PAAA-PoC

This repository is a proof-of-concept for a versioned storage as per the Plazi Actionable Accessible Archive (PAAA) arhitecture.

The repository contains all treatments in the Plazi Root Format GG-XML that pass the TreatmentBank Gatekeeper rules for LOD data, all other formats offered by Plazi can be derived from this format. A GitHub Workflow exemplifies the transformation to another format. It uses xalan and rapper to transform the documents to RDF whenever they are changed or added.

Workflow: How Changes are translated to Synospecies

Changed XML is uploaded to this repository (currently this is always from TreatmentBank). All XML Documents and their history is available in the data folder in this Git Repository.
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A webhook is sent to our server where https://github.com/plazi/gg2rdf transform all changed XML to RDF turtle.

to do so it uses this XSLT and the Raptor RDF Library.
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The same Github Action uploads the genrated RDF to the treatments-rdf repository
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That repository triggers a Webhook on our server, where PSPS takes in the data and stores it in an internal triplestore. (Exposed SPARQL-Endpoint at https://treatment.ld.plazi.org/sparql )
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PSPS then uploads all this data to lindas, which reloads itself every 24h, from where Synospecies gets its data by default

GateKeeper rules

source	destination	check	type	message
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'missingRank' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/missingRank	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'missingAuthority' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/missingAuthority	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'missingFamily' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/missingFamily	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'missingOrder' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/missingOrder	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'missingKingdom' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/missingKingdom	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'brokenFamily' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/brokenFamily	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'taxonomicNames']/type[./@name = 'brokenOrder' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	taxonomicNames/brokenOrder	Unresolved treatment taxon issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'missingTaxon' and $detailId and ./@errors-blocker > 0])	treatments/missingTaxon	Unresolved treatment boundary issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'brokenBoundaries' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	treatments/brokenBoundaries	Unresolved treatment boundary issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'brokenStructure' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	treatments/brokenStructure	Unresolved treatment structure issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'missingStructure' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	treatments/missingStructure	Unresolved treatment structure issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'missingNomenclature' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	treatments/missingNomenclature	Unresolved treatment structure issues
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'spuriousTreatment' and $detailId and ./@errors-blocker > 0])	treatments/spuriousTreatment	Treatment too small to be valid
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'mingledTreatments' and $detailId and ./@errors-blocker > 0])	treatments/mingledTreatments	Treatment might be aggregate of multiple treatments
SRS	LOD	(./category[./@name = 'treatments']/type[./@name = 'brokenReferenceGroup' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)])	treatments/brokenReferenceGroup	Reference group cites suspicious taxon names
//	fallback for missing error protocol: uploaded 2020-06-01 or later
SRS	LOD	(./@checkinTime > 1590926399000)	document/missingQc	QC is required for LOD export of treatments extracted from IMF documents uploaded after 2020-05-31