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Merge pull request #3 from PharmCat/dev
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update 0.2.5
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@PharmCat
PharmCat committed Jan 13, 2023
2 parents d4c71b2 + 1ed7f8d commit 290376f
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Showing 5 changed files with 90 additions and 20 deletions.
2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "ODMXMLTools"
uuid = "2456a17b-6ca2-4f51-9342-f0287e829718"
authors = ["PharmCat <[email protected]>"]
version = "0.2.4"
version = "0.2.5"

[deps]

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85 changes: 73 additions & 12 deletions src/odmxml.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,17 @@ function appendelements!(inds::AbstractVector, n::AbstractODMNode, nname::Symbol
end
inds
end

function appendelements!(inds::AbstractVector, n::AbstractODMNode, nname::Union{Set{Symbol}, AbstractVector{Symbol}})
for i in n.el
if name(i) in nname
push!(inds, i)
end
end
inds
end


function content(n::ODMTextNode)
getfield(n, :content)
end
Expand All @@ -191,6 +202,7 @@ function content(n::AbstractODMNode)
nothing
end


t_collect(a::Tuple) = [i for i in a];
t_collect(a::Vector) = a;
t_collect(a) = collect(a);
Expand Down Expand Up @@ -728,27 +740,58 @@ end


"""
clinicaldatatable(cd::AbstractODMNode; itemgroup = nothing)
clinicaldatatable(cd::AbstractODMNode;
itemgroup = nothing,
form = nothing,
item::Union{Nothing, AbstractString, <: AbstractVector{<:AbstractString}} = nothing,
categ = false,
addstudyid = false,
addstudyidcol = false,
idlnames = nothing)
Return clinical data table in long formal. `cd` should be ClinicalData.
* `itemgroup` - only this ItemGroupOID;
* `form` - only this FormOID;
* `item` - only this ItemOID;
* `categ` - make collumns categorical;
* `addstudyid` - add StudyOID as prefix to SubjectKey: "StudyOID_SubjectKey";
* `addstudyidcol` - add StudyOID as collumn to dataframe;
* `idlnames` - only this types of data will be collected, for example: ItemData, ItemDataInteger, ets (if `nothing`` - all will be collected).
"""
function clinicaldatatable(cd::AbstractODMNode;
itemgroup = nothing,
form = nothing,
item::Union{Nothing, AbstractString, <: AbstractVector{<:AbstractString}} = nothing,
categ = false, )
categ = false,
addstudyid = false,
addstudyidcol = false,
idlnames = nothing)


if name(cd) != :ClinicalData error("This is not ClinicalData") end
# For TypedData
datatype = String
#df = DataFrame(SubjectKey = String[], StudyEventOID = CategoricalArray(String[]), FormOID = CategoricalArray(String[]), ItemGroupOID = CategoricalArray(String[]), ItemGroupRepeatKey = CategoricalArray(String[]), ItemOID = CategoricalArray(String[]), Value = String[])
df = DataFrame(SubjectKey = String[], StudyEventOID = String[], FormOID = String[], ItemGroupOID = String[], ItemGroupRepeatKey = String[], ItemOID = String[], Value = String[])
df = DataFrame(SubjectKey = String[], StudyEventOID = String[], FormOID = String[], ItemGroupOID = String[], ItemGroupRepeatKey = String[], ItemOID = String[], Value = datatype[])
sdl = findelements(cd, :SubjectData)
edl = AbstractODMNode[]
fdl = AbstractODMNode[]
gdl = AbstractODMNode[]
idl = AbstractODMNode[]

if isnothing(idlnames)
idlnames = pushfirst!(collect(ITEMDATATYPE), :ItemData)
end

if isa(item, AbstractString) item = [item] end
#sdl = Iterators.filter(isSubjectData, cd.el)
for s in sdl
if addstudyid
subjid = attribute(cd, :StudyOID)*"_"*attribute(s, :SubjectKey)
else
subjid = attribute(s, :SubjectKey)
end
resize!(edl, 0)
appendelements!(edl, s, :StudyEventData)
#edl = Iterators.filter(isStudyEventData, s.el)
Expand All @@ -768,19 +811,34 @@ function clinicaldatatable(cd::AbstractODMNode;
if attribute(f, :FormOID) != form continue end
end
resize!(idl, 0)
appendelements!(idl, g, :ItemData)
#idl = Iterators.filter(isItemData, g.el)
appendelements!(idl, g, idlnames)
#idl = Iterators.filter(isItemData, g.el)
for i in idl
if !isnothing(item)
if !(attribute(i, :ItemOID) in item) continue end
end
push!(df, (attribute(s, :SubjectKey),
attribute(e, :StudyEventOID),
attribute(f, :FormOID),
attribute(g, :ItemGroupOID),
attribute(g, :ItemGroupRepeatKey),
attribute(i, :ItemOID),
attribute(i, :Value)))
if isItemData(i)
push!(df, (subjid,
attribute(e, :StudyEventOID),
attribute(f, :FormOID),
attribute(g, :ItemGroupOID),
attribute(g, :ItemGroupRepeatKey),
attribute(i, :ItemOID),
attribute(i, :Value)))
else
val = content(i)
if isnothing(val)
@warn "ItemData[TYPE] content is empty"
val = ""
end
push!(df, (subjid,
attribute(e, :StudyEventOID),
attribute(f, :FormOID),
attribute(g, :ItemGroupOID),
attribute(g, :ItemGroupRepeatKey),
attribute(i, :ItemOID),
val))
end
end
end
end
Expand All @@ -793,6 +851,9 @@ function clinicaldatatable(cd::AbstractODMNode;
transform!(df, :ItemGroupRepeatKey => categorical, renamecols=false)
transform!(df, :ItemOID => categorical, renamecols=false)
end
if addstudyidcol
insertcols!(df, 1, :StudyOID=>fill(attribute(cd, :StudyOID), size(df, 1)); copycols=false)
end
df
end
"""
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12 changes: 6 additions & 6 deletions src/spss.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -39,16 +39,16 @@ end


