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Perform some conventions code and fixed little bugs

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This commit is contained in:
Marsa Haoua
2013-09-16 11:55:01 +02:00
committed by Pascal-Nicolas Becker
parent 404bc1c6bf
commit 7fa57d84ca
4 changed files with 130 additions and 95 deletions
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4
dspace-api/src/main/java/org/dspace/identifier/DOIIdentifierProvider.java
View File

@@ -335,7 +335,7 @@ public class DOIIdentifierProvider
TableRow doiRow = null; TableRow doiRow = null;
try try
{ {
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi); doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length()));
} }
catch (SQLException sqle) catch (SQLException sqle)
{ {
@@ -492,7 +492,7 @@ public class DOIIdentifierProvider
try try
{ {
doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi); doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length()));
} }
catch (SQLException sqle) catch (SQLException sqle)
{ {

171
dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java
View File

@@ -92,7 +92,7 @@ public class DOIOrganiser {
Option registerByItemOrHandle = OptionBuilder.withArgName("ItemID or Handle") Option registerByItemOrHandle = OptionBuilder.withArgName("ItemID or Handle")
.hasArgs(1) .hasArgs(1)
.withDescription("Reserve an identifier for a given ItemID or Handle." .withDescription("Register an identifier for a given ItemID or Handle."
+ " An ItemID or a Handle is needed. ").create('t'); + " An ItemID or a Handle is needed. ").create('t');
options.addOption(registerByItemOrHandle); options.addOption(registerByItemOrHandle);
@@ -104,15 +104,16 @@ public class DOIOrganiser {
options.addOption(reserveByItemOrHandle); options.addOption(reserveByItemOrHandle);
Option udate = OptionBuilder.withArgName("DOI identifier or ItemID or Handle") Option update = OptionBuilder.withArgName("DOI identifier or ItemID or Handle")
.hasArgs(1) .hasArgs(1)
.withDescription("Update online an object for a given DOI identifier" .withDescription("Update online an object for a given DOI identifier"
+ " or ItemID or Handle. A DOI identifier or an ItemID or a Handle is needed. ") + " or ItemID or Handle. A DOI identifier or an ItemID or a Handle is needed. ")
.create('u'); .create('u');
options.addOption(udate); options.addOption(update);
Context context = null; Context context = null;
try { try {
context = new Context(); context = new Context();
} }
@@ -155,44 +156,55 @@ public class DOIOrganiser {
doiRequest(context, "toBeRegistered"); doiRequest(context, "toBeRegistered");
} }
if(line.hasOption('g')){ if(line.hasOption('g'))
{
String identifier = line.getOptionValue('g'); String identifier = line.getOptionValue('g');
if(null == identifier){
// LOG.info("A DOI identifier is needed"); if(null == identifier)
//throw new IllegalArgumentException("Identifier is null.", new NullPointerException()); {
}else{ printHelp(options);
}
else
{
doiRequestByDOI(context, identifier,"toBeRegistered"); doiRequestByDOI(context, identifier,"toBeRegistered");
} }
} }
if(line.hasOption('v')){
if(line.hasOption('v'))
{
String identifier = line.getOptionValue('v'); String identifier = line.getOptionValue('v');
if(null == identifier){
// LOG.info("A DOI identifier is needed"); if(null == identifier)
//throw new IllegalArgumentException("Identifier is null.", new NullPointerException()); {
printHelp(options);
} }
else else
{ {
doiRequestByDOI(context, identifier,"toBeReserved"); doiRequestByDOI(context, identifier,"toBeReserved");
} }
} }
if(line.hasOption('t')){
if(line.hasOption('t'))
{
String itemID_Hdl = line.getOptionValue('t'); String itemID_Hdl = line.getOptionValue('t');
if(null == itemID_Hdl){
if(null == itemID_Hdl)
{
printHelp(options); printHelp(options);
//LOG.info("A ItemID or a Handle is needed");
//throw new IllegalArgumentException("ItemID or Handle is null.", new NullPointerException());
} }
else else
{ {
doiRequestByItemID_Handle(context, itemID_Hdl,"toBeRegistered"); doiRequestByItemID_Handle(context, itemID_Hdl,"toBeRegistered");
} }
} }
if(line.hasOption('i')){
if(line.hasOption('i'))
{
String itemID_Hdl = line.getOptionValue('i'); String itemID_Hdl = line.getOptionValue('i');
if(null == itemID_Hdl){
if(null == itemID_Hdl)
{
printHelp(options); printHelp(options);
