Hyperlink DOIs to preferred resolver

petermr · Nov 19, 2019 · 33c1453 · 33c1453
1 parent ebfeeb5
commit 33c1453
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diff --git a/src/main/java/org/contentmine/cproject/metadata/CMDOI.java b/src/main/java/org/contentmine/cproject/metadata/CMDOI.java
@@ -17,16 +17,16 @@ public class CMDOI extends AbstractCM {
 
 	/**
 	 * 
-http://dx.doi.org/10.5539/cis.v9n2p126
-http://dx.doi.org/10.1530/edm-16-0003
-http://dx.doi.org/10.12968/bjsn.2016.11.4.166
-http://dx.doi.org/10.14358/pers.82.5.320
-http://dx.doi.org/10.3109/10715762.2016.1162299
-http://dx.doi.org/10.1127/ejm/2015/0027-2502
-http://dx.doi.org/10.7467/ksae.2016.24.3.285
-http://dx.doi.org/10.20488/austd.22645
-http://dx.doi.org/10.1177/2150135116645604
-http://dx.doi.org/10.1525/irqr.2016.9.1.29
+https://doi.org/10.5539/cis.v9n2p126
+https://doi.org/10.1530/edm-16-0003
+https://doi.org/10.12968/bjsn.2016.11.4.166
+https://doi.org/10.14358/pers.82.5.320
+https://doi.org/10.3109/10715762.2016.1162299
+https://doi.org/10.1127/ejm/2015/0027-2502
+https://doi.org/10.7467/ksae.2016.24.3.285
+https://doi.org/10.20488/austd.22645
+https://doi.org/10.1177/2150135116645604
+https://doi.org/10.1525/irqr.2016.9.1.29
 	 */
 
 	static Pattern PATTERN = Pattern.compile("https?://dx\\.doi\\.org/(10\\.\\d{3,8})/(.*)");

diff --git a/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java b/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java
@@ -29,8 +29,8 @@ public class DOIResolver {
 		LOG.setLevel(Level.DEBUG);
 	}
 
-	private static final String HTTP_DOI_ORG_API_HANDLES = "http://doi.org/api/handles/";
-	private static final String HTTP_DX_DOI_ORG = "http://dx.doi.org/";
+	private static final String HTTP_DOI_ORG_API_HANDLES = "https://doi.org/api/handles/";
+	private static final String HTTP_DX_DOI_ORG = "https://doi.org/";
 	private static final String VALUE = "value";
 	private static final String DATA = "data";
 	private static final String VALUES = "values";

diff --git a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java
@@ -19,7 +19,7 @@
  */
 public class QSRecord {
 
-	private static final String HTTP_DX_DOI_ORG = "http://dx.doi.org/";
+	private static final String HTTP_DX_DOI_ORG = "https://doi.org/";
 	private static final Logger LOG = Logger.getLogger(QSRecord.class);
 	static {
 		LOG.setLevel(Level.DEBUG);

diff --git a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java
@@ -39,7 +39,7 @@ public class QuickscrapeLog {
 
 	// info: URL processed
 	private final static Pattern OUTER = Pattern.compile("(trace|debug|info|warn|error)\\:\\s(.*)");
-	// [debug] [phantom] opening url: http://dx.doi.org/10.1093/mnras/stw468, HTTP GET
+	// [debug] [phantom] opening url: https://doi.org/10.1093/mnras/stw468, HTTP GET
 	private final static Pattern INNER1 = Pattern.compile("\\s*\\[(trace|debug|info|warn|error)\\]\\s+\\[(phantom)\\]\\s+(.*)");
 //	private final static Pattern INNER2 = Pattern.compile("\\[(^\\])+\\]\\s+(.*)");
 

diff --git a/src/main/java/org/contentmine/cproject/util/CMineUtil.java b/src/main/java/org/contentmine/cproject/util/CMineUtil.java
@@ -43,7 +43,7 @@ public class CMineUtil {
 		LOG.setLevel(Level.DEBUG);
 	}
 
-	private static final String HTTP_DX_DOI_ORG2 = "http://dx.doi.org/";
+	private static final String HTTP_DX_DOI_ORG2 = "https://doi.org/";
 	private static final String HTML_START = "<";
 	private static final String PDF_START = "%PDF";
 	private static final String URL_PUNCT = "[\\/\\$\\%\\*\\(\\)\\[\\]]";
@@ -310,7 +310,7 @@ public static String stripChars(String s, String regex, String replace) {
 		return s == null ? null : s.replaceAll(regex, replace);
 	}
 
