R/taxonx.R
In pensoft/ropenbio: R Package of the Open Biodiveristy Knowledge Management System
#' @include xml.R
#' TaxonX Schema
#'
#' @export
taxonx = XmlSchema$new(
schema_name = "taxonx",
xpath = "/",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
title = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:titleInfo/mods:title",
date = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:date",
doi = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='DOI']",
zenodo = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='Zenodo-Dep']",
zoobank = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='ZooBank']",
publisher = NA,
journal = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:titleInfo/mods:title",
journal_abbrev = NA,
issn = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='ISSN']",
eIssn = NA,
issue = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='issue']/mods:number",
volume = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='volume']/mods:number",
starting_page = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:start",
ending_page = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:end",
pensoft_pub = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='Pensoft-Pub']"
),
atom_lang = c(
title = NA,
date = NA,
doi = NA,
zenodo = NA,
publisher = NA,
journal = NA,
journal_abbrev = NA,
issn = NA,
eIssn = NA,
issue = NA,
volume = NA,
starting_page = NA,
ending_page = NA,
pensoft_pub = NA
),
atom_types = list(
title = rdf4r::xsd_string,
date = rdf4r::xsd_date,
doi = rdf4r::xsd_string,
zenodo = rdf4r::xsd_string,
publisher = rdf4r::xsd_string,
journal = rdf4r::xsd_string,
journal_abbrev = rdf4r::xsd_string,
issn = rdf4r::xsd_string,
eIssn = rdf4r::xsd_string,
issue = rdf4r::xsd_integer,
volume = rdf4r::xsd_integer,
starting_page = rdf4r::xsd_integer,
ending_page = rdf4r::xsd_integer,
pensoft_pub = rdf4r::xsd_string
),
constructor = metadata,
#injector = standard_injector,
components = list(
# Author
XmlSchema$new(
schema_name = "taxonx_author",
xpath = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:name[@type='personal']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
full_name = "./mods:namePart",
role = "./mods:role/mods:roleTerm"
),
atom_lang = c(
full_name = NA,
role = NA
),
atom_types = list(
full_name = rdf4r::xsd_string,
role = rdf4r::xsd_string
),
constructor = author,
components = NULL
),
# Treatment
XmlSchema$new(
schema_name = "taxonx_treatment",
xpath = "/tax:taxonx/tax:taxonxBody/tax:treatment",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
# injector = standard_injector,
constructor = treatment,
components = list(
# Nomenclature
XmlSchema$new(
schema_name = "nomenclature_section",
xpath = ".//tax:nomenclature", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = nomenclature
),
XmlSchema$new(
schema_name = "materials_examined",
xpath = ".//tax:div[@type='materials_examined']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = materials_examined
),
#taxonx_diagnosis
XmlSchema$new(
schema_name = "diagnosis_section",
xpath = ".//tax:div[@type='diagnosis']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = diagnosis
),
# distribution
XmlSchema$new(
schema_name = "distribution_section",
xpath = ".//tax:div[@type='distribution']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = distribution
)
)
),
# DISCUSSION
XmlSchema$new(
schema_name = "discussion_section",
xpath = ".//tax:div[@type='discussion']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = discussion
),
# Taxonomic Key
XmlSchema$new(
schema_name = "taxonx_taxonomic_key",
xpath = "/tax:taxonx/tax:taxonxBody//tax:div[@type='key']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = taxonomic_key,
components = NULL
),
# Figure
XmlSchema$new(
schema_name = "taxonx_figure",
xpath = ".//tax:figure",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = figure,
components = NULL
),
# Taxonomic Name Usage
XmlSchema$new(
schema_name = "taxonx_taxonomic_name_usage",
xpath = ".//tax:name",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
date = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:date",
kingdom = ".//dwc:Kingdom",
phylum = ".//dwc:Phylum",
class = ".//dwc:Class",
order = ".//dwc:Order",
family = ".//dwc:Family",
genus = ".//dwc:Genus",
subgenus = ".//dwc:Subgenus",
species = ".//dwc:Species", ## This is an error in TaxonX, not ropenbio!!!
subspecies = ".//dwc:Subspecies",
verbatim_rank = ".//dwc:taxonRank",
verbatim_status = NA,
authorship = ".//dwc:scientificNameAuthorship",
secundum_literal = NA
),
atom_lang = c(
date = NA,
kingdom = NA,
phylum = NA,
class = NA,
order = NA,
family = NA,
genus = NA,
subgenus = NA,
species = NA, ## This is an error in TaxonX, not DwC!
