import PMID field in Pubmed (#11513)

* import PMID field in Pubmed Fixes #11488 * fix tests --------- Co-authored-by: Carl Christian Snethlage <[email protected]>
JabRef · Jul 18, 2024 · 234ee2e · 234ee2e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
 - The 'Check for updates' menu bar button is now always enabled. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
 

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
@@ -149,6 +149,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
 
                 // store the fields in a map
                 Map<String, Field> hashMap = new HashMap<>();
+                hashMap.put("PMID", StandardField.PMID);
                 hashMap.put("PG", StandardField.PAGES);
                 hashMap.put("PL", StandardField.ADDRESS);
                 hashMap.put("PHST", new UnknownField("history"));

diff --git a/src/test/java/org/jabref/logic/importer/fileformat/MedlinePlainImporterTest.java b/src/test/java/org/jabref/logic/importer/fileformat/MedlinePlainImporterTest.java
@@ -117,11 +117,13 @@ void importMultipleEntriesInSingleFile() throws IOException, URISyntaxException
         assertEquals(Optional.of("Inproceedings book title"), testEntry.getField(StandardField.BOOKTITLE));
 
         BibEntry expectedEntry5 = new BibEntry(StandardEntryType.Proceedings)
-                .withField(StandardField.KEYWORDS, "Female");
+                .withField(StandardField.KEYWORDS, "Female")
+                        .withField(StandardField.PMID, "96578310");
         assertEquals(expectedEntry5, entries.get(5));
 
         BibEntry expectedEntry6 = new BibEntry(StandardEntryType.Misc)
-                .withField(StandardField.KEYWORDS, "Female");
+                .withField(StandardField.KEYWORDS, "Female")
+                        .withField(StandardField.PMID, "45984220");
         assertEquals(expectedEntry6, entries.get(6));
     }
 
@@ -158,19 +160,49 @@ private void assertImportOfMedlineFileEqualsBibtexFile(String medlineFile, Strin
 
     @Test
     void multiLineComments() throws IOException {
-        try (BufferedReader reader = readerForString("PMID-22664220" + "\n" + "CON - Comment1" + "\n" + "CIN - Comment2"
-                + "\n" + "EIN - Comment3" + "\n" + "EFR - Comment4" + "\n" + "CRI - Comment5" + "\n" + "CRF - Comment6"
-                + "\n" + "PRIN- Comment7" + "\n" + "PROF- Comment8" + "\n" + "RPI - Comment9" + "\n" + "RPF - Comment10"
-                + "\n" + "RIN - Comment11" + "\n" + "ROF - Comment12" + "\n" + "UIN - Comment13" + "\n"
-                + "UOF - Comment14" + "\n" + "SPIN- Comment15" + "\n" + "ORI - Comment16")) {
+        try (BufferedReader reader = readerForString("""
+                PMID-22664220
+                CON - Comment1
+                CIN - Comment2\
+
+                EIN - Comment3
+                EFR - Comment4
+                CRI - Comment5
+                CRF - Comment6\
+
+                PRIN- Comment7
+                PROF- Comment8
+                RPI - Comment9
+                RPF - Comment10\
+
+                RIN - Comment11
+                ROF - Comment12
+                UIN - Comment13
+                UOF - Comment14
+                SPIN- Comment15
+                ORI - Comment16""")) {
             List<BibEntry> actualEntries = importer.importDatabase(reader).getDatabase().getEntries();
             BibEntry expectedEntry = new BibEntry();
 
+            expectedEntry.setField(StandardField.PMID, "22664220");
             expectedEntry.setField(StandardField.COMMENT,
-                    "Comment1" + "\n" + "Comment2" + "\n" + "Comment3" + "\n" + "Comment4" + "\n" + "Comment5" + "\n"
-                            + "Comment6" + "\n" + "Comment7" + "\n" + "Comment8" + "\n" + "Comment9" + "\n"
-                            + "Comment10" + "\n" + "Comment11" + "\n" + "Comment12" + "\n" + "Comment13" + "\n"
-                            + "Comment14" + "\n" + "Comment15" + "\n" + "Comment16");
+                    """
+                            Comment1
+                            Comment2
+                            Comment3
+                            Comment4
+                            Comment5
+                            Comment6
+                            Comment7
+                            Comment8
+                            Comment9
+                            Comment10
+                            Comment11
+                            Comment12
+                            Comment13
+                            Comment14
+                            Comment15
+                            Comment16""");
             assertEquals(Collections.singletonList(expectedEntry), actualEntries);
         }
     }
@@ -184,6 +216,7 @@ void keyWords() throws IOException {
             List<BibEntry> actualEntries = importer.importDatabase(reader).getDatabase().getEntries();
 
