package eu.dnetlib.doiboost.orcid.xml; import java.io.IOException; import java.util.*; import org.apache.commons.lang3.StringUtils; import org.mortbay.log.Log; import com.ximpleware.*; import eu.dnetlib.dhp.parser.utility.VtdException; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.dhp.schema.orcid.AuthorHistory; import eu.dnetlib.dhp.schema.orcid.AuthorSummary; import eu.dnetlib.doiboost.orcid.model.WorkData; public class XMLRecordParser { private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; private static final String NS_COMMON = "common"; private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; private static final String NS_PERSON = "person"; private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; private static final String NS_DETAILS = "personal-details"; private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; private static final String NS_OTHER = "other-name"; private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; private static final String NS_RECORD = "record"; private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; private static final String NS_ACTIVITIES = "activities"; private static final String NS_ACTIVITIES_URL = "http://www.orcid.org/ns/activities"; private static final String NS_WORK = "work"; private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; private static final String NS_HISTORY = "history"; private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; private static final String NS_ERROR = "error"; public static AuthorData VTDParseAuthorData(byte[] bytes) throws VtdException, EncodingException, EOFException, EntityException, ParseException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); ap.declareXPathNameSpace(NS_HISTORY, NS_HISTORY_URL); AuthorData authorData = new AuthorData(); final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); if (!errors.isEmpty()) { authorData.setErrorCode(errors.get(0)); return authorData; } List recordNodes = VtdUtilityParser .getTextValuesWithAttributes( ap, vn, "//record:record", Arrays.asList("path")); if (!recordNodes.isEmpty()) { final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); authorData.setOid(oid); } else { return null; } final List names = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names"); if (!names.isEmpty()) { authorData.setName(names.get(0)); } final List surnames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name"); if (!surnames.isEmpty()) { authorData.setSurname(surnames.get(0)); } final List creditNames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name"); if (!creditNames.isEmpty()) { authorData.setCreditName(creditNames.get(0)); } final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); if (!otherNames.isEmpty()) { authorData.setOtherNames(otherNames); } // final String creationMethod = VtdUtilityParser.getSingleValue(ap, vn, "//history:creation-method"); // if (StringUtils.isNoneBlank(creationMethod)) { // authorData.setCreationMethod(creationMethod); // } // // final String completionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:completion-date"); // if (StringUtils.isNoneBlank(completionDate)) { // authorData.setCompletionDate(completionDate); // } // // final String submissionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:submission-date"); // if (StringUtils.isNoneBlank(submissionDate)) { // authorData.setSubmissionDate(submissionDate); // } // // final String claimed = VtdUtilityParser.getSingleValue(ap, vn, "//history:claimed"); // if (StringUtils.isNoneBlank(claimed)) { // authorData.setClaimed(Boolean.parseBoolean(claimed)); // } // // final String verifiedEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-email"); // if (StringUtils.isNoneBlank(verifiedEmail)) { // authorData.setVerifiedEmail(Boolean.parseBoolean(verifiedEmail)); // } // // final String verifiedPrimaryEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-primary-email"); // if (StringUtils.isNoneBlank(verifiedPrimaryEmail)) { // authorData.setVerifiedPrimaryEmail(Boolean.parseBoolean(verifiedPrimaryEmail)); // } // // final String deactivationDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:deactivation-date"); // if (StringUtils.isNoneBlank(deactivationDate)) { // authorData.setDeactivationDate(deactivationDate); // } // // final String lastModifiedDate = VtdUtilityParser // .getSingleValue(ap, vn, "//history:history/common:last-modified-date"); // if (StringUtils.isNoneBlank(lastModifiedDate)) { // authorData.setLastModifiedDate(lastModifiedDate); // } return authorData; } public static WorkData VTDParseWorkData(byte[] bytes) throws VtdException, EncodingException, EOFException, EntityException, ParseException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); WorkData workData = new WorkData(); final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); if (!errors.isEmpty()) { workData.setErrorCode(errors.get(0)); return workData; } List workNodes = VtdUtilityParser .