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Revision cd602b47

IDcd602b47083a92013943d43fae314ce076ea1040
Parent 651101eb
Child 8376de88

Added by Andreas M├╝ller about 3 years ago

ref #6636 firs incomplete version of RIS reference import

View differences:

cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/IoResultBase.java
20 20
 */
21 21
public abstract class IoResultBase {
22 22

  
23
    private List<Error> errors = new ArrayList<>();
24
    private List<String> warnings = new ArrayList<>();
25
    private List<Error> exceptions = new ArrayList<>();
23
    private List<IoInfo> ioInfos = new ArrayList<>();
24
    private List<IoInfo> warnings = new ArrayList<>();
25
    private List<IoInfo> exceptions = new ArrayList<>();
26 26

  
27
    public class Error{
27
    public class IoInfo{
28 28
        String message;
29 29
        Exception exception;
30
        private Error(String msg, Exception e){this.message = msg; this.exception = e;}
30
        String location;
31
        private IoInfo(String msg, Exception e){
32
            this.message = msg;
33
            this.exception = e;
34
        }
35
        private IoInfo(String msg, Exception e, String location){
36
            this.message = msg;
37
            this.exception = e;
38
            this.location = location;
39
        }
31 40

  
32 41
        public String getMessage(){
33 42
            return message;
......
40 49

  
41 50
// ************* GETTERS / SETTERS / ADDERS ***********************/
42 51

  
43
    public List<Error> getErrors() {return errors;}
44
    public void setErrors(List<Error> errors) {this.errors = errors;}
52
    public List<IoInfo> getErrors() {return ioInfos;}
53
    public void setErrors(List<IoInfo> ioInfos) {this.ioInfos = ioInfos;}
45 54
    public void addError(String error) {
46
        errors.add(new Error(error, null));
55
        ioInfos.add(new IoInfo(error, null));
47 56
    }
48 57
    public void addError(String error, Exception e) {
49
        errors.add(new Error(error, e));
58
        ioInfos.add(new IoInfo(error, e));
59
    }
60
    public void addError(String message, int location) {
61
        ioInfos.add(new IoInfo(message, null, String.valueOf(location)));
50 62
    }
51 63

  
52
    public List<String> getWarnings() {return warnings;}
53
    public void setWarnings(List<String> warnings) {this.warnings = warnings;}
64
    public List<IoInfo> getWarnings() {return warnings;}
65
    public void setWarnings(List<IoInfo> warnings) {this.warnings = warnings;}
54 66
    public void addWarning(String warning) {
55 67
//       warnings.add(warning.getBytes(StandardCharsets.UTF_8));
56
        warnings.add(warning);
68
        warnings.add(new IoInfo(warning, null));
69
    }
70
    public void addWarning(String message, int location) {
71
        warnings.add(new IoInfo(message, null, String.valueOf(location)));
57 72
    }
58 73

  
59
    public List<Error> getExceptions() {return exceptions;}
60
    public void setExceptions(List<Error> exceptions) {this.exceptions = exceptions;}
74
    public List<IoInfo> getExceptions() {return exceptions;}
75
    public void setExceptions(List<IoInfo> exceptions) {this.exceptions = exceptions;}
61 76
    public void addException(Exception e) {
62
        exceptions.add(new Error(null, e));
77
        exceptions.add(new IoInfo(null, e));
63 78
        setExceptionState();
64 79
    }
65 80
    public void addException(Exception e, String message) {
66
        exceptions.add(new Error(message, e));
81
        exceptions.add(new IoInfo(message, e));
67 82
        setExceptionState();
68 83
    }
69 84

  
......
85 100
     */
86 101
    public StringBuffer createReport() {
87 102
        StringBuffer report = new StringBuffer("");
88
        addErrorReport(report, "Errors", errors);
103
        addErrorReport(report, "Errors", ioInfos);
89 104
        addErrorReport(report, "Exceptions", exceptions);
90
        addWarnings(report, "Warnings", warnings);
105
        addErrorReport(report, "Warnings", warnings);
91 106
        return report;
92 107
    }
108
//    /**
109
//     * @param report
110
//     * @param string
111
//     * @param warnings2
112
//     */
113
//    private void addWarnings(StringBuffer report, String label, List<String> list) {
114
//        if (!list.isEmpty()){
115
//            report.append("\n\n" + label + ":\n" + StringUtils.leftPad("", label.length()+1, "="));
116
//            for (String warning : list){
117
//                String str = String.valueOf(warning);
118
//                report.append("\n" + str);
119
//            }
120
//        }
121
//    }
122

