Merge pull request #43 from bcbi/dev

Add named functions and support arrays

Project.toml

@@ -1,7 +1,7 @@
 name = "REDCap"
 uuid = "ba918724-fbf9-5e4a-a61c-87e95654e718"
 authors = ["Cory Cothrum", "Dilum Aluthge <dilum@aluthge.com>", "Ashlin Harris <ashlin_harris@brown.edu>"]
-version = "2.3.0"
+version = "2.4.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

src/api_methods/arms.jl

@@ -1,3 +1,10 @@
+#TODO: consider changing all functions to the following form:
+#=
+function delete_arms(;kwargs...)
+    REDCap.request(;kwargs...)
+end
+=#
+
 function delete_arms(; url=get_url(), token=get_token(), arms=nothing,)
 	REDCap.request(;
 		url=REDCap_url(url),
@@ -15,7 +22,7 @@ end
 #All examples use JSON
 #TODO: what is the proper format for multi-item XML? I can't find this anywhere...
 # #TODO: is this ata paratamet required, given the action parameter?
-function import_arms(; url=get_url(), token=get_token(), format=nothing, data=nothing, returnFormat=nothing, override=0,)
+function import_arms(; url=get_url(), token=get_token(), format=nothing, data=nothing, returnFormat=nothing, override=nothing,)
 	REDCap.request(;
 		url=REDCap_url(url),
 		data=REDCap_data(data,REDCap_format(format),xml_tag="arms"),

src/api_methods/events.jl

@@ -14,7 +14,7 @@ function export_events(; url=get_url(), token=get_token(), format=nothing, retur
 end
 
 #TODO: data parameter required?
-function import_events(; url=get_url(), token=get_token(), format=nothing, returnFormat=nothing, data=nothing, override=0,)
+function import_events(; url=get_url(), token=get_token(), format=nothing, returnFormat=nothing, data=nothing, override=nothing,)
 
 	REDCap.request(;
 		url=REDCap_url(url),

src/api_methods/field_names.jl

@@ -1,7 +1,11 @@
-function export_list_of_export_field_names(; url=get_url(), token=get_token(), format=nothing, returnFormat=nothing, field=nothing)
+#TODO: retire this old function name?
+##TODO: what about export_fields?
+function export_list_of_export_field_names(; url=get_url(), token=get_token(), format=nothing, field=nothing)
 #TODO: field could be a single entry or an array
+##TODO: returnFormat has no effect, which I think is generally the case for export functions
 	REDCap.request(;
 		url=REDCap_url(url),
-		kwargs = (; token=REDCap_token(token), content=:exportFieldNames, format=REDCap_format(format), field, returnFormat=REDCap_format(returnFormat),),
+		kwargs = (; token=REDCap_token(token), content=:exportFieldNames, format=REDCap_format(format), field, ),
 	)
 end
+export_field_names = export_list_of_export_field_names

src/api_methods/file_repository.jl

@@ -26,6 +26,7 @@ function export_list_of_folders(; url=get_url(), token=get_token(), format=nothi
 		kwargs = (; token=REDCap_token(token), content=:fileRepository, action=:list, name, format=REDCap_format(format), folder_id, returnFormat=REDCap_format(returnFormat),),
 	)
 end
+export_folders = export_list_of_folders
 
 function import_file_from_file_repository(; url=get_url(), token=get_token(), format=nothing, returnFormat=nothing, name=nothing, file=nothing, folder_id=nothing,)
 	REDCap.request(;

src/api_methods/records.jl

@@ -7,11 +7,12 @@ function delete_records(; url=get_url(), token=get_token(), records, arm=nothing
 end
 
