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Merge pull request #19 from PharmCat/dev
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Dev
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@PharmCat
PharmCat authored May 9, 2024
2 parents d5c48da + 9d51ff3 commit bd8e54e
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Showing 12 changed files with 124 additions and 31 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/Documenter.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
runs-on: ubuntu-latest
timeout-minutes: 30
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: julia-actions/setup-julia@latest
with:
version: '1.6.4'
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2 changes: 1 addition & 1 deletion .github/workflows/Tier1.yml
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Expand Up @@ -31,8 +31,8 @@ jobs:
matrix:
version:
- '1.6'
- '1.7'
- '1.8'
- '1'
os:
- ubuntu-latest
- macOS-latest
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7 changes: 7 additions & 0 deletions .github/workflows/dependabot.yml
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@@ -0,0 +1,7 @@
# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/" # Location of package manifests
schedule:
interval: "weekly"
4 changes: 2 additions & 2 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "ODMXMLTools"
uuid = "2456a17b-6ca2-4f51-9342-f0287e829718"
authors = ["PharmCat <[email protected]>"]
version = "0.6.3"
version = "0.7.0"

[deps]

Expand All @@ -17,7 +17,7 @@ Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
AbstractTrees = "0.3, 0.4"
CategoricalArrays = "0.10"
DataFrames = "1"
EzXML = "1.1"
EzXML = "1.1, 1.2"
julia = "1"

[extras]
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4 changes: 0 additions & 4 deletions docs/Project.toml
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Expand Up @@ -2,7 +2,3 @@
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
ODMXMLTools = "2456a17b-6ca2-4f51-9342-f0287e829718"


