ࡱ> $&!"#q` &nbjbjqPqP ."::&f*******>",>=Z6kZń$;hV*ԅkkԅԅ**222ԅ& **2ԅ22**N |H`\ 0=^^,*"2+?=ԅԅԅԅ>>>$=bD$;>>>bD>>>****** Introduction Dryad Project The Dryad project is a funded National Science Foundation grant under the Directorate for Biological Sciences' Biological Databases and Informatics program. The goal of the Dryad project is to develop a metadata and data provider that supports the discovery and management of data associated with publications in the field of evolutionary biology. In addition, the Dryad repository will act as a clearing-house for data/metadata from related fields in biological and environmental sciences. To achieve data/metadata interoperability, the Dryad will adopt the OAI-PMH standard and become both an OAI-PMH repository and harvester, thereby exchanging metadata (and references to data) with other OAI-PMH compliant repositories. A sub-goal of the Dryad project is to perform metadata exchange with the Metacat XML database that underlies the LTER Data Catalog. As such, this particular goal is the focus of this document, and requires the design and development of an OAI-PMH service interface for Metacat. The Dryad project (and Metacat) will also support implementation of the Library of Congress Search and Retrieve via URL (SRU) standard, which will allow on-the-fly access to repository contents by third parties through a web-service protocol, and will also enable syndication of repository contents (the SRU work is scheduled for year 2 of the NESCent/Dryad LTER subcontract). OAI-PMH The Open Archives Initiative Protocol for Metadata Harvesting was first developed in the late 1990's as a standard for harvesting metadata from distributed metadata/data repositories. The current version of the OAI-PMH standard is 2.0 as of June 2002, with minor updates in December 2008 (http://www.openarchives.org/OAI/ openarchivesprotocol.html). The OAI-PMH standard uses the Hyper-text Transport Protocol (HTTP) as a transport layer and specifies six query methods (called verbs) that must be supported by an OAI-PMH compliant repository (see Section 7.1). These methods are: GetRecord retrieves zero or one complete metadata record from a repository; Identify retrieves information about a repository; ListIdentifiers retrieves zero or more metadata record headers (not the complete metadata record) from a repository; ListMetadataFormats retrieves a list of available metadata record formats supported by a repository; ListRecords retrieves zero or more complete metadata records from a respository; and ListSets retrieves the set structure from a repository. The OAI-PMH compliant repository must accept requests in both HTTP-GET and HTTP-POST formats. Responses from the repository must be returned as an XML-encoded (version 1.0) stream. Error handling must be supported by the repository and provide the correct error response code back to the harvester. Detailed specifications and examples of all six methods may be viewed in Section 4 of the standards document (http://www.openarchives.org/OAI/openarchivesprotocol.html# ProtocolMessages). Metadata Cross-walks EML and DC Effort will include identifying the mapping of content elements between the EML and DC. The EML (described above) is a fine-grained structure that has many content elements in common with DC. For transformations from the EML to DC, only simple or unqualified Dublin Core (using only the 15 canonical elements) will be the target of the transformation OAI-PMH requires unqualified Dublin Core metadata be supported as a minimum. The cross-walk mapping will be approved by the primary contractor prior to development of the XSLT script. Once the mapping elements are identified, an Extensible Stylesheet Language Transformation (XSLT) script will be written for performing the actual transformation. The XSLT will be tested for accuracy and completeness. EML and Dryad Application Profile Effort will include identifying the mapping of content elements between the EML and Dryad Application Profile (DAP). The DAP includes content elements from DC, the Data Documentation Initiative, Darwin Core, EML, and PREMIS. The cross-walk mapping will be approved by the primary contractor prior to development of the XSLT script. Once the mapping elements are identified, an