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getting rid of code in fromJSONString, addressing #33
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@hettling
hettling committed Dec 11, 2018
1 parent d9d7231 commit 56e8dae
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Showing 62 changed files with 1,357 additions and 1,582 deletions.
5 changes: 3 additions & 2 deletions R/Agent.r
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Expand Up @@ -93,8 +93,9 @@ Agent <- R6::R6Class(
AgentJson,
simplifyVector = FALSE
)
self[["agentText"]] <-
AgentList[["agentText"]]
self <- self$fromList(AgentList)
# self[["agentText"]] <-
# AgentList[["agentText"]]
invisible(self)
}
)
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9 changes: 5 additions & 4 deletions R/AssociatedTaxon.r
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Expand Up @@ -109,10 +109,11 @@ AssociatedTaxon <- R6::R6Class(
AssociatedTaxonJson,
simplifyVector = FALSE
)
self[["name"]] <-
AssociatedTaxonList[["name"]]
self[["relationType"]] <-
AssociatedTaxonList[["relationType"]]
self <- self$fromList(AssociatedTaxonList)
# self[["name"]] <-
# AssociatedTaxonList[["name"]]
# self[["relationType"]] <-
# AssociatedTaxonList[["relationType"]]
invisible(self)
}
)
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61 changes: 31 additions & 30 deletions R/BioStratigraphy.r
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Expand Up @@ -313,36 +313,37 @@ BioStratigraphy <- R6::R6Class(
BioStratigraphyJson,
simplifyVector = FALSE
)
self[["youngBioDatingQualifier"]] <-
BioStratigraphyList[["youngBioDatingQualifier"]]
self[["youngBioName"]] <-
BioStratigraphyList[["youngBioName"]]
self[["youngFossilZone"]] <-
BioStratigraphyList[["youngFossilZone"]]
self[["youngFossilSubZone"]] <-
BioStratigraphyList[["youngFossilSubZone"]]
self[["youngBioCertainty"]] <-
BioStratigraphyList[["youngBioCertainty"]]
self[["youngStratType"]] <-
BioStratigraphyList[["youngStratType"]]
self[["bioDatingQualifier"]] <-
BioStratigraphyList[["bioDatingQualifier"]]
self[["bioPreferredFlag"]] <-
BioStratigraphyList[["bioPreferredFlag"]]
self[["rangePosition"]] <-
BioStratigraphyList[["rangePosition"]]
self[["oldBioName"]] <-
BioStratigraphyList[["oldBioName"]]
self[["bioIdentifier"]] <-
BioStratigraphyList[["bioIdentifier"]]
self[["oldFossilzone"]] <-
BioStratigraphyList[["oldFossilzone"]]
self[["oldFossilSubzone"]] <-
BioStratigraphyList[["oldFossilSubzone"]]
self[["oldBioCertainty"]] <-
BioStratigraphyList[["oldBioCertainty"]]
self[["oldBioStratType"]] <-
BioStratigraphyList[["oldBioStratType"]]
self <- self$fromList(BioStratigraphyList)
# self[["youngBioDatingQualifier"]] <-
# BioStratigraphyList[["youngBioDatingQualifier"]]
# self[["youngBioName"]] <-
# BioStratigraphyList[["youngBioName"]]
# self[["youngFossilZone"]] <-
# BioStratigraphyList[["youngFossilZone"]]
# self[["youngFossilSubZone"]] <-
# BioStratigraphyList[["youngFossilSubZone"]]
# self[["youngBioCertainty"]] <-
# BioStratigraphyList[["youngBioCertainty"]]
# self[["youngStratType"]] <-
# BioStratigraphyList[["youngStratType"]]
# self[["bioDatingQualifier"]] <-
# BioStratigraphyList[["bioDatingQualifier"]]
# self[["bioPreferredFlag"]] <-
# BioStratigraphyList[["bioPreferredFlag"]]
# self[["rangePosition"]] <-
# BioStratigraphyList[["rangePosition"]]
# self[["oldBioName"]] <-
# BioStratigraphyList[["oldBioName"]]
# self[["bioIdentifier"]] <-
# BioStratigraphyList[["bioIdentifier"]]
# self[["oldFossilzone"]] <-
# BioStratigraphyList[["oldFossilzone"]]
# self[["oldFossilSubzone"]] <-
# BioStratigraphyList[["oldFossilSubzone"]]
# self[["oldBioCertainty"]] <-
# BioStratigraphyList[["oldBioCertainty"]]
# self[["oldBioStratType"]] <-
# BioStratigraphyList[["oldBioStratType"]]
invisible(self)
