All Classes and Interfaces
Class
Description
Java offers uniform database access through the use of JDBC.
Exception thrown when an error occurs during access control
A Class that loads eml-access.xml file containing ACL for a metadata
document into relational DB.
A Class that loads eml-access.xml file containing ACL for a metadata
document into relational DB.
Exception thrown when an error occurs in a configuration administrative
class
(on insert of XML document)
Generates a unique Accession Number or if provided check it
for uniqueness and register it into the db connection
(on update or delete of XML document)
Check for existance of provided Accession Number
Exception thrown when an error occurs because an AccessionNumber was
invalid or used incorrectly.
A Class that represents an XML access rule.
Exception thrown when an error occurs in a configuration administrative
class
This class is in order to fix a problem.
Control the display of the Authentication configuration page and the processing of the
configuration values.
Exception class will be used in the authentication process
This an authentication class base on a username/password file.
A class to use the BCryptHash algorithm to generate the hash.
This an interface for different hash algorithms using to protect users' password
in the username/password file
An interface representing the methods that should be
implemented by an authentication service.
An implementation of the AuthInterface interface that allows Metacat to use
the LDAP protocol for directory services.
Implementation of AuthInterface for ORCID auth (see orcid.org).
AuthPropertiesDelegate handles Authentication-related properties for metacat configuration.
A Class that implements session tracking for MetaCatServlet users.
An implementation of the AuthInterface interface that
allows Metacat to use the LDAP protocol for directory services.
An implementation of the AuthInterface interface that
allows Metacat to use the LDAP protocol for directory services.
Exception thrown when an error occurs in a configuration administrative
class
Control the display of the login page
BackupPropertiesDelegate handles functionality related to backing up the main properties for
metacat configuration.
Exception thrown when an error occurs in a configuration administrative
class
A suite of utility classes for querying DB
A Class that represents an XML node and its contents
A client class to access the BookKeeper service
Class to query data
A Class implementing callback bethods for the SAX parser to
call when processing the XML messages from the replication handler
A file object with the expected checksum
Description information for the ClientView bean.
Represents Metacat's implementation of the DataONE Coordinating Node service API.
Represents Metacat's implementation of the DataONE Coordinating Node service
API.
CN REST service implementation handler
****************** CNCore -- DONE create() - POST /d1/cn/object/PID
listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID
getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve
listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID
CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET
/d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET
/d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not
implemented in Metacat
CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET
/d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules
CNIdentity - not implemented at all on Metacat
CNReplication setReplicationStatus() - PUT /replicaNotifications/PID
updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy()
- PUT /replicaPolicies/PID isNodeAuthorized() - GET
/replicaAuthorizations/PID
CNRegister -- not implemented at all in Metacat ******************
CN REST service implementation handler
****************** CNCore -- DONE create() - POST /d1/cn/object/PID
listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID
getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve
listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID
CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET
/d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET
/d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not
implemented in Metacat
CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET
/d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules
CNIdentity - not implemented at all on Metacat
CNReplication setReplicationStatus() - PUT /replicaNotifications/PID
updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy()
- PUT /replicaPolicies/PID isNodeAuthorized() - GET
/replicaAuthorizations/PID
CNRegister -- not implemented at all in Metacat ******************
Routes CN REST service requests to the appropriate handler
Routes CN REST service requests to the appropriate handler
A suite of utility classes for the metadata catalog server
This class will figure out which content type it is for a given data file.
This class represents a task to report a creation of a usage to the remote bookkeeper server and
set the reported date in the local usages table after the succeeded reporting
Control the display of the database configuration page and the processing of the configuration
values.
This is delegate class for D1NodeService and subclasses.
This class will contact the CN to figure out the version of the service
for the given node
Base class for handling D1 REST calls in Metacat
Metacat implementation of DataONE REST API as a servlet.
A factory abstract class to generate the datacite metadata (xml format) for an DOI object.
A utility class for configuring DataONE setting
Control the display of the database configuration page and the processing
of the configuration values.
A class represent a connection object, it includes connection itself,
index, status, age, createtime, connection time, usageCount, warning message
A class represent a DBConnection pool.