  
93 123
    /**
94 124
     * @param report
95
     * @param string
96
     * @param warnings2
97
     */
98
    private void addWarnings(StringBuffer report, String label, List<String> list) {
99
        if (!list.isEmpty()){
100
            report.append("\n\n" + label + ":\n" + StringUtils.leftPad("", label.length()+1, "="));
101
            for (String warning : list){
102
                String str = String.valueOf(warning);
103
                report.append("\n" + str);
104
            }
105
        }
106
    }
107
    /**
108
     * @param report
109
     * @param string
110
     * @param newRecords2
125
     * @param label
126
     * @param list
111 127
     */
112
    private void addErrorReport(StringBuffer report, String label, List<Error> list) {
113
        if (!errors.isEmpty()){
128
    private void addErrorReport(StringBuffer report, String label, List<IoInfo> list) {
129
        if (!ioInfos.isEmpty()){
114 130
            report.append("\n\n" + label + ":\n" + StringUtils.leftPad("", label.length()+1, "="));
115
            for (Error error : list){
116
                String message = error.message != null ? error.message : error.exception != null ? error.exception.getMessage() : "";
131
            for (IoInfo ioInfo : list){
132
                String location = ioInfo.location == null ? "" : (ioInfo.location + ": ");
133
                String message = ioInfo.message != null ? ioInfo.message : ioInfo.exception != null ? ioInfo.exception.getMessage() : "";
117 134
                message = StringUtils.isBlank(message)? "no message" : message;
118
                Object stacktrace = error.exception.getStackTrace();
135
                Object stacktrace = ioInfo.exception.getStackTrace();
119 136
                String available = (stacktrace == null ? " not" : "");
120
                report.append("\n" + message + "(stacktrace" + available + ")");
137
                report.append("\n" + location + message + "(stacktrace" + available + ")");
121 138
            }
122 139
        }
123 140
    }
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisRecordReader.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
import java.io.BufferedReader;
12
import java.io.IOException;
13
import java.io.InputStreamReader;
14
import java.util.HashMap;
15
import java.util.Map;
16

  
17
import org.apache.commons.lang3.StringUtils;
18

  
19
/**
20
 * @author a.mueller
21
 * @date 11.05.2017
22
 *
23
 */
24
public class RisRecordReader {
25

  
26
    private BufferedReader lineReader;
27
    private RisReferenceImportState state;
28
    private int lineNo = 0;
29
    private String lineNoStr;
30

  
31
    public static final Map<RisReferenceTag, String>  EOF = new HashMap<>();
32
    private static final String NL = "\n";
33

  
34

  
35
    /**
36
     * @param baseReader
37
     */
38
    public RisRecordReader(RisReferenceImportState state, InputStreamReader inputReader) {
39
        lineReader = new BufferedReader(inputReader);
40
        this.state = state;
41
    }
42

  
43
    public Map<RisReferenceTag, String> readRecord(){
44
        try {
45
            Map<RisReferenceTag, String> result = new HashMap<>();
46
            String line;
47
            int count = 0;
48
            boolean started = false;
49
            RisReferenceTag lastType = null;
50
            while ((line = lineReader.readLine()) != null) {
51
                lineNo++;
52
                if (isBlank(line)){
53
                   continue;
54
               }
55
               RisReferenceTag type;
56
               if (matchesRisLine(line)){
57
                   type = RisReferenceTag.TY;
58
                   if (isTypeLine(line)){
59
                       type = RisReferenceTag.TY;
60
                       result.put(type, replaceTag(line));
61
                       count++;
62
                   }else if (isErLine(line)){
63
                       return result;
64
                   }else{
65
                       //TODO
66
                       try {
67
                           type = RisReferenceTag.valueOf(line.substring(0, 2));
68
                       } catch (Exception e) {
69
                            //type stays null
70
                       }
71
                       if (type == null){
72
                           //TODO
73
                           //Sollte aber als als extension trotzdem ├╝bergeben werden
74
                           String message = "Unknown reference type %s . Reference attribute could not be added";
75
                           state.getResult().addWarning(message, lineNo);
76
                       }else{
77
                           result.put(type, replaceTag(line));
78
                       }
79
                       count++;
80
                   }
81
                   if (type != null){
82
                       lastType = type;
83
                   }
84
               }else{
85
                   if (started){
86
                       //add to prior
87
                       String prior = result.get(lastType);
88
                       result.put(lastType, prior + NL + line);
89
                   }else{
90
                       String message = lineNoStr + "RIS record does not start with TY. Can't create record";
91
                       state.getResult().addError(message, lineNo);
92
                   }
93