}
)
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105 changes: 53 additions & 52 deletions R/ChronoStratigraphy.r
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Expand Up @@ -489,58 +489,59 @@ ChronoStratigraphy <- R6::R6Class(
ChronoStratigraphyJson,
simplifyVector = FALSE
)
self[["youngRegionalSubstage"]] <-
ChronoStratigraphyList[["youngRegionalSubstage"]]
self[["youngRegionalStage"]] <-
ChronoStratigraphyList[["youngRegionalStage"]]
self[["youngRegionalSeries"]] <-
ChronoStratigraphyList[["youngRegionalSeries"]]
self[["youngDatingQualifier"]] <-
ChronoStratigraphyList[["youngDatingQualifier"]]
self[["youngInternSystem"]] <-
ChronoStratigraphyList[["youngInternSystem"]]
self[["youngInternSubstage"]] <-
ChronoStratigraphyList[["youngInternSubstage"]]
self[["youngInternStage"]] <-
ChronoStratigraphyList[["youngInternStage"]]
self[["youngInternSeries"]] <-
ChronoStratigraphyList[["youngInternSeries"]]
self[["youngInternErathem"]] <-
ChronoStratigraphyList[["youngInternErathem"]]
self[["youngInternEonothem"]] <-
ChronoStratigraphyList[["youngInternEonothem"]]
self[["youngChronoName"]] <-
ChronoStratigraphyList[["youngChronoName"]]
self[["youngCertainty"]] <-
ChronoStratigraphyList[["youngCertainty"]]
self[["oldDatingQualifier"]] <-
ChronoStratigraphyList[["oldDatingQualifier"]]
self[["chronoPreferredFlag"]] <-
ChronoStratigraphyList[["chronoPreferredFlag"]]
self[["oldRegionalSubstage"]] <-
ChronoStratigraphyList[["oldRegionalSubstage"]]
self[["oldRegionalStage"]] <-
ChronoStratigraphyList[["oldRegionalStage"]]
self[["oldRegionalSeries"]] <-
ChronoStratigraphyList[["oldRegionalSeries"]]
self[["oldInternSystem"]] <-
ChronoStratigraphyList[["oldInternSystem"]]
self[["oldInternSubstage"]] <-
ChronoStratigraphyList[["oldInternSubstage"]]
self[["oldInternStage"]] <-
ChronoStratigraphyList[["oldInternStage"]]
self[["oldInternSeries"]] <-
ChronoStratigraphyList[["oldInternSeries"]]
self[["oldInternErathem"]] <-
ChronoStratigraphyList[["oldInternErathem"]]
self[["oldInternEonothem"]] <-
ChronoStratigraphyList[["oldInternEonothem"]]
self[["oldChronoName"]] <-
ChronoStratigraphyList[["oldChronoName"]]
self[["chronoIdentifier"]] <-
ChronoStratigraphyList[["chronoIdentifier"]]
self[["oldCertainty"]] <-
ChronoStratigraphyList[["oldCertainty"]]
self <- self$fromList(ChronoStratigraphyList)
# self[["youngRegionalSubstage"]] <-
# ChronoStratigraphyList[["youngRegionalSubstage"]]
# self[["youngRegionalStage"]] <-
# ChronoStratigraphyList[["youngRegionalStage"]]
# self[["youngRegionalSeries"]] <-
# ChronoStratigraphyList[["youngRegionalSeries"]]
# self[["youngDatingQualifier"]] <-
# ChronoStratigraphyList[["youngDatingQualifier"]]
# self[["youngInternSystem"]] <-
# ChronoStratigraphyList[["youngInternSystem"]]
# self[["youngInternSubstage"]] <-
# ChronoStratigraphyList[["youngInternSubstage"]]
# self[["youngInternStage"]] <-
# ChronoStratigraphyList[["youngInternStage"]]
