run tp conversion on phytochemistry articles

[tcatapano]

starting with sample file Phytochemistry.103.67-75.pdf.xml

[tcatapano]

Problem with TP result:

Two consecutive treatments in the source are being merged into a single treatment, with the two nomenclature sections placed one after another at the start of the treatment: see

https://github.com/plazi/ggxml2taxpub/blob/8f605eab9dd119dea1f287c67768d1aa6dde6b45/level1/articles/non-tax/Phytochemistry.103.67-75.pdf_tp.xml#L1854C2-L1861C2

        <tp:mixed-nomenclature> 2.1. Floral scent composition of <tp:taxon-name>Nymphaea subg.
               Hydrocallis</tp:taxon-name>
         </tp:mixed-nomenclature>
         <tp:mixed-nomenclature> 2.2. Floral scent variations within
               <tp:taxon-name>Nymphaea</tp:taxon-name> and <tp:taxon-name>Victoria</tp:taxon-name>
         </tp:mixed-nomenclature>
         <tp:treatment-sec sec-type="description">
            <p> The six species and two subspecies of <tp:taxon-name> Nymphaea subg. Hydrocallis

[tcatapano]

Think the problem is here: (

ggxml2taxpub/xslt/gg2tp_l1.xsl

Lines 8 to 13 in 8f605ea

	<xsl:template match="//treatment">
	<tp:taxon-treatment>
	<xsl:call-template name="treatment-metadata"/>
	<xsl:apply-templates select="//subSubSection[@type = 'nomenclature']"/>
	<xsl:apply-templates select="//subSubSection[not(@type = 'nomenclature')]"/>
	</tp:taxon-treatment>

)

this should be

xsl:apply-templates select=".//subSubSection[@type = 'nomenclature']"/> 
         <xsl:apply-templates select=".//subSubSection[not(@type = 'nomenclature')]"/> 

to iterate over descendant subSubSection's of the current treatment, not in the document as a whole

[tcatapano]

The xpath fix worked. Resulting file is now valid. Now run over larger sample set.

[tcatapano]

Conversion on full batch results in most files being valid. Errors are in:

  22 Phytochemistry.157.168-174.pdf_tp.xml
   3 Phytochemistry.189.112824.pdf_tp.xml
   2 Phytochemistry.187.112776.pdf_tp.xml
   2 Phytochemistry.186.112741.pdf_tp.xml
   1 Phytochemistry.193.112970.pdf_tp.xml
   1 Phytochemistry.191.112908.pdf_tp.xml
   1 Phytochemistry.163.196-197.pdf_tp.xml
   1 Phytochemistry.157.158-167.pdf_tp.xml
   1 Phytochemistry.153.58-63.pdf_tp.xml

see: https://github.com/plazi/ggxml2taxpub/blob/master/errs/phytochemistry_errors_20240211_frq.txt:

ggxml2taxpub/errs/phytochemistry_errors_20240211_frq.txt

Lines 1 to 7 in 7c41161

	22 Unexpected character data "
	6 Unexpected element "title". The content of the parent element type must match "(sec-meta?,((label,title?)|title),(address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml:math|p|related-article|related-object|disp-quote|speech|statement|verse-group)*,(sec|tp
	2 Unexpected element "sec". The content of the parent element type must match "(sec-meta?,label?,title?,(address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml:math|p|related-article|related-object|disp-quote|speech|statement|verse-group)*,tp
	1 Unexpected element "tp:treatment-sec". The content of the parent element type must match "((address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml
	1 Unexpected element "tp:mixed-nomenclature". The content of the parent element type must match "((address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml
	1 Unexpected element "sec". The content of the parent element type must match "(tp:taxon-name|tp
	1 The content of element type "kwd-group" is incomplete, it must match "(label?,title?,(kwd|compound-kwd|nested-kwd)+)".