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<table> under <floats-group> excluded, breaks references #48

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wrought opened this issue Sep 16, 2014 · 5 comments
Open

<table> under <floats-group> excluded, breaks references #48

wrought opened this issue Sep 16, 2014 · 5 comments
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@wrought
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wrought commented Sep 16, 2014

10.3897/BDJ.2.e1161
log
wikisource
PMC4092324
NXML source

From nxml:

<table-wrap id="T581008" orientation="portrait" position="float"><label>Table 1.</label><caption><p>Island and mainland records for <italic><named-content content-type="taxon-name"><named content content-type="genus">Johngarthia</named-content>
@wrought wrought changed the title Table 1 <table-wrap> tag excluded from <table-wrap> tag (Table 1) excluded from 10.3897/BDJ.2.e1161 Sep 16, 2014
@wrought
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wrought commented Sep 17, 2014

Table works fine when run through xsltproc with jats-to-mediawiki.xsl, issue must be the table in context of rest of article. Here's the successfully transformed output of the table:

==Table 1.==
:"Island and mainland records for ''Johngarthia planata'' obtained from the literature (L) and photographs (P); new records highlighted by (*)."&lt;table frame="hsides" rules="all" border="1"&gt;&lt;tr&gt;&lt;th rowspan="1" colspan="1"&gt;Location&lt;/th&gt;&lt;th rowspan="1" colspan="1"&gt;Source&lt;/th&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Colombia'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Gorgona Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Prahl 1983 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Costa Rica'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Colorada Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Perger et al. 2013 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Caño Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Perger et al. 2013 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Nairita Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Perger et al. 2013 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Panama'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Iguana Island*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;María Elena Valencia 2006; Julio Larish 2013 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Mexico, islands'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Clipperton Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Lenz 1901, Rathbun 1918, Garth 1965 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Pájaros Island, Michoacán&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;García-Madrigal 2000 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Isabela Island, Nayarit&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Rathbun 1899 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Maria Cleofa Island, Nayarit&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Rathbun 1899 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Pájaros Island, Sinaloa&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Arzola-González et al. 2010 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;San Pedro Nolasco Island, Gulf of California&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Felger et al. 2011 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Socorro Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Rodriguez et al. 1996, Ortega-Rubio et al. 1997 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;San Benedicto Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Brattstrom and Howell 1956 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Clarion Island&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Hernández-Aguilera et al. 1986 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Bacochibampo Bay, Sonora (small reef)&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Manrique 1981 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Mexico, Baja California Peninsula'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Cabo San Lucas&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Stimpson 1860 (L)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;'''Mexico, mainland'''&lt;/td&gt;&lt;td rowspan="1" colspan="1"/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Mazatlán, Sinaloa*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Lisa Brettschneider 2008 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Sayulita, Nayarit*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Lisa Johnston 2005; Tania Beagley-Brown 2007; Daniel Brewer 2010; Madeline Milne 2013 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Mismaloya, Jalisco*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Darin Williams 2007 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Manzanillo, Colima*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Derek Zoebelein 2004 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Ixtapa, Guerrero*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Miguel Angel Morales 2012 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Mazunte, Oaxaca *&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Gustavo A. Zambrano Cabrera 2008 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Escondido Beach, Oaxaca*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Mike Gardiner 2010 (P)&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td rowspan="1" colspan="1"&gt;Zapotengo Beach, Oaxaca*&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;Claudia Glechner 2011 (P)&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;

@wrought
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wrought commented Sep 17, 2014

Ah, issue seems related to #23 and <floats-group> which was also an issue for <fig> elements, like the two present here: 10.3897/BDJ.2.e1161.

This table appears inside of a <floats-group> tag as well. perhaps a generalized solution is needed here to handle any content inside of these tags? Otherwise, at least handling <table-wrap> and table elements, etc is necessary.

@wrought wrought mentioned this issue Sep 17, 2014
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@wrought wrought changed the title <table-wrap> tag (Table 1) excluded from 10.3897/BDJ.2.e1161 <table-wrap> and <table> tags excluded under <floats-group> from 10.3897/BDJ.2.e1161 Sep 17, 2014
@wrought wrought changed the title <table-wrap> and <table> tags excluded under <floats-group> from 10.3897/BDJ.2.e1161 <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 Sep 17, 2014
@wrought wrought changed the title <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 Sep 17, 2014
@wrought wrought changed the title <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 Sep 17, 2014
@wrought wrought changed the title <table> under <floats-group> excluded from 10.3897/BDJ.2.e1161 <table> under <floats-group> excluded Sep 17, 2014
@wrought wrought changed the title <table> under <floats-group> excluded <table> under <floats-group> excluded, breaks references Sep 17, 2014
@Klortho
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Klortho commented Sep 17, 2014

Good detective work. Yes, the , which is at the top-level of the article, is not processed at all.

@wrought
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wrought commented Sep 17, 2014

I tried to take a pass at processing the <floats-group> but no luck. As far as I can tell, this element is a child of <article> and a sibling of <sec> elements. What would be the best way to handle the contents of a <floats-group> element as though it were another <sec>?

@Klortho
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Klortho commented Sep 18, 2014

Off the top of my head, I'd think we'd want to find and process the float-group items when they are referenced from the body of the article. So, when the XSLT encounters a figure in the body that references the item that exists inside the floats-group, then do a call-template to process that item. I will try to take a look this weekend.

@tcatapano tcatapano added the ready label Feb 9, 2017
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@Klortho @Daniel-Mietchen @wrought @tcatapano