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Add delete option. Delete DOI on command line

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This commit is contained in:
Marsa Haoua
2013-10-02 15:37:02 +02:00
committed by Pascal-Nicolas Becker
parent 0251a02190
commit 7d68f9936a
2 changed files with 177 additions and 39 deletions
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70
dspace-api/src/main/java/org/dspace/identifier/DOIIdentifierProvider.java
View File

@@ -73,7 +73,8 @@ public class DOIIdentifierProvider
public static final Integer UPDATE_RESERVERED = 5;
public static final Integer UPDATE_REGISTERED = 6;
public static final Integer UPDATE_BEFORE_REGISTERATION = 7;
public static final Integer DELETED = 8;
public static final Integer TO_BE_DELETED = 8;
public static final Integer DELETED = 9;
/**
* Prefix of DOI namespace. Set in dspace.cfg.
@@ -197,6 +198,7 @@ public class DOIIdentifierProvider
doiRow.setColumn("status", TO_BE_REGISTERED);
try {
DatabaseManager.update(context, doiRow);
context.commit();
}
catch (SQLException sqle)
{
@@ -581,11 +583,11 @@ public class DOIIdentifierProvider
{
String doi = DOI.formatIdentifier(identifier);
TableRow doiRow = null;
String oldStatus = null;
try
{
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length()));
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi",
doi.substring(DOI.SCHEME.length()));
}
catch (SQLException sqle)
{
@@ -626,6 +628,51 @@ public class DOIIdentifierProvider
// change doi status in db if necessary.
if (null != doiRow)
{
doiRow.setColumn("status", TO_BE_DELETED);
try {
DatabaseManager.update(context, doiRow);
context.commit();
}
catch (SQLException sqle)
{
log.warn("SQLException while changing status of DOI {} to be deleted.", doi);
throw new RuntimeException(sqle);
}
}
// DOI is a permanent identifier. DataCite for example does not delete
// DOIS. But it is possible to mark a DOI as "inactive".
}
public void deleteOnline(Context context, String identifier)
throws DOIIdentifierException
{
String doi = DOI.formatIdentifier(identifier);
TableRow doiRow = null;
try
{
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi",
doi.substring(DOI.SCHEME.length()));
}
catch (SQLException sqle)
{
throw new RuntimeException(sqle);
}
if(null == doiRow)
{
throw new DOIIdentifierException("This identifier: " + identifier
+ " isn't in our database",
DOIIdentifierException.DOI_DOES_NOT_EXIST);
}
if (TO_BE_DELETED != doiRow.getIntColumn("status"))
{
log.error("This identifier: {} couldn't be deleted",
DOI.SCHEME + doiRow.getStringColumn("doi"));
return;
}
connector.deleteDOI(context, doi);
doiRow.setColumn("status", DELETED);
try {
DatabaseManager.update(context, doiRow);
@@ -633,17 +680,11 @@ public class DOIIdentifierProvider
}
catch (SQLException sqle)
{
log.warn("SQLException while changing status of DOI {} to be registered.", doi);
log.warn("SQLException while changing status of DOI {} deleted.", doi);
throw new RuntimeException(sqle);
}
}
// DOI is a permanent identifier. DataCite for example does not delete
// DOIS. But it is possible to mark a DOI as "inactive".
connector.deleteDOI(context, doi);
}
/**
* Returns a DSpaceObject depending on its DOI.
* @param context the context
@@ -684,7 +725,7 @@ public class DOIIdentifierProvider
* Search the database for a DOI, using the type and id of an DSpaceObject.
*
* @param context
* @param dso DSpaceObject to find doi for. DOIs with status DELETED will be
* @param dso DSpaceObject to find doi for. DOIs with status TO_BE_DELETED will be
* ignored.
* @return The DOI as String or null if DOI was not found.
* @throws SQLException
@@ -693,10 +734,11 @@ public class DOIIdentifierProvider
throws SQLException
{
String sql = "SELECT * FROM Doi WHERE resource_type_id = ? " +
"AND resource_id = ? AND status != ?";
"AND resource_id = ? AND (status != ? OR status != ?)";
TableRow doiRow = DatabaseManager.querySingleTable(context,
"Doi", sql, dso.getType(), dso.getID(), DOIIdentifierProvider.DELETED);
TableRow doiRow = DatabaseManager.querySingleTable(context, "Doi", sql,
dso.getType(), dso.getID(), DOIIdentifierProvider.TO_BE_DELETED,
DOIIdentifierProvider.DELETED);
if (null == doiRow)
{
return null;