A database aware Class implementing DTDHandler interface for the SAX
parser to call when processing the XML stream and intercepting notations
and unparsed entities
A database aware Class implementing EntityResolver interface for the SAX
parser to call when processing the XML stream and intercepting any
external entities (including the external DTD subset and external
parameter entities, if any) before including them.
A database aware Class implementing callback bethods for the SAX parser to
call when processing the XML stream and generating events.
A Class that transforms XML documents utitlizing XSL style sheets
Building a transformer from the .xsl is expensive, so Templates are used
as an intermediate construct to allow lightweight construction of Transformers.
A suite of utility classes for querying DB
Name: DBValidate.java
Purpose: A Class that validates XML documents
This class is designed to be parser independent
i.e.
Default factory to generate a simple datacite metadata xml string
This class represents a thread task to report an event to delete of an exiting usage to the remote bookkeeper server.
A FileInputStream class with more information, such as the object of source file itself and the expected checksum of the source file.
A class to parse document ids
The docid is of the form siteCode.uniqueId.rev
A class that represents an XML document.
Exception thrown when the requested docid does not exist on the server
A suite of utility classes for the metadata catalog server
An exception that encapsulates errors from the DOI service.
An abstract class for the DOI service
A factory class to initialize an instance of DOIService
based on the configuration in the metacat.properties file
The class to back up dropped tables to the csv files during the upgrade process to 3.0.0
Provides eml-2.0.0 documents.
Provides eml-2.0.1 documents.
Before Metacat 1.8.1 release, Metacat uses the eml201 schema with the tag
RELEASE_EML_2_0_1_UPDATE_5.
Provides eml-2.1.0 documents.
Provides eml-2.1.1 documents.
A factory to generate data cite meta data for the scientific meta data standards - eml-2.*
Convert native "item" to oai_dc.
Exception thrown when an error occurs in a configuration administrative
class
Exception thrown when an error occurs in a utility method
EventLog is used to intialize and store a log of events that occur in an
application.
A data structure holding the information to be logged about an event.
This class represents a filter to prevent the events generated by some ip addresses and subjects
to be logged into db
Control the display of the ezid configuration page and the processing
of the configuration values.
Singleton for interacting with the EZID DOI library.
A timer to regenerate failed index tasks or index tasks in a given time frame.
This class periodically gets reporting usages which were failed to be reported to the
remote book keeper service (e.g.
This class represents an GetRecord response on either the server or on the
client
Class handling metacat scheme URLs by delegating connection requests
to the MetacatURLConnection class
Exception thrown when an error occurs in a configuration administrative
class
HarvesterVerb is the parent class for each of the OAI verbs.
Manage the relationship between Metacat local identifiers (LocalIDs) that are
codified as the (docid, rev) pair with globally unique string identifiers
(GUIDs) that are opaque strings.
This class represents an Identify response on either the server or on the
client
The IndexGenerator class will publish (send) the index information
to a RabbitMQ queue.
A timer to regenerate failed index tasks or index tasks in a given time frame.
Encapsulate an InputStream within a DataSource interface so that it is
accessible to MIME processors.
Exception thrown when an error occurs because a Metacat server operation
requires higher access rights than the currently logged in user has.
An exception class indicate the given system metadata is invalid.
The handler of JSON-LD objects to save bytes to disk
Collection of administrative initialization tasks that need to be performed automatically on
startup, when running in Kubernetes.
A class to save/retrieve the last re-index date.
This class represents an ListIdentifiers response on either the server or on
the client.
This class represents an ListMetadataFormats response on either the server or
on the client
This class represents an ListRecords response on either the server or on the
client
This class represents an ListSets response on either the server or on the
client
A child class of the Usage class of BookKeeper.
Control the display of the login page
This class represents a converter to convert an DataONE v2 Log object to a v1 Log object.
A class to convert a v2 LogEntry object to a v1 LogEntry object
A wrapper class to gap the difference in the signature of setEvent between the v2 and v1 LogEntry objects.
A wrapper class to gap the difference in the signature of setEvent between the v2 and v1 LogEntry objects.
Exception thrown when an error occurs because a document with a
given ID could not be found in the metacat database.
Exception thrown when an error occurs because a problem occurred in
the metacat database.