[compat]
Documenter = "≥0.26"
ODMXMLTools = "0.6"
43 changes: 43 additions & 0 deletions docs/src/api.md
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Expand Up @@ -156,6 +156,13 @@ ODMXMLTools.itemquestion
ODMXMLTools.nodedesq
```

## Decode

### ODMXMLTools.codelistitemdecode
```@docs
ODMXMLTools.codelistitemdecode
```

## Delete

### ODMXMLTools.deletestudy!
Expand Down Expand Up @@ -236,4 +243,40 @@ ODMXMLTools.sortelements!
### ODMXMLTools.writenode
```@docs
ODMXMLTools.writenode
```

Other:

### ODMXMLTools.oclformdetailslist
```@docs
ODMXMLTools.oclformdetailslist
```

### ODMXMLTools.countelements
```@docs
ODMXMLTools.countelements
```

### ODMXMLTools.findelementbyattr
```@docs
ODMXMLTools.findelementbyattr
```

### ODMXMLTools.buildelementsdata
```@docs
ODMXMLTools.buildelementsdata
```



## Base

### Base.findall
```@docs
Base.findall
```

### Base.findfirst
```@docs
Base.findfirst
```
2 changes: 1 addition & 1 deletion src/ODMXMLTools.jl
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Expand Up @@ -256,7 +256,7 @@ module ODMXMLTools
:UserType
:Value
:Version
:lang
Symbol("xml:lang")
:xmlns])

const ITEMDATATYPE = Set([:ItemDataAny
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4 changes: 2 additions & 2 deletions src/nodeinfo.jl
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Expand Up @@ -130,7 +130,7 @@ const NODEINFO = Dict{Symbol, NodeInfo}(
),
:TranslatedText => NodeInfo(:TranslatedText,
[:Decode, :ErrorMessage, :Question, :Symbol, :Description],
Tuple{Symbol, Symbol, Symbol}[(:lang, :?, :languageTag)],
Tuple{Symbol, Symbol, Symbol}[(Symbol("xml:lang"), :?, :languageTag)],
"text"
),
:MetaDataVersion => NodeInfo(:MetaDataVersion,
Expand Down Expand Up @@ -278,7 +278,7 @@ const NODEINFO = Dict{Symbol, NodeInfo}(
),
:Presentation => NodeInfo(:Presentation,
:MetaDataVersion,
[(:OID, :!, :oid), (:lang, :?, :languageTag)],
[(:OID, :!, :oid), (Symbol("xml:lang"), :?, :languageTag)],
"text"
),
:ConditionDef => NodeInfo(:ConditionDef,
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57 changes: 44 additions & 13 deletions src/odmxml.jl
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Expand Up @@ -84,16 +84,20 @@ function makenode(str, attr)
return ODMNode(Symbol(str), attr)
end
=#
function attributes_dict(n)
function attributes_dict(n, ns)
d = Dict{Symbol, String}()
for i in eachattribute(n)
d[Symbol(i.name)] = i.content
end
attributes_dict!(d, root, n)
d
end
function attributes_dict!(d, n)
for i in eachattribute(n)
d[Symbol(i.name)] = i.content
function attributes_dict!(d, ns, n)
for i in EzXML.attributes(n)
if EzXML.hasnamespace(i)
pref = ns[EzXML.namespace(i)]
k = Symbol(string(pref)*":"*i.name)
else
k = Symbol(i.name)
end
d[k] = i.content
end
d
end
Expand All @@ -109,11 +113,12 @@ function importxml(file::AbstractString)
nsv = namespaces(xodm)
if EzXML.hasnamespace(xodm)
nsv = namespaces(xodm)
push!(nsv, "xml" => "http://www.w3.org/XML/1998/namespace" )
else
nsv = ["" => ""]
nsv = ["xml" => "http://www.w3.org/XML/1998/namespace"]
end
ns = Dict([p[2] => Symbol(p[1]) for p in nsv]...)
odm = ODMRoot(attributes_dict(xodm), ns)
odm = ODMRoot(attributes_dict(xodm, ns), ns)
importxml_(odm, xodm, ns)
odm
end
Expand All @@ -125,7 +130,7 @@ function importxml_(parent, root, ns)
content = nothing
attr = Dict{Symbol, String}()
#if iselement(c)
attributes_dict!(attr, c)
attributes_dict!(attr, ns, c)
if !haselement(c)
tv = EzXML.eachnode(root)
for t in tv
Expand Down Expand Up @@ -1058,7 +1063,7 @@ function codelisttable(cd::AbstractODMNode; lang = "en")
text = content(first(tn))
if length(tn) > 1
for i = 2:length(tn)
if attribute(tn[i], :lang) == lang
if attribute(tn[i], Symbol("xml:lang")) == lang
text = content(tn[i])
break
end
Expand All @@ -1076,10 +1081,31 @@ function codelisttable(cd::AbstractODMNode; lang = "en")
df
end

"""
codelistitemdecode(cli; lang = nothing, nolangerr = true, nolangval = "")
Return TranslatedText content for Decode node.
"""
function codelistitemdecode(cli; lang = nothing, nolangerr = true, nolangval = "")
if name(cli) != :CodeListItem error("Wrong node name ($(name(cli)), not CodeListItem)") end
decodenode = findelement(cli, :Decode)
if isnothing(decodenode) error("No Decode node in CodeListItem") end
t = findelements(decodenode, :TranslatedText)
if length(t) == 0 error("No TranslatedText node in Decode") end
if isnothing(lang)
return content(first(t))
else
for tv in t
if attribute(tv, :lang) == lang return content(first(tv)) end
end
end
if nolangerr error("No TranslatedText for lang $lang found") end
return nolangval
end
"""
itemcodelisttable(cd::AbstractODMNode; lang = nothing) where T <: AbstractODMNode
Same as `codelisttable`, but return ItemDef.
Same as `codelisttable`, but return ItemDef (DataFrame).
"""
function itemcodelisttable(cd::AbstractODMNode; lang = nothing)
df = DataFrame(OID = String[], CodeListOID = String[], Name = String[], DataType = String[], Type = String[], CodedValue = String[], Rank = Union{Missing, String}[], OrderNumber = Union{Missing, String}[], Text = String[])
Expand All @@ -1096,7 +1122,7 @@ function itemcodelisttable(cd::AbstractODMNode; lang = nothing)
text = content(first(tn))
if length(tn) > 1
for i = 2:length(tn)
if attribute(tn[i], :lang) == lang
if attribute(tn[i], Symbol("xml:lang")) == lang
text = content(tn[i])
break
end
Expand All @@ -1117,6 +1143,11 @@ function itemcodelisttable(cd::AbstractODMNode; lang = nothing)
df
end






function dfpush!(df, s, e, f, g, i, null)
push!(df, (s,
attribute(e, :StudyEventOID),
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6 changes: 5 additions & 1 deletion src/spss.jl
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Expand Up @@ -58,7 +58,9 @@ end
"""
spss_form_variable_labels(mdb, form; variable = :OID, labels = :Name, source = :attr, lang = nothing)
SPSS command to set variable labels.
SPSS command to set variable labels:
```VARIABLE LABELS variable 'labels'.```
`variable` - varable names attribute, `OID` by default.
Expand All @@ -68,6 +70,8 @@ If `source` == `:Question` - try to get description from `TranslatedText` of `Qu
If `source` == `:Description` - try to get description from `TranslatedText` of `Description` element.
"""
function spss_form_variable_labels(mdb, form; variable = :OID, labels = :Name, source = :attr, lang = nothing)
df = itemformdefcontent_(mdb, form; optional = true)
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10 changes: 10 additions & 0 deletions test/runtests.jl
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Expand Up @@ -346,4 +346,14 @@ using EzXML
doc = EzXML.readxml(joinpath(dirname(@__FILE__), "test.xml"))
dtdn = EzXML.readdtd(joinpath(dirname(@__FILE__), "test-schema.dtd"))
EzXML.validate(doc, dtdn)
=#


