Merge pull request #640 from ropensci/occ_search

multivalue support for more args

R/occ_data.R

@@ -132,30 +132,30 @@ occ_data <- function(taxonKey=NULL,
     args <- rgbif_compact(
       list(
         hasCoordinate = hasCoordinate,
-        lastInterpreted = lastInterpreted,
-        decimalLatitude = decimalLatitude,
-        decimalLongitude = decimalLongitude,
         hasGeospatialIssue = hasGeospatialIssue,
         occurrenceStatus = occurrenceStatus,
         q = search,
         repatriated = repatriated,
-        elevation = elevation,
-        depth = depth, 
         limit = check_limit(as.integer(limit)),
-        eventDate = eventDate, 
-        month = month, 
-        year = year,
-        coordinateUncertaintyInMeters = coordinateUncertaintyInMeters,
-        organismQuantity = organismQuantity,
-        organismQuantityType = organismQuantityType,
-        relativeOrganismQuantity = relativeOrganismQuantity,
         isInCluster = isInCluster,
         offset = check_limit(as.integer(start))
       )
     )
     args <- c(
       args,
       parse_issues(issue),
+      convmany(lastInterpreted),
+      convmany(decimalLatitude),
+      convmany(decimalLongitude),
+      convmany(elevation),
+      convmany(depth), 
+      convmany(eventDate),
+      convmany(month),
+      convmany(year),
+      convmany(coordinateUncertaintyInMeters),
+      convmany(organismQuantity),
+      convmany(organismQuantityType),
+      convmany(relativeOrganismQuantity),
       convmany(taxonKey),
       convmany(scientificName),
       convmany(country),

R/occ_facet.R

@@ -55,31 +55,3 @@ occ_facet <- function(facet, facetMincount = NULL, curlopts = list(), ...) {
   }), vapply(tt$facets, function(x) to_camel(x$field), ""))
 }
 
-collargs <- function(x){
-  outlist <- list()
-  for (i in seq_along(x)) {
-    outlist[[i]] <- makemultiargs(x[[i]])
-  }
-  as.list(unlist(rgbif_compact(outlist)))
-}
-
-makemultiargs <- function(x){
-  value <- get(x, envir = parent.frame(n = 2))
-  if ( length(value) == 0 ) {
-    NULL
-  } else {
-    if ( any(sapply(value, is.na)) ) {
-      NULL
-    } else {
-      if ( !is.character(value) ) {
-        value <- as.character(value)
-      }
-      names(value) <- rep(x, length(value))
-      value
-    }
-  }
-}
-
-to_camel <- function(x) {
-  gsub("(_)([a-z])", "\\U\\2", tolower(x), perl = TRUE)
-}

R/occ_search.r

@@ -126,23 +126,11 @@ occ_search <- function(taxonKey=NULL,
     args <- rgbif_compact(
       list(
         hasCoordinate = hasCoordinate,
-        lastInterpreted = lastInterpreted,
-        decimalLatitude = decimalLatitude,
-        decimalLongitude = decimalLongitude,
         hasGeospatialIssue = hasGeospatialIssue,
         occurrenceStatus = occurrenceStatus,
         q = search,
         repatriated = repatriated,
-        elevation = elevation,
-        depth = depth, 
         limit = check_limit(as.integer(limit)),
-        eventDate = eventDate, 
-        month = month, 
-        year = year,
-        coordinateUncertaintyInMeters = coordinateUncertaintyInMeters,
-        organismQuantity = organismQuantity,
-        organismQuantityType = organismQuantityType,
-        relativeOrganismQuantity = relativeOrganismQuantity,
         isInCluster = isInCluster,
         offset = check_limit(as.integer(start))
       )
@@ -153,6 +141,18 @@ occ_search <- function(taxonKey=NULL,
       parse_issues(issue),
       collargs("facet"),
       yank_args(...),
+      convmany(lastInterpreted),
+      convmany(decimalLatitude),
+      convmany(decimalLongitude),
+      convmany(elevation),
+      convmany(depth), 
+      convmany(eventDate), 
+      convmany(month), 
+      convmany(year),
+      convmany(coordinateUncertaintyInMeters),
+      convmany(organismQuantity),
+      convmany(organismQuantityType),
+      convmany(relativeOrganismQuantity),
       convmany(taxonKey),
       convmany(scientificName),
       convmany(country),
@@ -197,7 +197,6 @@ occ_search <- function(taxonKey=NULL,
       convmany(lifeStage),
       convmany(distanceFromCentroidInMeters)
     )
-
     argscoll <<- args
 