subspecies = NA,
verbatim_rank = NA,
verbatim_status = NA,
authorship = NA,
secundum_literal = NA
),
atom_types = list(
date = rdf4r::xsd_date,
kingdom = rdf4r::xsd_string,
class = rdf4r::xsd_string,
order = rdf4r::xsd_string,
family = rdf4r::xsd_string,
genus = rdf4r::xsd_string,
subgenus = rdf4r::xsd_string,
species = rdf4r::xsd_string,
subspecies = rdf4r::xsd_string,
verbatim_rank = rdf4r::xsd_string,
taxonomic_rank = rdf4r::xsd_string,
taxonomic_status = rdf4r::xsd_string,
authorship = rdf4r::xsd_string,
secundum_literal = rdf4r::xsd_string
),
constructor = taxonomic_name_usage,
components = NULL
)
)
)
#' @include xml.R
#' Plazi XML schema (not TAXONX)
#'
#' @export
plazi_schema = XmlSchema$new(
schema_name = "plazi_schema",
xpath = "/",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
title = "/document/mods:mods/mods:titleInfo/mods:title",
date = "/document/mods:mods/mods:relatedItem/mods:part/mods:date",
doi = "/document/mods:mods/mods:identifier[@type='DOI']",
zenodo = "/document/mods:mods/mods:identifier[@type='Zenodo-Dep']",
zoobank = "/document/mods:mods/mods:identifier[@type='ZooBank']",
gbif_dataset = "/document/mods:mods/mods:identifier[@type='GBIF-Dataset']",
publisher = NA,
journal = "/document/mods:mods/mods:relatedItem/mods:titleInfo/mods:title",
journal_abbrev = NA,
issn = "/document/mods:mods/mods:identifier[@type='ISSN']",
eIssn = NA,
issue = "/document/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='issue']/mods:number",
volume = "/document/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='volume']/mods:number",
starting_page = "/document/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:start",
ending_page = "/document/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:end",
pensoft_pub = "/document/mods:mods/mods:identifier[@type='Pensoft-Pub']",
pensoft_uuid = "/document/mods:mods/mods:identifier[@type='Pensoft-UUID']"
),
atom_lang = c(
title = NA,
date = NA,
doi = NA,
zenodo = NA,
gbif_dataset = NA,
publisher = NA,
journal = NA,
journal_abbrev = NA,
issn = NA,
eIssn = NA,
issue = NA,
volume = NA,
starting_page = NA,
ending_page = NA,
pensoft_pub = NA,
pensoft_uuid = NA
),
atom_types = list(
title = rdf4r::xsd_string,
date = rdf4r::xsd_date,
doi = rdf4r::xsd_string,
zenodo = rdf4r::xsd_string,
gbif_dataset = rdf4r::xsd_string,
publisher = rdf4r::xsd_string,
journal = rdf4r::xsd_string,
journal_abbrev = rdf4r::xsd_string,
issn = rdf4r::xsd_string,
eIssn = rdf4r::xsd_string,
issue = rdf4r::xsd_integer,
volume = rdf4r::xsd_integer,
starting_page = rdf4r::xsd_integer,
ending_page = rdf4r::xsd_integer,
pensoft_pub = rdf4r::xsd_string,
pensoft_uuid = rdf4r::xsd_string
),
mongo_key = c(plazi_article = "/document/mods:mods/mods:identifier[@type='DOI']"),
constructor = plazi_metadata,
#injector = standard_injector,
components = list(
# Author
XmlSchema$new(
schema_name = "plazi_author",
xpath = "/document/mods:mods/mods:name[@type='personal']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
full_name = "./mods:namePart",
role = "./mods:role/mods:roleTerm"
),
atom_lang = c(
full_name = NA,
role = NA
),
atom_types = list(
full_name = rdf4r::xsd_string,
role = rdf4r::xsd_string
),
# injector = standard_injector,
mongo_key = c(plazi_author = "/document/mods:mods/mods:name[@type='personal']/mods:namePart"),
constructor = plazi_author,
components = NULL
),
# Treatment
XmlSchema$new(
schema_name = "plazi_treatment",
xpath = ".//treatment",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
#injector = standard_injector,
mongo_key = c(plazi_treatment = ".//treatment"),
constructor = plazi_treatment,
components = list(
# Nomenclature
XmlSchema$new(
schema_name = "nomenclature_section",
xpath = ".//subSubSection[@type='nomenclature']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(nomenclature = ".//subSubSection[@type='nomenclature']"),
constructor = nomenclature,
components = list(
XmlSchema$new(
schema_name = "nomenclature_citations-list",
xpath = "./paragraph", #rel path from nomenclature
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(nomenclature_citations = "."),
constructor = nomenclature_citations,
components = list(
XmlSchema$new(
schema_name = "treatment_citation",
xpath = "./../../subSubSection[@type='reference_group']/paragraph/treatmentCitationGroup", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".", #need to crossreference with the bibliography section,
bibr = ".//treatmentCitation/bibRefCitation/@refId"
),
atom_lang = c(
text_content = NA,
