ModelCrawler.App
- getChangesPerRelease(CrawlerAPI) - Static method in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- getChangeVersionDate(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getChangeVersionId(Change) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getCollection(URL) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getCollectionEndpoint() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getConfig() - Static method in class de.unirostock.sems.ModelCrawler.Config
-
Gets the config instance
- getContentDir() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getCrawledDate() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getCrawledDate() - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Returns the parsed CrawledDate if it is set, or null.
- getDatabases() - Method in class de.unirostock.sems.ModelCrawler.Config
- getDownloadedModels(App) - Static method in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- getEncoding() - Method in class de.unirostock.sems.ModelCrawler.Config
- getExtensionBlacklist() - Method in class de.unirostock.sems.ModelCrawler.Config
- getFile(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- getFile(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- getFile(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- getFileId() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- getFileId() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the file id.
- getFileId() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo.FileVersionInfo
- getFilePath() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the file path.
- getFtpDirectory() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getFtpPass() - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- getFtpUrl() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- getFtpUrl() - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- getFtpUser() - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- getHash() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- getHashAlgo() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getHttpAccessPath() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- getLatestChange() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- getLatestKnownVersionDate() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the latest known VersionDate.
- getLatestKnownVersionId() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the latest known VersionId.
- getLatestVersionDate() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the real latest versionDate.
- getLatestVersionId() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the real latest versionId.
- getLimit() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- getMeta(String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Returns the value of a meta field or null.
- getModelChange(Change, String) - Static method in class de.unirostock.sems.ModelCrawler.CrawlerAPI
-
Return a specific field within the provided model's change.
- getModelChanges(String) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- getModelChanges(String) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
Returns the ChangeSet only for one specific model.
- getModelChanges(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getModelChangeSet(Map<String, ChangeSet>, String) - Static method in class de.unirostock.sems.ModelCrawler.CrawlerAPI
-
Return all ChangeSet changes associated with the given modelName.
- getModelList() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getModelPath(String) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getModels() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- getModelStorage() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- getMorreClient() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- getMorreUrl() - Method in class de.unirostock.sems.ModelCrawler.Config
- getObjectMapper() - Static method in class de.unirostock.sems.ModelCrawler.Config
-
returns the default jackson object mapper for serializing and deserializing json objects
- getOrigin() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- getPathSeparator() - Method in class de.unirostock.sems.ModelCrawler.Config
- getPathSeparatorString() - Method in class de.unirostock.sems.ModelCrawler.Config
- getRelativeFile(File, File) - Static method in class de.unirostock.sems.ModelCrawler.helper.RelativPath
-
Returns the path of one File relative to another.
- getReleaseDate() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getReleaseName() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- getRepoListUrl() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getRepositoriesFromCollection() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- getRepositoryDirectory(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
-
Gets the Path to the Repository Directory out of Workspace config or null if it fails.
- getRepositoryList() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
-
Retrieves the txt Repository List and puts it in a list.
- getRepositoryUrl() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the repository url.
- getSingleModel(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- getStorage() - Method in class de.unirostock.sems.ModelCrawler.Config
- getTempDir() - Method in class de.unirostock.sems.ModelCrawler.Config
- getTempDirPrefix() - Method in class de.unirostock.sems.ModelCrawler.Config
- getTempFile() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
-
Returns a non existent temporary file.
- getType() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Gets the type.
- getUrnNamespace() - Method in class de.unirostock.sems.ModelCrawler.Config
- getVersionDate() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- getVersionDate() - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Returns the parsed VersionDate if it is set, or null.
- getVersions() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo.FileVersionInfo
- getWorkingDir() - Method in class de.unirostock.sems.ModelCrawler.Config
- getWorkingDir() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- getWorkingDirConfig() - Method in class de.unirostock.sems.ModelCrawler.Config
- getWorkingMode() - Static method in class de.unirostock.sems.ModelCrawler.Config
-
Gets the current working mode of the crawler
- getXmlFile() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
H
- HASH_ALGORITHM - Static variable in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- HASH_ALGORITHM_FALLBACK - Static variable in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- hashAlgo - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- hashCode() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- httpAccessPath - Variable in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- HttpException - Exception in de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions
- HttpException() - Constructor for exception de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions.HttpException
- HttpException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions.HttpException
- HttpException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions.HttpException
- HttpException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.PMR2.exceptions.HttpException
I
- init() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- init() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- initConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- initConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- initConnection() - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- isAvailable() - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Checks if the model dataholder is valid.
