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[Treebase-guts] SF.net SVN: treebase:[672] trunk/treebase-web
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From: <yo...@us...> - 2010-04-03 14:52:27
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Revision: 672
http://treebase.svn.sourceforge.net/treebase/?rev=672&view=rev
Author: youjun
Date: 2010-04-03 14:52:13 +0000 (Sat, 03 Apr 2010)
Log Message:
-----------
import oai-pmh-provider
Modified Paths:
--------------
trunk/treebase-web/pom.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java
trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-04-03 14:08:25 UTC (rev 671)
+++ trunk/treebase-web/pom.xml 2010-04-03 14:52:13 UTC (rev 672)
@@ -326,5 +326,20 @@
<version>3.0.4</version>
</dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools</artifactId>
+ <version>1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools-generic</artifactId>
+ <version>1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools-view</artifactId>
+ <version>1.1</version>
+ </dependency>
</dependencies>
</project>
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,275 @@
+package org.treebase.oai.web.controller;
+
+import java.lang.reflect.Method;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.validation.BindException;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.AbstractCommandController;
+import org.treebase.oai.web.command.Identify;
+import org.treebase.oai.web.command.OAIPMHCommand;
+import org.treebase.oai.web.util.IdentifyUtil;
+import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.domain.study.ArticleCitation;
+import org.cipres.treebase.domain.study.BookCitation;
+import org.cipres.treebase.domain.study.Citation;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.study.Submission;
+import org.cipres.treebase.domain.study.SubmissionService;
+import org.cipres.treebase.domain.study.StudyService;
+/**
+ * OAIPMHController.java
+ *
+ * Created on Nov. 1, 2009
+ *
+ * @author Youjun Guo
+ *
+ */
+public class OAIPMHController extends AbstractCommandController{
+
+ private SubmissionService submissionService;
+ private StudyService studyService;
+ private Identify identify;
+
+ public OAIPMHController(){
+ setCommandClass(OAIPMHCommand.class);
+ setCommandName("requestParams");
+ }
+
+ public SubmissionService getSubmissionService() {
+ return submissionService;
+ }
+
+ public void setSubmissionService(SubmissionService submissionService) {
+ this.submissionService = submissionService;
+ }
+
+ public StudyService getStudyService() {
+ return studyService;
+ }
+
+ public void setStudyService(StudyService studyService) {
+ this.studyService = studyService;
+ }
+
+ public Identify getIdentify() {
+ return identify;
+ }
+
+ public void setIdentify(Identify identify) {
+ this.identify = identify;
+ }
+
+
+
+ @Override
+ protected ModelAndView handle(HttpServletRequest request,
+ HttpServletResponse response, Object command, BindException errors)
+ throws Exception {
+ // TODO Auto-generated method stub
+
+ OAIPMHCommand params = (OAIPMHCommand) command;
+
+ Map model=errors.getModel();
+ model.put("requestParams", params);
+ model.put("identify", this.identify);
+
+ if(errors.getErrorCount()>0){
+ if(errors.hasFieldErrors("metadataPrefix")){
+ model.put("error_code", "cannotDisseminateFormat");
+ model.put("error", "bad metadataPrefix");
+ return new ModelAndView("error",model);
+ }
+ if(errors.hasFieldErrors("verb")){
+ model.put("error_code", "badVerb");
+ model.put("error", "no verb was found");
+ return new ModelAndView("error",model);
+ }
+ if(errors.hasFieldErrors("identifier")){
+ model.put("error_code", "idDoesNotExist");
+ model.put("error", "no id was found");
+ return new ModelAndView("error",model);
+ }
+ }
+
+ Method method=null;
+ try{
+ method=this.getClass().getMethod(params.getVerb(), new Class[]{OAIPMHCommand.class, Map.class});
+ }catch(NoSuchMethodException nsme){
+ model.put("error_code", "badVerb");
+ model.put("error", "invalid verb");
+ return new ModelAndView("error",model);
+ }catch(NullPointerException e){
+ model.put("error_code", "badVerb");
+ model.put("error", "missing verb");
+ return (new ModelAndView("error",model));