// LOG.info("A ItemID or a Handle is needed");
//throw new IllegalArgumentException("ItemID or Handle is null.", new NullPointerException());
} }
else else
{ {
@@ -200,9 +212,12 @@ public class DOIOrganiser {
} }
} }
if(line.hasOption('u')){ if(line.hasOption('u'))
{
String argument = line.getOptionValue('u'); String argument = line.getOptionValue('u');
if(null == argument){
if(null == argument)
{
printHelp(options); printHelp(options);
} }
else else
@@ -210,9 +225,11 @@ public class DOIOrganiser {
updateObject(context, argument); updateObject(context, argument);
} }
} }
try { try
{
context.complete(); context.complete();
} catch (SQLException sqle) }
catch (SQLException sqle)
{ {
System.err.println("Cannot save changes to database: " + sqle.getMessage()); System.err.println("Cannot save changes to database: " + sqle.getMessage());
System.exit(-1); System.exit(-1);
@@ -312,27 +329,39 @@ public class DOIOrganiser {
dso, dso,
doiRow.getStringColumn("doi")); doiRow.getStringColumn("doi"));
} }
} catch (SQLException ex) { }
catch (SQLException ex)
{
LOG.error("Error while trying to get data from database", ex); LOG.error("Error while trying to get data from database", ex);
throw new RuntimeException("Error while trying to get data from database", ex); throw new RuntimeException("Error while trying to get data from database", ex);
} catch (IdentifierException ex) { }
catch (IdentifierException ex)
{
LOG.error(ex); LOG.error(ex);
} catch (IllegalArgumentException ex) { }
catch (IllegalArgumentException ex)
{
LOG.error(ex); LOG.error(ex);
} }
} }
private static void doiRequestByDOI(Context context, String identifier, String status){ private static void doiRequestByDOI(Context context, String identifier, String status){
try { try
{
DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class); DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class);
String doi = DOI.formatIdentifier(identifier); String doi = DOI.formatIdentifier(identifier);
TableRow doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length())); TableRow doiRow = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length()));
if(null == doiRow) LOG.error("Identifier: "+ identifier + " is not fund. "); if(null == doiRow) LOG.error("Identifier: "+ identifier + " is not fund. ");
runRequest(context, doiRow, status); runRequest(context, doiRow, status);
} catch (SQLException ex) { }
catch (SQLException ex)
{
LOG.error("It wasn't possible to connect to the Database",ex); LOG.error("It wasn't possible to connect to the Database",ex);
} catch (IdentifierException ex) { }
catch (IdentifierException ex)
{
LOG.error(ex); LOG.error(ex);
} }
} }
@@ -370,20 +399,31 @@ public class DOIOrganiser {
private static void runRequestByItemID_Handle(Context context, Integer resource_type_id, Integer resource_id, String status ){ private static void runRequestByItemID_Handle(Context context, Integer resource_type_id, Integer resource_id, String status ){
DSpaceObject dso = null; DSpaceObject dso = null;
DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class); DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class);
try { try
{
dso = DSpaceObject.find(context, resource_type_id, resource_id); dso = DSpaceObject.find(context, resource_type_id, resource_id);
if (status.equals("toBeRegistered")) {
if (status.equals("toBeRegistered"))
{
doiIdentifierProvider.register(context, dso); doiIdentifierProvider.register(context, dso);
} else { }
else
{
String identifier = doiIdentifierProvider.mint(context, dso); String identifier = doiIdentifierProvider.mint(context, dso);
dso.update(); dso.update();
doiIdentifierProvider.reserve(context, dso, identifier); doiIdentifierProvider.reserve(context, dso, identifier);
} }
} catch (SQLException ex) { }
catch (SQLException ex)
{
LOG.error("It wasn't possible to connect to the Database", ex); LOG.error("It wasn't possible to connect to the Database", ex);
} catch (IdentifierException ex) { }
catch (IdentifierException ex)
{
LOG.error("It wasn't possible to reserved or to registered an DOI Identifier for the objact", ex); LOG.error("It wasn't possible to reserved or to registered an DOI Identifier for the objact", ex);
} catch (AuthorizeException ex) { }
catch (AuthorizeException ex)
{
LOG.error("It wasn't possible to update the dspace object", ex); LOG.error("It wasn't possible to update the dspace object", ex);
