net.imagej.updater

Class FilesCollection

java.lang.Object

java.util.AbstractMap<K,V>

java.util.HashMap<K,V>

java.util.LinkedHashMap<String,FileObject>

net.imagej.updater.FilesCollection

All Implemented Interfaces:

Serializable, Cloneable, Iterable<FileObject>, Map<String,FileObject>

public class FilesCollection
extends LinkedHashMap<String,FileObject>
implements Iterable<FileObject>

This class represents the database of available FileObjects.

By itself, a FilesCollection is fairly naive. If built around an existing installation, the first action to take after instantiation is often tryLoadingCollection() - which will then recognize update sites, etc...

After any updates to the FilesCollection, the write() method is used to persist configuration state to the db.xml.gz on disk. To rebuild the FilesCollection after such a modification, use reloadCollectionAndChecksum(Progress). This will, for example, provide FileObject instances for newly added update sites that are not yet installed. To make actual file changes (not just modifications to the database) you must first stage them with FileObject.stageForUninstall(FilesCollection) or FileObject.stageForUpdate(FilesCollection, boolean). At that point, an Installer can be used to create an update directory reflecting the staged changes, and apply them if needed.

Note that which files are incorporated into the FilesCollection is based on the behavior of the Checksummer.

Author:

Johannes Schindelin

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FilesCollection.DependencyMap
static interface	FilesCollection.Filter
static class	FilesCollection.FilteredIterator

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>

Field Summary

Fields

Modifier and Type	Field and Description
protected List<Conflicts.Conflict>	conflicts
static String	DEFAULT_UPDATE_SITE
protected Set<FileObject>	ignoredConflicts
org.scijava.log.LogService	log

Constructor Summary

Constructors

Constructor and Description
FilesCollection(File appRoot) This constructor takes the app root primarily for testing purposes.
FilesCollection(org.scijava.log.LogService log, File appRoot) This constructor takes the app root primarily for testing purposes.

