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CREATE TABLE systemMetadata (
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	guid   text,          -- the globally unique string identifier of the object that the system metadata describes
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	serial_version VARCHAR(256), --the serial version of the object
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	date_uploaded TIMESTAMP, -- the date/time the document was first submitted
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	rights_holder VARCHAR(250), --the user who has rights to the document, usually the first persons to upload it
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	checksum VARCHAR(512), --the checksum of the doc using the given algorithm (see below)
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	checksum_algorithm VARCHAR(250), --the algorithm used to calculate the checksum
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	origin_member_node VARCHAR(250), --the member node where the document was first uploaded
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	authoritive_member_node VARCHAR(250), --the member node that currently controls the document
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	date_modified TIMESTAMP, -- the last date/time that the file was changed
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	submitter VARCHAR(256), -- the user who originally submitted the doc
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	object_format VARCHAR(256), --the format of the object
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	size VARCHAR(256), --the size of the object
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	archived boolean,	 -- specifies whether this an archived object
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	replication_allowed boolean,	 -- replication allowed
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	number_replicas INT8, 	-- the number of replicas allowed
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	obsoletes   text,       -- the identifier that this record obsoletes
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	obsoleted_by   text,     -- the identifier of the record that replaces this record
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	CONSTRAINT systemMetadata_pk PRIMARY KEY (guid)
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);
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CREATE TABLE systemMetadataReplicationPolicy (
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	guid text,	-- the globally unique string identifier of the object that the system metadata describes
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	member_node VARCHAR(250),	 -- replication member node
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	policy text,	 -- the policy (preferred, blocked, etc...TBD)
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	CONSTRAINT systemMetadataReplicationPolicy_fk
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		FOREIGN KEY (guid) REFERENCES systemMetadata DEFERRABLE
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);
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CREATE TABLE systemMetadataReplicationStatus (
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	guid text,	-- the globally unique string identifier of the object that the system metadata describes
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	member_node VARCHAR(250),	 -- replication member node
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	status VARCHAR(250),	 -- replication status
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	date_verified TIMESTAMP, 	-- the date replication was verified
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	CONSTRAINT systemMetadataReplicationStatus_fk
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		FOREIGN KEY (guid) REFERENCES systemMetadata DEFERRABLE
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);
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/*
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 * Remove the old Identifier table (pre-2.0)
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 */
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DROP TABLE IF EXISTS identifier;
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/*
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 * Create the new one (DataONE features)
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 */
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CREATE TABLE identifier (
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   guid   text,          -- the globally unique string identifier
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   docid  VARCHAR(250),  -- the local document id #
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   rev    INT8,          -- the revision part of the local identifier
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   CONSTRAINT identifier_pk PRIMARY KEY (guid)
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);
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/*
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 * add the nodedatadate column to the tables that need it
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 */
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ALTER TABLE xml_nodes ADD COLUMN nodedatadate TIMESTAMP;
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ALTER TABLE xml_nodes_revisions ADD COLUMN nodedatadate TIMESTAMP;
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ALTER TABLE xml_path_index ADD COLUMN nodedatadate TIMESTAMP;
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CREATE INDEX xml_path_index_idx5 ON xml_path_index (nodedatadate);
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/**
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 * track the user-agent for the request
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 */
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ALTER TABLE access_log ADD COLUMN user_agent VARCHAR(512);
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/*
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 * Register the new schema
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 */
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('Schema', '@eml2_1_1namespace@', '/schema/eml-2.1.1/eml.xsd');
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/**
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 * Generate GUIDs for docid.rev
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 */
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INSERT INTO identifier (docid, rev, guid)
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	SELECT docid, rev, docid || '.' || rev FROM xml_documents
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	UNION
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	SELECT docid, rev, docid || '.' || rev FROM xml_revisions;
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--INSERT 0 156644
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/**
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 *  Add guid in xml_access table
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 */
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ALTER TABLE xml_access ADD COLUMN guid text;
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/**
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 *  Expand accessfileid in xml_access table to hold guids
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 */
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ALTER TABLE xml_access ALTER COLUMN accessfileid TYPE text;
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/**
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 * Upgrade xml_access records to use GUID from identifier table
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 * NOTE: This duplicates existing access rules for every revision of a document
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 */
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INSERT INTO xml_access (
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	guid, principal_name, permission, perm_type, perm_order,
