importxml(file::AbstractString)

Import odm.xml file.

mekenode!(root::AbstractODMNode, nname::Symbol, attrs::Dict = Dict(); content = nothing, namespace = Symbol(""), checkname = false, checkni = false)

Make ODM node in root.

makeclinicaldata!(odm::ODMRoot, soid::String, moid::String)

Make ClinicalData in ODM.

buildmetadata(odm::ODMRoot, soid::AbstractString, moid::AbstractString)

Build MetaData from MetaDataVersion by StudyOID (soid) and MetaDataVersionOID (moid).

clinicaldatatable(cd::AbstractODMNode;
    itemgroup = nothing,
    form = nothing,
    event = nothing,
    item::Union{Nothing, AbstractString, <: AbstractVector{<:AbstractString}} = nothing,
    categ = false, 
    addstudyid = false,
    addstudyidcol = false,
    idlnames = nothing,
    null = "NULL",
    drop = [:StudyEventRepeatKey, :FormRepeatKey])

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;
• null = "NULL" - default NULL values;
• idlnames - only this types of data will be collected, for example: ItemData, ItemDataInteger, ets (if nothing` - all will be collected).
• drop - drop columns.

clinicaldatatable(odm::ODMRoot, soid::AbstractString, moid::AbstractString; itemgroup = nothing)

Return ClinicalData table in long formal.

• soid - StudyOID;
• moid - MetaDataVersionOID.

clinicaldatatable(odm::ODMRoot, inds::AbstractVector{Int}; kwargs...)

Return ClinicalData table in long formal.

• inds - indexes of clinicaldatalist table.

clinicaldatatable(odm::ODMRoot, range::UnitRange{Int64}; kwargs...)

Return ClinicalData table in long formal.

• inds - indexes of clinicaldatalist table.

clinicaldatatable(odm::ODMRoot; kwargs...)

Return ClinicalData table in long formal.

clinicaldatatable(odm::ODMRoot, soid::AbstractString; kwargs...)

Return ClinicalData table in long formal.

subjectdatatable(cld::AbstractODMNode; optional = false, attrs::Union{AbstractVector, Nothing} = nothing)

Subject information table.

subjectdatatable(odm::ODMRoot; optional = false, attrs::Union{AbstractVector, Nothing} = nothing)

codelisttable(cd::AbstractODMNode; lang = nothing)

Return CodeList table (DataFrame).

itemcodelisttable(cd::AbstractODMNode; lang = nothing) where T <: AbstractODMNode

Same as codelisttable, but return ItemDef (DataFrame).

metadatalist(odm::ODMRoot)

Returm table of MetaDataVersion elements.

studylist(odm::ODMRoot; categ = false)

Returm table of Study elements.

clinicaldatalist(odm::ODMRoot)

Returm table of ClinicalData elements.

eventlist(md::AbstractODMNode; optional = false, attrs = nothing, categ = false)

Return StudyEventDef table (DataFrame).

Keywords:

• optional (true/false) - get optional attributes;
• attrs - get selected attributes;
• categ - return OID as categorical;

formlist(el::Vector{T}; attrs = nothing,  categ = false) where T <: AbstractODMNode

Return FormDef table (DataFrame).

Keywords:

• attrs - get selected attributes;
• categ - return OID as categorical;

formlist(md::AbstractODMNode)

Return FormDef table (DataFrame).

itemgrouplist(el::Vector{T}; optional = false, attrs = nothing, categ = false) where T <: AbstractODMNode

Return ItemGroupDef table (DataFrame).

Keywords:

• optional (true/false) - get optional attributes;
• attrs - get selected attributes;
• categ - return OID as categorical;

itemgrouplist(md::AbstractODMNode; optional = false, attrs::Union{AbstractVector, Nothing} = nothing)

Return ItemGroupDef table (DataFrame).

If optional == true - return all optional attributes.

attrs - get selected attributes.

itemlist(el::Vector{T}; optional = false, attrs = nothing, categ = false, datatype = nothing) where T <: AbstractODMNode

Return ItemDef table (DataFrame).