Extensible Stylesheet Language Transformation (XSLT) script will be written for performing the actual transformation. The XSLT will be tested for accuracy and completeness. OAI-PMH Metacat Service Interfaces Effort will include designing and implementing an OAI-PMH Metacat repository (also referred to as data provider) and harvester service interfaces. Repository (Data Provider) The design and implementation of the OAI-PHM Metacat Repository service interface will make available all six OAI-PMH methods (GetRecord, Identify, ListIdentifiers, ListMetadataFormats, ListRecords, and ListSets) as defined in the OAI-PMH Version 2 Specification (http://www.openarchives.org/OAI/ openarchivesprotocol.html) through a standard HTTP URL that accepts both HTTP-GET and HTTP-POST formats. The design will attempt to be metadata neutral with respect to other metadata standards residing within a Metacat instance, however the implementation will only address EML metadata. The design will utilize example OAI-PMH repositories (e.g., OCLC's OAIcat, UIUC provider, or the DLESE provider) as guidance. Harvester The design and implementation of the OAI-PMH Metacat Harvester service interface will utilize all six OAI-PMH methods to request metadata or related information from another OAI-PMH compliant repository using a standard HTTP URL in either an HTTP-GET or HTTP-POST format and transform such metadata into the EML standard, which will subsequently be inserted into a Metacat instance. The design will initially harvest DAP data, allowing fall-back to Dublin Core when DAP is not available. The design will allow harvesting of other metadata types in the future. The design will utilize example OAI-PMH harvesters (e.g., OCLC's OAIHarvester2, UIUC harvester, or the DLESE harvester) as guidance. Development Plan Metacat SVN Integration All project related artifacts, including source code, templates, examples, and/or documentation will be integrated directly with the ecoinformatics.org Metacat project from the project beginning. As such, all artifacts will be checked into and managed by the ecoinformatics.org Subversion version control system server (https://code.ecoinformatics.org) and under the code/metacat/trunk project directory. A directory hierarchy follows: for design/planning documents - metacat/docs/dev/oaipmh for shell scripts and other resources - metacat/lib/oaipmh for Java source code - metacat/src/edu/ucsb/nceas/metacat/oaipmh Design Details Crosswalks EML to DC crosswalk The following table summarizes the element mappings of the EML to DC crosswalk, including notes specific to each element mapping. EML ElementDC ElementNotesTitletitleOne-to-one mapping of contentCreatorcreatorUse only the creator's name (givenName and surName elements); could be an organization namekeywordsubjectOne subject element per keyword elementabstractdescriptionMust extract text formatting tagspublisherpublisherUse only the publisher's name (givenName and surName elements); could be an organization nameassociatedPartycontributorUse only the party's name (givenName and surName); could be an organization namepubDatedateOne-to-one mappingdataset | citation | protocol | softwaretypeType value is determined by the type of EML document rather than by a specific field valuephysicalformatUse a mime type as the Format value? For example, if EML has element within , then use 'text/plain' as the Format value?(1) packageId; (2) URL to the EML documentidentifierpackageId can be used as the value of one identifier element; a second identifier element can hold a URL to the EML documentdataSourcesourceUse the document URL of the referenced data source?CitationrelationUse the document URL of the referenced citation?geographicCoverage coverageAdd separate coverage elements for geographic description and geographic bounding coordinates. For bounding coordinates, use minimal labeling, for example: 81.505000 W, 81.495000 W, 31.170000 N, 31.163000 NtaxonomicCoveragecoverageUse only genus/species binomials; place each binomial in a separate coverage elementtemporalCoveragecoverageInclude begin date and end date when available. For example: 1915-01-01 to 2004-12-31intellectualRightsrightsMust extract text formatting tags Repository (Data Provider) The Metacat OAI-PMH