Method Summary

Modifier and Type	Method and Description
void	activateUpdateSite(UpdateSite updateSite, Progress progress) Activate the given update site.
void	add(FileObject file)
UpdateSite	addUpdateSite(String name, String url, String sshHost, String uploadDirectory, long timestamp)
protected void	addUpdateSite(String name, UpdateSite updateSite)
UpdateSite	addUpdateSite(UpdateSite site)
Iterable<String>	analyzeDependencies(FileObject file)
FilesCollection.Filter	and(FilesCollection.Filter a, FilesCollection.Filter b)
Iterable<FileObject>	changes()
String	checkConsistency()
FilesCollection	clone(Iterable<FileObject> iterable)
int	deactivateUpdateSite(UpdateSite site) Deactivates the given update site.
FilesCollection.Filter	doesPlatformMatch()
String	downloadIndexAndChecksum(Progress progress)
FilesCollection.Filter	endsWith(String suffix)
boolean	fileExists(String filename)
Iterable<FileObject>	filter(FilesCollection.Filter filter)
static Iterable<FileObject>	filter(FilesCollection.Filter filter, Iterable<FileObject> files)
static Iterable<FileObject>	filter(String search, Iterable<FileObject> files)
Iterable<FileObject>	forUpdateSite(String name)
Iterable<FileObject>	forUpdateSite(String name, boolean includeObsoletes)
FileObject	get(int index) Deprecated.
FileObject	get(Object filename)
FileObject.Action[]	getActions(FileObject file) Deprecated.
FileObject.Action[]	getActions(Iterable<FileObject> files) Deprecated.
File	getAppRoot()
List<Conflicts.Conflict>	getConflicts()
FilesCollection.DependencyMap	getDependencies(boolean overridingOnes) Gets a map listing all the dependencees of files to be installed or updated.
FilesCollection.DependencyMap	getDependencies(Iterable<FileObject> files, boolean overridingOnes) Gets a map listing all the dependencees of the specified files.
FileObject	getFileFromDigest(String filename, String digest)
static String	getInstalledVersions(File ijDirectory, Progress progress) Utility method for the Bug Submitter
Collection<String>	getProtocols(Iterable<FileObject> selected)
Collection<String>	getSiteNamesToUpload()
UpdateSite	getUpdateSite(String name) Deprecated. use getUpdateSite(String, boolean) instead
UpdateSite	getUpdateSite(String name, boolean evenDisabled)
Collection<String>	getUpdateSiteNames() Deprecated. use getUpdateSiteNames(boolean) instead
Collection<String>	getUpdateSiteNames(boolean evenDisabled) Gets the names of known update sites.
Collection<UpdateSite>	getUpdateSites(boolean evenDisabled) Gets the list of known update sites.
String	getURL(FileObject file)
Set<GroupAction>	getValidActions()
Set<GroupAction>	getValidActions(Iterable<FileObject> selected)
boolean	has(FilesCollection.Filter filter)
boolean	hasChanges()
boolean	hasForcableUpdates()
FilesCollection.Filter	hasMetadataChanges()
boolean	hasUpdateSitesChanges()
boolean	hasUploadableSites()
boolean	hasUploadOrRemove()
Iterable<FileObject>	installed()
FilesCollection.Filter	is(FileObject.Action action)
FilesCollection.Filter	is(FileObject.Status status)
boolean	isActivePlatform(String platform)
FilesCollection.Filter	isNoAction()
FilesCollection.Filter	isUpdateSite(String updateSite)
Iterator<FileObject>	iterator()
Iterable<FileObject>	locallyModified()
Iterable<FileObject>	localOnly()
Iterable<FileObject>	managedFiles()
void	markForUpdate(boolean evenForcedUpdates)
FilesCollection.Filter	not(FilesCollection.Filter filter)
Iterable<FileObject>	notHidden()
FilesCollection.Filter	oneOf(FileObject.Action... actions)
FilesCollection.Filter	oneOf(FileObject.Status... states)
FilesCollection.Filter	or(FilesCollection.Filter a, FilesCollection.Filter b)
String	platform()
File	prefix(FileObject file)
File	prefix(String path)
File	prefixUpdate(String path)
String	protocolsMissingUploaders(UploaderService uploaderService, Progress progress)
FileObject	put(String key, FileObject file)
void	read()
void	read(File file)
void	read(FileInputStream in)
String	reloadCollectionAndChecksum(Progress progress)
FileObject	remove(Object file)
void	removeUpdateSite(String name)
void	renameUpdateSite(String oldName, String newName)
void	replaceUpdateSites(List<UpdateSite> sites)
void	reReadUpdateSite(String name, Progress progress)
void	setActivePlatforms(String... platforms)
void	setUpdateSitesChanged(boolean updateSitesChanged)
Iterable<FileObject>	shownByDefault()
void	sort()
FilesCollection.Filter	startsWith(String... prefixes)
FilesCollection.Filter	startsWith(String prefix)
Iterable<FileObject>	toInstall()
Iterable<FileObject>	toInstallOrUpdate()
Iterable<FileObject>	toRemove()
String	toString()
Iterable<FileObject>	toUninstall()
Iterable<FileObject>	toUpdate()
Iterable<FileObject>	toUpload()
Iterable<FileObject>	toUpload(boolean includeMetadataChanges)
Iterable<FileObject>	toUpload(String updateSite)
Iterable<FileObject>	toUploadOrRemove()
void	tryLoadingCollection()
Iterable<FileObject>	uninstalled()
Iterable<FileObject>	updateable(boolean evenForcedOnes)
void	updateDependencies(FileObject file)
Iterable<FileObject>	uploadable()
Iterable<FileObject>	uploadable(boolean assumeModified) Gets the list of uploadable files.
Iterable<FileObject>	upToDate()
void	write()
FilesCollection.Filter	yes()

Methods inherited from class java.util.LinkedHashMap

clear, containsValue, entrySet, forEach, getOrDefault, keySet, removeEldestEntry, replaceAll, values

Methods inherited from class java.util.HashMap

clone, compute, computeIfAbsent, computeIfPresent, containsKey, isEmpty, merge, putAll, putIfAbsent, remove, replace, replace, size

Methods inherited from class java.util.AbstractMap

equals, hashCode

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, containsKey, equals, hashCode, isEmpty, merge, putAll, putIfAbsent, remove, replace, replace, size

Field Detail

DEFAULT_UPDATE_SITE

public static final String DEFAULT_UPDATE_SITE

See Also:

Constant Field Values

log

public final org.scijava.log.LogService log

ignoredConflicts

protected Set<FileObject> ignoredConflicts

conflicts

protected List<Conflicts.Conflict> conflicts

Constructor Detail

FilesCollection

public FilesCollection(File appRoot)

This constructor takes the app root primarily for testing purposes.

Parameters:

appRoot - the application base directory

FilesCollection

public FilesCollection(org.scijava.log.LogService log,
                       File appRoot)

This constructor takes the app root primarily for testing purposes.