  
94
               }
95
            }
96
            if (count>0){
97
                String message = lineNoStr + "Unexpected end of file. Some records may not have been imported";
98
                state.getResult().addError(message, lineNo);
99
            }
100
            return EOF;
101

  
102
        } catch (IOException e) {
103
            String message = "Unexpected exception during RIS Reference Import";
104
            state.getResult().addException(e, message);
105
            return EOF;
106
        }
107
    }
108

  
109

  
110
    /**
111
     * @param line
112
     * @return
113
     */
114
    private String replaceTag(String line) {
115
        return line.substring(5).trim();
116
    }
117

  
118

  
119
    private static final String risLineReStr = "[A-Z1-9]{2}\\s\\s-\\s.*";
120
    private static final String typeLineReStr = "TY\\s\\s-\\s.*";
121
    private static final String erLineReStr = "ER\\s\\s-\\s+";
122

  
123

  
124
    /**
125
     * @param line
126
     * @return
127
     */
128
    private boolean isErLine(String line) {
129
        return line.matches(erLineReStr);
130
    }
131

  
132

  
133
    /**
134
     * @param line
135
     * @return
136
     */
137
    private boolean isTypeLine(String line) {
138
        return line.matches(typeLineReStr);
139
    }
140

  
141

  
142
    /**
143
     * @param line
144
     * @return
145
     */
146
    private boolean matchesRisLine(String line) {
147
        return line.matches(risLineReStr);
148
    }
149

  
150
    private boolean isBlank(String str){
151
        return StringUtils.isBlank(str);
152
    }
153
}
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisRecordType.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
import eu.etaxonomy.cdm.model.reference.ReferenceType;
12

  
13
/**
14
 * @author a.mueller
15
 * @date 12.05.2017
16
 *
17
 */
18
public enum RisRecordType {
19
    AGGR("Aggregated Database" , ReferenceType.Database ),
20
    ANCIENT("Ancient Text"  ),
21
    ART("Art Work"  ),
22
    BILL("Bill"  ),
23
    BLOG("Blog"  ),
24
    BOOK("Whole book" , ReferenceType.Book ),
25
    CASE("Case"  ),
26
    CHAP("Book chapter" , ReferenceType.BookSection ),
27
    CHART("Chart"  ),
28
    CLSWK("Classical Work"  ),
29
    COMP("Computer program"  ),
30
    CONF("Conference proceeding" , ReferenceType.InProceedings ),
31
    CPAPER("Conference paper"  ),
32
    CTLG("Catalog"  ),
33
    DATA("Data file"  ),
34
    DBASE("Online Database" , ReferenceType.Database ),
35
    DICT("Dictionary"  ),
36
    EBOOK("Electronic Book"  ),
37
    ECHAP("Electronic Book Section"  ),
38
    EDBOOK("Edited Book" , ReferenceType.Book ),
39
    EJOUR("Electronic Article"  ),
40
    ELEC("Web Page" , ReferenceType.WebPage ),
41
    ENCYC("Encyclopedia"  ),
42
    EQUA("Equation"  ),
43
    FIGURE("Figure"  ),
44
    GEN("Generic" , ReferenceType.Generic ),
45
    GOVDOC("Government Document"  ),
46
    GRANT("Grant"  ),
47
    HEAR("Hearing"  ),
48
    ICOMM("Internet Communication"  ),
49
    INPR("In Press"  ),
50
    JFULL("Journal (full)" , ReferenceType.Journal ),
51
    JOUR("Journal" , ReferenceType.Article ),
52
    LEGAL("Legal Rule or Regulation"  ),
53
    MANSCPT("Manuscript"  ),
54
    MAP("Map" , ReferenceType.Map ),
55
    MGZN("Magazine article" , ReferenceType.Article ),
56
    MPCT("Motion picture"  ),
57
    MULTI("Online Multimedia"  ),
58
    MUSIC("Music score"  ),
59
    NEWS("Newspaper"  ),
60
    PAMP("Pamphlet"  ),
61
    PAT("Patent"  ),
62
    PCOMM("Personal communication" , ReferenceType.PersonalCommunication ),
63
    RPRT("Report" , ReferenceType.Report ),
64
    SER("Serial publication" , ReferenceType.PrintSeries ),
65
    SLIDE("Slide"  ),
66
    SOUND("Sound recording"  ),
67
    STAND("Standard"  ),
68
    STAT("Statute"  ),
69
    THES("Thesis/Dissertation" , ReferenceType.Thesis ),
70
    UNPB("Unpublished work"  ),
71
    VIDEO("Video recording"  ),
72

