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Merge remote-tracking branch 'upstream/master' into removecommonslogging
* upstream/master: Extend RIS import with multiple fields (#3642) Fix ICAR fetcher test which resulted in build failure (#3654)
2 parents eff166b + 733da31 commit ea7744f

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‎CHANGELOG.md‎

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@@ -24,6 +24,7 @@ For more details refer to the [field mapping help page](http://help.jabref.org/e
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### Fixed
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- We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
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- Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
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- We fixed and extended the RIS import functionality to cover more fields. [#3634](https://github.com/JabRef/jabref/issues/3634) [#2607](https://github.com/JabRef/jabref/issues/2607)
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### Removed
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- We removed the [Look and Feels from JGoodies](http://www.jgoodies.com/freeware/libraries/looks/), because the open source version is not compatible with Java 9.

‎src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java‎

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@@ -19,12 +19,6 @@
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import org.jabref.model.entry.FieldName;
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import org.jabref.model.entry.Month;
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/**
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* Imports a Biblioscape Tag File. The format is described on
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* http://www.biblioscape.com/manual_bsp/Biblioscape_Tag_File.htm
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* Several Biblioscape field types are ignored. Others are only included in the BibTeX
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* field "comment".
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*/
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public class RisImporter extends Importer {
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private static final Pattern RECOGNIZED_FORMAT_PATTERN = Pattern.compile("TY - .*");
@@ -129,21 +123,21 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
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fields.put(FieldName.TITLE, fields.get(FieldName.TITLE).replaceAll("\\s+", " ")); // Normalize whitespaces
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} else if ("BT".equals(tag)) {
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fields.put(FieldName.BOOKTITLE, value);
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} else if ("T2".equals(tag) && (fields.get(FieldName.JOURNAL) == null || "".equals(fields.get(FieldName.JOURNAL)))) {
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} else if (("T2".equals(tag) || "J2".equals(tag) || "JA".equals(tag)) && (fields.get(FieldName.JOURNAL) == null || "".equals(fields.get(FieldName.JOURNAL)))) {
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//if there is no journal title, then put second title as journal title
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fields.put(FieldName.JOURNAL, value);
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} else if ("JO".equals(tag)) {
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} else if ("JO".equals(tag) || "J1".equals(tag) || "JF".equals(tag)) {
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//if this field appears then this should be the journal title
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fields.put(FieldName.JOURNAL, value);
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} else if ("T3".equals(tag)) {
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fields.put(FieldName.SERIES, value);
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} else if ("AU".equals(tag) || "A1".equals(tag)) {
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} else if ("AU".equals(tag) || "A1".equals(tag) || "A2".equals(tag) || "A3".equals(tag) || "A4".equals(tag)) {
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if ("".equals(author)) {
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author = value;
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} else {
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author += " and " + value;
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}
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} else if ("A2".equals(tag) || "A3".equals(tag) || "A4".equals(tag)) {
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} else if ("ED".equals(tag)) {
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if (editor.isEmpty()) {
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editor = value;
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} else {