Repository service was implemented using the Online Computer Library Center (OCLC) OAICat Open Source Software as the basis for the implementation, with substantial customizations and modifications added to facilitate integration with Metacat. Customizations and additions to the set of OAICat classes are described in the following table: Package NameClass Name(s)Modified Class vs. New ClassDescriptionedu.ucsb.nceas.metacat.oaipmh.provider.serverOAIHandler.javaModifiedOAIHandler is the primary servlet class for OAICat. It has been customized to allow loading of Metacat configuration values.edu.ucsb.nceas.metacat.oaipmh.provider.server.catalogMetacatCatalog.javaNewMetacatCatalog is an implementation of AbstractCatalog interface. It is responsible for determining which documents exist in Metacat, their document types, and their datestamps.edu.ucsb.nceas.metacat.oaipmh.provider.server.catalogMetacatRecordFactory.javaNewMetacatRecordFactory, a subclass of RecordFactory, converts native Metacat documents to OAI-PMH records. edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalkEml200.java Eml201.java Eml210.java NewThe set of Eml2xx.java classes are responsible for retrieving EML documents in their native format. Although these classes are subclasses of the Crosswalk class, no actual XSLT transformation is performed by them.edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalkEml2oai_dc.javaNewEml2oai_dc, a subclass of Crosswalk, is responsible for retrieving EML 2.x.y documents and transforming them to oai_dc (Dublin Core) format. With the exception of OAIHandler.java, all other native OAICat classes are used in their original (non-modified) form and are contained in the Java archive file: metacat/lib/oaipmh/oaicat.jar The XSLT stylesheets used by the Eml2oai_dc.java class reside in files: metacat/lib/oaipmh/eml200toDublinCore.xsl metacat/lib/oaipmh/eml201toDublinCore.xsl metacat/lib/oaipmh/eml210toDublinCore.xsl Repository Design Issues 1. 'Deleted' Status OAI-PMH repositories can optionally flag records with a 'deleted' status, indicating that a record in the metadata format specified by the metadataPrefix is no longer available. Since the Metacat database does not provide a readily apparent mechanism for retrieving a list of deleted documents, the use of the 'deleted' status is not supported in this implementation of the OAI-PMH repository. This represents a possible future enhancement to the repository design. 2. Sets OAI-PMH repositories can optionally support set hierarchies. Since it has not been determined how set hierarchies should be structured in Metacat, this implementation of the OAI-PMH repository does not support set hierarchies. This represents a possible future enhancement to the repository design. 3. Datestamp Granularity When expressing datestamps for repository documents, OAI-PMH allows two levels of granularity day granularity and seconds granularity. Since the Metacat database stores the value of its xml_documents.date_updated field in day granularity, that is the level that is supported by the Metacat OAI-PMH Repository. Harvester The Metacat OAI-PMH Harvester client was implemented using OCLC's OAIHarvester2 open source code as its base implementation, with customizations and additions as needed to support integration with Metacat. Customizations and additions to the set of OAIHarvester2 classes are described in the following table: Package NameClass Name(s)Modified Class vs. New ClassDescriptionedu.ucsb.nceas.metacat.oaipmh.harvesterOaipmhHarvester.javaNewOaipmhHarvester is the primary Java class for executing the code, containing the main() method. It is a heavily modified version of the RawWrite.java class included in the OAIHarvester2 source code.edu.ucsb.nceas.metacat.oaipmh.harvesterHarvesterVerb.javaModifiedHarvesterVerb is a parent claass to the six verb subclasses. This is a heavily modified version of the original HarvesterVerb class in the OAIHarvester2 source code.edu.ucsb.nceas.metacat.oaipmh.harvesterGetRecord.java ListIdentifiers.javaModifiedThese two verb classes are used to drive the harvest engine. The program first runs the 'ListIdentifiers' verb to determine which records exist in the remote respository, as well as their datestamps. Then it runs the 'Get