} }
} }
@@ -393,58 +433,85 @@ public class DOIOrganiser {
TableRow doiRow = null; TableRow doiRow = null;
DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class); DOIIdentifierProvider doiIdentifierProvider = new DSpace().getSingletonService(DOIIdentifierProvider.class);
String sql = "Select * From Doi Where resource_type_id = ? and resource_id = ? "; String sql = "Select * From Doi Where resource_type_id = ? and resource_id = ? ";
try { try
if (argument.matches("\\d*")) { {
if (argument.matches("\\d*"))
{
System.err.println("I'm an Item"); System.err.println("I'm an Item");
Integer itemID = Integer.valueOf(argument); Integer itemID = Integer.valueOf(argument);
row = DatabaseManager.findByUnique(context, "Item", "item_id", itemID); row = DatabaseManager.findByUnique(context, "Item", "item_id", itemID);
if (null != row) {
if (null != row)
{
System.err.println("I'm not null"); System.err.println("I'm not null");
doiRow = DatabaseManager.querySingleTable(context, doiRow = DatabaseManager.querySingleTable(context,
"Doi", sql, row.getIntColumn("submitter_id"), row.getIntColumn("item_id")); "Doi", sql, row.getIntColumn("submitter_id"), row.getIntColumn("item_id"));
if (null != doiRow) {
if (null != doiRow)
{
DSpaceObject dso = DSpaceObject.find(context, DSpaceObject dso = DSpaceObject.find(context,
doiRow.getIntColumn("resource_type_id"), doiRow.getIntColumn("resource_type_id"),
doiRow.getIntColumn("resource_id")); doiRow.getIntColumn("resource_id"));
doiIdentifierProvider.updateMetadata(context, dso, doiRow.getStringColumn("doi")); doiIdentifierProvider.updateMetadata(context, dso, doiRow.getStringColumn("doi"));
return; return;
} else { }
else
{
LOG.error("There are no DOI Identifier for this Value : " + argument); LOG.error("There are no DOI Identifier for this Value : " + argument);
} }
} else { }
else
{
LOG.error("This Item : " + argument + "doesn't exist"); LOG.error("This Item : " + argument + "doesn't exist");
} }
} }
row = DatabaseManager.findByUnique(context, "Handle", "handle", argument); row = DatabaseManager.findByUnique(context, "Handle", "handle", argument);
if (null != row) {
if (null != row)
{
doiRow = DatabaseManager.querySingleTable(context, doiRow = DatabaseManager.querySingleTable(context,
"Doi", sql, row.getIntColumn("resource_type_id"), row.getIntColumn("resource_id")); "Doi", sql, row.getIntColumn("resource_type_id"), row.getIntColumn("resource_id"));
if (null != doiRow) {
if (null != doiRow)
{
DSpaceObject dso = DSpaceObject.find(context, DSpaceObject dso = DSpaceObject.find(context,
doiRow.getIntColumn("resource_type_id"), doiRow.getIntColumn("resource_type_id"),
doiRow.getIntColumn("resource_id")); doiRow.getIntColumn("resource_id"));
doiIdentifierProvider.updateMetadata(context, dso, doiRow.getStringColumn("doi")); doiIdentifierProvider.updateMetadata(context, dso, doiRow.getStringColumn("doi"));
return; return;
} else { }
else
{
LOG.error("There are no DOI Identifier for this Value : " + argument); LOG.error("There are no DOI Identifier for this Value : " + argument);
} }
} else { }
else
{
LOG.error("This Handle: " + argument + "doesn't exist"); LOG.error("This Handle: " + argument + "doesn't exist");
} }
String doi = doiIdentifierProvider.formatIdentifier(argument);
String doi = DOI.formatIdentifier(argument);
row = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length())); row = DatabaseManager.findByUnique(context, "Doi", "doi", doi.substring(DOI.SCHEME.length()));
if (null != row) {
if (null != row)
{
DSpaceObject dso = DSpaceObject.find(context, DSpaceObject dso = DSpaceObject.find(context,
row.getIntColumn("resource_type_id"), row.getIntColumn("resource_type_id"),
row.getIntColumn("resource_id")); row.getIntColumn("resource_id"));
doiIdentifierProvider.updateMetadata(context, dso, row.getStringColumn("doi")); doiIdentifierProvider.updateMetadata(context, dso, row.getStringColumn("doi"));
} else { }
else
{
LOG.error("This DOI identifier: " + argument + "doesn't exist"); LOG.error("This DOI identifier: " + argument + "doesn't exist");
} }
} catch (SQLException ex) { }
catch (SQLException ex)
{
LOG.error(ex); LOG.error(ex);
} catch (IdentifierException ex) { }
LOG.error("It wasn't possible to format the DOI Identifier", ex); catch (IdentifierException ex)
{
LOG.error("It wasn't possible to update The object", ex);
} }
} }
} }