@@ -161,7 +155,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
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fields.put("caption", value);
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} else if ("DB".equals(tag)) {
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fields.put("database", value);
164-
} else if ("IS".equals(tag)) {
158+
} else if ("IS".equals(tag) || "AN".equals(tag) || "C7".equals(tag) || "M1".equals(tag)) {
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fields.put(FieldName.NUMBER, value);
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} else if ("SP".equals(tag)) {
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startPage = value;
@@ -171,7 +165,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
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} else {
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fields.put(FieldName.PUBLISHER, value);
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}
174-
} else if ("AD".equals(tag) || "CY".equals(tag)) {
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} else if ("AD".equals(tag) || "CY".equals(tag) || "PP".equals(tag)) {
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fields.put(FieldName.ADDRESS, value);
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} else if ("EP".equals(tag)) {
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endPage = value;
@@ -191,9 +185,9 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
191185
} else {
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fields.put(FieldName.ABSTRACT, oldAb + OS.NEWLINE + value);
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}
194-
} else if ("UR".equals(tag)) {
188+
} else if ("UR".equals(tag) || "L2".equals(tag) || "LK".equals(tag)) {
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fields.put(FieldName.URL, value);
196-
} else if (("Y1".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4)) {
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} else if (("Y1".equals(tag) || "Y2".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4)) {
197191
fields.put(FieldName.YEAR, value.substring(0, 4));
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String[] parts = value.split("/");
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if ((parts.length > 1) && !parts[1].isEmpty()) {
@@ -216,12 +210,39 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
216210
comment = comment + " ";
217211
}
218212
comment = comment + value;
213+
} else if ("M3".equals(tag) || "DO".equals(tag)) {
214+
addDoi(fields, value);
215+
} else if ("C3".equals(tag)) {
216+
fields.put(FieldName.EVENTTITLE, value);
217+
} else if ("N1".equals(tag) || "RN".equals(tag)) {
218+
fields.put(FieldName.NOTE, value);
219+
} else if ("ST".equals(tag)) {
220+
fields.put(FieldName.SHORTTITLE, value);
221+
} else if ("C2".equals(tag)) {
222+
fields.put(FieldName.EPRINT, value);
223+
fields.put(FieldName.EPRINTTYPE, "pubmed");
224+
} else if ("TA".equals(tag)) {
225+
fields.put(FieldName.TRANSLATOR, value);
219226
}
220-
// Added ID import 2005.12.01, Morten Alver:
221-
else if ("ID".equals(tag)) {
227+
// fields for which there is no direct mapping in the bibtext standard
228+
else if ("AV".equals(tag)) {
229+
fields.put("archive_location", value);
230+
} else if ("CN".equals(tag) || "VO".equals(tag)) {
231+
fields.put("call-number", value);
232+
} else if ("DB".equals(tag)) {
233+
fields.put("archive", value);
234+
} else if ("NV".equals(tag)) {
235+
fields.put("number-of-volumes", value);
236+
} else if ("OP".equals(tag)) {
237+
fields.put("original-title", value);
238+
} else if ("RI".equals(tag)) {
239+
fields.put("reviewed-title", value);
240+
} else if ("RP".equals(tag)) {
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fields.put("status", value);
242+
} else if ("SE".equals(tag)) {
243+
fields.put("section", value);
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} else if ("ID".equals(tag)) {
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fields.put("refid", value);
223-
} else if ("M3".equals(tag) || "DO".equals(tag)) {
224-
addDoi(fields, value);
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}
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}
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// fix authors
@@ -245,11 +266,11 @@ else if ("ID".equals(tag)) {
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// create one here
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// type is set in the loop above
248-
BibEntry b = new BibEntry(type);
249-
b.setField(fields);
269+
BibEntry entry = new BibEntry(type);
270+
entry.setField(fields);
250271
// month has a special treatment as we use the separate method "setMonth" of BibEntry instead of directly setting the value
251-
month.ifPresent(parsedMonth -> b.setMonth(parsedMonth));
252-
bibitems.add(b);
272+
month.ifPresent(parsedMonth -> entry.setMonth(parsedMonth));
273+
bibitems.add(entry);
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}
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return new ParserResult(bibitems);