             BibEntry expectedEntry = new BibEntry();
+            expectedEntry.setField(StandardField.PMID, "22664795");
             expectedEntry.setField(StandardField.KEYWORDS, "Female, Male");
 
             assertEquals(Collections.singletonList(expectedEntry), actualEntries);
@@ -200,7 +233,7 @@ void withNbibFile() throws IOException, URISyntaxException {
     }
 
     @Test
-    void withMultipleEntries() throws IOException, URISyntaxException {
+    void withMultipleEntriesInvalidFormat() throws IOException, URISyntaxException {
         Path file = Path.of(MedlinePlainImporter.class.getResource("MedlinePlainImporterStringOutOfBounds.txt").toURI());
 
         List<BibEntry> entries = importer.importDatabase(file).getDatabase().getEntries();
@@ -229,14 +262,20 @@ void nullReader() throws IOException {
 
     @Test
     void allArticleTypes() throws IOException {
-        try (BufferedReader reader = readerForString("PMID-22664795" + "\n" + "MH  - Female\n" + "PT  - journal article"
-                + "\n" + "PT  - classical article" + "\n" + "PT  - corrected and republished article" + "\n"
-                + "PT  - introductory journal article" + "\n" + "PT  - newspaper article")) {
+        try (BufferedReader reader = readerForString("""
+                PMID-22664795
+                MH  - Female
+                PT  - journal article\
+
+                PT  - classical article
+                PT  - corrected and republished article
+                PT  - introductory journal article
+                PT  - newspaper article""")) {
             List<BibEntry> actualEntries = importer.importDatabase(reader).getDatabase().getEntries();
 
-            BibEntry expectedEntry = new BibEntry();
-            expectedEntry.setType(StandardEntryType.Article);
-            expectedEntry.setField(StandardField.KEYWORDS, "Female");
+            BibEntry expectedEntry = new BibEntry(StandardEntryType.Article)
+                    .withField(StandardField.KEYWORDS, "Female")
+                    .withField(StandardField.PMID, "22664795");
 
             assertEquals(Collections.singletonList(expectedEntry), actualEntries);
         }

diff --git a/.../resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterStringOutOfBounds.bib b/.../resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterStringOutOfBounds.bib
@@ -1,6 +1,9 @@
 @misc{,
-  title = {This is a test title}
+  title = {This is a test title},
+  pmid = {27433151 SO  invalid line},
+
 }
 @misc{,
-  title = {This is also a test title}
+  title = {This is also a test title},
+  pmid = {27394443 SO- another invalid line},
 }
diff --git a/.../resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestCompleteEntry.bib b/.../resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestCompleteEntry.bib
@@ -15,6 +15,7 @@ @article{
   other-id = {NLM: PMC4513071},
   owner = {NLM},
   pages = {454-81},
+  pmid = {20481061},
   print-issn = {0955-2359},
   publication-status = {ppublish},
   revised = {20150731},

diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestDOI.bib b/src/test/resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestDOI.bib
@@ -1,3 +1,4 @@
 @TechReport{,
-  doi                    = {10.1016/j.cpr.2005.02.002}
+  doi                    = {10.1016/j.cpr.2005.02.002},
+  pmid                   = {22664220},
 }
diff --git a/...t/resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestInproceeding.bib b/...t/resources/org/jabref/logic/importer/fileformat/MedlinePlainImporterTestInproceeding.bib
@@ -1,3 +1,5 @@
 @InProceedings{,
-  Booktitle                = {Inproceedings book title}
+  Booktitle                = {Inproceedings book title},
+  pmid                     = {22664238},
+
 }
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/NbibImporterTest.bib b/src/test/resources/org/jabref/logic/importer/fileformat/NbibImporterTest.bib
@@ -29,6 +29,7 @@ @article{
   other-abstract = {other abstract infos},
   owner = {NLM},
   pages = {67},
+  pmid = {27169098},
   publication-status = {epublish},
   registry-number = {123456789},
   second-id = {12563},