14
dspace/config/crosswalks/DIM2DataCite.xsl
View File

@@ -248,14 +248,14 @@
Adds contributor and contributorType information Adds contributor and contributorType information
--> -->
<xsl:template match="//dspace:field[@mdschema='dc' and @element='contributor'][not(@qualifier='author')]"> <xsl:template match="//dspace:field[@mdschema='dc' and @element='contributor'][not(@qualifier='author')]">
<xsl:element name="contributor"> <xsl:if test="@qualifier='editor'">
<xsl:if test="@qualifier='editor'"> <xsl:element name="contributor">
<xsl:attribute name="contributorType">Editor</xsl:attribute> <xsl:attribute name="contributorType">Editor</xsl:attribute>
</xsl:if> <contributorName>
<contributorName> <xsl:value-of select="." />
<xsl:value-of select="." /> </contributorName>
</contributorName> </xsl:element>
</xsl:element> </xsl:if>
</xsl:template> </xsl:template>
<!-- <!--

36
dspace/etc/oracle/database_schema_30-31.sql
View File

@@ -21,39 +21,7 @@
-- DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST. -- DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST. DUMP YOUR DATABASE FIRST.
-- --
ALTER TABLE resourcepolicy
ADD (
rpname VARCHAR2(30),
rptype VARCHAR2(30),
rpdescription VARCHAR2(100)
);
ALTER TABLE item ADD discoverable NUMBER(1);
CREATE TABLE versionhistory
(
versionhistory_id INTEGER NOT NULL PRIMARY KEY
);
CREATE TABLE versionitem
(
versionitem_id INTEGER NOT NULL PRIMARY KEY,
item_id INTEGER REFERENCES Item(item_id),
version_number INTEGER,
eperson_id INTEGER REFERENCES EPerson(eperson_id),
version_date TIMESTAMP,
version_summary VARCHAR2(255),
versionhistory_id INTEGER REFERENCES VersionHistory(versionhistory_id)
);
CREATE SEQUENCE versionitem_seq;
CREATE SEQUENCE versionhistory_seq;
------------------------------------------- -------------------------------------------
-- New columns and longer hash for salted password hashing DS-861 -- -- New columns for Doi Table status --
------------------------------------------- -------------------------------------------
ALTER TABLE EPerson modify( password VARCHAR(128)); ALTER TABLE DOI ADD status VARCHAR(20);
ALTER TABLE EPerson ADD salt VARCHAR(32);
ALTER TABLE EPerson ADD digest_algorithm VARCHAR(16);