  
73

  
74
    ;
75

  
76
    private String description;
77
    private ReferenceType refType;
78

  
79
    private RisRecordType(String description){
80
        this.description = description;
81
    }
82

  
83
    private RisRecordType(String description, ReferenceType refType){
84
        this.description = description;
85
        this.refType = refType;
86
    }
87

  
88
    /**
89
     * @return the description
90
     */
91
    public String getDescription() {
92
        return description;
93
    }
94

  
95
    /**
96
     * @return
97
     */
98
    public ReferenceType getCdmReferenceType() {
99
        return refType;
100
    }
101
}
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisReferenceImport.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
import java.io.InputStreamReader;
12
import java.util.HashSet;
13
import java.util.Map;
14
import java.util.Set;
15

  
16
import org.apache.log4j.Logger;
17
import org.springframework.stereotype.Component;
18

  
19
import eu.etaxonomy.cdm.common.DOI;
20
import eu.etaxonomy.cdm.io.common.CdmImportBase;
21
import eu.etaxonomy.cdm.model.agent.Person;
22
import eu.etaxonomy.cdm.model.common.Annotation;
23
import eu.etaxonomy.cdm.model.common.AnnotationType;
24
import eu.etaxonomy.cdm.model.common.Language;
25
import eu.etaxonomy.cdm.model.common.TimePeriod;
26
import eu.etaxonomy.cdm.model.reference.Reference;
27
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
28
import eu.etaxonomy.cdm.model.reference.ReferenceType;
29
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
30

  
31
/**
32
 * @author a.mueller
33
 * @date 11.05.2017
34
 *
35
 */
36
@Component
37
public class RisReferenceImport
38
    extends CdmImportBase<RisReferenceImportConfigurator, RisReferenceImportState>{
39

  
40
    private static final long serialVersionUID = 7022034669942979722L;
41
    @SuppressWarnings("unused")
42
    private static final Logger logger = Logger.getLogger(RisReferenceImport.class);
43

  
44
    /**
45
     * {@inheritDoc}
46
     */
47
    @Override
48
    protected void doInvoke(RisReferenceImportState state) {
49
        RisReferenceImportConfigurator config = state.getConfig();
50
        try {
51
//            new FileReader(file)
52
            InputStreamReader inputReader = config.getSource();
53
            RisRecordReader risReader = new RisRecordReader(state, inputReader);
54

  
55
            Set<Reference> referencesToSave = new HashSet<>();
56

  
57

  
58
            Map<RisReferenceTag, String> next = risReader.readRecord();
59
            while (next != RisRecordReader.EOF){
60
                Reference ref = makeReference(next);
61
                referencesToSave.add(ref);
62
                next = risReader.readRecord();
63
            }
64

  
65
            getReferenceService().saveOrUpdate(referencesToSave);
66

  
67
        } catch (Exception e) {
68
            String message = "Unexpected exception during RIS Reference Import";
69
            state.getResult().addException(e, message);
70
        }
71
    }
72

  
73
    /**
74
     * @param next
75
     * @return
76
     */
77
    private Reference makeReference(Map<RisReferenceTag, String> record) {
78
        ReferenceType type = makeReferenceType(record);
79
        Reference result = ReferenceFactory.newReference(type);
80
        ReferenceType inRefType = type == ReferenceType.Article ? ReferenceType.Journal : ReferenceType.Generic;
81
        Reference inRef = ReferenceFactory.newReference(inRefType);
82

  
83
        for (RisReferenceTag tag : record.keySet()){
84
            String value = record.get(tag);
85