-	/** removes "http://dx.doi.org/" from start of string.
+	/** removes "https://doi.org/" from start of string.
 	 * 
 	 * @param string
 	 * @return

diff --git a/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java b/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java
@@ -87,7 +87,7 @@ public class EPMCResultsJsonEntry extends AbstractMetadata {
 		new CellRenderer(SOURCE).setVisible(false),
 		new CellRenderer(AUTHOR_STRING).setBrief(20),
 		new CellRenderer(ABSTRACT_TEXT).setBrief(20),
-		new CellRenderer(DOI).setHref0("http://doi.org/"),
+		new CellRenderer(DOI).setHref0("https://doi.org/"),
 		new CellRenderer(ID).setVisible(false),
 		new CellRenderer(PMID).setVisible(false),
 		new CellRenderer(PMCID).setHref0("foo/").setHref1("/bar").setVisible(false),

diff --git a/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml b/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml
diff --git a/src/main/resources/org/contentmine/ami/plugins/dictionary/organization.xml b/src/main/resources/org/contentmine/ami/plugins/dictionary/organization.xml
diff --git a/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml b/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml
@@ -8,7 +8,7 @@
               Volume 2014 (2014), Article ID 801626, 8 pages
               <br></br>
           // doi
-              <a href="http://dx.doi.org/10.1155/2014/801626">http://dx.doi.org/10.1155/2014/801626</a>
+              <a href="https://doi.org/10.1155/2014/801626">https://doi.org/10.1155/2014/801626</a>
             </pre>
             // articleType
             <div class="article_type">Research Article</div>