+ }
+
+ return (ModelAndView) method.invoke(this, params, model);
+
+ }
+
+ public ModelAndView ListRecords(OAIPMHCommand params, Map model){
+
+ List<Submission> list=null;
+ try {
+ list = (List)submissionService.findSubmissionByCreateDateRange(IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedFrom()),
+ IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedUntil()));
+ } catch (ParseException e) {
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid from or until format");
+ return (new ModelAndView("error",model));
+ }
+ model.put("recordList", getRecordList(list));
+ return (new ModelAndView("ListRecords",model));
+
+ }
+
+
+ public ModelAndView ListIdentifiers( OAIPMHCommand params, Map model){
+
+ List<Submission> list=null;
+ try {
+ list = (List)submissionService.findSubmissionByCreateDateRange(IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedFrom()),
+ IdentifyUtil.parseGranularity(identify.getGranularityPattern(), params.getModifiedUntil()));
+ } catch (ParseException e) {
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid from or until format");
+ return (new ModelAndView("error",model));
+ }
+ model.put("recordList", getRecordList(list));
+ return (new ModelAndView(params.getMetadataPrefix()+"_ListIdentifiers",model));
+
+ }
+
+ public ModelAndView GetRecord( OAIPMHCommand params, Map model){
+
+ Submission submission = null;
+
+ try{
+ long id = IdentifyUtil.parseID(params);
+ submission = studyService.findByID(id).getSubmission();
+ }catch(NumberFormatException nfe){
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid id format");
+ return (new ModelAndView("error",model));
+
+ }
+ catch (NullPointerException e){
+
+ model.put("error_code", "idDoesNotExist");
+ model.put("error", "invalid id");
+ return (new ModelAndView("error",model));
+
+ }
+ model.put("record", getRecordMap(submission));
+ return (new ModelAndView("GetRecord",model));
+
+ }
+
+ public ModelAndView Identify(OAIPMHCommand params, Map model){
+
+
+ return (new ModelAndView("Identify",model));
+
+ }
+
+ public ModelAndView ListSets(OAIPMHCommand params, Map model){
+ model.put("error_code", "noSetHierarchy");
+ model.put("error", "This repository does not support sets");
+ return (new ModelAndView("error",model));
+
+ }
+
+ public ModelAndView ListMetadataFormats(OAIPMHCommand params, Map model){
+
+ Submission submission = null;
+
+ try{
+ long id = IdentifyUtil.parseID(params);
+ submission = studyService.findByID(id).getSubmission();
+ }catch(NumberFormatException nfe){
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid id format");
+ return (new ModelAndView("error",model));
+
+ }
+ catch (NullPointerException e){
+ //id is optional for ListMetadataFormats
+ //return (new ModelAndView("error",model));
+ }
+
+
+ return (new ModelAndView("ListMetadataFormats",model));
+
+ }
+
+
+ private Map getRecordMap(Submission submission){
+
+ Map map= new HashMap();
+
+ Study study=submission.getStudy();
+ Citation citation=study.getCitation();
+ String publisher=null;
+ if(!study.isPublished())return null;
+
+ //System.out.println("ctype: "+citation.getCitationType());
+ try{
+ if(citation.getCitationType().toUpperCase().contains("BOOK"))
+ publisher=((BookCitation)citation).getPublisher();
+ else publisher=((ArticleCitation)citation).getJournal();
+
+
+ List<Person> authors=citation.getAuthors();
+
+
+ map.put("title", citation.getTitle());
+ map.put("creator", authors);
+ map.put("subject", citation.getKeywords());
+ if(study.getName()!=null&study.getNotes()!=null)
+ map.put("description", study.getName()+" "+study.getNotes());
+ else if(study.getNotes()==null)
+ map.put("description",study.getName());
+ else
+ map.put("description",study.getNotes());
+ map.put("publisher", publisher);
+ map.put("date", "published on "+citation.getPublishYear());
+ map.put("identifier", "TreeBASE.org/study/TB2:s"+study.getId());
+ map.put("datestamp", study.getReleaseDate());
+
+ }catch(NullPointerException e){
+ //study 253 citation= null, data should be fixed
+ System.err.println("study "+study.getId()+
+ " citation= "+e.getMessage());
+ return null;
+ }
+
+ //map.put("type", "text");
+ //map.put("language", "en");