Parameters:

log - the log service

appRoot - the application base directory

Method Detail

getAppRoot

public File getAppRoot()

addUpdateSite

public UpdateSite addUpdateSite(String name,
                                String url,
                                String sshHost,
                                String uploadDirectory,
                                long timestamp)

addUpdateSite

public UpdateSite addUpdateSite(UpdateSite site)

addUpdateSite

protected void addUpdateSite(String name,
                             UpdateSite updateSite)

renameUpdateSite

public void renameUpdateSite(String oldName,
                             String newName)

removeUpdateSite

public void removeUpdateSite(String name)

replaceUpdateSites

public void replaceUpdateSites(List<UpdateSite> sites)

getUpdateSite

@Deprecated
public UpdateSite getUpdateSite(String name)

Deprecated. use getUpdateSite(String, boolean) instead

getUpdateSite

public UpdateSite getUpdateSite(String name,
                                boolean evenDisabled)

getUpdateSiteNames

@Deprecated
public Collection<String> getUpdateSiteNames()

Deprecated. use getUpdateSiteNames(boolean) instead

getUpdateSiteNames

public Collection<String> getUpdateSiteNames(boolean evenDisabled)

Gets the names of known update sites.

getUpdateSites

public Collection<UpdateSite> getUpdateSites(boolean evenDisabled)

Gets the list of known update sites.

getSiteNamesToUpload

public Collection<String> getSiteNamesToUpload()

hasUploadableSites

public boolean hasUploadableSites()

hasUpdateSitesChanges

public boolean hasUpdateSitesChanges()

setUpdateSitesChanged

public void setUpdateSitesChanged(boolean updateSitesChanged)

deactivateUpdateSite

public int deactivateUpdateSite(UpdateSite site)

Deactivates the given update site.

Parameters:

site - the site to deactivate

Returns:

the number of files marked for update/install/uninstall

activateUpdateSite

public void activateUpdateSite(UpdateSite updateSite,
                               Progress progress)
                        throws ParserConfigurationException,
                               IOException,
                               SAXException

Activate the given update site.

Parameters:

updateSite - the update site to activate

progress - the object to display the progress

Throws:

ParserConfigurationException

IOException

SAXException

reReadUpdateSite

public void reReadUpdateSite(String name,
                             Progress progress)
                      throws ParserConfigurationException,
                             IOException,
                             SAXException

Throws:

ParserConfigurationException

IOException

SAXException

protocolsMissingUploaders

public String protocolsMissingUploaders(UploaderService uploaderService,
                                        Progress progress)

getValidActions

public Set<GroupAction> getValidActions()

getValidActions

public Set<GroupAction> getValidActions(Iterable<FileObject> selected)

getActions

@Deprecated
public FileObject.Action[] getActions(FileObject file)

Deprecated.

getActions

@Deprecated
public FileObject.Action[] getActions(Iterable<FileObject> files)

Deprecated.

read

public void read()
          throws IOException,
                 ParserConfigurationException,
                 SAXException

Throws:

IOException

ParserConfigurationException

SAXException

read

public void read(File file)
          throws IOException,
                 ParserConfigurationException,
                 SAXException

Throws:

IOException

ParserConfigurationException

SAXException

read

public void read(FileInputStream in)
          throws IOException,
                 ParserConfigurationException,
                 SAXException

Throws:

IOException

ParserConfigurationException

SAXException

write

public void write()
           throws IOException,
                  SAXException,
                  TransformerConfigurationException

Throws:

IOException

SAXException

TransformerConfigurationException

clone

public FilesCollection clone(Iterable<FileObject> iterable)

toUploadOrRemove

public Iterable<FileObject> toUploadOrRemove()

toUpload

public Iterable<FileObject> toUpload()

toUpload

public Iterable<FileObject> toUpload(boolean includeMetadataChanges)

toUpload

public Iterable<FileObject> toUpload(String updateSite)

toUninstall

public Iterable<FileObject> toUninstall()

toRemove

public Iterable<FileObject> toRemove()

toUpdate

public Iterable<FileObject> toUpdate()

upToDate

public Iterable<FileObject> upToDate()

toInstall

public Iterable<FileObject> toInstall()

toInstallOrUpdate

public Iterable<FileObject> toInstallOrUpdate()

notHidden

public Iterable<FileObject> notHidden()

uninstalled

public Iterable<FileObject> uninstalled()

installed

public Iterable<FileObject> installed()

locallyModified

public Iterable<FileObject> locallyModified()

forUpdateSite

public Iterable<FileObject> forUpdateSite(String name)

forUpdateSite

public Iterable<FileObject> forUpdateSite(String name,
                                          boolean includeObsoletes)

managedFiles

public Iterable<FileObject> managedFiles()

localOnly

public Iterable<FileObject> localOnly()

shownByDefault

public Iterable<FileObject> shownByDefault()

uploadable

public Iterable<FileObject> uploadable()

uploadable

public Iterable<FileObject> uploadable(boolean assumeModified)

Gets the list of uploadable files.

Parameters:

assumeModified - true if we want the potentially uploadable files if they (or their metadata) were to be changed.