Record' verb, as needed, to retrieve individual records from the remote respository for insertion/update into Metacat.edu.ucsb.nceas.metacat.oaipmh.harvesterIdentify.java ListRecords.java ListSets.java ListMetadataFormats.javaUnmodifiedThese verb classes are essentially unmodified from their corresponding classes in the OAIHarvester2 source code. They are not actively used by the Metacat OAI-PMH Harvester code, but are included with the source code for completeness and for potential future development. Harvester Design Issues 1. Dryad Identifiers Dryad stores documents using identifiers like the following: oai:dryad-dev.nescent.org:10255/dryad.12 When harvested into Metacat, these identifiers are converted to a Metacat-legal equivalent, for example: 10255-dryad.12 (Note the use of a '-' character in place of a '/' character. It was discovered during development that the '/' character caused errors when used in Metacat identifiers.) 2. Handling of 'Deleted' status The Metacat OAI-PMH Harvester program does check to see whether a 'deleted' status is flagged for a harvested document, and if it is, the document is correspondingly deleted from the Metacat repository. 3. Datestamp Granularity When expressing datestamps for repository documents, OAI-PMH allows two levels of granularity day granularity and seconds granularity. Since the Metacat database stores the value of its 'xml_documents.last_updated' field in day granularity, that is the level that is supported by both the Metacat OAI-PMH Repository and the Metacat OAI-PMH Harvester. This has implications when Metacat OAI-PMH Harvester (MOH) interacts with the Dryad repository, which stores its documents with seconds granularity. For example, consider the following sequence of events: On January 1, 2010, MOH harvests a document from the Dryad repository with datestamp '2010-01-01T10:00:00Z', and stores its local copy with datestamp '2010-01-01'. Later that same day, the Dryad repository updates the document to a newer revision, with a new datestamp such as '2010-01-01T20:00:0Z'. On the following day, MOH runs another harvest. It determines that it has a local copy of the document with datestamp '2010-01-01' and does not re-harvest the document, despite the fact that its local copy is not the latest revision. Configuring and Running Configuring and Running the Metacat OAI-PMH Data Provider Servlet Uncomment the servlet-name and servlet-mapping entries for the DataProvider servlet in file: metacat/lib/web.xml.tomcat5 Edit properties in the OAI-PMH section of file metacat/lib/metacat.properties The following table describes the properties stored in metacat.properties that are used by the DataProvider servlet: Property NameSample ValueDescriptionoaipmh.maxListSize 5Maximum number of records returned by each call to the ListIdentifiers and ListRecords verbs.oaipmh.repositoryIdentifiermetacat.lternet.edu An identifier string for the respository.AbstractCatalog. oaiCatalogClassNameedu.ucsb.nceas.metacat.oaipmh. provider.server.catalog. MetacatCatalog The class that implements the AbstractCatalog interface. This class determines which records exist in the repository and their datestamps.AbstractCatalog. recordFactoryClassNameedu.ucsb.nceas.metacat.oaipmh. provider.server.catalog. MetacatRecordFactory The class that extends the RecordFactory class. This class creates OAI-PMH metadata records.AbstractCatalog. secondsToLive3600The lifetime, in seconds, of the resumptionToken.AbstractCatalog. granularityYYYY-MM-DD or YYYY-MM-DDThh:mm:ssZGranularity of datestamps. Either days granularity or seconds granularity values can be used.Identify.repositoryNameMetacat OAI-PMH Data ProviderA name for the repository.Identify.earliestDatestamp2000-01-01T00:00:00ZEarliest datestamp supported by this repositoryIdentify.deletedRecordyes or noUse yes if the repository indicates the status of deleted records; use no if it doesnt.Identify.adminEmailmailto:tech_support@LTERnet.edu Email address of the repository administrator.Crosswalks.oai_dcedu.ucsb.nceas.metacat.oaipmh. provider.server.crosswalk. Eml2oai_dc Class that controls the EML to oai_dc crosswalk.Crosswalks.eml2.0.0edu.ucsb.nceas.metacat.oaipmh. provider.server.crosswalk. Eml200 Class that furnishes EML 2.0.0 