# self[["youngInternSeries"]] <-
# ChronoStratigraphyList[["youngInternSeries"]]
# self[["youngInternErathem"]] <-
# ChronoStratigraphyList[["youngInternErathem"]]
# self[["youngInternEonothem"]] <-
# ChronoStratigraphyList[["youngInternEonothem"]]
# self[["youngChronoName"]] <-
# ChronoStratigraphyList[["youngChronoName"]]
# self[["youngCertainty"]] <-
# ChronoStratigraphyList[["youngCertainty"]]
# self[["oldDatingQualifier"]] <-
# ChronoStratigraphyList[["oldDatingQualifier"]]
# self[["chronoPreferredFlag"]] <-
# ChronoStratigraphyList[["chronoPreferredFlag"]]
# self[["oldRegionalSubstage"]] <-
# ChronoStratigraphyList[["oldRegionalSubstage"]]
# self[["oldRegionalStage"]] <-
# ChronoStratigraphyList[["oldRegionalStage"]]
# self[["oldRegionalSeries"]] <-
# ChronoStratigraphyList[["oldRegionalSeries"]]
# self[["oldInternSystem"]] <-
# ChronoStratigraphyList[["oldInternSystem"]]
# self[["oldInternSubstage"]] <-
# ChronoStratigraphyList[["oldInternSubstage"]]
# self[["oldInternStage"]] <-
# ChronoStratigraphyList[["oldInternStage"]]
# self[["oldInternSeries"]] <-
# ChronoStratigraphyList[["oldInternSeries"]]
# self[["oldInternErathem"]] <-
# ChronoStratigraphyList[["oldInternErathem"]]
# self[["oldInternEonothem"]] <-
# ChronoStratigraphyList[["oldInternEonothem"]]
# self[["oldChronoName"]] <-
# ChronoStratigraphyList[["oldChronoName"]]
# self[["chronoIdentifier"]] <-
# ChronoStratigraphyList[["chronoIdentifier"]]
# self[["oldCertainty"]] <-
# ChronoStratigraphyList[["oldCertainty"]]
invisible(self)
}
)
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9 changes: 5 additions & 4 deletions R/Crs.r
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Expand Up @@ -105,10 +105,11 @@ Crs <- R6::R6Class(
CrsJson,
simplifyVector = FALSE
)
self[["type"]] <-
CrsList[["type"]]
self[["properties"]] <-
CrsList[["properties"]]
self <- self$fromList(CrsList)
# self[["type"]] <-
# CrsList[["type"]]
# self[["properties"]] <-
# CrsList[["properties"]]
invisible(self)
}
)
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45 changes: 23 additions & 22 deletions R/DefaultClassification.r
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Expand Up @@ -253,28 +253,29 @@ DefaultClassification <- R6::R6Class(
DefaultClassificationJson,
simplifyVector = FALSE
)
self[["kingdom"]] <-
DefaultClassificationList[["kingdom"]]
self[["phylum"]] <-
DefaultClassificationList[["phylum"]]
self[["className"]] <-
DefaultClassificationList[["className"]]
self[["order"]] <-
DefaultClassificationList[["order"]]
self[["superFamily"]] <-
DefaultClassificationList[["superFamily"]]
self[["family"]] <-
DefaultClassificationList[["family"]]
self[["genus"]] <-
DefaultClassificationList[["genus"]]
self[["subgenus"]] <-
DefaultClassificationList[["subgenus"]]
self[["specificEpithet"]] <-
DefaultClassificationList[["specificEpithet"]]
self[["infraspecificEpithet"]] <-
DefaultClassificationList[["infraspecificEpithet"]]
self[["infraspecificRank"]] <-
DefaultClassificationList[["infraspecificRank"]]
self <- self$fromList(DefaultClassificationList)