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path")); if (!workNodes.isEmpty()) { final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; workData.setOid(oid); } else { return null; } final List dois = VtdUtilityParser .getTextValue( ap, vn, "//common:external-id-type[text()=\"doi\"]/../common:external-id-value"); if (!dois.isEmpty()) { workData.setDoi(dois.get(0)); workData.setDoiFound(true); } return workData; } public static String retrieveOrcidIdFromSummary(byte[] bytes, String defaultValue) throws VtdException, ParseException { return retrieveOrcidId(bytes, defaultValue, NS_RECORD, NS_RECORD_URL, "//record:record", "path").substring(1); } public static String retrieveOrcidIdFromActivity(byte[] bytes, String defaultValue) throws VtdException, ParseException { return retrieveOrcidId(bytes, defaultValue, NS_WORK, NS_WORK_URL, "//work:work", "put-code"); } public static String retrieveWorkIdFromSummary(byte[] bytes, String defaultValue) throws VtdException, ParseException { return retrieveOrcidId( bytes, defaultValue, NS_ACTIVITIES, NS_ACTIVITIES_URL, "//work:work-summary", "put-code"); } private static String retrieveOrcidId(byte[] bytes, String defaultValue, String ns, String nsUrl, String xpath, String idAttributeName) throws VtdException, ParseException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); ap.declareXPathNameSpace(ns, nsUrl); ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); List recordNodes = VtdUtilityParser .getTextValuesWithAttributes( ap, vn, xpath, Arrays.asList(idAttributeName)); if (!recordNodes.isEmpty()) { return (recordNodes.get(0).getAttributes().get(idAttributeName)); } Log.info("id not found - default: " + defaultValue); return defaultValue; } public static Map retrieveWorkIdLastModifiedDate(byte[] bytes) throws ParseException, XPathParseException, NavException, XPathEvalException, IOException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); Map workIdLastModifiedDate = new HashMap<>(); ap.selectXPath("//work:work-summary"); String workId = ""; while (ap.evalXPath() != -1) { String lastModifiedDate = ""; int attr = vn.getAttrVal("put-code"); if (attr > -1) { workId = vn.toNormalizedString(attr); } if (vn.toElement(VTDNav.FIRST_CHILD, "common:last-modified-date")) { int val = vn.getText(); if (val != -1) { lastModifiedDate = vn.toNormalizedString(val); workIdLastModifiedDate.put(workId, lastModifiedDate); } vn.toElement(VTDNav.PARENT); } } return workIdLastModifiedDate; } public static AuthorSummary VTDParseAuthorSummary(byte[] bytes) throws VtdException, ParseException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); ap.declareXPathNameSpace(NS_HISTORY, NS_HISTORY_URL); AuthorData authorData = retrieveAuthorData(ap, vn, bytes); AuthorHistory authorHistory = retrieveAuthorHistory(ap, vn, bytes); AuthorSummary authorSummary = new AuthorSummary(); authorSummary.setAuthorData(authorData); authorSummary.setAuthorHistory(authorHistory); return authorSummary; } private static AuthorData retrieveAuthorData(AutoPilot ap, VTDNav vn, byte[] bytes) throws VtdException { AuthorData authorData = new AuthorData(); final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); if (!errors.isEmpty()) { authorData.setErrorCode(errors.get(0)); return authorData; } List recordNodes = VtdUtilityParser .getTextValuesWithAttributes( ap, vn, "//record:record", Arrays.asList("path")); if (!recordNodes.isEmpty()) { final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); authorData.setOid(oid); } else { return null; } final List names = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names"); if (!names.isEmpty()) { authorData.setName(names.get(0)); } final List surnames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name"); if (!surnames.isEmpty()) { authorData.setSurname(surnames.get(0)); } final List creditNames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name"); if (!creditNames.isEmpty()) { authorData.setCreditName(creditNames.get(0)); } final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); if (!otherNames.isEmpty()) { authorData.setOtherNames(otherNames); } return authorData; } private static AuthorHistory retrieveAuthorHistory(AutoPilot ap, VTDNav vn, byte[] bytes) throws VtdException { AuthorHistory authorHistory = new AuthorHistory(); final String creationMethod = VtdUtilityParser.getSingleValue(ap, vn, "//history:creation-method"); if (StringUtils.isNoneBlank(creationMethod)) { authorHistory.setCreationMethod(creationMethod); } final String completionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:completion-date"); if (StringUtils.isNoneBlank(completionDate)) { authorHistory.setCompletionDate(completionDate); } final String submissionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:submission-date"); if (StringUtils.isNoneBlank(submissionDate)) { authorHistory.setSubmissionDate(submissionDate); } final String claimed = VtdUtilityParser.getSingleValue(ap, vn, "//history:claimed"); if (StringUtils.isNoneBlank(claimed)) { authorHistory.setClaimed(Boolean.parseBoolean(claimed)); } final String verifiedEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-email"); if (StringUtils.isNoneBlank(verifiedEmail)) { authorHistory.setVerifiedEmail(Boolean.parseBoolean(verifiedEmail)); } final String verifiedPrimaryEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-primary-email"); if (StringUtils.isNoneBlank(verifiedPrimaryEmail)) { authorHistory.setVerifiedPrimaryEmail(Boolean.parseBoolean(verifiedPrimaryEmail)); } final String deactivationDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:deactivation-date"); if (StringUtils.isNoneBlank(deactivationDate)) { authorHistory.setDeactivationDate(deactivationDate); } final String lastModifiedDate = VtdUtilityParser .getSingleValue(ap, vn, "//history:history/common:last-modified-date"); if (StringUtils.isNoneBlank(lastModifiedDate)) { authorHistory.setLastModifiedDate(lastModifiedDate); } return authorHistory; } }