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eblondeleblondel
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impl #309 #376 
1 parent 33771d9 commit a72a9bf

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+77
-34
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4 files changed

+77
-34
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‎R/executeWorkflowJob.R

+10-4
Original file line numberDiff line numberDiff line change
@@ -29,6 +29,7 @@ executeWorkflowJob <- function(config, jobdir = NULL, queue = NULL, monitor = NU
2929
skipDataDownload = config$profile$options$skipFileDownload
3030
}
3131
skipDataDownload <- if(!is.null(config$profile$options$skipDataDownload)) config$profile$options$skipDataDownload else FALSE
32+
skipEnrichWithData = if(!is.null(config$profile$options$skipEnrichWithData)) config$profile$options$skipEnrichWithData else FALSE
3233

3334
#Actions onstart
3435
config$log_separator("-")
@@ -136,17 +137,22 @@ executeWorkflowJob <- function(config, jobdir = NULL, queue = NULL, monitor = NU
136137
entity$copyDataToJobDir(config, jobdir)
137138
#vector data: we enrich entity with features
138139
#control is added in case of entity already enriched with features/coverages (when loaded from custom R entity handlers)
139-
if(is.null(entity$data$features) && is.null(entity$data$coverages)){
140+
if(!skipEnrichWithData) if(is.null(entity$data$features) && is.null(entity$data$coverages)){
140141
entity$enrichWithData(config, jobdir)
141142
}
142143

143144
setwd(entity$getEntityJobDirPath(config, jobdir)) #make sure we are in entity jobdir
144145
#we check if the source and upload are both different file format (csv,shp,gpkg) and process automatically to conversion from source to upload type
145146
entity$prepareFeaturesToUpload(config)
146147
}else{
147-
config$logger.info("SkipDataDownload is true: fetching spatial coverage from data (for DB sources only)...")
148-
#alternative behaviors in case we don't download data, applies to DB only
149-
entity$enrichSpatialCoverageFromDB(config)
148+
config$logger.info("SkipDataDownload is true:")
149+
if(!skipEnrichWithData){
150+
config$logger.info("SkipEnrichWithData is false: Fetching spatial coverage from data (for DB sources only)...")
151+
#alternative behaviors in case we don't download data, applies to DB only
152+
entity$enrichSpatialCoverageFromDB(config)
153+
}else{
154+
config$logger.info("SkipEnrichWithData is true")
155+
}
150156
}
151157

152158
#extra identifiers to use in entity identification/actions

‎R/geoflow_featuremember.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -49,8 +49,8 @@ geoflow_featuremember <- R6Class("geoflow_featuremember",
4949
initialize = function(type, code, name, def, defSource = NULL,
5050
minOccurs = NULL, maxOccurs = NULL, uom = NULL,
5151
registerId = NULL){
52-
if(!type %in% c("attribute", "variable")){
53-
stop("The member type should be either 'attribute' or 'variable'")
52+
if(!(type %in% c("attribute", "variable") | startsWith(type, "gml:"))){
53+
stop("The member type should be either 'attribute' or 'variable' or be a GML geometry type")
5454
}
5555
self$id = code
5656
self$type = type

‎doc/documentation.Rmd

+2-1
Original file line numberDiff line numberDiff line change
@@ -176,8 +176,9 @@ The ``options`` are by definition optional. The table below defines the possible
176176
Name|Definition|Default value
177177
----|----------|-------------
178178
``line_separator``|Defines the suite of characters used for splitting metadata components with a single tabular cell of an _entity_ (eg. Description field)|**_\n**
179-
``skipDataDownload``|Indicates whether data associated to an entity should be download|**false**
179+
``skipDataDownload``|Indicates whether downloading data associated to an entity should be skipped|**false**
180180
``skipFileDownload``|Deprecated, use `skipDataDownload` instead.|**false**
181+
``skipEnrichWithData``|Indicates whether actual data objects (features/coverages) reading and association with entity data should be skipped or not|**false**
181182
``skipDynamicBbox``|Indicates whether bbox inherited from data should be ignored.|**false**
182183
``enrichDataStrategy``|Strategy to use when inheriting spatial bbox from multiple data objects, either "first" (take the first data object for the bbox, or "union" (union of bboxes from the different data objects).|**"first"*
183184

‎inst/actions/geometa_create_iso_19110.R

+63-27
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,8 @@ function(action, entity, config){
66

77
ISOMetadataNamespace$GML$uri <- "http://www.opengis.net/gml/3.2"
88

9+
skipEnrichWithData = if(!is.null(config$profile$options$skipEnrichWithData)) config$profile$options$skipEnrichWithData else FALSE
10+
911
#manage multiple sources (supposes a common data structure to expose as ISO 19110)
1012
data_objects <- list()
1113
if(is.null(entity$data$dir)){
@@ -15,11 +17,25 @@ function(action, entity, config){
1517
}
1618

1719
#features if any
20+
build_catalog_from_features = TRUE
1821
features = do.call("rbind", lapply(data_objects, function(data_object){data_object$features}))
1922
if(is.null(features)){
20-
warnMsg <- sprintf("No data features associated to entity '%s'. Skip feature catalogue creation", entity$identifiers[["id"]])
21-
config$logger.warn(warnMsg)
22-
return(FALSE)
23+
if(!skipEnrichWithData){
24+
warnMsg <- sprintf("No data features associated to entity '%s' and global option 'skipEnrichWithData' is false. Skip feature catalogue creation", entity$identifiers[["id"]])
25+
config$logger.warn(warnMsg)
26+
return(FALSE)
27+
}else{
28+
fto <- entity$data$featureTypeObj
29+
if(!is.null(fto)){
30+
infoMsg <- "Global option 'skipEnrichWithData' is true. Feature catalogue will be created based on the dictionary only"
31+
config$logger.info(infoMsg)
32+
build_catalog_from_features = FALSE
33+
}else{
34+
warnMsg <- "Global option 'skipEnrichWithData' is true, but no dictionary available. Skip feature catalogue creation"
35+
config$logger.warn(warnMsg)
36+
return(FALSE)
37+
}
38+
}
2339
}
2440