Returns:

the list of uploadable files

changes

public Iterable<FileObject> changes()

filter

public static Iterable<FileObject> filter(FilesCollection.Filter filter,
                                          Iterable<FileObject> files)

filter

public static Iterable<FileObject> filter(String search,
                                          Iterable<FileObject> files)

yes

public FilesCollection.Filter yes()

doesPlatformMatch

public FilesCollection.Filter doesPlatformMatch()

is

public FilesCollection.Filter is(FileObject.Action action)

isNoAction

public FilesCollection.Filter isNoAction()

oneOf

public FilesCollection.Filter oneOf(FileObject.Action... actions)

is

public FilesCollection.Filter is(FileObject.Status status)

hasMetadataChanges

public FilesCollection.Filter hasMetadataChanges()

isUpdateSite

public FilesCollection.Filter isUpdateSite(String updateSite)

oneOf

public FilesCollection.Filter oneOf(FileObject.Status... states)

startsWith

public FilesCollection.Filter startsWith(String prefix)

startsWith

public FilesCollection.Filter startsWith(String... prefixes)

endsWith

public FilesCollection.Filter endsWith(String suffix)

not

public FilesCollection.Filter not(FilesCollection.Filter filter)

or

public FilesCollection.Filter or(FilesCollection.Filter a,
                                 FilesCollection.Filter b)

and

public FilesCollection.Filter and(FilesCollection.Filter a,
                                  FilesCollection.Filter b)

filter

public Iterable<FileObject> filter(FilesCollection.Filter filter)

getFileFromDigest

public FileObject getFileFromDigest(String filename,
                                    String digest)

analyzeDependencies

public Iterable<String> analyzeDependencies(FileObject file)

updateDependencies

public void updateDependencies(FileObject file)

has

public boolean has(FilesCollection.Filter filter)

hasChanges

public boolean hasChanges()

hasUploadOrRemove

public boolean hasUploadOrRemove()

hasForcableUpdates

public boolean hasForcableUpdates()

updateable

public Iterable<FileObject> updateable(boolean evenForcedOnes)

markForUpdate

public void markForUpdate(boolean evenForcedUpdates)

getURL

public String getURL(FileObject file)

getDependencies

public FilesCollection.DependencyMap getDependencies(boolean overridingOnes)

Gets a map listing all the dependencees of files to be installed or updated.

Parameters:

overridingOnes - whether to include files that override a particular dependency

Returns:

the map

getDependencies

public FilesCollection.DependencyMap getDependencies(Iterable<FileObject> files,
                                                     boolean overridingOnes)

Gets a map listing all the dependencees of the specified files.

Parameters:

files - the dependencies

overridingOnes - whether to include files that override a particular dependency

Returns:

the map

sort

public void sort()

checkConsistency

public String checkConsistency()

prefix

public File prefix(FileObject file)

prefix

public File prefix(String path)

prefixUpdate

public File prefixUpdate(String path)

fileExists

public boolean fileExists(String filename)

toString

public String toString()

Overrides:

toString in class AbstractMap<String,FileObject>

get

@Deprecated
public FileObject get(int index)

Deprecated.

add

public void add(FileObject file)

get

public FileObject get(Object filename)

Specified by:

get in interface Map<String,FileObject>

Overrides:

get in class LinkedHashMap<String,FileObject>

put

public FileObject put(String key,
                      FileObject file)

Specified by:

put in interface Map<String,FileObject>

Overrides:

put in class HashMap<String,FileObject>

remove

public FileObject remove(Object file)

Specified by:

remove in interface Map<String,FileObject>

Overrides:

remove in class HashMap<String,FileObject>

iterator

public Iterator<FileObject> iterator()

Specified by:

iterator in interface Iterable<FileObject>

tryLoadingCollection

public void tryLoadingCollection()
                          throws ParserConfigurationException,
                                 SAXException

Throws:

ParserConfigurationException

SAXException

reloadCollectionAndChecksum

public String reloadCollectionAndChecksum(Progress progress)

downloadIndexAndChecksum

public String downloadIndexAndChecksum(Progress progress)
                                throws ParserConfigurationException,
                                       SAXException

Throws:

ParserConfigurationException

SAXException

getConflicts

public List<Conflicts.Conflict> getConflicts()

getInstalledVersions

public static String getInstalledVersions(File ijDirectory,
                                          Progress progress)

Utility method for the Bug Submitter

Returns:

the list of files known to the Updater, with versions, as a String

getProtocols

public Collection<String> getProtocols(Iterable<FileObject> selected)

platform

public String platform()

isActivePlatform

public boolean isActivePlatform(String platform)

setActivePlatforms

public void setActivePlatforms(String... platforms)