"""
spss_form_variable_labels(mdb, form; variable, labels)
spss_form_variable_labels(mdb, form; variable = :OID, labels = :Comment)
SPSS command to set variable labels.
`variable` - varable names attribute, `SASFieldName` by default.
`variable` - varable names attribute, `OID` by default.
`labels` - labels names attribute, `Comment` by default.
"""
function spss_form_variable_labels(mdb, form; variable = :SASFieldName, labels = :Comment)
function spss_form_variable_labels(mdb, form; variable = :OID, labels = :Comment)
df = itemformcontent_(mdb, form; optional = true)
v = Vector{Pair}(undef, length(df))
for i = 1:size(df, 1)
Expand All @@ -70,13 +70,13 @@ function spss_form_variable_labels(mdb, form, pairs; kwargs...)
end

"""
spss_form_value_labels(mdb, form; variable = :SASFieldName)
spss_form_value_labels(mdb, form; variable = :OID)
SPSS command to set value labels.
`variable` - varable names attribute, `SASFieldName` by default.
`variable` - varable names attribute, `OID` by default.
"""
function spss_form_value_labels(mdb, form; variable = :SASFieldName)
function spss_form_value_labels(mdb, form; variable = :OID)
items = itemformcontent_(mdb, form)
v = Vector{Pair}(undef, 0)
for i = 1:length(items)
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2 changes: 2 additions & 0 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@ using Test

@test_nowarn ODMXMLTools.validateodm(odm)

@test_nowarn ODMXMLTools.clinicaldatatable(odm, addstudyid= true, addstudyidcol = true)

cdat = ODMXMLTools.findclinicaldata(odm, "ST1", "v2")

@test_nowarn ODMXMLTools.clinicaldatatable(cdat)
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9 changes: 8 additions & 1 deletion test/test.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -65,11 +65,14 @@
<Include StudyOID="DEFS" MetaDataVersionOID="v1"/>
<ItemGroupDef OID="IG_1" Name="Item group 1" Repeating="No" SASDatasetName="UNGRP">
<ItemRef ItemOID="I_1" OrderNumber="1" Mandatory="Yes" />
<ItemRef ItemOID="I_2" OrderNumber="1" Mandatory="Yes" />
<ItemRef ItemOID="I_2" OrderNumber="2" Mandatory="Yes" />
<ItemRef ItemOID="I_3" OrderNumber="3" Mandatory="Yes" />
</ItemGroupDef>
<ItemDef OID="I_2" Name="Item 2" DataType="integer" Length="3" SASFieldName="IT2" Comment="Comments 2">
<CodeListRef CodeListOID="CL_1"/>
</ItemDef>
<ItemDef OID="I_3" Name="Item 3" DataType="integer" Length="3" SASFieldName="IT3" Comment="Comments 3">
</ItemDef>
<CodeList OID="CL_1" Name="NP" DataType="integer" SASFormatName="NP">
<CodeListItem CodedValue="0">
<Decode>
Expand All @@ -90,6 +93,8 @@
<FormData FormOID="FORM_1">
<ItemGroupData ItemGroupOID="IG_1" TransactionType="Insert">
<ItemData ItemOID="I_1" Value="FieldValue"/>
<ItemData ItemOID="I_2" Value="2"/>
<ItemDataInteger ItemOID="I_3">4</ItemDataInteger>
</ItemGroupData>
</FormData>
</StudyEventData>
Expand All @@ -102,6 +107,7 @@
<ItemGroupData ItemGroupOID="IG_1" TransactionType="Insert">
<ItemData ItemOID="I_1" Value="FieldValue"/>
<ItemData ItemOID="I_2" Value="1"/>
<ItemDataInteger ItemOID="I_3">1</ItemDataInteger>
</ItemGroupData>
</FormData>
</StudyEventData>
Expand All @@ -112,6 +118,7 @@
<ItemGroupData ItemGroupOID="IG_1" TransactionType="Insert">
<ItemData ItemOID="I_1" Value="FieldValue"/>
<ItemData ItemOID="I_2" Value="3"/>
<ItemDataInteger ItemOID="I_3">2</ItemDataInteger>
</ItemGroupData>
</FormData>
</StudyEventData>
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2 comments on commit 290376f

@PharmCat
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Registration pull request created: JuliaRegistries/General/75649

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.5 -m "<description of version>" 290376ffe6e88ad871d427df322c295953e4a306
git push origin v0.2.5

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