diff --git a/src/main/java/fr/osug/doi/Const.java b/src/main/java/fr/osug/doi/Const.java
index 0e44f5dd2d9f7f7f65fc7a46649ec9d8d74df3b1..95bbaf1ccea483c8bbec4f546f51008685849717 100644
--- a/src/main/java/fr/osug/doi/Const.java
+++ b/src/main/java/fr/osug/doi/Const.java
@@ -7,15 +7,22 @@ package fr.osug.doi;
*
*/
public interface Const {
-
- /** datacite schema version '3.1' or '4.0' */
- public final static String SCHEMA_VERSION = "3.1";
-
+
+ public final static String SCHEMA_VERSION_3_1 = "3.1";
+ public final static String SCHEMA_VERSION_4_1 = "4.1";
+
+ public final static float F_SCHEMA_VERSION_3_1 = Float.valueOf(SCHEMA_VERSION_3_1);
+ public final static float F_SCHEMA_VERSION_4_1 = Float.valueOf(SCHEMA_VERSION_4_1);
+
+ /** datacite schema version '3.1' or '4.1' */
+ public final static String SCHEMA_VERSION = SCHEMA_VERSION_3_1;
+ public final static float F_SCHEMA_VERSION = Float.valueOf(SCHEMA_VERSION);
+
public final static String DOI_PREFIX_TEST = "10.5072";
public final static char SEPARATOR = ';';
public final static char COMMENT = '#';
-
+
public final static String FILE_EXT_CSV = ".csv";
public final static String FILE_EXT_XML = ".xml";
@@ -25,20 +32,26 @@ public interface Const {
public static final String KEY_CREATOR_NAME = "creatorName";
public static final String KEY_CONTRIBUTOR_NAME = "contributorName";
-
+ public static final String KEY_CONTRIBUTOR_FUNDER_NAME = "contributorName:Funder";
+ public static final String KEY_FUNDER_NAME = "funderName";
+
public static final String KEY_REL_ID_START = "relatedIdentifier:";
public static final String KEY_REL_ID_DOI = ":DOI";
public static final String[] KEY_ORDER = new String[]{
//# 1 [identifier]
- "identifier", KEY_IDENTIFIER,
+ KEY_IDENTIFIER,
//# 2 [creators]
KEY_CREATOR_NAME,
+ // # v4.1
+ "creatorName:Organizational",
+ "creatorName:Personal",
//# 3 [titles]
KEY_TITLE,
"title:AlternativeTitle",
"title:Subtitle",
"title:TranslatedTitle",
+ "title:Other",
//# 4 [publisher]
"publisher",
// # 5 [publicationYear]
@@ -54,7 +67,8 @@ public interface Const {
"contributorName:DataManager",
"contributorName:Distributor",
"contributorName:Editor",
- "contributorName:Funder",
+ // Funder is deprecated in v4.0
+ KEY_CONTRIBUTOR_FUNDER_NAME,
"contributorName:HostingInstitution",
"contributorName:Other",
"contributorName:Producer",
@@ -77,6 +91,7 @@ public interface Const {
"date:Copyrighted",
"date:Created",
"date:Issued",
+ "date:Other",
"date:Submitted",
"date:Updated",
"date:Valid",
@@ -84,15 +99,18 @@ public interface Const {
"language",
//# 10 [resourceType] (PARTIAL)
"resourceType:Dataset",
+ "resourceType:DataPaper",
"resourceType:Service",
"resourceType:Software",
- "resourceType:Text",
"resourceType:Other",
//# 11 [alternateIdentifiers] (IGNORED)
+ "alternateIdentifier:URL",
+ "alternateIdentifier:DOI",
//# 12 [relatedIdentifiers]
// URL:
"relatedIdentifier:Cites:URL",
"relatedIdentifier:References:URL",
+ "relatedIdentifier:HasPart:URL",
// DOI:
"relatedIdentifier:IsCitedBy:DOI",
"relatedIdentifier:Cites:DOI",
@@ -132,28 +150,37 @@ public interface Const {
"description:Abstract",
"description:Methods",
"description:SeriesInformation",
+ "description:TechnicalInfo",
"description:TableOfContents",
"description:Other",
//# 18 [geoLocations]
KEY_GEO_LOCATION_PLACE,
"geoLocationPoint",
- "geoLocationBox"
+ "geoLocationBox",
+ //# 19 [funder]
+ KEY_FUNDER_NAME
};
public static final String[] KEY_ATTRS = new String[]{
// creator / contributor attributes:
// nameIdentifier variants:
-// "nameIdentifier:AUTHORCLAIM",
-// "nameIdentifier:ISNI",
+ // "nameIdentifier:AUTHORCLAIM",
