treat conference refs as book instead of journal (#162)

README.md

@@ -146,7 +146,7 @@ This XSL changes `<boxed-text>` into a `<sec>` element because encoda and EPP do
 
 ### [/src/conf-ref-workaround.xsl](/src/boxed-text-workaround.xsl)
 
-For conference proceeding references, the name of a conference is usually captured using the element `<conf-name>`. Encoda does not decode/encode this element, as such it is missing in the HTML rendered by EPP. Encoda also does not distinguish in the reference type (still encoded as `Article`). This XSL converts a conference reference into a journal reference (as best as possible) so that the details can be showin in the HTML. 
+For conference proceeding references, the name of a conference is usually captured using the element `<conf-name>`. Encoda does not decode/encode this element, as such it is missing in the HTML rendered by EPP. Encoda also does not distinguish in the reference type (still encoded as `Article`). This XSL converts a conference reference into a book reference (as best as possible) so that the details can be showin in the HTML. 
 
 ### [/src/extra-abstract-workaround.xsl](/src/extra-abstract-workaround.xsl)
 

src/conf-ref-workaround.xsl

@@ -15,24 +15,21 @@
 
     <xsl:template match="mixed-citation[@publication-type=('conference','confproc')]">
         <xsl:copy>
-            <xsl:attribute name="publication-type">journal</xsl:attribute>
+            <xsl:attribute name="publication-type">book</xsl:attribute>
             <xsl:apply-templates select="*|@*[name()!='publication-type']|text()|comment()|processing-instruction()"/>
         </xsl:copy>
     </xsl:template>
 
     <xsl:template match="mixed-citation[@publication-type=('conference','confproc')]/conf-name">
-        <xsl:choose>
-            <xsl:when test="parent::mixed-citation/article-title">
-                <source>
-                    <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
-                </source>
-            </xsl:when>
-            <xsl:otherwise>
-                <article-title>
-                    <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
-                </article-title>
-            </xsl:otherwise>
-        </xsl:choose>
+        <source>
+            <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
+        </source>
+    </xsl:template>
+
+    <xsl:template match="mixed-citation[@publication-type=('conference','confproc')]/article-title">
+        <chapter-title>
+            <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
+        </chapter-title>
     </xsl:template>
 