  
86
            if (isNotBlank(value)){
87
                switch (tag) {
88
                    case T1:
89
                        result.setTitle(value);
90
                        break;
91
                    case AU:
92
                        Person author = Person.NewTitledInstance(value);
93
                        result.setAuthorship(author);
94
                        break;
95
                    case Y1:
96
                        TimePeriod y1 = TimePeriodParser.parseString(value);
97
                        result.setDatePublished(y1);
98
                        break;
99
                    case PY:
100
                        //TODO
101
                        TimePeriod py = TimePeriodParser.parseString(value);
102
                        result.setDatePublished(py);
103
                        break;
104
                    case DA:
105
                        //TODO
106
                        TimePeriod da = TimePeriodParser.parseString(value);
107
                        result.setDatePublished(da);
108
                        break;
109
                    case N1:
110
                        Annotation annotation = Annotation.NewInstance(value, AnnotationType.EDITORIAL(), Language.DEFAULT());
111
                        result.addAnnotation(annotation);
112
                        break;
113
                    case DO:
114
                        DOI doi = DOI.fromString(value);
115
                        result.setDoi(doi);
116
                        break;
117
                    case T2:
118
                        inRef.setTitle(value);
119
                        break;
120
                    case JF:
121
                        inRef.setTitle(value);
122
                        break;
123
                    case JO:
124
                        inRef.setTitle(value);
125
                        break;
126
                    case SP:
127
                        String startPage = value;
128
                        result.setPages(startPage);
129
                        break;
130
                    case EP:
131
                        String endPage = value;
132
                        result.setPages(endPage);
133
                        break;
134
                    case VL:
135
                        String volume = value;
136
                        result.setVolume(volume);
137
                        break;
138
                    case IS:
139
                        String issueNumber = value;
140
                        result.setVolume(issueNumber);
141
                        break;
142
                    case PB:
143
                        String publisher = value;
144
                        result.setPublisher(publisher);
145
                        break;
146
                    case N2:
147
                        String n2Str = value;
148
                        result.setReferenceAbstract(n2Str);
149
                        break;
150
                    case AB:
151
                        String abstractStr = value;
152
                        result.setReferenceAbstract(abstractStr);
153
                        break;
154
                    case SN:
155
                        String issn = value;
156
                        result.setIssn(issn);
157
                        break;
158
                    default:
159
                        //TODO
160
                        break;
161
                }
162
            }else {
163
                //TODO isBlank
164
            }
165

  
166
        }
167
        return result;
168
    }
169

  
170
    /**
171
     * @param record
172
     * @return
173
     */
174
    private ReferenceType makeReferenceType(Map<RisReferenceTag, String> record) {
175
        RisReferenceTag tyTag = RisReferenceTag.TY;
176
        String typeStr = record.get(tyTag);
177
        RisRecordType type = RisRecordType.valueOf(typeStr);
178
        ReferenceType cdmType = type.getCdmReferenceType();
179
        record.remove(tyTag);
180
        return cdmType;
181
    }
182

  
183
    /**
184
     * {@inheritDoc}
185
     */
186
    @Override
187
    protected boolean doCheck(RisReferenceImportState state) {
188
        return true;
189
    }
190

  
191
    /**
192
     * {@inheritDoc}
193
     */
194
    @Override
195
    protected boolean isIgnore(RisReferenceImportState state) {
196
        return false;
197
    }
198
}
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisReferenceImportConfigurator.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
import java.io.IOException;
12
import java.io.InputStream;
13
import java.io.InputStreamReader;
14
import java.net.MalformedURLException;
15
import java.net.URI;
16
import java.net.URL;
17

  
18
import eu.etaxonomy.cdm.database.ICdmDataSource;
19
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
20
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
21
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
22
import eu.etaxonomy.cdm.model.reference.Reference;
23
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
24

  
25
/**
26
 * @author a.mueller
27
 * @date 11.05.2017
28
 *
29
 */
30
public class RisReferenceImportConfigurator
31
        extends ImportConfiguratorBase<RisReferenceImportState, InputStreamReader>{
32

  
33
    private static final long serialVersionUID = -5982826645441621962L;
34
    private static IInputTransformer defaultTransformer = null;
35