- isDownloaded() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- isEnabled() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- isExtracted() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- iterateRelevantVersions(Git, File, List<RelevantFile>, List<RevCommit>) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
L
- limit - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- linkFiles(String, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- linkFiles(String, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- linkFiles(String, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- linkModelVersion(String, String, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- linkModelVersion(String, String, String) - Method in class de.unirostock.sems.ModelCrawler.storage.ModelStorage
-
Links the source Version to the target Version (The target Version should exist already).
- listChanges() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- listChanges() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
Returns a map with all changes made after the last crawl
the fileId is the map key. - listChanges() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- listModels() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- listModels() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
-
lists all Models in the latest revision
- listModels() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- load(File) - Static method in class de.unirostock.sems.ModelCrawler.Config
-
Loads the config from a Json file.
M
- main(String[]) - Static method in class de.unirostock.sems.ModelCrawler.App
- main(String[]) - Static method in class de.unirostock.sems.ModelCrawler.CrawlerAPI
-
Class demo.
- makeDirs(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- makeDirs(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- makeDirs(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- makeRepositoryDirectory(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
-
Creates the directory for the given Repository.
- META_HASH - Static variable in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- ModelDatabase - Class in de.unirostock.sems.ModelCrawler.databases.Interface
- ModelDatabase() - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- ModelDatabase.DatabaseTypes - Class in de.unirostock.sems.ModelCrawler.databases.Interface
- modelStorage - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- ModelStorage - Class in de.unirostock.sems.ModelCrawler.storage
- ModelStorage() - Constructor for class de.unirostock.sems.ModelCrawler.storage.ModelStorage
- ModelStorage.Types - Class in de.unirostock.sems.ModelCrawler.storage
- morreClient - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
N
- NO_MORRE - de.unirostock.sems.ModelCrawler.Config.WorkingMode
- NONE - Static variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase.DatabaseTypes
- NORMAL - de.unirostock.sems.ModelCrawler.Config.WorkingMode
O
- obtainWorkingDir() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
P
- PATH_SPLIT_REGEX - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- PMR2 - Static variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase.DatabaseTypes
- PmrChange - Class in de.unirostock.sems.ModelCrawler.databases.PMR2
- PmrChange(URL, String, String, Date, Date) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChange
- PmrChangeSet - Class in de.unirostock.sems.ModelCrawler.databases.PMR2
- PmrChangeSet(String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChangeSet
- PmrChangeSet(URL, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChangeSet
- PmrDb - Class in de.unirostock.sems.ModelCrawler.databases.PMR2
- PmrDb() - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
-
Default dataholder
- PmrDb.ExposureTransformJob - Class in de.unirostock.sems.ModelCrawler.databases.PMR2
- processRelease(BioModelRelease) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
-
Downloads, extracts and indexes the gives release must called for each new release CHRONOLOGICAL.
- processRepository(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
R
- RelativPath - Class in de.unirostock.sems.ModelCrawler.helper
- RelativPath() - Constructor for class de.unirostock.sems.ModelCrawler.helper.RelativPath
- RelevantFile - Class in de.unirostock.sems.ModelCrawler.databases.PMR2
-
The Class RelevantFile.
- RelevantFile(String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
The Constructor.
- RelevantFile(String, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
The Constructor.
- repoListUrl - Variable in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- REPOSITORY_URL - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- repositoryUrl - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- retrieveReleaseList() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
S
- save(File) - Method in class de.unirostock.sems.ModelCrawler.Config
-
Saves the current config to disk.
- saveProperties() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- saveProperties() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- scanAndTransferRepository(String, File, Git) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- scanRepository(File) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- searchLatestKnownVersion(RelevantFile) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- setArchivFile(File) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- setBaseDir(File) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- setCollectionEndpoint(URL) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- setContentDir(File, Map<String, File>) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- setCrawledDate(Date) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- setCrawledDate(Date) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Sets the CrawledDate in the Meta Field.
- setDatabases(List<ModelDatabase>) - Method in class de.unirostock.sems.ModelCrawler.Config
- setEnabled(boolean) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- setEncoding(String) - Method in class de.unirostock.sems.ModelCrawler.Config
- setExtensionBlacklist(String[]) - Method in class de.unirostock.sems.ModelCrawler.Config
- setFileId(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo.FileVersionInfo
- setFtpPass(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- setFtpUrl(URL) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsDb
- setFtpUrl(URL) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- setFtpUser(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- setHashAlgo(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- setHttpAccessPath(URL) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- setLatestKnownVersion(String, Date) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Sets the latest known Version of this model.