bibr = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
bibr = rdf4r::xsd_string
),
mongo_key = c(nomenclature_citation = "."),
constructor = plazi_nomenclature_citation,
components = NULL
)
)
)
)
)
,
XmlSchema$new(
schema_name = "materials_examined",
xpath = ".//subSubSection[@type='materials_examined'] | .//subSubSection[@type='types'] ", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
#paragraph = ".//paragraph"
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(type_material = "subSubSection[@type='materials_examined']"),
constructor = type_material,
components = list(
XmlSchema$new(
schema_name = "materials_examined_paragraph",
xpath = "./paragraph", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(occurrence_info_list = "."),
constructor = occurrence_list
)
)
),
#taxonx_diagnosis
XmlSchema$new(
schema_name = "diagnosis_section",
xpath = ".//subSubSection[@type='diagnosis']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(diagnosis = "."),
constructor = diagnosis
),
# distribution
XmlSchema$new(
schema_name = "distribution_section",
xpath = ".//subSubSection[@type='distribution']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(distribution = "."),
constructor = distribution
)
,
# DISCUSSION
XmlSchema$new(
schema_name = "discussion_section",
xpath = ".//subSubSection[@type='discussion']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(discussion = ".//subSubSection[@type='discussion']"),
constructor = discussion
)
,
# Taxonomic Key
XmlSchema$new(
schema_name = "taxonomic_key",
xpath = ".//subSubSection[@type='taxonomicKey']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(taxonomic_key = "."),
constructor = taxonomic_key,
components = NULL
),
# Figure
XmlSchema$new(
schema_name = "figure",
xpath = ".//figureCitation[@figureDoi]",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
caption = "./@captionText",
download_link = "./@httpUri",
doi = "./@figureDoi"
),
atom_lang = c(
text_content = NA,
caption = NA,
download_link = NA,
doi = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
caption = rdf4r::xsd_string,
download_link = rdf4r::xsd_string,
doi = rdf4r::xsd_string
),
mongo_key = c(plazi_figure = "."),
constructor = figure,
components = NULL
),
# Taxonomic Name Usage
XmlSchema$new(
schema_name = "taxonomic_name_usage",
xpath = ".//taxonomicName",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
authorship = "./@authority",
kingdom = "./@kingdom",
phylum = "./@phylum",
class = "./@class",
order = "./@order",
family = "./@family",
genus = "./@genus",
species = "./@species",
rank = "./@rank",
status = "./@status"
),
atom_lang = c(
text_content = NA,
authorship = NA,
kingdom = NA,
phylum = NA,
class = NA,
order = NA,
family = NA,
genus = NA,
species = NA,
rank = NA,
status = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
authorship = rdf4r::xsd_string,
kingdom = rdf4r::xsd_string,
phylum = rdf4r::xsd_string,
class = rdf4r::xsd_string,
order = rdf4r::xsd_string,
family = rdf4r::xsd_string,
genus = rdf4r::xsd_string,
species = rdf4r::xsd_string,
rank = rdf4r::xsd_string,
status = rdf4r::xsd_string
),
mongo_key = c(
kingdom = "./@kingdom",
phylum = "./@phylum",
class = "./@class",
order = "./@order",
family = "./@family",
subfamily = NA,
genus = "./@genus",
subgenus = NA,
species = "./@species",
subspecies = NA,
#rank = "./@rank",
#status = "./@status",
authorship = "./@authority",
secundum_literal = NA
),
constructor = taxonomic_name_usage,
components = NULL
),
#REFERENCE
XmlSchema$new(
schema_name = "reference",
xpath = ".//bibRefCitation",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
reference_id = "./@refId",
verbatim = ".",
author = "./@author",
refString = "./@refString",
year = "./@year"
),
atom_lang = c(
reference_id = NA,
verbatim = NA,
author = NA,
refString = NA,
year = NA
),
atom_types = list(
reference_id = rdf4r::xsd_string,
verbatim = rdf4r::xsd_string,
author = rdf4r::xsd_string,
refString = rdf4r::xsd_string,
year = rdf4r::xsd_string
),
mongo_key = c(reference = "."),
constructor = plazi_reference,
components = NULL
)
)
)
)
)
#' Plazi Internal
#'
#' @export
plazi_int =
XmlSchema$new(schema_name = "plazi_int",
file_pattern = ".*\\.plazixml",
extension = ".plazixml",
prefix = "http://tb.plazi.org/GgServer/xml/",
atoms = c(lang = "/document/@docLanguage"))
#' Plazi Feed
#'
#' @export
plazi_feed_schema =
XmlSchema$new(schema_name = "plazi_feed",
atoms = c(link = "/rss/channel/item/link",
pub_date = "/rss/channel/item/pubDate"))
pensoft/ropenbio documentation built on Dec. 17, 2020, 5:50 a.m.