+
+ //map.put("issued", citation.getPublishYear());
+ //map.put("abstract", citation.getAbstract());
+
+
+ return map;
+ }
+
+ private List getRecordList(List<Submission> sList)
+ {
+ List recordList=new ArrayList<Map>();
+
+ for(int i =0; i< sList.size(); i++){
+ Map map=getRecordMap(sList.get(i));
+ if(map!=null)recordList.add(map);
+ }
+ return recordList;
+ }
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,125 @@
+package org.treebase.oai.web.command;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.SimpleTimeZone;
+import java.util.TimeZone;
+/**
+ *
+ * @author youjun
+ * class hold identify data about the service
+ */
+
+public class Identify {
+
+
+ private String baseURL;
+ private String repositoryName;
+ private String protocolVersion;
+ private String adminEmail;
+ private String earliestDatestamp;
+ private String deletedRecord;
+ private String granularity;
+ private String granularityPattern;
+ private String repositoryIdentifier;
+ private String sampleIdentifier;
+ private String dryadPerfix;
+ private String identifierDelimiter;
+ private String dublinPerfix;
+
+
+ public String getGranularityPattern() {
+ return granularityPattern;
+ }
+ public void setGranularityPattern(String granularityPattern) {
+ this.granularityPattern = granularityPattern;
+ }
+
+
+ public String getIdentifierDelimiter() {
+ return identifierDelimiter;
+ }
+ public void setIdentifierDelimiter(String identifierDelimiter) {
+ this.identifierDelimiter = identifierDelimiter;
+ }
+ public String getDublinPerfix() {
+ return dublinPerfix;
+ }
+ public void setDublinPerfix(String dublinPerfix) {
+ this.dublinPerfix = dublinPerfix;
+ }
+ public String getDryadPerfix() {
+ return dryadPerfix;
+ }
+ public void setDryadPerfix(String dryadPerfix) {
+ this.dryadPerfix = dryadPerfix;
+ }
+
+ public String getRepositoryIdentifier() {
+ return repositoryIdentifier;
+ }
+ public void setRepositoryIdentifier(String repositoryIdentifier) {
+ this.repositoryIdentifier = repositoryIdentifier;
+ }
+ public String getSampleIdentifier() {
+ return sampleIdentifier;
+ }
+ public void setSampleIdentifier(String sampleIdentifier) {
+ this.sampleIdentifier = sampleIdentifier;
+ }
+
+ public String getBaseURL() {
+ return baseURL;
+ }
+ public void setBaseURL(String baseRUL) {
+ this.baseURL = baseRUL;
+ }
+ public String getRepositoryName() {
+ return repositoryName;
+ }
+ public void setRepositoryName(String repositoryName) {
+ this.repositoryName = repositoryName;
+ }
+ public String getProtocolVersion() {
+ return protocolVersion;
+ }
+ public void setProtocolVersion(String protocolVersion) {
+ this.protocolVersion = protocolVersion;
+ }
+ public String getAdminEmail() {
+ return adminEmail;
+ }
+ public void setAdminEmail(String adminEmail) {
+ this.adminEmail = adminEmail;
+ }
+ public String getEarliestDatestamp() {
+ return earliestDatestamp;
+ }
+ public void setEarliestDatestamp(String earliestDatestamp) {
+ this.earliestDatestamp = earliestDatestamp;
+ }
+ public String getDeletedRecord() {
+ return deletedRecord;
+ }
+ public void setDeletedRecord(String deletedRecord) {
+ this.deletedRecord = deletedRecord;
+ }
+ public String getGranularity() {
+ return granularity;
+ }
+ public void setGranularity(String granularity) {
+ this.granularity = granularity;
+ }
+
+ // return a current date object in UTC
+ public String getResponseDate(){
+ SimpleDateFormat format = new SimpleDateFormat(granularityPattern);
+ Calendar cal = Calendar.getInstance(new SimpleTimeZone(0, "GMT"));
+ format.setCalendar(cal);
+ return format.format(new Date());
+
+ }
+
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,74 @@
+package org.treebase.oai.web.command;
+/**
+ *
+ * @author youjun
+ * class transfer page/query input data to controller
+ */
+public class OAIPMHCommand {
+
+ private String from;
+ private String until;
+ private String resumptionToken;
+ private String identifier;
+ private String metadataPrefix;
+ private String set;
+ private String verb;
+
+ public String getVerb() {
+ return verb;
+ }
+ public void setVerb(String verb) {
+ this.verb = verb;
+ }
+ public String getModifiedFrom() {
+ if(from!=null&&from.trim()!="")return from;