  
36
    /**
37
     * @param uri
38
     * @param object
39
     * @return
40
     * @throws IOException
41
     * @throws MalformedURLException
42
     */
43
    public static IImportConfigurator NewInstance(URI uri, ICdmDataSource cdm) throws MalformedURLException, IOException {
44
        return NewInstance(uri.toURL(), cdm);
45
    }
46

  
47
    /**
48
     * @param url
49
     * @param object
50
     * @return
51
     * @throws IOException
52
     */
53
    public static IImportConfigurator NewInstance(URL url, ICdmDataSource cdm) throws IOException {
54
        InputStream stream = url.openStream();
55
        InputStreamReader reader = new InputStreamReader(stream);
56
        RisReferenceImportConfigurator result = new RisReferenceImportConfigurator(reader, cdm);
57
        return result;
58
    }
59

  
60
    /**
61
     * @param transformer
62
     */
63
    protected RisReferenceImportConfigurator() {
64
        super(defaultTransformer);
65
    }
66

  
67
    protected RisReferenceImportConfigurator(InputStreamReader source, ICdmDataSource cdm) {
68
        super(defaultTransformer);
69
        this.setSource(source);
70
        this.setDestination(cdm);
71
    }
72

  
73

  
74
    /**
75
     * {@inheritDoc}
76
     */
77
    @Override
78
    public RisReferenceImportState getNewState() {
79
        return new RisReferenceImportState(this);
80
    }
81

  
82

  
83
    /**
84
     * {@inheritDoc}
85
     */
86
    @Override
87
    protected void makeIoClassList() {
88
        ioClassList = new Class[]{
89
                RisReferenceImport.class
90
            };
91
    }
92

  
93

  
94
    /**
95
     * {@inheritDoc}
96
     */
97
    @Override
98
    public Reference getSourceReference() {
99
        if (this.sourceReference == null){
100
            sourceReference = ReferenceFactory.newGeneric();
101
            if (this.getSource() == null){
102
                sourceReference.setTitleCache("RIS Reference Import " + getDateString(), true);
103
            }else{
104
                sourceReference.setTitleCache(getSource().toString(), true);
105
            }
106
        }
107
        return sourceReference;
108
    }
109

  
110

  
111
}
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisReferenceImportState.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
import eu.etaxonomy.cdm.io.common.ImportStateBase;
12

  
13
/**
14
 * @author a.mueller
15
 * @date 11.05.2017
16
 *
17
 */
18
public class RisReferenceImportState
19
        extends ImportStateBase<RisReferenceImportConfigurator, RisReferenceImport>{
20

  
21
    /**
22
     * @param config
23
     */
24
    protected RisReferenceImportState(RisReferenceImportConfigurator config) {
25
        super(config);
26
    }
27

  
28
}
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/ris/in/RisReferenceTag.java
1
/**
2
* Copyright (C) 2017 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9
package eu.etaxonomy.cdm.io.reference.ris.in;
10

