Fix for issue 6199: EndNote .xml import to JabRef: PDF links are not …

…imported correctly. (JabRef#6199)
devinluo27 · Apr 24, 2021 · 40245c7 · 40245c7
1 parent 23d7573
commit 40245c7
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Showing 6 changed files with 380 additions and 5 deletions.
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/EndnoteXmlImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/EndnoteXmlImporter.java
@@ -260,10 +260,32 @@ private Optional<String> getUrl(Record record) {
     }
 
     private Optional<String> getUrlValue(Url url) {
-        return Optional.ofNullable(url)
-                       .map(Url::getStyle)
-                       .map(Style::getContent)
-                       .map(this::clean);
+        Optional<List<Object>> urlContent = Optional.ofNullable(url).map(Url::getContent);
+        List<Object> list = urlContent.orElse(null);
+        Optional<String> ret;
+        if (list==null || list.size() == 0) {
+            return Optional.empty();
+        }
+        else {
+            boolean isStyleExist = false;
+            int style_index = -1;
+            for(int i =0 ; i < list.size(); i++) {
+                if(list.get(i) instanceof Style){
+                    isStyleExist = true;
+                    style_index = i;
+                }
+            }
+            if (!isStyleExist) {
+                ret =  Optional.ofNullable((String) list.get(0))
+                        .map(this::clean);
+            }
+            else {
+                ret = Optional.ofNullable((Style)list.get(style_index))
+                        .map(Style::getContent)
+                        .map(this::clean);
+            }
+        }
+        return ret;
     }
 
     private List<String> getKeywords(Record record) {

diff --git a/src/main/resources/xjc/endnote/endnote.xsd b/src/main/resources/xjc/endnote/endnote.xsd
@@ -668,7 +668,7 @@
         </xs:complexType>
     </xs:element>
     <xs:element name="url">
-        <xs:complexType>
+        <xs:complexType mixed="true">
             <xs:sequence>
                 <xs:element minOccurs="0" ref="style"/>
             </xs:sequence>

diff --git a/...resources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle.bib b/...resources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle.bib
@@ -0,0 +1,16 @@
+@article{,
+  abstract = {test abstract},
+  author = {Ahmad, AS and Ormiston-Smith, N and Sasieni, PD},
+  doi = {10.1038/bjc.2014.606},
+  file = {:file\://localhost/Users/user/Documents/Bookends/Attachments/Ahmad%20et%20al%202015.pdf:PDF},
+  isbn = {1532-1827 (Electronic) 0007-0920 (Linking)},
+  keywords = {Age Factors; Aged; Aged, 80 and over; Female; Great Britain/epidemiology; Humans; Male; Middle Aged; Models, Statistical; Neoplasms/*epidemiology; Risk Assessment; Risk Factors; Sex Characteristics},
+  number = {5},
+  pages = {943-7},
+  title = {Trends in the lifetime risk of developing cancer in Great Britain: comparison of risk for those born from 1930 to 1960},
+  volume = {112},
+  year = {2015},
+  journal = {Br J Cancer},
+  note = {some notes},
+  url = {http://www.ncbi.nlm.nih.gov/pubmed/25647015},
+}
diff --git a/...resources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle.xml b/...resources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle.xml
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xml>
+    <records>
+        <record>
+            <database name="Library1.bdb" path="/Users/user/Documents/Bookends/Library1.bdb">Library1.bdb</database>
+            <source-app name="Bookends" version="13.0.5">Bookends</source-app>
+            <rec-number>2954</rec-number>
+            <ref-type name="Journal Article">17</ref-type>
+            <contributors>
+                <authors>
+                    <author>
+                        <style face="normal" size="100%">Ahmad, AS</style>
+                    </author>
+                    <author>
+                        <style face="normal" size="100%">Ormiston-Smith, N</style>
+                    </author>
+                    <author>
+                        <style face="normal" size="100%">Sasieni, PD</style>
+                    </author>
+                </authors>
+            </contributors>
+            <auth-address>
+                <style face="normal" size="100%">Queen Mary University of London, Centre for Cancer Prevention, Wolfson
+                    Institute of Preventive Medicine, Charterhouse Square, London EC1M 6BQ, UK.&#xA;Cancer Research UK,
+                    Head of Statistical Information, Angel Building, 407 St John Street, London EC1V 4AD, UK.
+                </style>
+            </auth-address>
+            <titles>
+                <title>
+                    <style face="normal" size="100%">Trends in the lifetime risk of developing cancer in Great Britain:
+                        comparison of risk for those born from 1930 to 1960
+                    </style>
+                </title>
+                <secondary-title>
+                    <style face="normal" size="100%">Br J Cancer</style>
+                </secondary-title>
+            </titles>
+            <pages>
+                <style face="normal" size="100%">943-7</style>
+            </pages>
+            <number>
+                <style face="normal" size="100%">5</style>
+            </number>
+            <volume>
+                <style face="normal" size="100%">112</style>
+            </volume>
+            <dates>
+                <year>
+                    <style face="normal" size="100%">2015</style>
+                </year>
+                <pub-dates>
+                    <date>
+                        <style face="normal" size="100%">Mar 3</style>
+                    </date>
+                </pub-dates>
+            </dates>
+            <keywords>
+                <keyword>
+                    <style face="normal" size="100%">Age Factors</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Aged</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Aged, 80 and over</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Female</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Great Britain/epidemiology</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Humans</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Male</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Middle Aged</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Models, Statistical</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Neoplasms/*epidemiology</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Risk Assessment</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Risk Factors</style>
+                </keyword>
+                <keyword>
+                    <style face="normal" size="100%">Sex Characteristics</style>
+                </keyword>
+            </keywords>
+            <abstract>
+                <style face="normal" size="100%">test abstract
+                </style>
+            </abstract>
+            <notes>
+                <style face="normal" size="100%">some notes
+                </style>
+            </notes>
+            <urls>
+                <related-urls>
+                    <url>
+                        <style face="normal" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/25647015</style>
+                    </url>
+                </related-urls>
+                <pdf-urls>
+                    <url>
+                            file://localhost/Users/user/Documents/Bookends/Attachments/Ahmad%20et%20al%202015.pdf
+                    </url>
+                </pdf-urls>
+            </urls>
+            <isbn>
+                <style face="normal" size="100%">1532-1827 (Electronic)&#xD;0007-0920 (Linking)</style>
+            </isbn>
+            <electronic-resource-num>
+                <style face="normal" size="100%">10.1038/bjc.2014.606</style>
+            </electronic-resource-num>
+            <accession-num>
+                <style face="normal" size="100%">25647015</style>
+            </accession-num>
+        </record>
+    </records>
+</xml>
diff --git a/...esources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle2.bib b/...esources/org/jabref/logic/importer/fileformat/EndnoteXmlImporterTest_WithoutUrlStyle2.bib
@@ -0,0 +1,24 @@
+@article{,
+  author = {Chapman, A. G.},
+  isbn = {0012-9658},
+  number = {1},
+  pages = {93-105},
+  title = {An ecological basis for reforestation of submariginal lands in the Central Hardwood Region},
+  volume = {18},
+  year = {1937},
+  journal = {Ecology},
+  note = {some notes},
+  url = {<Go to ISI>://000200148800007}
+}
+@book{,
+  author = {Strohecker, H. F.},
+  isbn = {0012-9658},
+  number = {1},
+  journal = {Ecology},
+  note = {some other notes},
+  pages = {162-168},
+  title = {A survey of soil temperatures in the Chicago area},
+  volume = {18},
+  url = {<Go to ISI>://000200148800014},
+  year = {1937}
+}