+ // "nameIdentifier:ISNI",
"nameIdentifier:ORCID",
-// "nameIdentifier:RESEARCHERID",
-// "nameIdentifier:VIAF",
-// "nameIdentifier:URL",
+ // "nameIdentifier:RESEARCHERID",
+ // "nameIdentifier:VIAF",
+ // "nameIdentifier:URL",
// affiliation:
"affiliation",
+ // givenName
+ // familyName
// rights attribute:
- "rightsURI"
+ "rightsURI",
+ // funder attributes:
+ // funderIdentifier
+ "awardNumber",
+ "awardTitle"
};
-
+
public static final String[] KEY_IGNORE = new String[]{
"Préfixe enregistrement doi",
"Prénom Nom",
diff --git a/src/main/java/fr/osug/doi/DoiCsvData.java b/src/main/java/fr/osug/doi/DoiCsvData.java
index 2284a211a833a3ac94c0acaf34bf29577ac8a8bb..999a9678716c4c40cbb5d72a1607575bfb3c7e70 100644
--- a/src/main/java/fr/osug/doi/DoiCsvData.java
+++ b/src/main/java/fr/osug/doi/DoiCsvData.java
@@ -20,6 +20,7 @@ import java.util.Set;
public final class DoiCsvData extends CsvData {
static final Set<String> KEY_SET = new HashSet<String>(128);
+ static final Set<String> KEY_ATTR_SET = new HashSet<String>(32);
static final Map<String, Integer> KEY_ORDER_INDEX = new HashMap<String, Integer>(128);
static {
@@ -31,7 +32,7 @@ public final class DoiCsvData extends CsvData {
}
// supported attributes (extra CSV columns):
for (String key : Const.KEY_ATTRS) {
- KEY_SET.add(key);
+ KEY_ATTR_SET.add(key);
}
}
@@ -94,7 +95,7 @@ public final class DoiCsvData extends CsvData {
// Check keys:
if (i % 2 == 0) {
- if (!KEY_SET.contains(v)) {
+ if (!KEY_SET.contains(v) && ((i == 0) || !KEY_ATTR_SET.contains(v))) {
if (!shouldIgnoreKey(v)) {
logger.warn("Invalid key found [{}] for row: {}", v, Arrays.toString(cols));
}
diff --git a/src/main/java/fr/osug/doi/ProcessPipeline.java b/src/main/java/fr/osug/doi/ProcessPipeline.java
index 18897b9be348d9de3746c159caf4da2e8d81ed10..ba69c36c8eb8350f7bf651dd700143ee69c68dda 100644
--- a/src/main/java/fr/osug/doi/ProcessPipeline.java
+++ b/src/main/java/fr/osug/doi/ProcessPipeline.java
@@ -18,6 +18,7 @@ import java.io.FileInputStream;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
import java.util.LinkedHashSet;
@@ -252,6 +253,9 @@ public final class ProcessPipeline extends AbstractPipeline<ProcessPipelineData>
mergeCSV(projectConfig, data, doiData);
}
+ // Upgrade metadata:
+ upgradeData(data, doiData);
+
// Validate metadata:
validateData(projectConfig, data, doiData);
@@ -322,54 +326,6 @@ public final class ProcessPipeline extends AbstractPipeline<ProcessPipelineData>
}
}
- private void validateData(final ProjectConfig projectConfig, final DoiCsvData data, final ProcessPipelineDoiData doiData) throws IOException {
- logger.debug("validateData [{}]", doiData.getDoiId());
-
- // check title
- if (data.getTitle().isEmpty()) {
- doiData.addWarning("Empty title.");
- }
-
- final List<String[]> rows = data.getRows();
-
- // check all values:
- for (ListIterator<String[]> it = rows.listIterator(); it.hasNext();) {
- String[] cols = it.next();
- if (cols != null && cols.length >= 2) {
- if (cols[1].toLowerCase().contains("todo")) {
- doiData.addWarning("TODO detected for key [" + cols[0] + ']');
- }
-
- // Collect name references and override specific name entries:
- final String key = cols[0];
- if (key.startsWith(Const.KEY_CREATOR_NAME) || key.startsWith(Const.KEY_CONTRIBUTOR_NAME)) {
- final String name = cols[1];
- final String simpleName = ValidationUtil.simplifyName(name);
-
- // Check in override names:
- final NameEntry override = projectConfig.getOverrideNameEntry(simpleName);
-
- if (override != null) {
- logger.debug("override: {}", override);
- cols = NameEntry.toCsv(override);
- cols[0] = key;