  
11
/**
12
 * @author a.mueller
13
 * @date 11.05.2017
14
 *
15
 */
16
public enum RisReferenceTag {
17
    TY("Type of reference"),
18
    A1("First Author"),
19
    A2("Secondary Author (each author on its own line preceded by the tag)"),
20
    A3("Tertiary Author (each author on its own line preceded by the tag)"),
21
    A4("Subsidiary Author (each author on its own line preceded by the tag)"),
22
    AB("Abstract"),
23
    AD("Author Address"),
24
    AN("Accession Number"),
25
    AU("Author (each author on its own line preceded by the tag)"),
26
    AV("Location in Archives"),
27
    BT("This field can contain alphanumeric characters. There is no practical limit to the length of this field."),
28
    C1("Custom 1"),
29
    C2("Custom 2"),
30
    C3("Custom 3"),
31
    C4("Custom 4"),
32
    C5("Custom 5"),
33
    C6("Custom 6"),
34
    C7("Custom 7"),
35
    C8("Custom 8"),
36
    CA("Caption"),
37
    CN("Call Number"),
38
    CP("This field can contain alphanumeric characters. There is no practical limit to the length of this field."),
39
    CT("Title of unpublished reference"),
40
    CY("Place Published"),
41
    DA("Date"),
42
    DB("Name of Database"),
43
    DO("DOI"),
44
    DP("Database Provider"),
45
    ED("Editor"),
46
    EP("End Page"),
47
    ET("Edition"),
48
    ID("Reference ID"),
49
    IS("Issue number"),
50
    J1("Periodical name: user abbreviation 1. This is an alphanumeric field of up to 255 characters."),
51
    J2("Alternate Title (this field is used for the abbreviated title of a book or journal name, the latter mapped to T2)"),
52
    JA("Periodical name: standard abbreviation. This is the periodical in which the article was (or is to be, in the case of in-press references) published. This is an alphanumeric field of up to 255 characters."),
53
    JF("Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters."),
54
    JO("Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters."),
55
    KW("Keywords (keywords should be entered each on its own line preceded by the tag)"),
56
    L1("Link to PDF. There is no practical limit to the length of this field. URL addresses can be entered individually, one per tag or multiple addresses can be entered on one line using a semi-colon as a separator."),
57
    L2("Link to Full-text. There is no practical limit to the length of this field. URL addresses can be entered individually, one per tag or multiple addresses can be entered on one line using a semi-colon as a separator."),
58
    L3("Related Records. There is no practical limit to the length of this field."),
59
    L4("Image(s). There is no practical limit to the length of this field."),
60
    LA("Language"),
61
    LB("Label"),
62
    LK("Website Link"),
63
    M1("Number"),
64
    M2("Miscellaneous 2. This is an alphanumeric field and there is no practical limit to the length of this field."),
65
    M3("Type of Work"),
66
    N1("Notes"),
67
    N2("Abstract. This is a free text field and can contain alphanumeric characters. There is no practical length limit to this field."),
68
    NV("Number of Volumes"),
69
    OP("Original Publication"),
70
    PB("Publisher"),
71
    PP("Publishing Place"),
72
    PY("Publication year (YYYY/MM/DD)"),
73
    RI("Reviewed Item"),
74
    RN("Research Notes"),
75
    RP("Reprint Edition"),
76
    SE("Section"),
77
    SN("ISBN/ISSN"),
78
    SP("Start Page"),
79
    ST("Short Title"),
80
    T1("Primary Title"),
81
    T2("Secondary Title (journal title, if applicable)"),
82
    T3("Tertiary Title"),
83
    TA("Translated Author"),
84
    TI("Title"),
85
    TT("Translated Title"),
86
    U1("User definable 1. This is an alphanumeric field and there is no practical limit to the length of this field."),
87
    U2("User definable 2. This is an alphanumeric field and there is no practical limit to the length of this field."),
88
    U3("User definable 3. This is an alphanumeric field and there is no practical limit to the length of this field."),
89
    U4("User definable 4. This is an alphanumeric field and there is no practical limit to the length of this field."),
90
    U5("User definable 5. This is an alphanumeric field and there is no practical limit to the length of this field."),
91
    UR("URL"),
92
    VL("Volume number"),
93
    VO("Published Standard number"),
94
    Y1("Primary Date"),
95
    Y2("Access Date"),
96
    ER("End of Reference")
97
    ;
98

  
99
    private String description;
100

  
101
    private RisReferenceTag(String description){
102
        this.description = description;
103
    }
104

  
105
    /**
106
     * @return the description
107
     */
108
    public String getDescription() {
109
        return description;
110
    }
111

  
112

  
113
}
cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/reference/RisReferenceImportTest.java
1
/**
2
* Copyright (C) 2007 EDIT
3
* European Distributed Institute of Taxonomy
4
* http://www.e-taxonomy.eu
5
*
6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7
* See LICENSE.TXT at the top of this package for the full license terms.
8
*/
9

  
10
package eu.etaxonomy.cdm.io.reference;
11

  
12
import static org.junit.Assert.assertNotNull;
13

  
14
import java.io.FileNotFoundException;
15
import java.net.URL;
16

  
17
import org.junit.Assert;
18
import org.junit.Before;
19
import org.junit.Ignore;
20
import org.junit.Test;
21
import org.unitils.spring.annotation.SpringBeanByName;
22
import org.unitils.spring.annotation.SpringBeanByType;
23

  
24
import eu.etaxonomy.cdm.api.service.INameService;
25
import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
26
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
27
import eu.etaxonomy.cdm.io.common.ImportResult;
28
import eu.etaxonomy.cdm.io.reference.ris.in.RisReferenceImportConfigurator;
29
import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
30

  
31
/**
32
 * @author andy
33
 *
34
 */
35
public class RisReferenceImportTest extends CdmTransactionalIntegrationTest {
36