metadata.Crosswalks.eml2.0.1edu.ucsb.nceas.metacat.oaipmh. provider.server.crosswalk. Eml201 Class that furnishes EML 2.0.1 metadata.Crosswalks.eml2.1.0edu.ucsb.nceas.metacat.oaipmh. provider.server.crosswalk. Eml210 Class that furnishes EML 2.1.0 metadata. The properties whose values will need to be changed for a particular Metacat installation are the oaipmh.repositoryIdentifier and the Identify.adminEmail properties. The remaining properties can usually be left as is, retaining their default values as they appear in the metacat.properties file. Example URLs Examples of URLs that demonstrate use of the Data Provider servlet follow: OAI-PMH VerbDescriptionURLGetRecordGet an EML 2.0.1 record using its LSID identifier HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider" http://scoria.lternet.edu:8080/knb/dataProvider? verb=GetRecord&metadataPrefix=eml-2.0.1& identifier=urn:lsid:knb.ecoinformatics.org:knb-lter-gce:26GetRecordGet an oai_dc record using its LSID identifier HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider" http://scoria.lternet.edu:8080/knb/dataProvider? verb=GetRecord&metadataPrefix=oai_dc& identifier=urn:lsid:knb.ecoinformatics.org:knb-lter-gce:26IdentifyIdentify this data provider HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider?verb=Identify" http://scoria.lternet.edu:8080/knb/dataProvider?verb=IdentifyListIdentifiersList all EML 2.1.0 identifiers in the repository HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListIdentifiers&metadataPrefix=eml-2.1.0&from=2001-01-01&until=2010-01-01" http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListIdentifiers&metadataPrefix=eml-2.1.0ListIdentifiersList all oai_dc identifiers in the repository between a range of dates HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider" http://scoria.lternet.edu:8080/knb/dataProvider? verb=ListIdentifiers&metadataPrefix=oai_dc& from=2006-01-01&until=2010-01-01ListMetadataFormatsList metadata formats supported by this repository HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider" http://scoria.lternet.edu:8080/knb/dataProvider? verb=ListMetadataFormatsListRecordsList all EML 2.0.0 records in the repository HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListRecords&metadataPrefix=eml-2.0.0" http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListRecords&metadataPrefix=eml-2.0.0 ListRecordsList all oai_dc records in the repository HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListRecords&metadataPrefix=oai_dc" http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListRecords&metadataPrefix=oai_dcListSetsList sets supported by this repository HYPERLINK "http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListSets" http://scoria.lternet.edu:8080/knb/dataProvider?verb=ListSets Running the Metacat OAI-PMH Harvester The Metacat OAI-PMH Harvester (MOH) is executed as a command-line program: sh runHarvester.sh -dn \ -password \ -metadataPrefix \ [-from ] \ [-until ] \ [-setSpec ] \ The following example illustrates how the MOH is run from the command line: % cd $METACAT_HOME/lib/oaipmh % sh runHarvester.sh -dn uid=dryad,o=LTER,dc=ecoinformatics,dc=org \ -password some_password \ -metadataPrefix oai_dc \  HYPERLINK "http://baseurl.repository.org/knb/dataProvider" http://baseurl.repository.org/knb/dataProvider Command line options and parameters are described in the following table: Command Option or ParameterExampleDescription-dn-dn uid=dryad,o=LTER,dc=ecoinformatics,dc=orgFull distinguished name of the LDAP account used when harvesting documents into Metacat. (Required)-password-password some_passwordPassword of the LDAP account used when harvesting documents into Metacat. (Required)-metadataPrefix-metadataPrefix oai_dcThe type of documents being harvested from the remote repository. (Required)-from-from 2000-01-01The lower limit of the datestamp for harvested documents. (Optional)-until-until 2010-12-31The upper limit of the datestamp for harvested documents. (Optional)-setSpec-setSpec someSetHarvest documents belonging to this set. (Optional)base_url HYPERLINK "http://baseurl.repository.org/knb/dataProvider" http://baseurl.repository.org/knb/dataProviderBase URL of the remote repository Generalized Definitions OAI-PMH (see OAI-PMH specification Section 2 for details - http://www.openarchives.org/OAI/ openarchivesprotocol.html# DefinitionsConcepts) Datestamp a datestamp is an optional construct for categorizing or grouping items based on a time frame for the purpose of selective harvesting; datestamps use a day granularity and can specify either or both beginning and ending values; datestamps can be used to identify creation, modified, and deletion events associated with an item. Harvester a client application that use the OAI-PMH methods to retrieve metadata from and/or information about a repository. Item an informational container of metadata within a repository that can serve as the origin of content when constructing an OAI-PMH metadata record; each item is considered unique within the repository. Record metadata expressed as a single format and as an XML-encoded stream that is returned in response to an OAI-PMH request; each record consists of a header, metadata, and about (optional) sections. The concept of deleted records must be supported by the repository. Repository a network accessible server that hosts metadata and complies with the OAI-PMH standard for serving metadata requests. Selective Harvesting selective harvesting allows a harvester to limit harvest requests to subsets of the metadata available from a repository based on either datestamps and/or sets. Set a set is an optional construct for categorizing or grouping items based on a logical theme for the purpose of selective harvesting; a set can be flat or hierarchical. Unique Identifier a unique identifier (UID) unambiguously identifies an item in a repository; the UID must conform to the Uniform Resource Identifier (IETF RCC 2396) syntax (http://www.ietf.org/rfc/rfc2396.txt?number=2396). Informational Links Dublin Core Metadata Initiative  HYPERLINK "http://dublincore.org/" http://dublincore.org/. Ecological Metadata Language (EML)  HYPERLINK "http://knb.ecoinformatics.org/software/eml" http://knb.ecoinformatics.org/software/eml Knowledge Network for Biocomplexity (KNB) (NSF DEB9980154) http://knb.ecoinformatics.org. LTER Data Catalog  HYPERLINK "http://metacat.lternet.edu" http://metacat.lternet.edu Metacat http://knb.ecoinformatics.org/software/metacat/. OCLC OAICat -  HYPERLINK "http://www.oclc.org/research/software/oai/cat.htm" http://www.oclc.org/research/software/oai/cat.htm OAICat was used as the base implementation of the Metacat OAI-PMH Repository (the DataProvider servlet). OCLC OAIHarvester2 -  HYPERLINK "http://www.oclc.org/research/software/oai/harvester2.htm" http://www.oclc.org/research/software/oai/harvester2.htm OAIHarvester2 was used as the base implementation of the Metacat OAI-PMH Harvester. Open Archives Initiative  HYPERLINK "http://www.openarchives.org/" http://www.openarchives.org/ OAI-PMH Error Codes Error CodeDescriptionApplicable VerbsbadArgumentThe request includes illegal arguments, is missing required arguments, includes a repeated argument, or values for arguments have an illegal syntax.all verbsbadResumptionTokenThe value of the resumptionToken argument is invalid or expired.ListIdentifiers ListRecords ListSetsbadVerbValue of the verb argument is not a legal OAI-PMH verb, the verb argument is missing, or the verb argument is repeated. N/AcannotDisseminateFormatThe metadata format identified by the value given for the metadataPrefix argument is not supported by the item or by the repository.GetRecord ListIdentifiers ListRecordsidDoesNotExistThe value of the identifier argument is unknown or illegal in this repository.GetRecord ListMetadataFormatsnoRecordsMatchThe combination of the values of the from, until, set and metadataPrefix arguments results in an empty list.ListIdentifiers ListRecordsnoMetadataFormatsThere are no metadata formats available for the specified item.ListMetadataFormatsnoSetHierarchyThe repository does not support sets.ListSets ListIdentifiers ListRecords  ,4apALwzI"J""""""##' '(P()2)o){))))*8+++/[1ȬȬ'h>@$B*CJOJPJQJ^JaJphh>@$CJOJQJaJh>@$5CJ\aJ'h>@$B*CJOJPJQJ^JaJphh*#CJaJh>@$CJaJh>@$5CJ\aJ h&#h&#h&#he{p h>@$5\ h>@$hO$h#.h>@$2  ,aA%H & F x*$1$gd>@$ & Fgd>@$gd>@$gdO$ gd>@$ & F x*$1$gdO$&nI!h!!!"+"6"J"""""" $Ifgd>@$`gd&#gd&# & Fgd>@$gd>@$ gd>@$ & F x*$1$gd>@$gdO$ & F x*$1$gd>@$""""###7Vkd$$IfF} $} 6   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