+ return "1995-11-04T00:00:00Z";
+ }
+
+ public String getFrom() {
+ return from;
+ }
+
+ public void setFrom(String from) {
+ this.from = from;
+ }
+ public String getModifiedUntil() {
+ if(until != null && until.trim()!="") return until;
+ return "";
+ }
+
+ public String getUntil() {
+ return until;
+ }
+
+ public void setUntil(String until) {
+ this.until = until;
+ }
+ public String getResumptionToken() {
+ return resumptionToken;
+ }
+ public void setResumptionToken(String resumptionToken) {
+ this.resumptionToken = resumptionToken;
+ }
+ public String getIdentifier() {
+ return identifier;
+ }
+ public void setIdentifier(String identifier) {
+ this.identifier = identifier;
+ }
+ public String getMetadataPrefix() {
+ return metadataPrefix;
+ }
+ public void setMetadataPrefix(String metadataPrefix) {
+ this.metadataPrefix = metadataPrefix;
+ }
+ public String getSet() {
+ return set;
+ }
+ public void setSet(String set) {
+ this.set = set;
+ }
+
+
+
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,51 @@
+package org.treebase.oai.web.util;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.TimeZone;
+
+import org.treebase.oai.web.command.Identify;
+import org.treebase.oai.web.command.OAIPMHCommand;
+/*
+ *
+ * @author youjun
+ *
+ */
+public class IdentifyUtil {
+
+ // return a studyID by parsing params.identifier
+
+ public static long parseID(OAIPMHCommand params)
+ {
+ String [] ids = params.getIdentifier().split("[/:.]");
+
+ return Long.parseLong(ids[ids.length-1].replaceAll("[a-zA-Z]",""));
+ }
+
+
+ // convert a time String to date object based on granularity
+
+ public static Date parseGranularity(String granularity, String time ) throws ParseException
+ {
+ if(time=="")return new Date();
+ SimpleDateFormat sdf = new SimpleDateFormat(granularity);
+ Date utcDate = sdf.parse(time);
+ return utcToLocal(utcDate);
+
+
+ }
+
+ //convert a date object from utc to local
+
+ protected static Date utcToLocal(Date utcDate)
+ {
+ long utcMiliseconds = utcDate.getTime();
+
+ Calendar cal = new GregorianCalendar();
+ cal.setTimeInMillis(utcMiliseconds);
+ return new Date(utcMiliseconds + cal.get(Calendar.ZONE_OFFSET) + cal.get(Calendar.DST_OFFSET));
+ }
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,40 @@
+package org.treebase.oai.web.validator;
+
+import org.springframework.validation.Errors;
+import org.springframework.validation.ValidationUtils;
+import org.springframework.validation.Validator;
+import org.treebase.oai.web.command.OAIPMHCommand;
+
+public class OAIPMHValidator implements Validator {
+
+ public boolean supports(Class pClass) {
+ return OAIPMHCommand.class.equals(pClass);
+ }
+
+ public void validate(Object pValidatable, Errors pError) {
+ // ValidationUtils.rejectIfEmpty(e, "name", "name.empty");
+ OAIPMHCommand command = (OAIPMHCommand) pValidatable;
+
+ String verb = command.getVerb();
+ String fPrefix = command.getMetadataPrefix();
+
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "verb", "empyt verb");
+
+
+ if(verb!=null && verb.equals("GetRecord"))
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "identifier", "empyt id");
+
+ // check format prefix
+ if(verb!=null){
+ if(verb.equals("GetRecord")||verb.equals("ListIdentifiers")||verb.equals("ListRecords")){
+
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "metadataPrefix", "cannotDisseminateFormat");
+
+ if(fPrefix!=null)
+ if(!(fPrefix.equals("oai_dc")||fPrefix.equals("dryad")))
+ pError.rejectValue("metadataPrefix","cannotDisseminateFormat");
+ }
+ }
+ }
+
+}
Added: trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,13 @@
+identify.baseURL=www.***.***:port/top
+identify.repositoryName=TreeBASE repository
+identify.protocolVersion=2.0
+identify.adminEmail=you...@ya...
+identify.earliestDatestamp=1995-11-04T00:00:00Z
+identify.deletedRecord=transient
+identify.granularity=YYYY-MM-DDThh:mm:ssZ
+identify.granularityPattern=yyyy-MM-dd'T'hh:mm:ss'Z'
+identify.sampleIdentifier=TreeBASE.org/study/TB2:s6705
+identify.repositoryIdentifier=TreeBASE.org
+identify.identifierDelimiter=:
+identify.dublinPerfix=oai_dc
+identify.dryadPerfix=dryad
\ No newline at end of file
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