  
37
	@SpringBeanByName
38
	private CdmApplicationAwareDefaultImport<?> defaultImport;
39

  
40
	@SpringBeanByType
41
	private INameService nameService;
42

  
43
	private IImportConfigurator configurator;
44

  
45
	@Before
46
	public void setUp() {
47
		String inputFile = "/eu/etaxonomy/cdm/io/reference/RisReferenceImportTest-input.ris";
48
		URL url = this.getClass().getResource(inputFile);
49
		assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
50
		try {
51
			configurator = RisReferenceImportConfigurator.NewInstance(url, null);
52
		} catch (Exception e) {
53
			e.printStackTrace();
54
			Assert.fail();
55
		}
56
		assertNotNull("Configurator could not be created", configurator);
57
	}
58

  
59
//***************************** TESTS *************************************//
60

  
61
	@Test
62
	public void testInit() {
63
//		assertNotNull("XXX should not be null", defaultImport);
64
		assertNotNull("nameService should not be null", nameService);
65
		assertNotNull("configurator should not be null", configurator);
66
	}
67

  
68
	@Test
69
	public void testDoInvokeWithoutExceptions() {
70
		ImportResult result = defaultImport.invoke(configurator);
71
		String report = result.createReport().toString();
72
		System.out.println(report);
73
	}
74

  
75
	@Test
76
	@Ignore("Import does not fully work yet")
77
	public void testDoInvoke() {
78
		boolean result = defaultImport.invoke(configurator).isSuccess();
79
		//TODO result is still false
80
		logger.warn("No real testing for ris import yet");
81
		Assert.assertTrue("Return value for import.invoke() should be true", result);
82
//		assertEquals("Number of TaxonNames should be 5", 5, nameService.count());
83
	}
84

  
85
    @Override
86
    public void createTestDataSet() throws FileNotFoundException {}
87
}
cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/reference/RisReferenceImportTest-input.ris
1

  
2

  
3

  
4
TY  - JOUR
5
T1  - Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea
6
AU  - Jongkind, Carel C. H.
7
Y1  - 2017/02/13
8
PY  - 2017
9
DA  - 2017/04/01
10
N1  - doi: 10.3372/wi.47.47105
11
DO  - 10.3372/wi.47.47105
12
T2  - Willdenowia
13
JF  - Willdenowia
14
JO  - Willdenowia
15
SP  - 43
16
EP  - 47
17
VL  - 47
18
IS  - 1
19
PB  - Botanic Garden and Botanical Museum Berlin (BGBM)
20
N2  - Abstract: A new species of Violaceae, Decorsella arborea Jongkind, is described and illustrated. The new species differs from the only other species in the genus, D. paradoxa A. Chev., by the larger size of the plants, smaller leaves, more slender flowers, and stamen filaments that are free for a much larger part. Both species are from the Guineo-Congolian forest of tropical Africa. The differences between Decorsella and Rinorea are discussed. Confirming recent reports, some species of Rinorea can have zygomorphic flowers and some of these can be almost equal in shape to Decorsella flowers. Citation: Jongkind C. C. H. 2017: Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea. ? Willdenowia 47: 43?47. doi: https://doi.org/10.3372/wi.47.47105 Version of record first published online on 13 February 2017 ahead of inclusion in April 2017 issue.
21
AB  - Abstract: A new species of Violaceae, Decorsella arborea Jongkind, is described and illustrated. The new species differs from the only other species in the genus, D. paradoxa A. Chev., by the larger size of the plants, smaller leaves, more slender flowers, and stamen filaments that are free for a much larger part. Both species are from the Guineo-Congolian forest of tropical Africa. The differences between Decorsella and Rinorea are discussed. Confirming recent reports, some species of Rinorea can have zygomorphic flowers and some of these can be almost equal in shape to Decorsella flowers. Citation: Jongkind C. C. H. 2017: Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea. ? Willdenowia 47: 43?47. doi: https://doi.org/10.3372/wi.47.47105 Version of record first published online on 13 February 2017 ahead of inclusion in April 2017 issue.
22
SN  - 0511-9618
23
M3  - doi: 10.3372/wi.47.47105
24
UR  - http://dx.doi.org/10.3372/wi.47.47105
25
Y2  - 2017/04/25
26
ER  - 

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