 </xsl:stylesheet>

test/all/kitchen-sink.xml

@@ -437,7 +437,7 @@ return :shrug:
 <ref id="c61"><label>61.</label><mixed-citation publication-type="other"><string-name><given-names>J. H.</given-names> <surname>Krijthe</surname></string-name>, <article-title>Rtsne: T-distributed stochastic neighbor embedding using Barnes-Hut implementation</article-title>. <italic>R package version 0.13</italic>, URL <ext-link ext-link-type="uri" xlink:href="https://github.com/jkrijthe/Rtsne">https://github.com/jkrijthe/Rtsne</ext-link> (<year>2015</year>).</mixed-citation></ref>
 <ref id="c62"><label>62.</label><mixed-citation publication-type="other"><string-name><given-names>Z.</given-names> <surname>Sethna</surname></string-name>, <string-name><given-names>Y.</given-names> <surname>Elhanati</surname></string-name>, C. G. C. Jr, <string-name><given-names>T.</given-names> <surname>Mora</surname></string-name>, <article-title>OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs</article-title>, <volume>8</volume>.</mixed-citation></ref>
 <ref id="c63"><label>63.</label><mixed-citation publication-type="journal"><string-name><surname>Liu</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Brincat</surname> <given-names>SL</given-names></string-name>, <string-name><surname>Miller</surname> <given-names>EK</given-names></string-name>, <string-name><surname>Hasselmo</surname> <given-names>ME</given-names></string-name>. <article-title>A Geometric Characterization of Population Coding in the Prefrontal Cortex and Hippocampus during a Paired-Associate Learning Task</article-title>. <source>Journal of Cognitive Neuroscience</source>. <year>2020</year> 8; <volume>32</volume>(). doi: 10.1162/jocn{\_}a{\_}01569.</mixed-citation></ref>
-<ref id="c64"><label>64.</label><mixed-citation publication-type="journal"><string-name><given-names>T.</given-names> <surname>Stuart</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Comprehensive Integration of Single-Cell Data</article-title>. <source>Cell</source> <volume>177</volume>, <fpage>1888</fpage>&#x2013;<lpage>1902</lpage>.<page-range>e1821</page-range> (<year>2019</year>).</mixed-citation></ref><ref id="c65"><label>65.</label><mixed-citation publication-type="journal"><string-name><given-names>M. S.</given-names> <surname>Kowalczyk</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells</article-title>. <source>Genome Res</source> <volume>25</volume>, <fpage>1860</fpage>&#x2013;<lpage>1872</lpage> (<year>2015</year>).</mixed-citation></ref><ref id="c66"><label>66.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Reversed graph embedding resolves complex single-cell trajectories</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>979</fpage>&#x2013;<lpage>982</lpage> (<year>2017</year>).</mixed-citation></ref><ref id="c67"><label>67.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Single-cell mRNA quantification and differential analysis with Census</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>309</fpage>&#x2013;<lpage>315</lpage> (<year>2017</year>).</mixed-citation></ref><ref id="c68"><label>68.</label><mixed-citation publication-type="other"><string-name><surname>Nykanen</surname> <given-names>L</given-names></string-name>, <string-name><surname>Nykanen</surname>, <given-names>I.</given-names></string-name> (<year>1991</year>) <article-title>Distilled beverages</article-title>. <source>Volatile Compounds in Foods and Beverages</source>, ed <string-name><surname>Maarse</surname> <given-names>H</given-names></string-name> (<publisher-name>Dekker Inc, New York</publisher-name>), pp <fpage>548</fpage>&#x2013;<lpage>580</lpage>.</mixed-citation></ref><ref id="c69"><label>69.</label><mixed-citation publication-type="journal"><string-name><surname>Flatla</surname>, <given-names>D. R.</given-names></string-name> <article-title>Accessibility for individuals with color vision deficiency</article-title>. in <source>Proc. 24th Annu. ACM Symp. Adjun. User Interface Softw. Technol</source>. <fpage>31</fpage>–<lpage>34</lpage> (<publisher-name>Association for Computing Machinery</publisher-name>, <year>2011</year>). doi:<pub-id pub-id-type="doi">10.1145/2046396.2046412</pub-id>.</mixed-citation></ref></ref-list>
+<ref id="c64"><label>64.</label><mixed-citation publication-type="journal"><string-name><given-names>T.</given-names> <surname>Stuart</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Comprehensive Integration of Single-Cell Data</article-title>. <source>Cell</source> <volume>177</volume>, <fpage>1888</fpage>&#x2013;<lpage>1902</lpage>.<page-range>e1821</page-range> (<year>2019</year>).</mixed-citation></ref><ref id="c65"><label>65.</label><mixed-citation publication-type="journal"><string-name><given-names>M. S.</given-names> <surname>Kowalczyk</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells</article-title>. <source>Genome Res</source> <volume>25</volume>, <fpage>1860</fpage>&#x2013;<lpage>1872</lpage> (<year>2015</year>).</mixed-citation></ref><ref id="c66"><label>66.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Reversed graph embedding resolves complex single-cell trajectories</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>979</fpage>&#x2013;<lpage>982</lpage> (<year>2017</year>).</mixed-citation></ref><ref id="c67"><label>67.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <string-name><surname>et al.</surname></string-name>, <article-title>Single-cell mRNA quantification and differential analysis with Census</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>309</fpage>&#x2013;<lpage>315</lpage> (<year>2017</year>).</mixed-citation></ref><ref id="c68"><label>68.</label><mixed-citation publication-type="other"><string-name><surname>Nykanen</surname> <given-names>L</given-names></string-name>, <string-name><surname>Nykanen</surname>, <given-names>I.</given-names></string-name> (<year>1991</year>) <article-title>Distilled beverages</article-title>. <source>Volatile Compounds in Foods and Beverages</source>, ed <string-name><surname>Maarse</surname> <given-names>H</given-names></string-name> (<publisher-name>Dekker Inc, New York</publisher-name>), pp <fpage>548</fpage>&#x2013;<lpage>580</lpage>.</mixed-citation></ref><ref id="c69"><label>69.</label><mixed-citation publication-type="book"><string-name><surname>Flatla</surname>, <given-names>D. R.</given-names></string-name> <chapter-title>Accessibility for individuals with color vision deficiency</chapter-title>. in <source>Proc. 24th Annu. ACM Symp. Adjun. User Interface Softw. Technol</source>. <fpage>31</fpage>–<lpage>34</lpage> (<publisher-name>Association for Computing Machinery</publisher-name>, <year>2011</year>). doi:<pub-id pub-id-type="doi">10.1145/2046396.2046412</pub-id>.</mixed-citation></ref></ref-list>
 <ack>
 <title>Acknowledgments:</title>
 <p>The authors would like to express their gratitude to the organ donors and their families who allowed the collection of samples for research under sad circumstances. The authors would also like to thank Prof. Pascal Leprince, Dr. Guillaume Lebreton, and Dr. Marina Rigolet of the cardiac surgery team, Prof. Bruno Riou and the graft coordination team of the Piti&#x00E9;-Salp&#x00EA;tri&#x00E8;re hospital for their invaluable contribution to sample collection. The authors thank the UMR 8199 LIGAN-PM Genomics platform (Lille, France) for efficient sequencing. We also thank Thierry Mora, and Aleksandra Walczak for helpful discussion.</p>