‎src/main/java/org/jabref/model/entry/FieldName.java‎

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@@ -110,6 +110,7 @@ public class FieldName {
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public static final String SERIES = "series";
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public static final String SHORTAUTHOR = "shortauthor";
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public static final String SHORTEDITOR = "shorteditor";
113+
public static final String SHORTTITLE = "shorttitle";
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public static final String SORTNAME = "sortname";
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public static final String SUBTITLE = "subtitle";
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public static final String TITLE = "title";

‎src/test/java/org/jabref/logic/importer/fetcher/IacrEprintFetcherTest.java‎

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@@ -71,12 +71,12 @@ public void setUp() {
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delgado2017.setField("bibtexkey", "cryptoeprint:2017:1095");
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delgado2017.setField(FieldName.ABSTRACT, "dummy");
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delgado2017.setField(FieldName.AUTHOR, "Sergi Delgado-Segura and Cristina Pérez-Solà and Guillermo Navarro-Arribas and Jordi Herrera-Joancomartí");
74-
delgado2017.setField(FieldName.DATE, "2017-11-10");
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delgado2017.setField(FieldName.DATE, "2018-01-19");
7575
delgado2017.setField(FieldName.HOWPUBLISHED, "Cryptology ePrint Archive, Report 2017/1095");
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delgado2017.setField(FieldName.NOTE, "\\url{https://eprint.iacr.org/2017/1095}");
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delgado2017.setField(FieldName.TITLE, "Analysis of the Bitcoin UTXO set");
78-
delgado2017.setField(FieldName.URL, "https://eprint.iacr.org/2017/1095/20171110:183926");
79-
delgado2017.setField(FieldName.VERSION, "20171110:183926");
78+
delgado2017.setField(FieldName.URL, "https://eprint.iacr.org/2017/1095/20180119:113352");
79+
delgado2017.setField(FieldName.VERSION, "20180119:113352");
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delgado2017.setField(FieldName.YEAR, "2017");
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}
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‎src/test/java/org/jabref/logic/importer/fileformat/RISImporterTestFiles.java‎

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@@ -40,7 +40,7 @@ public void setUp() throws URISyntaxException {
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@Parameters(name = "{0}")
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public static Collection<String> fileNames() {
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return Arrays.asList("RisImporterTest1", "RisImporterTest3", "RisImporterTest4a", "RisImporterTest4b",
43-
"RisImporterTest4c", "RisImporterTest5a", "RisImporterTest5b", "RisImporterTest6",
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"RisImporterTest4c", "RisImporterTest5a", "RisImporterTest5b", "RisImporterTest6", "RisImporterTest7",
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"RisImporterTestDoiAndJournalTitle", "RisImporterTestScopus", "RisImporterTestScience");
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}
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‎src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest1.bib‎

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@@ -2,13 +2,12 @@ @phdthesis{
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abstract = {abstract0
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abstract1},
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address = {32 peralta avenue los gatos ca},
5-
author = {Cocke and Harrison, Warren Levenshtein Morris},
6-
booktitle = {kmptnz},
5+
author = {Cocke and Harrison, Warren Levenshtein Morris and Rives and Kasami},
6+
booktitle = {kmptne},
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comment = {comment0
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comment1
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comment2},
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doi = {whatever},
11-
editor = {Rives and Kasami},
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issn = {kmptns},
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journal = {kmptnd},
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keywords = {keyword0, keyword1},

‎src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib‎

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@@ -4,7 +4,8 @@ @incollection{
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doi = {10.1201/b19107-2},
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issn = {978-1-4822-5326-9},
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journal = {Dermoscopy Image Analysis},
7-
month = {#sep#},
7+
month = {#nov#},
8+
number = {0},
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pages = {1-22},
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publisher = {CRC Press},
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series = {Digital Imaging and Computer Vision},

‎src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest4b.bib‎

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@@ -1,5 +1,6 @@
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@book{,
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address = {Cambridge},
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editor = {Robinson, W. F. and Huxtable, C. R. R.},
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publisher = {Cambridge University Press},
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refid = {robinson},
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title = {Clinicopathologic Principles For Veterinary Medicine},

‎src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest5a.bib‎

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@@ -5,6 +5,7 @@ @article{
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issn = {0032-5910},
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journal = {Powder Technology},
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keywords = {ibuprofen beta cyclodextrin inclusion complex tablet},
8+
number = {Copyright (C) 2016 American Chemical Society (ACS). All Rights Reserved.},
89
pages = {245--251},
910
publisher = {Elsevier B.V.},
1011
title = {Release profile of ibuprofen in β-cyclodextrin complexes from two different solid dosage forms.},

‎src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib‎

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@@ -5,6 +5,7 @@ @article{
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issn = {1537-744X},
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journal = {The Scientific World Journal},
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month = {#mar#},
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number = {PMC3654245},
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pages = {219840},
910
publisher = {Hindawi Publishing Corporation},
1011
title = {Chelation: Harnessing and Enhancing Heavy Metal Detoxification--A Review},

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