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#' @include xml.R
#' TaxonX Schema
#'
#' @export
taxonx = XmlSchema$new(
schema_name = "taxonx",
xpath = "/",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
title = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:titleInfo/mods:title",
date = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:date",
doi = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='DOI']",
zenodo = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='Zenodo-Dep']",
zoobank = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='ZooBank']",
publisher = NA,
journal = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:titleInfo/mods:title",
journal_abbrev = NA,
issn = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='ISSN']",
eIssn = NA,
issue = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='issue']/mods:number",
volume = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='volume']/mods:number",
starting_page = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:start",
ending_page = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:end",
pensoft_pub = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:identifier[@type='Pensoft-Pub']"
),
atom_lang = c(
title = NA,
date = NA,
doi = NA,
zenodo = NA,
publisher = NA,
journal = NA,
journal_abbrev = NA,
issn = NA,
eIssn = NA,
issue = NA,
volume = NA,
starting_page = NA,
ending_page = NA,
pensoft_pub = NA
),
atom_types = list(
title = rdf4r::xsd_string,
date = rdf4r::xsd_date,
doi = rdf4r::xsd_string,
zenodo = rdf4r::xsd_string,
publisher = rdf4r::xsd_string,
journal = rdf4r::xsd_string,
journal_abbrev = rdf4r::xsd_string,
issn = rdf4r::xsd_string,
eIssn = rdf4r::xsd_string,
issue = rdf4r::xsd_integer,
volume = rdf4r::xsd_integer,
starting_page = rdf4r::xsd_integer,
ending_page = rdf4r::xsd_integer,
pensoft_pub = rdf4r::xsd_string
),
constructor = metadata,
#injector = standard_injector,
components = list(
# Author
XmlSchema$new(
schema_name = "taxonx_author",
xpath = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:name[@type='personal']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
full_name = "./mods:namePart",
role = "./mods:role/mods:roleTerm"
),
atom_lang = c(
full_name = NA,
role = NA
),
atom_types = list(
full_name = rdf4r::xsd_string,
role = rdf4r::xsd_string
),
constructor = author,
components = NULL
),
# Treatment
XmlSchema$new(
schema_name = "taxonx_treatment",
xpath = "/tax:taxonx/tax:taxonxBody/tax:treatment",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
# injector = standard_injector,
constructor = treatment,
components = list(
# Nomenclature
XmlSchema$new(
schema_name = "nomenclature_section",
xpath = ".//tax:nomenclature", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = nomenclature
),
XmlSchema$new(
schema_name = "materials_examined",
xpath = ".//tax:div[@type='materials_examined']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = materials_examined
),
#taxonx_diagnosis
XmlSchema$new(
schema_name = "diagnosis_section",
xpath = ".//tax:div[@type='diagnosis']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = diagnosis
),
# distribution
XmlSchema$new(
schema_name = "distribution_section",
xpath = ".//tax:div[@type='distribution']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = distribution
)
)
),
# DISCUSSION
XmlSchema$new(
schema_name = "discussion_section",
xpath = ".//tax:div[@type='discussion']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = discussion
),
# Taxonomic Key
XmlSchema$new(
schema_name = "taxonx_taxonomic_key",
xpath = "/tax:taxonx/tax:taxonxBody//tax:div[@type='key']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = taxonomic_key,
components = NULL
),
# Figure
XmlSchema$new(
schema_name = "taxonx_figure",
xpath = ".//tax:figure",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
constructor = figure,
components = NULL
),
# Taxonomic Name Usage
XmlSchema$new(
schema_name = "taxonx_taxonomic_name_usage",
xpath = ".//tax:name",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = "http://tb.plazi.org/GgServer/taxonx/",
atoms = c(
date = "/tax:taxonx/tax:taxonxHeader/mods:mods/mods:relatedItem/mods:part/mods:date",
kingdom = ".//dwc:Kingdom",
phylum = ".//dwc:Phylum",
class = ".//dwc:Class",
order = ".//dwc:Order",
family = ".//dwc:Family",
genus = ".//dwc:Genus",
subgenus = ".//dwc:Subgenus",
species = ".//dwc:Species", ## This is an error in TaxonX, not ropenbio!!!