diff --git a/src/main/resources/org/contentmine/graphics/html/badhtml1.html b/src/main/resources/org/contentmine/graphics/html/badhtml1.html
diff --git a/src/main/resources/org/contentmine/graphics/html/badhtml1a.html b/src/main/resources/org/contentmine/graphics/html/badhtml1a.html
@@ -182,7 +182,7 @@
                      <em>Arts</em> 
                      <b>2014</b>, 
                      <em>3</em>(1), 27-45; doi:
-                     <a href="http://dx.doi.org/10.3390/arts3010027">10.3390/arts3010027</a>
+                     <a href="https://doi.org/10.3390/arts3010027">10.3390/arts3010027</a>
                     </div> 
                     <div class="pubdates">
                      Received: 30 September 2013; in revised form: 28 October 2013 / Accepted: 1 December 2013 / Published: 3 January 2014
@@ -221,7 +221,7 @@
                      <em>Symmetry</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 23-66; doi:
-                     <a href="http://dx.doi.org/10.3390/sym6010023">10.3390/sym6010023</a>
+                     <a href="https://doi.org/10.3390/sym6010023">10.3390/sym6010023</a>
                     </div> 
                     <div class="pubdates">
                      Received: 28 October 2013; in revised form: 13 December 2013 / Accepted: 13 December 2013 / Published: 3 January 2014
@@ -263,7 +263,7 @@
                      <em>Processes</em> 
                      <b>2014</b>, 
                      <em>2</em>(1), 34-57; doi:
-                     <a href="http://dx.doi.org/10.3390/pr2010034">10.3390/pr2010034</a>
+                     <a href="https://doi.org/10.3390/pr2010034">10.3390/pr2010034</a>
                     </div> 
                     <div class="pubdates">
                      Received: 18 September 2013; in revised form: 5 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
@@ -310,7 +310,7 @@
                      <em>Plants</em> 
                      <b>2014</b>, 
                      <em>3</em>(1), 27-57; doi:
-                     <a href="http://dx.doi.org/10.3390/plants3010027">10.3390/plants3010027</a>
+                     <a href="https://doi.org/10.3390/plants3010027">10.3390/plants3010027</a>
                     </div> 
                     <div class="pubdates">
                      Received: 4 November 2013; in revised form: 18 December 2013 / Accepted: 20 December 2013 / Published: 3 January 2014
@@ -362,7 +362,7 @@
                      <em>Forests</em> 
                      <b>2014</b>, 
                      <em>5</em>(1), 21-71; doi:
-                     <a href="http://dx.doi.org/10.3390/f5010021">10.3390/f5010021</a>
+                     <a href="https://doi.org/10.3390/f5010021">10.3390/f5010021</a>
                     </div> 
                     <div class="pubdates">
                      Received: 4 November 2013; in revised form: 15 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014
@@ -404,7 +404,7 @@
                      <em>Adm. Sci.</em> 
                      <b>2014</b>, 
                      <em>4</em>(1), 1-14; doi:
-                     <a href="http://dx.doi.org/10.3390/admsci4010001">10.3390/admsci4010001</a>
+                     <a href="https://doi.org/10.3390/admsci4010001">10.3390/admsci4010001</a>
                     </div> 
                     <div class="pubdates">
                      Received: 8 October 2013; in revised form: 16 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
@@ -442,7 +442,7 @@
                      <em>Arts</em> 
                      <b>2014</b>, 
                      <em>3</em>(1), 15-26; doi:
-                     <a href="http://dx.doi.org/10.3390/arts3010015">10.3390/arts3010015</a>
+                     <a href="https://doi.org/10.3390/arts3010015">10.3390/arts3010015</a>
                     </div> 
                     <div class="pubdates">
                      Received: 27 October 2013; in revised form: 2 December 2013 / Accepted: 17 December 2013 / Published: 3 January 2014
@@ -485,7 +485,7 @@
                      <em>J. Funct. Biomater.</em> 
                      <b>2014</b>, 
                      <em>5</em>(1), 1-14; doi:
-                     <a href="http://dx.doi.org/10.3390/jfb5010001">10.3390/jfb5010001</a>
+                     <a href="https://doi.org/10.3390/jfb5010001">10.3390/jfb5010001</a>
                     </div> 
                     <div class="pubdates">
                      Received: 27 August 2013; in revised form: 26 November 2013 / Accepted: 27 November 2013 / Published: 3 January 2014
@@ -526,7 +526,7 @@
                      <em>Int. J. Environ. Res. Public Health</em> 
                      <b>2014</b>, 
                      <em>11</em>(1), 713-733; doi:
-                     <a href="http://dx.doi.org/10.3390/ijerph110100713">10.3390/ijerph110100713</a>
+                     <a href="https://doi.org/10.3390/ijerph110100713">10.3390/ijerph110100713</a>
                     </div> 
                     <div class="pubdates">
                      Received: 14 October 2013; in revised form: 16 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014
@@ -567,7 +567,7 @@
                      <em>Diversity</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 33-42; doi:
-                     <a href="http://dx.doi.org/10.3390/d6010033">10.3390/d6010033</a>
+                     <a href="https://doi.org/10.3390/d6010033">10.3390/d6010033</a>
                     </div> 
                     <div class="pubdates">
                      Received: 2 October 2013; in revised form: 20 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -618,7 +618,7 @@
                      <em>Diversity</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 18-32; doi:
-                     <a href="http://dx.doi.org/10.3390/d6010018">10.3390/d6010018</a>
+                     <a href="https://doi.org/10.3390/d6010018">10.3390/d6010018</a>
                     </div> 
                     <div class="pubdates">
                      Received: 27 October 2013; in revised form: 3 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
@@ -652,7 +652,7 @@
                      <em>Sustainability</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 251-266; doi:
-                     <a href="http://dx.doi.org/10.3390/su6010251">10.3390/su6010251</a>
+                     <a href="https://doi.org/10.3390/su6010251">10.3390/su6010251</a>
                     </div> 
                     <div class="pubdates">
                      Received: 11 November 2013; in revised form: 13 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -698,7 +698,7 @@
                      <em>Membranes</em> 
                      <b>2014</b>, 
                      <em>4</em>(1), 20-39; doi:
-                     <a href="http://dx.doi.org/10.3390/membranes4010020">10.3390/membranes4010020</a>
+                     <a href="https://doi.org/10.3390/membranes4010020">10.3390/membranes4010020</a>
                     </div> 
                     <div class="pubdates">
                      Received: 6 November 2013; in revised form: 26 November 2013 / Accepted: 21 December 2013 / Published: 3 January 2014
@@ -743,7 +743,7 @@
                      <em>Energies</em> 
                      <b>2014</b>, 
                      <em>7</em>(1), 130-149; doi:
-                     <a href="http://dx.doi.org/10.3390/en7010130">10.3390/en7010130</a>
+                     <a href="https://doi.org/10.3390/en7010130">10.3390/en7010130</a>
                     </div> 
                     <div class="pubdates">
                      Received: 21 October 2013; in revised form: 11 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -781,7 +781,7 @@
                      <em>Societies</em> 
                      <b>2014</b>, 
                      <em>4</em>(1), 16-29; doi:
-                     <a href="http://dx.doi.org/10.3390/soc4010016">10.3390/soc4010016</a>
+                     <a href="https://doi.org/10.3390/soc4010016">10.3390/soc4010016</a>
                     </div> 
                     <div class="pubdates">
                      Received: 31 October 2013; in revised form: 24 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
@@ -820,7 +820,7 @@
                      <em>J. Sens. Actuator Netw.</em> 
                      <b>2014</b>, 
                      <em>3</em>(1), 44-63; doi:
-                     <a href="http://dx.doi.org/10.3390/jsan3010044">10.3390/jsan3010044</a>
+                     <a href="https://doi.org/10.3390/jsan3010044">10.3390/jsan3010044</a>
                     </div> 
                     <div class="pubdates">
                      Received: 26 November 2013; in revised form: 15 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
@@ -859,7 +859,7 @@
                      <em>Mar. Drugs</em> 
                      <b>2014</b>, 
                      <em>12</em>(1), 115-127; doi:
-                     <a href="http://dx.doi.org/10.3390/md12010115">10.3390/md12010115</a>
+                     <a href="https://doi.org/10.3390/md12010115">10.3390/md12010115</a>
                     </div> 
                     <div class="pubdates">
                      Received: 14 October 2013; in revised form: 25 November 2013 / Accepted: 12 December 2013 / Published: 3 January 2014
@@ -914,7 +914,7 @@
                      <em>Energies</em> 
                      <b>2014</b>, 
                      <em>7</em>(1), 115-129; doi:
-                     <a href="http://dx.doi.org/10.3390/en7010115">10.3390/en7010115</a>
+                     <a href="https://doi.org/10.3390/en7010115">10.3390/en7010115</a>
                     </div> 
                     <div class="pubdates">
                      Received: 22 October 2013; in revised form: 17 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -961,7 +961,7 @@
                      <em>Materials</em> 
                      <b>2014</b>, 
                      <em>7</em>(1), 218-231; doi:
-                     <a href="http://dx.doi.org/10.3390/ma7010218">10.3390/ma7010218</a>
+                     <a href="https://doi.org/10.3390/ma7010218">10.3390/ma7010218</a>
                     </div> 
                     <div class="pubdates">
                      Received: 28 November 2013; in revised form: 17 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
@@ -1007,7 +1007,7 @@
                      <em>Int. J. Mol. Sci.</em> 
                      <b>2014</b>, 
                      <em>15</em>(1), 525-544; doi:
-                     <a href="http://dx.doi.org/10.3390/ijms15010525">10.3390/ijms15010525</a>
+                     <a href="https://doi.org/10.3390/ijms15010525">10.3390/ijms15010525</a>
                     </div> 
                     <div class="pubdates">
                      Received: 13 November 2013; in revised form: 19 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
@@ -1051,7 +1051,7 @@
                      <em>Materials</em> 
                      <b>2014</b>, 
                      <em>7</em>(1), 206-217; doi:
-                     <a href="http://dx.doi.org/10.3390/ma7010206">10.3390/ma7010206</a>
+                     <a href="https://doi.org/10.3390/ma7010206">10.3390/ma7010206</a>
                     </div> 
                     <div class="pubdates">
                      Received: 8 October 2013; in revised form: 14 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
@@ -1107,7 +1107,7 @@
                      <em>Int. J. Mol. Sci.</em> 
                      <b>2014</b>, 
                      <em>15</em>(1), 504-524; doi:
-                     <a href="http://dx.doi.org/10.3390/ijms15010504">10.3390/ijms15010504</a>
+                     <a href="https://doi.org/10.3390/ijms15010504">10.3390/ijms15010504</a>
                     </div> 
                     <div class="pubdates">
                      Received: 30 October 2013; in revised form: 16 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -1152,7 +1152,7 @@
                      <em>Remote Sens.</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 540-554; doi:
-                     <a href="http://dx.doi.org/10.3390/rs6010540">10.3390/rs6010540</a>
+                     <a href="https://doi.org/10.3390/rs6010540">10.3390/rs6010540</a>
                     </div> 
                     <div class="pubdates">
                      Received: 30 October 2013; in revised form: 25 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
@@ -1193,7 +1193,7 @@
                      <em>Remote Sens.</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 521-539; doi:
-                     <a href="http://dx.doi.org/10.3390/rs6010521">10.3390/rs6010521</a>
+                     <a href="https://doi.org/10.3390/rs6010521">10.3390/rs6010521</a>
                     </div> 
                     <div class="pubdates">
                      Received: 27 September 2013; in revised form: 13 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
@@ -1238,7 +1238,7 @@
                      <em>Toxins</em> 
                      <b>2014</b>, 
                      <em>6</em>(1), 229-253; doi:
-                     <a href="http://dx.doi.org/10.3390/toxins6010229">10.3390/toxins6010229</a>
+                     <a href="https://doi.org/10.3390/toxins6010229">10.3390/toxins6010229</a>
                     </div> 
                     <div class="pubdates">
                      Received: 11 November 2013; in revised form: 24 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014