This interface provides methods for initializing and logging in to a
Metacat server, and then querying, reading, transforming, inserting,
updating and deleting documents from that server.
A suite of utility classes for querying DB
Entry servlet for the metadata configuration utility
Exception thrown when a Metacat server denies a login authentication
request.
MetacatCatalog is an implementation of AbstractCatalog interface.
This interface provides methods for initializing and logging in to a
Metacat server, and then querying, reading, transforming, inserting,
updating and deleting documents from that server.
Exception thrown when an error occurs during a metacat operation.
This class is a factory which allows the caller to create an instance of
a Metacat object for accessing a metacat server.
General entry point for the Metacat server which is called from various mechanisms such as the
standard MetacatServlet class and the various web service servlets such as RestServlet class.
Exception thrown when a Metacat server is not accessible for the
operation requested.
A class to initialize Metacat
MetacatRecordFactory converts native Metacat documents to OAI-PMH records.
This interface provides methods for initializing and logging in to a
Metacat REST API, and then querying, reading, transforming, inserting,
updating and deleting documents from that server.
A metadata catalog server implemented as a Java Servlet
All actions are disabled since Metacat 3.0.0
This class handles the request for getting the solr engine description.
This class will query the solr server and return the result.
Handle requests for metacat scheme URLs
A suite of utility classes for the metadata catalog server
Exception thrown when an error occurs in a utility method
Represents Metacat's implementation of the DataONE Member Node service API.
Represents Metacat's implementation of the DataONE Member Node
service API, v1.
MN REST service implementation handler
******************
MNCore -- DONE
ping() - GET /d1/mn/monitor/ping
log() - GET /d1/mn/log
**getObjectStatistics() - GET /d1/mn/monitor/object
getOperationsStatistics - GET /d1/mn/monitor/event
**getStatus - GET /d1/mn/monitor/status
getCapabilities() - GET /d1/mn/ and /d1/mn/node
MNRead -- DONE
get() - GET /d1/mn/object/PID
getSystemMetadata() - GET /d1/mn/meta/PID
describe() - HEAD /d1/mn/object/PID
getChecksum() - GET /d1/mn/checksum/PID
listObjects() - GET /d1/mn/object
synchronizationFailed() - POST /d1/mn/error
MNAuthorization -- DONE
isAuthorized() - GET /d1/mn/isAuthorized/PID
setAccessPolicy() - PUT /d1/mn/accessRules/PID
MNStorage - DONE
create() - POST /d1/mn/object/PID
update() - PUT /d1/mn/object/PID
delete() - DELETE /d1/mn/object/PID
archive() - PUT /d1/mn/archive/PID
systemMetadataChanged() - POST /dirtySystemMetadata/PID
MNReplication
replicate() - POST /d1/mn/replicate
getReplica() - GET /d1/mn/replica
******************
MN REST service implementation handler
******************
MNCore
ping() - GET /d1/mn/monitor/ping
log() - GET /d1/mn/log
**getObjectStatistics() - GET /d1/mn/monitor/object
getOperationsStatistics - GET /d1/mn/monitor/event
**getStatus - GET /d1/mn/monitor/status
getCapabilities() - GET /d1/mn/ and /d1/mn/node
MNRead
get() - GET /d1/mn/object/PID
getSystemMetadata() - GET /d1/mn/meta/PID
describe() - HEAD /d1/mn/object/PID
getChecksum() - GET /d1/mn/checksum/PID
listObjects() - GET /d1/mn/object
synchronizationFailed() - POST /d1/mn/error
MNAuthorization
isAuthorized() - GET /d1/mn/isAuthorized/PID
setAccessPolicy() - PUT /d1/mn/accessRules/PID
MNStorage
create() - POST /d1/mn/object/PID
update() - PUT /d1/mn/object/PID
delete() - DELETE /d1/mn/object/PID
archive() - PUT /d1/mn/archive/PID
updateSystemMetadata() - PUT /d1/mn/meta
systemMetadataChanged() - POST /dirtySystemMetadata/PID
MNReplication
replicate() - POST /d1/mn/replicate
getReplica() - GET /d1/mn/replica
MNAdmin
reindex() - PUT /d1/mn/index
updateIdMetadata() - PUT /d1/mn/identifiers
******************
Routes MN REST service requests to the appropriate handler
Routes MN REST service requests to the appropriate handler
A class extends from the MultipartRequest class with the extra information of system meta data
A collection of static utility methods for networking
A utility class that sorts two node records.