subspecies = ".//dwc:Subspecies",
verbatim_rank = ".//dwc:taxonRank",
verbatim_status = NA,
authorship = ".//dwc:scientificNameAuthorship",
secundum_literal = NA
),
atom_lang = c(
date = NA,
kingdom = NA,
phylum = NA,
class = NA,
order = NA,
family = NA,
genus = NA,
subgenus = NA,
species = NA, ## This is an error in TaxonX, not DwC!
subspecies = NA,
verbatim_rank = NA,
verbatim_status = NA,
authorship = NA,
secundum_literal = NA
),
atom_types = list(
date = rdf4r::xsd_date,
kingdom = rdf4r::xsd_string,
class = rdf4r::xsd_string,
order = rdf4r::xsd_string,
family = rdf4r::xsd_string,
genus = rdf4r::xsd_string,
subgenus = rdf4r::xsd_string,
species = rdf4r::xsd_string,
subspecies = rdf4r::xsd_string,
verbatim_rank = rdf4r::xsd_string,
taxonomic_rank = rdf4r::xsd_string,
taxonomic_status = rdf4r::xsd_string,
authorship = rdf4r::xsd_string,
secundum_literal = rdf4r::xsd_string
),
constructor = taxonomic_name_usage,
components = NULL
)
)
)
#' @include xml.R
#' Plazi XML schema (not TAXONX)
#'
#' @export
plazi_schema = XmlSchema$new(
schema_name = "plazi_schema",
xpath = "/",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
title = "/document/mods:mods/mods:titleInfo/mods:title",
date = "/document/mods:mods/mods:relatedItem/mods:part/mods:date",
doi = "/document/mods:mods/mods:identifier[@type='DOI']",
zenodo = "/document/mods:mods/mods:identifier[@type='Zenodo-Dep']",
zoobank = "/document/mods:mods/mods:identifier[@type='ZooBank']",
gbif_dataset = "/document/mods:mods/mods:identifier[@type='GBIF-Dataset']",
publisher = NA,
journal = "/document/mods:mods/mods:relatedItem/mods:titleInfo/mods:title",
journal_abbrev = NA,
issn = "/document/mods:mods/mods:identifier[@type='ISSN']",
eIssn = NA,
issue = "/document/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='issue']/mods:number",
volume = "/document/mods:mods/mods:relatedItem/mods:part/mods:detail[@type='volume']/mods:number",
starting_page = "/document/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:start",
ending_page = "/document/mods:mods/mods:relatedItem/mods:part/mods:extent[@unit='page']/mods:end",
pensoft_pub = "/document/mods:mods/mods:identifier[@type='Pensoft-Pub']",
pensoft_uuid = "/document/mods:mods/mods:identifier[@type='Pensoft-UUID']"
),
atom_lang = c(
title = NA,
date = NA,
doi = NA,
zenodo = NA,
gbif_dataset = NA,
publisher = NA,
journal = NA,
journal_abbrev = NA,
issn = NA,
eIssn = NA,
issue = NA,
volume = NA,
starting_page = NA,
ending_page = NA,
pensoft_pub = NA,
pensoft_uuid = NA
),
atom_types = list(
title = rdf4r::xsd_string,
date = rdf4r::xsd_date,
doi = rdf4r::xsd_string,
zenodo = rdf4r::xsd_string,
gbif_dataset = rdf4r::xsd_string,
publisher = rdf4r::xsd_string,
journal = rdf4r::xsd_string,
journal_abbrev = rdf4r::xsd_string,
issn = rdf4r::xsd_string,
eIssn = rdf4r::xsd_string,
issue = rdf4r::xsd_integer,
volume = rdf4r::xsd_integer,
starting_page = rdf4r::xsd_integer,
ending_page = rdf4r::xsd_integer,
pensoft_pub = rdf4r::xsd_string,
pensoft_uuid = rdf4r::xsd_string
),
mongo_key = c(plazi_article = "/document/mods:mods/mods:identifier[@type='DOI']"),
constructor = plazi_metadata,
#injector = standard_injector,
components = list(
# Author
XmlSchema$new(
schema_name = "plazi_author",
xpath = "/document/mods:mods/mods:name[@type='personal']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
full_name = "./mods:namePart",
role = "./mods:role/mods:roleTerm"
),
atom_lang = c(
full_name = NA,
role = NA
),
atom_types = list(
full_name = rdf4r::xsd_string,
role = rdf4r::xsd_string
),
# injector = standard_injector,
mongo_key = c(plazi_author = "/document/mods:mods/mods:name[@type='personal']/mods:namePart"),
constructor = plazi_author,
components = NULL
),
# Treatment
XmlSchema$new(
schema_name = "plazi_treatment",
xpath = ".//treatment",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
#injector = standard_injector,