diff --git a/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt b/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt
@@ -106,7 +106,7 @@
               Volume 2014 (2014), Article ID 801626, 8 pages
               <br></br>
           // doi
-              <a href="http://dx.doi.org/10.1155/2014/801626">http://dx.doi.org/10.1155/2014/801626</a>
+              <a href="https://doi.org/10.1155/2014/801626">https://doi.org/10.1155/2014/801626</a>
             </pre>
             // article type
             <div class="article_type">Research Article</div>

diff --git a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl
@@ -6,7 +6,7 @@
 
     <xsl:output method="xhtml"/>
 
-    <xsl:variable name="doiroot">https://dx.doi.org/</xsl:variable>
+    <xsl:variable name="doiroot">https://doi.org/</xsl:variable>
     <xsl:variable name="nlmroot">http://www.ncbi.nlm.nih.gov/pubmed/</xsl:variable>    
 	<xsl:variable name="lowercase" select="'abcdefghijklmnopqrstuvwxyz'" />
 	<xsl:variable name="uppercase" select="'ABCDEFGHIJKLMNOPQRSTUVWXYZ'" />
@@ -817,7 +817,7 @@
 	<xsl:template match="*[local-name()='fig']">
 	 <div class="fig" title="fig">
 	  <div class="figure" title="figure">
-	    <a href="http://doi.org/{*[local-name()='object-id' and @pub-id-type='doi']}"><xsl:apply-templates select="*[local-name()='label']"/></a>
+	    <a href="https://doi.org/{*[local-name()='object-id' and @pub-id-type='doi']}"><xsl:apply-templates select="*[local-name()='label']"/></a>
 	  </div>
 	  <caption class="caption" title="caption"><xsl:apply-templates select="*[local-name()='caption']"/></caption>
 	  <!--  the <graphic> links to files we don't have -->

diff --git a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl
@@ -9,7 +9,7 @@
 	<xsl:variable name="publisher">Generic NLM</xsl:variable>
 	<xsl:variable name="prefix">10.0000</xsl:variable>
 
-    <xsl:variable name="doiroot">https://dx.doi.org/</xsl:variable>
+    <xsl:variable name="doiroot">https://doi.org/</xsl:variable>
     <xsl:variable name="nlmroot">http://www.ncbi.nlm.nih.gov/pubmed/</xsl:variable>    
 	<xsl:variable name="lowercase" select="'abcdefghijklmnopqrstuvwxyz'" />
 	<xsl:variable name="uppercase" select="'ABCDEFGHIJKLMNOPQRSTUVWXYZ'" />
@@ -885,7 +885,7 @@ UNKNOWN nlm: alt-text:
 	<xsl:template match="*[local-name()='fig']">
 	 <div class="fig" title="fig">
 	  <div class="figure" title="figure">
-	    <a href="http://doi.org/{*[local-name()='object-id' and @pub-id-type='doi']}"><xsl:apply-templates select="*[local-name()='label']"/></a>
+	    <a href="https://doi.org/{*[local-name()='object-id' and @pub-id-type='doi']}"><xsl:apply-templates select="*[local-name()='label']"/></a>
 	  </div>
 	  <caption class="caption" title="caption"><xsl:apply-templates select="*[local-name()='caption']"/></caption>
 	  <!--  the <graphic> links to files we don't have -->