A utility class that encapsulates a node and its data
This class enforces the node replication policies such as the allowed node list,
maximum size and allowed format list
The abstract class to validate non-xml meta data objects
The factory and utility methods for the NonXMLMetadataHandlers
OAIHandler is the primary Servlet for OAICat.
Implements a subset of the DataONE CNCore services in Metacat.
The Oracle db adapter implementation.
The implementation class for the OSTI
(DOE Office of Scientific and Technical Information) DOI service
Details of OSTI eink: https://www.osti.gov/elink/241-6api.jsp
A class sends emails to clients when errors happened during the
interaction process between Metacat and the OSTI Elink service.
A class that handles downloading data packages under the V2 format.
PathIndexEntry contains all of the data fields needed to insert an path into
the xml_index table or the xml_path_index table, depending on which
constructor is used.
Exception thrown when an error occurs with a permission order
A class enforce the portal quota service, which controls how many portals
users can create
The PostgreSQL db adapter implementation.
This class will ensure the upgrade process to 3.0.0 is from version 2.19.*.
Control the display of the main properties configuration page and the
processing of the configuration values.
A Class that provides a wrapper around standard java.util.Properties to provide backwards
compatibility with metacat's original properties implementation
A suite of utility classes for the metadata configuration utility
Control the display of the quota -service configuration page and the processing
of the configuration values.
Represents a class to manipulate the usages table for the quota service in the postgresql database
A class represents an abstract quota service.
A class manages the quota service for users
A class to decide the quota type (storage, portal and etc) based on the given name space
A checker to determine if the Metacat is in the read-only mode by checking
the property of database.readOnly.
This class will create a new resource map by modifying a given resourceMap input stream.
A database aware Class to handle schema location.
Exception thrown when an error occurs in a configuration administrative
class
A Sitemap represents a document that lists all of the content of the Metacat
server for use by harvesting spiders that wish to index the contents of the
Metacat site.
A suite of utility classes for the skin configuration utility
Class to generate Styled Layer Descriptors allowing geoserver to
filter the feature rendering based on various contraints
such as permissions, non-spatial queries and skin configuration.
Control the display of the Solr configuration page and the processing
of the configuration values.
This class represents an object to upgrade the solrconfig.xml on the Metacat upgrade process.
A class to find the version of a JVM against which the solr is running
A class to upgrade solr configuration files in the upgrade process to Metacat 3.0.0
An exception happens when an administrator modified a the schema.xml in the solr home.
This class will overwrite the existing schema under the /solr-home/conf/schema.xml
Here is the algorithm:
1.
This class will check if the given solr home directory is for an embedded solr server
which is used in the earlier Metacat versions.
Class providing direct read/write access to the
persistent spatial cache.
Class representing the spatial portions of an xml document as a geotools
Feature.
Class representing the geotools feature schemas and file paths
for the spatial data cache.
Harvests spatial data from metacat database
and saves to persistent cache
Class to query the persistent spatial cache
and returns docids matching spatial constraints
The MS SQL Server db adapter implementation.
An implementation of ServletContextListener that is called automatically by the servlet
container on startup, and used to verify that we have the essential components in place for
Metacat to run successfully.
This class will stream the file parts of the multipart request into a temporary file.
A class to validate the given system metadata object
Updates existing DOI registrations for EML versions
This class represents a thread task to report a updating of an exiting usage to the remote bookkeeper server.
Run this class when the users upgrade their Metacat instances to 3.0.0.
The parent class reporting usages to the remote book keeper server and logging the quota usages events
into the local database.
This class will parse the root element to figure out the namespace of the root element(we also call
it the namespace of the element).
Historically, early versions of Metacat only store the metadata documents in the xml_nodes and
xml_nodes_revsions tables rather than the files.
This class represents the information for a schema without a namespace
A class will parse an schema file to get information - such as included
xsd files in this schema
A Class that transforms XML documents utitlizing XSL style sheets.