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	docid, accessfileid, begin_time, end_time, ticket_count, subtreeid, startnodeid, endnodeid
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)
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	SELECT
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		id.guid, xa.principal_name, xa.permission, xa.perm_type, xa.perm_order,
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		xa.docid, xa.accessfileid, xa.begin_time, xa.end_time, xa.ticket_count, xa.subtreeid, xa.startnodeid, xa.endnodeid
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	FROM identifier id, xml_access xa
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	WHERE id.docid = xa.docid;
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--INSERT 0 311224
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/**
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 * Include inline data access rows -- they have a special guid: 'scope.docid.rev.index'
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 */
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INSERT INTO xml_access (
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	guid, principal_name, permission, perm_type, perm_order,
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	docid, accessfileid, begin_time, end_time, ticket_count, subtreeid, startnodeid, endnodeid
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)
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	SELECT
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		docid, principal_name, permission, perm_type, perm_order,
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		docid, accessfileid, begin_time, end_time, ticket_count, subtreeid, startnodeid, endnodeid
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	FROM xml_access
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	WHERE docid like '%.%.%.%';
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--INSERT 0 18
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/**
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 * Update the accessfileid to use their guid
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 * NOTE: uses the last revision's guid as the new value for accessfileid
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 * uses a temporary table
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 **/
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CREATE TABLE max_identifier (guid text, docid VARCHAR(250), rev INT8);
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/** insert the max rev identifier for each document **/
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INSERT INTO max_identifier (docid, rev, guid)
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SELECT docid, MAX(rev), docid || '.' || MAX(rev)
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FROM identifier
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GROUP BY docid;
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--INSERT 0 57841
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/** create some indexes to speed up the join **/
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CREATE INDEX maxid_docid_index ON max_identifier (docid);
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CREATE INDEX maxid_guid_index ON max_identifier (docid);
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CREATE INDEX accessfileid_index on xml_access (accessfileid);
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CREATE INDEX xml_access_guid_index on xml_access (guid);
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UPDATE xml_access xa
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SET accessfileid = maxid.guid
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FROM max_identifier maxid
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WHERE xa.accessfileid = maxid.docid
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AND xa.guid IS NOT null;
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--UPDATE 310427
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DROP INDEX maxid_docid_index;
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DROP INDEX maxid_guid_index;
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DROP INDEX accessfileid_index;
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DROP INDEX xml_access_guid_index;
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DROP TABLE max_identifier;
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/**
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 * Remove old access rules
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 */
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DELETE FROM xml_access WHERE guid is null;
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--DELETE 105432
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/**
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 * clean up the xml_access table
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 */
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ALTER TABLE xml_access DROP COLUMN docid;
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/**
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 * expand xml_path_index 'path' column to hold larger strings
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 */
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ALTER TABLE xml_path_index ALTER COLUMN path TYPE text;
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/**
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 * include 2.0.0beta4 DTD
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 */
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-access-@eml-beta4-version@//EN',
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         '/dtd/eml-access-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-attribute-@eml-beta4-version@//EN',
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          '/dtd/eml-attribute-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-constraint-@eml-beta4-version@//EN',
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          '/dtd/eml-constraint-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-coverage-@eml-beta4-version@//EN',
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          '/dtd/eml-coverage-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-dataset-@eml-beta4-version@//EN',
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          '/dtd/eml-dataset-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-entity-@eml-beta4-version@//EN',
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          '/dtd/eml-entity-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-literature-@eml-beta4-version@//EN',
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          '/dtd/eml-literature-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-physical-@eml-beta4-version@//EN',
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          '/dtd/eml-physical-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-project-@eml-beta4-version@//EN',
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          '/dtd/eml-project-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-protocol-@eml-beta4-version@//EN',
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          '/dtd/eml-protocol-@eml-beta4-version@.dtd');
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INSERT INTO xml_catalog (entry_type, public_id, system_id)
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  VALUES ('DTD', '-//ecoinformatics.org//eml-software-@eml-beta4-version@//EN',
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          '/dtd/eml-software-@eml-beta4-version@.dtd');
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/*
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 * update the database version
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 */
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UPDATE db_version SET status=0;
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INSERT INTO db_version (version, status, date_created)
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  VALUES ('2.0.0', 1, CURRENT_DATE);