#=
txt = """<?xml version="1.0" encoding="UTF-8"?>
<t1>
<t2 xml:name="Homo"></t2>
<t2 b:name="Homo"></t2>
</t1>"""
root(EzXML.parsexml(txt));
=#
14 changes: 8 additions & 6 deletions test/test.xml
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Expand Up @@ -117,24 +117,26 @@
<CodeList OID="CL_1" Name="Race codelist" DataType="integer" SASFormatName="CL_1">
<CodeListItem CodedValue="1">
<Decode>
<TranslatedText>Asian</TranslatedText>
<TranslatedText xml:lang = "en-US">Asian</TranslatedText>
<TranslatedText xml:lang = "ru">Азиатская</TranslatedText>
</Decode>
</CodeListItem>
<CodeListItem CodedValue="2">
<Decode>
<TranslatedText>Caucasian</TranslatedText>
<TranslatedText xml:lang = "en-US">Caucasian</TranslatedText>
<TranslatedText xml:lang = "ru">Европеоидная</TranslatedText>
</Decode>
</CodeListItem>
</CodeList>
<CodeList OID="CL_2" Name="Sex codelist" DataType="string" SASFormatName="CL_2">
<CodeListItem CodedValue="M">
<Decode>
<TranslatedText>Male</TranslatedText>
<TranslatedText xml:lang = "en-US">Male</TranslatedText>
</Decode>
</CodeListItem>
<CodeListItem CodedValue="F">
<Decode>
<TranslatedText>Female</TranslatedText>
<TranslatedText xml:lang = "en-US">Female</TranslatedText>
</Decode>
</CodeListItem>
</CodeList>
Expand All @@ -154,12 +156,12 @@
<CodeList OID="CL_2" Name="Sex codelist" DataType="integer" SASFormatName="CL_2">
<CodeListItem CodedValue="1">
<Decode>
<TranslatedText>Male</TranslatedText>
<TranslatedText xml:lang = "en-US">Male</TranslatedText>
</Decode>
</CodeListItem>
<CodeListItem CodedValue="2">
<Decode>
<TranslatedText>Female</TranslatedText>
<TranslatedText xml:lang = "en-US">Female</TranslatedText>
</Decode>
</CodeListItem>
</CodeList>
Expand Down

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Registration pull request created: JuliaRegistries/General/106491

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

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 v0.7.0 -m "<description of version>" bd8e54e5f7c96f19c588a2a3c47d638c661d9d0d
git push origin v0.7.0

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