-
- it.set(cols);
- }
-
- pipeData.addNameRef(cols);
- }
- }
- }
-
- final Set<String> refs = data.getReferences();
- if (refs != null) {
- logger.debug("References: {}", refs);
- }
- // anyway: add the doi entry:
- pipeData.addRefs(doiData.getDoiId(), refs);
- }
-
private void saveData(final ProjectConfig projectConfig, final DoiCsvData data, final ProcessPipelineDoiData doiData) throws IOException {
// Sort keys:
data.sort();
@@ -452,4 +408,82 @@ public final class ProcessPipeline extends AbstractPipeline<ProcessPipelineData>
FileUtils.writeFile(xmlDoc, fileXML);
}
}
+
+ private void validateData(final ProjectConfig projectConfig, final DoiCsvData data, final ProcessPipelineDoiData doiData) throws IOException {
+ logger.debug("validateData [{}]", doiData.getDoiId());
+
+ // check title
+ if (data.getTitle().isEmpty()) {
+ doiData.addWarning("Empty title.");
+ }
+
+ // check all values:
+ for (ListIterator<String[]> it = data.getRows().listIterator(); it.hasNext();) {
+ String[] cols = it.next();
+ if (cols != null && cols.length >= 2) {
+ if (cols[1].toLowerCase().contains("todo")) {
+ doiData.addWarning("TODO detected for key [" + cols[0] + ']');
+ }
+
+ // Collect name references and override specific name entries:
+ final String key = cols[0];
+ if (key.startsWith(Const.KEY_CREATOR_NAME)
+ || key.startsWith(Const.KEY_CONTRIBUTOR_NAME)
+ || key.startsWith(Const.KEY_FUNDER_NAME)) {
+
+ final String name = cols[1];
+ final String simpleName = ValidationUtil.simplifyName(name);
+
+ // Check in override names:
+ final NameEntry override = projectConfig.getOverrideNameEntry(simpleName);
+
+ if (override != null) {
+ logger.debug("override: {}", override);
+ cols = NameEntry.toCsv(override);
+ cols[0] = key;
+
+ it.set(cols);
+ }
+
+ pipeData.addNameRef(cols);
+ }
+ }
+ }
+
+ final Set<String> refs = data.getReferences();
+ if (refs != null) {
+ logger.debug("References: {}", refs);
+ }
+ // anyway: add the doi entry:
+ pipeData.addRefs(doiData.getDoiId(), refs);
+ }
+
+ private void upgradeData(final DoiCsvData data, final ProcessPipelineDoiData doiData) throws IOException {
+ if (Const.F_SCHEMA_VERSION >= Const.F_SCHEMA_VERSION_4_1) {
+ logger.debug("upgradeData [{}] to schema {}", doiData.getDoiId(), Const.SCHEMA_VERSION);
+
+ for (ListIterator<String[]> it = data.getRows().listIterator(); it.hasNext();) {
+ String[] cols = it.next();
+ if (cols != null && cols.length >= 2) {
+ final String key = cols[0];
+
+ // Convert 'contributorName:Funder' (deprecated ContributorType=Funder) to 'funderName' (fundingReference)
+ if (Const.KEY_CONTRIBUTOR_FUNDER_NAME.equals(key)) {
+ if (cols.length > 2) {
+ logger.warn("upgradeData [{}] : Complex Contributor::Funder = {}", Arrays.toString(cols));
+ // trim (optional attributes like affiliation or orcid)
+ final String value = cols[1];
+ cols = new String[2];
+ cols[1] = value;
+ }
+ cols[0] = Const.KEY_FUNDER_NAME;
+
+ logger.info("upgradeData [{}]: Fixed Funder = {}", doiData.getDoiId(), cols[1]);
+ it.set(cols);
+ }
+ }
+ }
+ }
+
+ }
}
diff --git a/src/test/java/fr/osug/doi/DOITextToXmlTest.java b/src/test/java/fr/osug/doi/DOITextToXmlTest.java
index d7d898b53c21af9e411ee491e99039e057d25592..6aa8b0b1403834351e44ccc413f8b4b7b43a31a1 100644
--- a/src/test/java/fr/osug/doi/DOITextToXmlTest.java
+++ b/src/test/java/fr/osug/doi/DOITextToXmlTest.java
@@ -92,6 +92,7 @@ public class DOITextToXmlTest {
// redirect outputs:
projectConfig.initInputDir(DIR_TEST, true);
+ projectConfig.initMetadataDir(DIR_TEST + "xml/", true);
projectConfig.initTmpDir(DIR_OUTPUT);
projectConfig.initStagingDir(DIR_STAGING);