mongo_key = c(plazi_treatment = ".//treatment"),
constructor = plazi_treatment,
components = list(
# Nomenclature
XmlSchema$new(
schema_name = "nomenclature_section",
xpath = ".//subSubSection[@type='nomenclature']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(nomenclature = ".//subSubSection[@type='nomenclature']"),
constructor = nomenclature,
components = list(
XmlSchema$new(
schema_name = "nomenclature_citations-list",
xpath = "./paragraph", #rel path from nomenclature
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(nomenclature_citations = "."),
constructor = nomenclature_citations,
components = list(
XmlSchema$new(
schema_name = "treatment_citation",
xpath = "./../../subSubSection[@type='reference_group']/paragraph/treatmentCitationGroup", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".", #need to crossreference with the bibliography section,
bibr = ".//treatmentCitation/bibRefCitation/@refId"
),
atom_lang = c(
text_content = NA,
bibr = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
bibr = rdf4r::xsd_string
),
mongo_key = c(nomenclature_citation = "."),
constructor = plazi_nomenclature_citation,
components = NULL
)
)
)
)
)
,
XmlSchema$new(
schema_name = "materials_examined",
xpath = ".//subSubSection[@type='materials_examined'] | .//subSubSection[@type='types'] ", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
#paragraph = ".//paragraph"
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(type_material = "subSubSection[@type='materials_examined']"),
constructor = type_material,
components = list(
XmlSchema$new(
schema_name = "materials_examined_paragraph",
xpath = "./paragraph", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(occurrence_info_list = "."),
constructor = occurrence_list
)
)
),
#taxonx_diagnosis
XmlSchema$new(
schema_name = "diagnosis_section",
xpath = ".//subSubSection[@type='diagnosis']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(diagnosis = "."),
constructor = diagnosis
),
# distribution
XmlSchema$new(
schema_name = "distribution_section",
xpath = ".//subSubSection[@type='distribution']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(distribution = "."),
constructor = distribution
)
,
# DISCUSSION
XmlSchema$new(
schema_name = "discussion_section",
xpath = ".//subSubSection[@type='discussion']", #rel path from treatment
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
collecting_date = ".//collectingDate/@value",
collection_code = ".//collectionCode",
institution_name = ".//collectionCode/@name",
institution_uri = ".//collectionCode/@httpUri",
collector_name = ".//collectorName",
country = ".//collectingCountry",
elevation = ".//elevation",
locality = ".//location",
type_status = ".//typeStatus",
specimen_sex = ".//specimenCount[@type]",
decimal_lat = ".//geoCoordinate[@orientation='latitude']/@value",
decimal_long = ".//geoCoordinate[@orientation='longitude']/@value"
),
atom_lang = c(
text_content = NA,
collecting_date = NA,
collection_code = NA,
institution_name = NA,
institution_uri = NA,
collector_name = NA,
country = NA,
elevation = NA,
locality = NA,
type_status = NA,
specimen_sex = NA,
decimal_lat = NA,
decimal_long = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
collecting_date = rdf4r::xsd_string,
collection_code = rdf4r::xsd_string,
institution_name = rdf4r::xsd_string,
institution_uri = rdf4r::xsd_string,
collector_name = rdf4r::xsd_string,
country = rdf4r::xsd_string,
elevation = rdf4r::xsd_string,
locality = rdf4r::xsd_string,
type_status = rdf4r::xsd_string,
specimen_sex = rdf4r::xsd_string,
decimal_lat = rdf4r::xsd_string,
decimal_long = rdf4r::xsd_string
),
mongo_key = c(discussion = ".//subSubSection[@type='discussion']"),
constructor = discussion
)
,
# Taxonomic Key
XmlSchema$new(
schema_name = "taxonomic_key",
xpath = ".//subSubSection[@type='taxonomicKey']",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = "."
