Fix DOI import in RIS Importer

Use DOI parse and only add valid DOIs Follow up from #6557 Fixes #6530
JabRef · Jun 6, 2020 · 835e778 · 835e778
1 parent 9faf500
commit 835e778
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Showing 9 changed files with 61 additions and 61 deletions.
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
@@ -9,7 +9,6 @@
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Locale;
 import java.util.Map;
 import java.util.Optional;
 import java.util.regex.Pattern;
@@ -24,6 +23,7 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.field.UnknownField;
+import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.entry.types.EntryType;
 import org.jabref.model.entry.types.IEEETranEntryType;
 import org.jabref.model.entry.types.StandardEntryType;
@@ -204,7 +204,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                         }
                     } else if ("UR".equals(tag) || "L2".equals(tag) || "LK".equals(tag)) {
                         fields.put(StandardField.URL, value);
-                    } else if ((tagPriority = dateTags.indexOf(tag)) != -1 && value.length() >= 4) {
+                    } else if (((tagPriority = dateTags.indexOf(tag)) != -1) && (value.length() >= 4)) {
 
                         if (tagPriority < datePriority) {
                             String year = value.substring(0, 4);
@@ -312,12 +312,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
     }
 
   private void addDoi(Map<Field, String> hm, String val) {
-    String doi = val.toLowerCase(Locale.ENGLISH);
-    if (doi.startsWith("doi:")) {
-      doi = doi.replaceAll("(?i)doi:", "").trim();
-      hm.put(StandardField.DOI, doi);
-    } else {
-      hm.put(StandardField.DOI, doi);
-    }
+      Optional<DOI> parsedDoi = DOI.parse(val);
+      parsedDoi.ifPresent(doi -> hm.put(StandardField.DOI, doi.getDOI()));
   }
 }
diff --git a/src/test/java/org/jabref/logic/importer/RisImporterTest.java b/src/test/java/org/jabref/logic/importer/RisImporterTest.java
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest1.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest1.bib
@@ -7,7 +7,6 @@ @phdthesis{
   comment = {comment0
 comment1
 comment2},
-  doi = {whatever},
   issn = {kmptns},
   journal = {kmptnd},
   keywords = {keyword0, keyword1},

diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest5a.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest5a.bib
@@ -2,6 +2,7 @@ @article{
   abstract = {The objective of this work was to develop solid dosage forms using powders contg. inclusion complexes (ibuprofen with β-cyclodextrin) which were used to produce tablets (direct compression without addnl. excipients) and pellets (extrusion/spheronization) from wet mass contg. 40% (wt./wt.) of microcryst. cellulose.  The pellets also demonstrated that during prepn. of the wet mass, the inclusion process occurred in a same yield that when pre-complexation was used.  The particles characteristics were evaluated after being obtained through different complexation methods.  The results showed that the tensile strength and profile dissoln. were as expected for both dosage forms.  Tablets contg. inclusion complexes showed higher soly. when compared with a ref. formulation and with two com. formulations.  The ibuprofen released from the two pellets formulations didn't show relevant differences between them.  The drug released was analyzed considering different dissoln. parameters.  The advantages of these new methodologies can be summarized as: (a) tablets were produced at a lower cost for the total process; and (b) in the pellet's prepn. there was no need of the previous complexation method resulting in a decrease in time and energy required. [on SciFinder(R)]},
   author = {Salustio, P. J. and Feio, G. and Figueirinhas, J. L. and Cabral-Marques, H. M. and Costa, P. C. and Pinto, J. F.},
   comment = {CAPLUS AN 2012:446586(Journal; Online Computer File)},
+  doi = {10.1016/j.powtec.2012.01.008},
   issn = {0032-5910},
   journal = {Powder Technology},
   keywords = {ibuprofen beta cyclodextrin inclusion complex tablet},

diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
@@ -1,6 +1,7 @@
 @article{,
   author = {Sears, Margaret E.},
   comment = {23690738[pmid]},
+  doi = {10.1155/2013/219840},
   database = {PMC},
   issn = {1537-744X},
   journal = {The Scientific World Journal},

diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestDOI.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestDOI.bib
@@ -0,0 +1,22 @@
+% Encoding: UTF-8
+
+@Article{,
+  author    = {Jung, Sang In and Lee, Na Kyung and Kang, Kyung Woo and Kim, Kyoung and Lee, Do Youn},
+  title     = {The effect of smartphone usage time on posture and respiratory function},
+  doi       = {10.1589/jpts.28.186},
+  issn      = {2187-5626},
+  language  = {eng},
+  number    = {26957754},
+  pages     = {186--189},
+  url       = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756000/},
+  volume    = {28},
+  comment   = {26957754[pmid]
+PMC4756000[pmcid]},
+  database  = {PubMed},
+  edition   = {2016/01/30},
+  journal   = {Journal of physical therapy science},
+  keywords  = {Posture, Respiratory function, Smartphone},
+  month     = jan,
+  publisher = {The Society of Physical Therapy Science},
+  year      = {2016},
+}
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestDOI.ris b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestDOI.ris
@@ -0,0 +1,31 @@
+TY  - JOUR
+DB  - PubMed
+AU  - Jung, Sang In
+AU  - Lee, Na Kyung
+AU  - Kang, Kyung Woo
+AU  - Kim, Kyoung
+AU  - Lee, Do Youn
+T1  - The effect of smartphone usage time on posture and respiratory function
+LA  - eng
+SN  - 0915-5287
+SN  - 2187-5626
+Y1  - 2016/01/
+ET  - 2016/01/30
+SP  - 186
+EP  - 189
+VL  - 28
+IS  - 1
+AN  - 26957754
+UR  - https://pubmed.ncbi.nlm.nih.gov/26957754
+DO  - 10.1589/jpts.28.186
+L2  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756000/
+U1  - 26957754[pmid]
+U2  - PMC4756000[pmcid]
+U4  - jpts-2015-817[PII]
+J2  - J Phys Ther Sci
+JF  - Journal of physical therapy science
+KW  - Posture
+KW  - Respiratory function
+KW  - Smartphone
+PB  - The Society of Physical Therapy Science
+ER  - 
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestScience.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestScience.bib
@@ -1,5 +1,6 @@
 @Article{,
   author        = {Ghosh, Chanchal and Basu, Joysurya and Ramachandran, Divakar and Mohandas, E.},
+  doi = {10.1016/j.actamat.2016.09.028},
   title         = {Phase separation and ω transformation in binary V-Ti and ternary V-Ti-Cr alloys},
   journal       = {Acta Materialia},
   year          = {2016},

diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestScopus.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTestScopus.bib
@@ -10,6 +10,7 @@ @Article{
   comment  = {Cited By :44
 Export Date: 1 April 2016},
   database = {Scopus},
+  doi = {10.1016/j.jmps.2004.03.010},
   keywords = {Composite, Inclusions, Statistical distribution, Transverse isotropy},
   url      = {http://www.scopus.com/inward/record.url?eid=2-s2.0-4544289390&partnerID=40&md5=ad1a4baab95650b103a3467b787b83aa},
 }