138
dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java
View File

@@ -135,6 +135,14 @@ public class DOIOrganiser {
options.addOption(update);
Option delete = OptionBuilder.withArgName("DOI identifier")
.withLongOpt("delete")
.hasArgs(1)
.withDescription("Delete a specified identifier.")
.create('d');
options.addOption(delete);
// initialize parser
CommandLineParser parser = new PosixParser();
@@ -337,6 +345,35 @@ public class DOIOrganiser {
}
}
}
if(line.hasOption('d'))
{
String identifier = line.getOptionValue('d');
if (null == identifier)
{
helpformater.printHelp("\nDOI organiser\n", options);
}
else {
try {
TableRow doiRow = organiser.findTableRow(identifier);
DSpaceObject dso = DSpaceObject.find(
context,
doiRow.getIntColumn("resource_type_id"),
doiRow.getIntColumn("resource_id"));
organiser.delete(doiRow, dso);
} catch (SQLException ex) {
LOG.error(ex);
} catch (IllegalArgumentException ex) {
LOG.error(ex);
} catch (IllegalStateException ex) {
LOG.error(ex);
} catch (IdentifierException ex) {
LOG.error(ex);
}
}
}
}
@@ -608,6 +645,54 @@ public class DOIOrganiser {
}
}
public void delete(TableRow doiRow, DSpaceObject dso)
{
if(null == doiRow)
{
if (!quiet)
{
System.err.println("The DOI identifier that should be deleted doesn't exist.");
}
LOG.error("The DOI identifier that should be deleted doesn't exist.");
return;
}
try
{
provider.deleteOnline(context, doiRow.getStringColumn("doi"));
if(!quiet)
{
System.out.println("This identifier : "
+ DOI.SCHEME + doiRow.getStringColumn("doi")
+ " is successfully delete.");
}
}
catch (DOIIdentifierException ex)
{
try
{
sendAlertMail("Delete", dso,
DOI.SCHEME + doiRow.getStringColumn("doi"),
ex.codeToString(ex.getCode()));
}
catch (IOException ioe)
{
LOG.error("Couldn't send mail", ioe);
}
LOG.error("It wasn't possible to delete the identifier online. "
+ " Exceptions code: "
+ ex.codeToString(ex.getCode()), ex);
if(!quiet)
{
System.err.println("It wasn't possible to delete this identifier: "
+ DOI.SCHEME + doiRow.getStringColumn("doi"));
}
}
}
/**
* Finds the TableRow in the Doi table that belongs to the specified
* DspaceObject.
@@ -665,6 +750,29 @@ public class DOIOrganiser {
}
}
// detect handle
DSpaceObject dso = HandleManager.resolveToObject(context, identifier);
if (null != dso)
{
if (dso.getType() != Constants.ITEM)
{
throw new IllegalArgumentException(
"Currently DSpace supports DOIs for Items only. "
+ "Cannot process specified handle as it does not identify an Item.");
}
doiRow = DatabaseManager.querySingleTable(context, "Doi", sql,
Constants.ITEM, dso.getID());
if (null == doiRow)
{
doi = provider.mint(context, dso);
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi",
doi.substring(DOI.SCHEME.length()));
}
return doiRow;
}
// detect DOI
try {
doi = DOI.formatIdentifier(identifier);
@@ -676,34 +784,22 @@ public class DOIOrganiser {
throw new IllegalStateException("You specified a valid DOI,"
+ " that is not stored in our database.");
}
return doiRow;
}
catch (DOIIdentifierException ex)
{
// Identifier was not recognized as DOI => must be a handle.
// Will check for handle outside try-catch-block...
}
// Identifier was not recognized as DOI.
LOG.error("It wasn't possible to detect this identifier: "
+ identifier
+ " Exceptions code: "
+ ex.codeToString(ex.getCode()), ex);
// detect handle
DSpaceObject dso = HandleManager.resolveToObject(context, identifier);
if (dso.getType() != Constants.ITEM)
if(!quiet)
{
throw new IllegalArgumentException(
"Currently DSpace supports DOIs for Items only. "
+ "Cannot process specified handle as it does not identify an Item.");
System.err.println("It wasn't possible to detect this identifier: "
+ DOI.SCHEME + doiRow.getStringColumn("doi"));
}
doiRow = DatabaseManager.querySingleTable(context, "Doi", sql,
Constants.ITEM, dso.getID());
if (null == doiRow)
{
doi = provider.mint(context, dso);
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi",
doi.substring(DOI.SCHEME.length()));
return doiRow;
}
return doiRow;
}