 #TODO: this format parameter allows odm, unlike most other format args
-function export_records(; url=get_url(), token=get_token(), format=nothing, type=nothing, records=nothing, fields=nothing, forms=nothing, events=nothing, rawOrLabel=nothing, rawOrLabelHeaders=nothing, exportCheckboxLabel=false, returnFormat=nothing, exportSurveyFields=false, exportDataAccessGroups=false, filterLogic=nothing, dateRangeBegin=nothing, dateRangeEnd=nothing, csvDelimiter=nothing, decimalCharacter=nothing, exportBlankForGrayFormStatus=nothing)
+# The REDCap_listlike turns an input like [:a, :b, :c] into "a, b, c"
+# TODO: what other parameters need this sort of treatment?
+function export_records(; url=get_url(), token=get_token(), format=nothing, type=nothing, records=nothing, fields=nothing, forms=nothing, events=nothing, rawOrLabel=nothing, rawOrLabelHeaders=nothing, exportCheckboxLabel=nothing, returnFormat=nothing, exportSurveyFields=nothing, exportDataAccessGroups=nothing, filterLogic=nothing, dateRangeBegin=nothing, dateRangeEnd=nothing, csvDelimiter=nothing, decimalCharacter=nothing, exportBlankForGrayFormStatus=nothing)
 	REDCap.request(
-		data=REDCap_data(data,REDCap_format(format),xml_tag="records"),
 		url=REDCap_url(url),
-		kwargs = (; token=REDCap_token(token), content=:record, format=REDCap_format(format), type, records, forms, events, rawOrLabel, rawOrLabelHeaders, exportCheckboxLabel, returnFormat=REDCap_format(returnFormat), exportSurveyFields, exportDataAccessGroups, filterLogic, dateRangeBegin, dateRangeEnd, csvDelimiter, decimalCharacter, exportBlankForGrayFormStatus,),
+		kwargs = (; token=REDCap_token(token), content=:record, format=REDCap_format(format), type, records, fields, forms, events, rawOrLabel, rawOrLabelHeaders, exportCheckboxLabel, returnFormat=REDCap_format(returnFormat), exportSurveyFields, exportDataAccessGroups, filterLogic, dateRangeBegin, dateRangeEnd, csvDelimiter, decimalCharacter, exportBlankForGrayFormStatus,),
 		)
 end
 

src/export.jl

@@ -13,8 +13,10 @@ delete_users,
 export_arms,
 export_DAGs,
 export_events,
+export_field_names,
 export_file,
 export_file_from_file_repository,
+export_folders,
 export_instrument_event_mappings,
 export_instruments,
 export_list_of_export_field_names,

src/request.jl

@@ -52,9 +52,11 @@ function generate_request_body(; data=nothing, odm=nothing, kwargs)
 end
 
 append_as_redcap_pair!(d::Dict, parameter::Symbol, value::Nothing) = nothing
-function append_as_redcap_pair!(parameter::Symbol, value::Array)
+function append_as_redcap_pair!(d::Dict, parameter::Symbol, value::Vector)
 	for (i, item) in enumerate(value)
-		d[string(parameter,'[',i-1,']')] = string(item)
+		# I believe either method should work:
+		d[string(parameter)] = join(value, ',')
+		#d[string(parameter,'[',i-1,']')] = string(item)
 	end
 end
 function append_as_redcap_pair!(d::Dict, parameter::Symbol, value)

src/types.jl

@@ -1,3 +1,4 @@
+#TODO: It might make sense to deprecate all internal types, instead checking values based on argument name
 REDCap_url(x) = occursin(r"^https:\/\/.*\/api\/$", x) ? URIs.URI(x) : throw(ArgumentError("Invalid REDCap url (must be \"https:// ... /api/\")"))
 
 REDCap_datetime(x::String) = DateTime(x,"yyyy-m-dd H:M")
@@ -58,4 +59,3 @@ REDCap_data(x::NamedTuple, format::Union{REDCap_format,Nothing}; xml_tag=nothing
 REDCap_data(x::String, format::Union{REDCap_format, Nothing}; xml_tag=nothing) = x
 #TODO: handle large files?
 REDCap_data(x::IOStream, format::Union{REDCap_format, Nothing}; xml_tag=nothing) = read(x,String)
-

src/utils.jl

@@ -1,3 +1,4 @@
+#TODO: Add conversion functions (maybe functinos can accept a sink 
 function get_token()
 	if !haskey(ENV, "REDCAP_API_TOKEN")
 		@error("No REDCap API token found")

test/code/workflows/basic_demography.jl

@@ -19,7 +19,7 @@ field_names = export_list_of_export_field_names(token=demography_token, format=:
        ]
 
 import_records(token=demography_token,data=(record_id=1,first_name="A",last_name="Person"))
-@test generate_next_record_name(token=demography_token) == "2"
+@test "2" == generate_next_record_name(token=demography_token)
 for i in 2:4
 	import_records(
 	       token=demography_token,
@@ -28,4 +28,6 @@ for i in 2:4
 			first_name = "A",
 			last_name = "NotherPerson"))
 end
-@test generate_next_record_name(token=demography_token) == "5"
+@test "5" == generate_next_record_name(token=demography_token)
+@test ["A","A","A","A"] == DataFrame(export_records(fields=[:age, :bmi, :first_name],token=demography_token,format=:json) |> JSON.parse).first_name
+