2541
#options
@@ -154,7 +170,14 @@ function(action, entity, config){
154170
ft$setCode(entity$identifiers$id)
155171
ft$setIsAbstract(FALSE)
156172

157-
columns <- c(colnames(features), unlist(extra_attributes))
173+
columns <- if(build_catalog_from_features){
174+
#from data features
175+
c(colnames(features), unlist(extra_attributes))
176+
}else{
177+
#from dictionary
178+
fto <- entity$data$featureTypeObj
179+
sapply(fto$getMembers(), function(x){x$id})
180+
}
158181
for(featureAttrName in columns){
159182

160183
if(featureAttrName %in% exclude_attributes){
@@ -221,13 +244,12 @@ function(action, entity, config){
221244
}
222245

223246
#add listed values
224-
if(featureAttrName %in% colnames(features)){
247+
featureAttrValues <- fat_attr_register$data$code
248+
if(build_catalog_from_features) if(featureAttrName %in% colnames(features)){
225249
featureAttrValues <- switch(class(features)[1],
226250
"sf" = features[,featureAttrName][[1]],
227251
"data.frame" = features[,featureAttrName]
228252
)
229-
}else{
230-
featureAttrValues <- fat_attr_register$data$code
231253
}
232254

233255
addValues <- TRUE
@@ -242,7 +264,7 @@ function(action, entity, config){
242264
if(fat_attr$type == "variable") addValues <- FALSE
243265
}
244266
}
245-
if(addValues){
267+
if(!is.null(featureAttrValues) & addValues){
246268
config$logger.info(sprintf("Listing values for feature Attribute '%s'...", featureAttrName))
247269
featureAttrValues <- unique(featureAttrValues)
248270
featureAttrValues <- featureAttrValues[order(featureAttrValues)]
@@ -273,26 +295,40 @@ function(action, entity, config){
273295
}
274296

275297
#add primitive type + data type (attribute or variable) as valueType
276-
fat_type <- switch(class(featureAttrValues[1])[1],
277-
"integer" = "xsd:int",
278-
"numeric" = "xsd:decimal",
279-
"character" = "xsd:string",
280-
"logical" = "xsd:boolean",
281-
"Date" = "xsd:date",
282-
"POSIXct" = "xsd:datetime",
283-
"sfc_POINT" = "gml:PointPropertyType",
284-
"sfc_MULTIPOINT" = "gml:MultiPointPropertyType",
285-
"sfc_LINESTRING" = "gml:LineStringPropertyType",
286-
"sfc_MULTILINESTRING" = "gml:MultiLineStringPropertyType",
287-
"sfc_POLYGON" = "gml:PolygonPropertyType",
288-
"sfc_MULTIPOLYGON" = "gml:MultiPolygonPropertyType"
289-
)
298+
fat_type <- if(build_catalog_from_features){
299+
switch(class(featureAttrValues[1])[1],
300+
"integer" = "xsd:int",
301+
"numeric" = "xsd:decimal",
302+
"character" = "xsd:string",
303+
"logical" = "xsd:boolean",
304+
"Date" = "xsd:date",
305+
"POSIXct" = "xsd:datetime",
306+
"sfc_POINT" = "gml:PointPropertyType",
307+
"sfc_MULTIPOINT" = "gml:MultiPointPropertyType",
308+
"sfc_LINESTRING" = "gml:LineStringPropertyType",
309+
"sfc_MULTILINESTRING" = "gml:MultiLineStringPropertyType",
310+
"sfc_POLYGON" = "gml:PolygonPropertyType",
311+
"sfc_MULTIPOLYGON" = "gml:MultiPolygonPropertyType"
312+
)
313+
}else{
314+
type = if(!is.null(fto)) fto$getMemberById(featureAttrName)$type else "attribute"
315+
switch(type,
316+
"attribute" = "xsd:string",
317+
"variable" = "xsd:decimal",
318+
type
319+
)
320+
}
290321
config$logger.info(sprintf("Set primitive type '%s' for feature Attribute '%s'...", fat_type, featureAttrName))
291-
fat_generic_type <- switch(class(featureAttrValues[1])[1],
292-
"integer" = "variable",
293-
"numeric" = "variable",
294-
"attribute"
295-
)
322+
fat_generic_type <- if(build_catalog_from_features){
323+
switch(class(featureAttrValues[1])[1],
324+
"integer" = "variable",
325+
"numeric" = "variable",
326+
"attribute"
327+
)
328+
}else{
329+
if(!is.null(fto)) fto$getMemberById(featureAttrName)$type else "attribute"
330+
}
331+
config$logger.info(sprintf("Feature member generic type for '%s': %s", featureAttrName, fat_generic_type))
296332
if(!is.null(fat_attr)) fat_generic_type <- fat_attr$type
297333
fat_type_anchor <- ISOAnchor$new(name = fat_type, href = fat_generic_type)
298334
fat$setValueType(fat_type_anchor)

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