A B C D E F G H I L M N O P R S T U V X

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

A B C D E F G H I L M N O P R S T U V X