# self[["kingdom"]] <-
# DefaultClassificationList[["kingdom"]]
# self[["phylum"]] <-
# DefaultClassificationList[["phylum"]]
# self[["className"]] <-
# DefaultClassificationList[["className"]]
# self[["order"]] <-
# DefaultClassificationList[["order"]]
# self[["superFamily"]] <-
# DefaultClassificationList[["superFamily"]]
# self[["family"]] <-
# DefaultClassificationList[["family"]]
# self[["genus"]] <-
# DefaultClassificationList[["genus"]]
# self[["subgenus"]] <-
# DefaultClassificationList[["subgenus"]]
# self[["specificEpithet"]] <-
# DefaultClassificationList[["specificEpithet"]]
# self[["infraspecificEpithet"]] <-
# DefaultClassificationList[["infraspecificEpithet"]]
# self[["infraspecificRank"]] <-
# DefaultClassificationList[["infraspecificRank"]]
invisible(self)
}
)
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23 changes: 11 additions & 12 deletions R/Expert.r
View file
Expand Up @@ -124,18 +124,17 @@ Expert <- R6::R6Class(
ExpertJson,
simplifyVector = FALSE
)
self[["agentText"]] <-
ExpertList[["agentText"]]
self[["fullName"]] <-
ExpertList[["fullName"]]
self[["organization"]] <-
Organization$new()$fromJSONString(
jsonlite::toJSON(
ExpertList[["organization"]],
auto_unbox = TRUE
),
typeMapping = typeMapping
)
self <- self$fromList(ExpertList)
# self[["agentText"]] <-
# ExpertList[["agentText"]]
# self[["fullName"]] <-
# ExpertList[["fullName"]]
# self[["organization"]] <-
# Organization$new()$fromJSONString(
# jsonlite::toJSON(
# ExpertList[["organization"]],
# auto_unbox = TRUE),
# typeMapping = typeMapping)
invisible(self)
}
)
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31 changes: 15 additions & 16 deletions R/Feature.r
View file
Expand Up @@ -152,22 +152,21 @@ Feature <- R6::R6Class(
FeatureJson,
simplifyVector = FALSE
)
self[["crs"]] <-
Crs$new()$fromJSONString(
jsonlite::toJSON(
FeatureList[["crs"]],
auto_unbox = TRUE
),
typeMapping = typeMapping
)
self[["bbox"]] <-
FeatureList[["bbox"]]
self[["properties"]] <-
FeatureList[["properties"]]
self[["geometry"]] <-
FeatureList[["geometry"]]
self[["id"]] <-
FeatureList[["id"]]
self <- self$fromList(FeatureList)
# self[["crs"]] <-
# Crs$new()$fromJSONString(
# jsonlite::toJSON(
# FeatureList[["crs"]],
# auto_unbox = TRUE),
# typeMapping = typeMapping)
# self[["bbox"]] <-
# FeatureList[["bbox"]]
# self[["properties"]] <-
# FeatureList[["properties"]]
# self[["geometry"]] <-
# FeatureList[["geometry"]]
# self[["id"]] <-
# FeatureList[["id"]]
invisible(self)
}
)
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38 changes: 16 additions & 22 deletions R/FeatureCollection.r
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Expand Up @@ -138,28 +138,22 @@ FeatureCollection <- R6::R6Class(
FeatureCollectionJson,
simplifyVector = FALSE
)
self[["crs"]] <-
Crs$new()$fromJSONString(
jsonlite::toJSON(
FeatureCollectionList[["crs"]],
auto_unbox = TRUE
),
typeMapping = typeMapping
)
self[["bbox"]] <-
FeatureCollectionList[["bbox"]]
self[["features"]] <- lapply(
FeatureCollectionList[["features"]],
function(x) {
Feature$new()$fromJSONString(
jsonlite::toJSON(
x,
auto_unbox = TRUE
),
typeMapping = typeMapping
)
}
)
self <- self$fromList(FeatureCollectionList)
# self[["crs"]] <-
# Crs$new()$fromJSONString(
# jsonlite::toJSON(
# FeatureCollectionList[["crs"]],
# auto_unbox = TRUE),
# typeMapping = typeMapping)
# self[["bbox"]] <-
# FeatureCollectionList[["bbox"]]
# self[["features"]] <- lapply(FeatureCollectionList[["features"]],
# function(x) {
# Feature$new()$fromJSONString(
# jsonlite::toJSON(
# x,
# auto_unbox = TRUE),
# typeMapping = typeMapping)})
invisible(self)
}
)
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