),
atom_lang = c(
text_content = NA
),
atom_types = list(
text_content = rdf4r::xsd_string
),
mongo_key = c(taxonomic_key = "."),
constructor = taxonomic_key,
components = NULL
),
# Figure
XmlSchema$new(
schema_name = "figure",
xpath = ".//figureCitation[@figureDoi]",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
caption = "./@captionText",
download_link = "./@httpUri",
doi = "./@figureDoi"
),
atom_lang = c(
text_content = NA,
caption = NA,
download_link = NA,
doi = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
caption = rdf4r::xsd_string,
download_link = rdf4r::xsd_string,
doi = rdf4r::xsd_string
),
mongo_key = c(plazi_figure = "."),
constructor = figure,
components = NULL
),
# Taxonomic Name Usage
XmlSchema$new(
schema_name = "taxonomic_name_usage",
xpath = ".//taxonomicName",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
text_content = ".",
authorship = "./@authority",
kingdom = "./@kingdom",
phylum = "./@phylum",
class = "./@class",
order = "./@order",
family = "./@family",
genus = "./@genus",
species = "./@species",
rank = "./@rank",
status = "./@status"
),
atom_lang = c(
text_content = NA,
authorship = NA,
kingdom = NA,
phylum = NA,
class = NA,
order = NA,
family = NA,
genus = NA,
species = NA,
rank = NA,
status = NA
),
atom_types = list(
text_content = rdf4r::xsd_string,
authorship = rdf4r::xsd_string,
kingdom = rdf4r::xsd_string,
phylum = rdf4r::xsd_string,
class = rdf4r::xsd_string,
order = rdf4r::xsd_string,
family = rdf4r::xsd_string,
genus = rdf4r::xsd_string,
species = rdf4r::xsd_string,
rank = rdf4r::xsd_string,
status = rdf4r::xsd_string
),
mongo_key = c(
kingdom = "./@kingdom",
phylum = "./@phylum",
class = "./@class",
order = "./@order",
family = "./@family",
subfamily = NA,
genus = "./@genus",
subgenus = NA,
species = "./@species",
subspecies = NA,
#rank = "./@rank",
#status = "./@status",
authorship = "./@authority",
secundum_literal = NA
),
constructor = taxonomic_name_usage,
components = NULL
),
#REFERENCE
XmlSchema$new(
schema_name = "reference",
xpath = ".//bibRefCitation",
file_pattern = ".*\\.xml",
extension = ".xml",
prefix = c(openbiodiv = "http://openbiodiv.net/"),
atoms = c(
reference_id = "./@refId",
verbatim = ".",
author = "./@author",
refString = "./@refString",
year = "./@year"
),
atom_lang = c(
reference_id = NA,
verbatim = NA,
author = NA,
refString = NA,
year = NA
),
atom_types = list(
reference_id = rdf4r::xsd_string,
verbatim = rdf4r::xsd_string,
author = rdf4r::xsd_string,
refString = rdf4r::xsd_string,
year = rdf4r::xsd_string
),
mongo_key = c(reference = "."),
constructor = plazi_reference,
components = NULL
)
)
)
)
)
#' Plazi Internal
#'
#' @export
plazi_int =
XmlSchema$new(schema_name = "plazi_int",
file_pattern = ".*\\.plazixml",
extension = ".plazixml",
prefix = "http://tb.plazi.org/GgServer/xml/",
atoms = c(lang = "/document/@docLanguage"))
#' Plazi Feed
#'
#' @export
plazi_feed_schema =
XmlSchema$new(schema_name = "plazi_feed",
atoms = c(link = "/rss/channel/item/link",
pub_date = "/rss/channel/item/pubDate"))
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