Merge pull request #18 from PharmCat/dev

make clin dat, write file, docs

Project.toml

@@ -1,7 +1,7 @@
 name = "ODMXMLTools"
 uuid = "2456a17b-6ca2-4f51-9342-f0287e829718"
 authors = ["PharmCat <[email protected]>"]
-version = "0.6.2"
+version = "0.6.3"
 
 [deps]
 

docs/src/api.md

@@ -5,6 +5,18 @@
 ODMXMLTools.importxml
 ```
 
+## Make node
+
+### ODMXMLTools.mekenode!
+```@docs
+ODMXMLTools.mekenode!
+```
+
+### ODMXMLTools.makeclinicaldata!
+```@docs
+ODMXMLTools.makeclinicaldata!
+```
+
 ## Build metadata
 
 ### ODMXMLTools.buildmetadata
@@ -221,7 +233,7 @@ ODMXMLTools.name
 ODMXMLTools.sortelements!
 ```
 
-### ODMXMLTools.writenode!
+### ODMXMLTools.writenode
 ```@docs
-ODMXMLTools.writenode!
+ODMXMLTools.writenode
 ```

src/ODMXMLTools.jl

@@ -7,6 +7,9 @@ module ODMXMLTools
     import Base: show, findfirst, findall, push!, deleteat!, length
 
     export importxml,
+
+	mekenode!,
+
     findclinicaldata,
     findstudy,
     findstudymetadata,

src/odmxml.jl

@@ -304,6 +304,11 @@ end
 ################################################################################
 # MAKE NODE
 ################################################################################
+"""
+    mekenode!(root::AbstractODMNode, nname::Symbol, attrs::Dict = Dict(); content = nothing, namespace = Symbol(""), checkname = false, checkni = false)
+
+Make ODM node in root.
+"""
 function mekenode!(root::AbstractODMNode, nname::Symbol, attrs::Dict = Dict(); content = nothing, namespace = Symbol(""), checkname = false, checkni = false)
     if checkname
         if nname ∉ ODMNAMESPACE error("Name $nname not in ODMNAMESPACE!") end
@@ -1560,6 +1565,15 @@ function writenode(io::IO, node::AbstractODMNode, sp::Int)
         println(io, "/>")
     end
 end
+function writenode(file::String, node::AbstractODMNode; sp = 1)
+    f = open(file, "w")
+    try
+        writenode(f, node, sp)
+    finally
+        close(f)
+    end
+    nothing
+end
 
 ##########################################################################
 ##
@@ -1635,4 +1649,24 @@ function sortelements!(node::AbstractODMNode, rec::Bool = true)
             end
         end
     end
+end
+
+
+#####################################################################
+## MAKE NODES
+#####################################################################
+"""
+    makeclinicaldata!(odm::ODMRoot, soid::String, moid::String)
+
+Make ClinicalData in ODM.
+"""
+function makeclinicaldata!(odm::ODMRoot, soid::String, moid::String)
+    for i in odm.el
+        if isClinicalData(i)
+            if attribute(i, "StudyOID") == soid && attribute(i, "MetaDataVersionOID") == moid
+                error("ODM has ClinicalData with same StudyOID and MetaDataVersionOID")
+            end
+        end
+    end
+    mekenode!(odm, :ClinicalData, Dict(:StudyOID => soid, :MetaDataVersionOID => moid))
 end

test/runtests.jl

@@ -221,6 +221,8 @@ using Test
     # Write
     ODMXMLTools.writenode(io, odm)
 
+    @test_nowarn ODMXMLTools.writenode("test_file.xml", odm)
+
     # SPSS
     spssvallab =  ODMXMLTools.spss_form_value_labels(mdb, "FORM_VD_1"; variable = :OID)
     @test_nowarn show(io, spssvallab)
@@ -280,6 +282,10 @@ using Test
     @test ODMXMLTools.name(cld) == :ClinicalData
     cdel = ODMXMLTools.findelements(odm, :ClinicalData)
     @test length(cdel) == 2
+
+    newcldat = ODMXMLTools.makeclinicaldata!(odm, "TestSOID", "TestMOID")
+    @test ODMXMLTools.isClinicalData(newcldat)
+
     #@test ODMXMLTools.ischild(c[1], odm)
     # Node information