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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, String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
Adds a parent to this model.
addParent(String) - Method in class de.unirostock.sems.ModelCrawler.helper.CrawledModelRecord
Adds a parent to this model with the same fileId.
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, File) - Constructor for class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelRelease
 
BioModelRelease(String, String, Date) - 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(URL, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.Interface.ChangeSet
 
ChangeSet(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 - Class in de.unirostock.sems.ModelCrawler
 
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.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(Throwable) - 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
 
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(Throwable) - 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
 

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(Throwable) - 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
 
FtpStorage - Class in de.unirostock.sems.ModelCrawler.storage
 
FtpStorage() - Constructor for class de.unirostock.sems.ModelCrawler.storage.FtpStorage
 

G

generateFileId(URL, String) - Static method in class de.unirostock.sems.ModelCrawler.databases.Interface.Change
 
generateFileId(String) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
Generate file id.
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(Throwable) - 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
 

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

NONE - Static variable in class de.unirostock.sems.ModelCrawler.databases.Interface.ModelDatabase.DatabaseTypes
 

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(URL, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.PmrChangeSet
 
PmrChangeSet(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, String) - Constructor for class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
The Constructor.
RelevantFile(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, PmrChangeSet) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
Sets the latest known Version of this model and the changeSet of it.
setLatestKnownVersion(String, Date) - Method in class de.unirostock.sems.ModelCrawler.databases.PMR2.RelevantFile
Sets the latest known Version of this model.
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, String) - Method in class de.unirostock.sems.ModelCrawler.databases.BioModelsDb.BioModelsChange
 
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
 
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(Throwable) - 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
 
storeFile(InputStream, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
 
storeFile(InputStream, String, boolean) - Method in class de.unirostock.sems.ModelCrawler.storage.FileBasedStorage
 
storeFile(InputStream, String) - Method in class de.unirostock.sems.ModelCrawler.storage.FileStorage
 
storeFile(InputStream, String, boolean) - 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.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
 
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(Throwable) - 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
 
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