- setLatestKnownVersion(String, Date, PmrChangeSet) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Sets the latest known Version of this model and the changeSet of it.
- setLimit(int) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- setMeta(String, String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Sets the value of a meta field and overrides the previous value.
- setModels(Map<String, FileBasedStorage.VersionInfo.FileVersionInfo>) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- setModelStorage(ModelStorage) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- setMorreClient(MorreCrawlerInterface) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- setMorreUrl(String) - Method in class de.unirostock.sems.ModelCrawler.Config
- setOrigin(String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
- setPathSeparator(char) - Method in class de.unirostock.sems.ModelCrawler.Config
- setRepoListUrl(URL) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- setStorage(ModelStorage) - Method in class de.unirostock.sems.ModelCrawler.Config
- setTempDir(File) - Method in class de.unirostock.sems.ModelCrawler.Config
- setTempDirPrefix(String) - Method in class de.unirostock.sems.ModelCrawler.Config
- setType(int) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
-
Sets the type.
- setUrnNamespace(String) - Method in class de.unirostock.sems.ModelCrawler.Config
- setVersionDate(Date) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- setVersionDate(Date) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
-
Sets the VersionDate in the Meta Field.
- setWorkingDir(File) - Method in class de.unirostock.sems.ModelCrawler.Config
- setWorkingDir(String) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- setWorkingDirConfig(String) - Method in class de.unirostock.sems.ModelCrawler.Config
- setWorkingMode(Config.WorkingMode) - Static method in class de.unirostock.sems.ModelCrawler.Config
-
Sets the current working mode of the crawler
- setXmlFile(File) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- setXmlFile(File) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- setXmlFile(File, boolean) - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- setXmlFile(File, String) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
- StorageException - Exception in de.unirostock.sems.ModelCrawler.exceptions
- StorageException() - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.StorageException
- StorageException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.StorageException
- StorageException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.StorageException
- StorageException(String, Throwable, boolean, boolean) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.StorageException
- StorageException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.exceptions.StorageException
- storeFile(InputStream, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- storeFile(InputStream, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- storeFile(InputStream, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- storeFile(InputStream, String, boolean) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- storeFile(InputStream, String, boolean) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
- storeFile(InputStream, String, boolean) - Method in class de.unirostock.sems.ModelCrawler.storage.FtpStorage
- storeModel(Change) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
- storeModel(Change) - Method in class de.unirostock.sems.ModelCrawler.storage.ModelStorage
-
Puts a model into the storage system and returns the URI.
- storeModelChangeSet(ChangeSet) - Method in class de.unirostock.sems.ModelCrawler.storage.ModelStorage
-
Puts a whole ChangeSet of models into the storage system.
T
- TEMP_DIR_POSIX_ATTRIBUTES - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- tempDir - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase
- TEMPLATE_CONFIG - de.unirostock.sems.ModelCrawler.Config.WorkingMode
- TEST - de.unirostock.sems.ModelCrawler.Config.WorkingMode
- toString() - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
- toString() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- toString() - Method in class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
- toString() - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChange
- transformExposureUrl(URL) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrDb
- Types() - Constructor for class de.unirostock.sems.ModelCrawler.storage.ModelStorage.Types
U
- URN_SEPARATOR - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- URN_START - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- URN_VERSION_PLACEHOLDER - Static variable in class de.unirostock.sems.ModelCrawler.Constants
V
- valueOf(String) - Static method in enum de.unirostock.sems.ModelCrawler.Config.WorkingMode
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum de.unirostock.sems.ModelCrawler.Config.WorkingMode
-
Returns an array containing the constants of this enum type, in the order they are declared.
- VERSION_DATE - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- VERSION_ID - Static variable in class de.unirostock.sems.ModelCrawler.CrawlerAPI
- VERSION_INFO_FILENAME - Static variable in class de.unirostock.sems.ModelCrawler.Constants
- versionId - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- VersionInfo() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage.VersionInfo
X
- xmlFile - Variable in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
- XmlNotFoundException - Exception in de.unirostock.sems.ModelCrawler.databases.Interface.exceptions
- XmlNotFoundException() - Constructor for exception de.unirostock.sems.ModelCrawler.databases.Interface.exceptions.XmlNotFoundException
- XmlNotFoundException(String) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.Interface.exceptions.XmlNotFoundException
- XmlNotFoundException(String, Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.Interface.exceptions.XmlNotFoundException
- XmlNotFoundException(Throwable) - Constructor for exception de.unirostock.sems.ModelCrawler.databases.Interface.exceptions.XmlNotFoundException
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