test/conf-ref-workaround/kitchen-sink.xml

@@ -848,7 +848,7 @@ return :shrug:
 <ref id="c66"><label>66.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <etal>et al.</etal>, <article-title>Reversed graph embedding resolves complex single-cell trajectories</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>979</fpage>&#x2013;<lpage>982</lpage> (<year>2017</year>).</mixed-citation></ref>
 <ref id="c67"><label>67.</label><mixed-citation publication-type="journal"><string-name><given-names>X.</given-names> <surname>Qiu</surname></string-name> <etal>et al.</etal>, <article-title>Single-cell mRNA quantification and differential analysis with Census</article-title>. <source>Nat Methods</source> <volume>14</volume>, <fpage>309</fpage>&#x2013;<lpage>315</lpage> (<year>2017</year>).</mixed-citation></ref>
 <ref id="c68"><label>68.</label><mixed-citation publication-type="other"><string-name><surname>Nykanen</surname> <given-names>L</given-names></string-name>, <string-name><surname>Nykanen</surname>, <given-names>I.</given-names></string-name> (<year>1991</year>) <article-title>Distilled beverages</article-title>. <source>Volatile Compounds in Foods and Beverages</source>, ed <string-name><surname>Maarse</surname> <given-names>H</given-names></string-name> (<publisher-name>Dekker Inc, New York</publisher-name>), pp <fpage>548</fpage>&#x2013;<lpage>580</lpage>.</mixed-citation></ref>
-<ref id="c69"><label>69.</label><mixed-citation publication-type="journal"><string-name><surname>Flatla</surname>, <given-names>D. R.</given-names></string-name> <article-title>Accessibility for individuals with color vision deficiency</article-title>. in <source>Proc. 24th Annu. ACM Symp. Adjun. User Interface Softw. Technol</source>. <fpage>31</fpage>–<lpage>34</lpage> (<publisher-name>Association for Computing Machinery</publisher-name>, <year>2011</year>). doi:<pub-id pub-id-type="doi">10.1145/2046396.2046412</pub-id>.</mixed-citation></ref>
+<ref id="c69"><label>69.</label><mixed-citation publication-type="book"><string-name><surname>Flatla</surname>, <given-names>D. R.</given-names></string-name> <chapter-title>Accessibility for individuals with color vision deficiency</chapter-title>. in <source>Proc. 24th Annu. ACM Symp. Adjun. User Interface Softw. Technol</source>. <fpage>31</fpage>–<lpage>34</lpage> (<publisher-name>Association for Computing Machinery</publisher-name>, <year>2011</year>). doi:<pub-id pub-id-type="doi">10.1145/2046396.2046412</pub-id>.</mixed-citation></ref>
 </ref-list>
 </back>
 </article>