     if (limit >= 300) {

R/zzz.r

@@ -763,3 +763,33 @@ prep_output <- function(x) {
   )
 }
 
+collargs <- function(x){
+  outlist <- list()
+  for (i in seq_along(x)) {
+    outlist[[i]] <- makemultiargs(x[[i]])
+  }
+  as.list(unlist(rgbif_compact(outlist)))
+}
+
+makemultiargs <- function(x){
+  value <- get(x, envir = parent.frame(n = 2))
+  if ( length(value) == 0 ) {
+    NULL
+  } else {
+    if ( any(sapply(value, is.na)) ) {
+      NULL
+    } else {
+      if ( !is.character(value) ) {
+        value <- as.character(value)
+      }
+      names(value) <- rep(x, length(value))
+      value
+    }
+  }
+}
+
+to_camel <- function(x) {
+  gsub("(_)([a-z])", "\\U\\2", tolower(x), perl = TRUE)
+}
+
+

tests/fixtures/occ_count.yml

@@ -19,13 +19,13 @@ http_interactions:
     body:
       encoding: ''
       file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjI4MDMzNTUx
+      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjI4NDgyMDU2
         NiwicmVzdWx0cyI6W10sImZhY2V0cyI6W119
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&offset=0
+    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&offset=0&facetLimit=&year=2000%2C2011&taxonKey=212
     body:
       encoding: ''
       string: ''
@@ -43,85 +43,13 @@ http_interactions:
     body:
       encoding: ''
       file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjI4MDMzNTUx
-        NiwicmVzdWx0cyI6W10sImZhY2V0cyI6W119
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&year=2000%2C2011&offset=0&facetLimit=&taxonKey=212
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjIyNzg4MzUw
-        LCJyZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&year=2000%2C2011&offset=0&taxonKey=212
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjIyNzg4MzUw
+      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjIyODMzOTM4
         LCJyZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&year=2012&offset=0&facetLimit=
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6Njc3NjkyMTUs
-        InJlc3VsdHMiOltdLCJmYWNldHMiOltdfQ==
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&year=2012&offset=0
+    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&offset=0&facetLimit=&year=2012
     body:
       encoding: ''
       string: ''
@@ -139,9 +67,9 @@ http_interactions:
     body:
       encoding: ''
       file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6Njc3NjkyMTUs
+      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6Njc4ODY4MjMs
         InJlc3VsdHMiOltdLCJmYWNldHMiOltdfQ==
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
@@ -163,37 +91,13 @@ http_interactions:
     body:
       encoding: ''
       file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6Mjg5OTMwNTUs
+      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjkwMTc3MTcs
         InJlc3VsdHMiOltdLCJmYWNldHMiOltdfQ==
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=ABSENT&limit=0&offset=0
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6Mjg5OTMwNTUs
-        InJlc3VsdHMiOltdLCJmYWNldHMiOltdfQ==
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&organismQuantity=5&offset=0&facetLimit=&basisOfRecord=MATERIAL_SAMPLE
+    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&offset=0&facetLimit=&organismQuantity=5&basisOfRecord=MATERIAL_SAMPLE
     body:
       encoding: ''
       string: ''
@@ -213,31 +117,7 @@ http_interactions:
       file: no
       base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6OTQxNTM5LCJy
         ZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&organismQuantity=5&offset=0&basisOfRecord=MATERIAL_SAMPLE
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6OTQxNTM5LCJy
-        ZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2
 - request:
     method: get
@@ -259,31 +139,7 @@ http_interactions:
     body:
       encoding: ''
       file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjY1ODQyLCJy
-        ZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
-  recorded_with: vcr/1.2.0, webmockr/0.8.2
-- request:
-    method: get
-    uri: https://api.gbif.org/v1/occurrence/search?occurrenceStatus=PRESENT&limit=0&offset=0&verbatimScientificName=Calopteryx%20splendens&verbatimScientificName=Calopteryx%20virgo
-    body:
-      encoding: ''
-      string: ''
-    headers:
-      Accept-Encoding: gzip, deflate
-      Accept: application/json, text/xml, application/xml, */*
-  response:
-    status:
-      status_code: '200'
-      message: OK
-      explanation: Request fulfilled, document follows
-    headers:
-      status: HTTP/1.1 200 OK
-      content-type: application/json
-    body:
-      encoding: ''
-      file: no
-      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjY1ODQyLCJy
+      base64_string: eyJvZmZzZXQiOjAsImxpbWl0IjowLCJlbmRPZlJlY29yZHMiOmZhbHNlLCJjb3VudCI6MjY1OTA1LCJy
         ZXN1bHRzIjpbXSwiZmFjZXRzIjpbXX0=
-  recorded_at: 2023-03-06 15:33:29 GMT
+  recorded_at: 2023-03-09 14:40:20 GMT
   recorded_with: vcr/1.2.0, webmockr/0.8.2