Keywords:

• if optional == true - return all optional attributes;
• attrs - get selected attributes;
• categ - return OID as categorical;
• datatype - select only this type of items (See DataType);

itemlist(md::AbstractODMNode; kwargs...)

Return ItemDef table (DataFrame).

itemsformlist(md, oid; optional = false)

Return ItemDef table (DataFrame) for concrete form (FormDef) by oid.

keywords see (itemlist)[@ref].

findelement(el::AbstractVector{AbstractODMNode}, nname::Symbol, oid::AbstractString)

Find first element by node name nname and oid.

findelement(n::AbstractODMNode, nname::Symbol, oid::AbstractString)

Find first element by node name nname and oid.

findelement(n::AbstractODMNode, nname::Symbol)

Find first element by node name nname.

findelements(n::AbstractODMNode, nname::Symbol)

Find all elements by node name nname.

findelements(n::AbstractODMNode, nnames::Vector{Symbol})

Find all elements by node name nnames (list).

findstudy(odm::ODMRoot, oid::AbstractString)

Find Study element by OID (oid), nothing` if not found.

findstudymetadata(odm::ODMRoot, soid::AbstractString, moid::AbstractString)

Find MeteDataVersion by StudyOID (soid) and MetaDataVersionOID (moid).

findclinicaldata(odm::ODMRoot, soid::AbstractString, moid::AbstractString)

Find ClinicalData by StudyOID (soid) and MetaDataVersionOID (moid).

Returns single element or nothing.

findclinicaldata(odm::ODMRoot, soid::AbstractString)

Find ClinicalData by StudyOID (soid).

Returns vector or empty vetctor if no elements found.

findclinicaldata(odm::ODMRoot)

Find all ClinicalData.

Returns vector or empty vetctor if no elements found.

function protocolcontent(md; optional = false, attrs = nothing, categ = false)

eventcontent(md; kwargs...)

Return FormRef table (DataFrame) for concrete form (StudyEventDef).

if optional == true - return all optional attributes.

eventcontent(md, oid; kwargs...)

Return FormRef table (DataFrame) for concrete form (StudyEventDef) by oid.

if optional == true - return all optional attributes.

formcontent(md; optional = false, attrs::Union{AbstractVector, Nothing} = nothing)

Return ItemGroupRef table (DataFrame) for concrete form (FormDef).

if optional == true - return all optional attributes.

formcontent(md, oid; optional = false, attrs::Union{AbstractVector, Nothing} = nothing)

Return ItemGroupRef table (DataFrame) for concrete form (FormDef) by oid.

if optional == true - return all optional attributes.

itemgroupcontent(md; kwargs...)

Return ItemRef table (DataFrame) for concrete group (ItemGroupDef).

itemgroupcontent(md, oid; kwargs...)

Return ItemRef table (DataFrame) for concrete group (ItemGroupDef) by oid.

itemdescription(md::AbstractODMNode; lang = ["en"])

ItemDef descriptions.

itemquestion(md::AbstractODMNode; lang = ["en"])

ItemDef questions.

nodedesq(md::AbstractODMNode, tnode::Symbol, nname::Symbol; lang = ["en"])

Get desctriptions or questions for node tnode.

nname can be only :Description or :Question.

codelistitemdecode(cli; lang = nothing, nolangerr = true, nolangval = "")

Return TranslatedText content for Decode node.

deletestudy!(odm::ODMRoot, soid::AbstractString)

Delete Study by StudyOID (soid).

deletestudy!(odm::ODMRoot, soid::AbstractString)

Delete ClinicalData by StudyOID (soid).

studyinfo(odm::ODMRoot, oid::AbstractString;  io = stdout)

Study information.

studyinfo(odm::ODMRoot;  io = stdout)

Study information.

studyinfo(st::AbstractODMNode;  io = stdout)

Study information.

validateodm(odm::AbstractODMNode)

Basic structure validation.

checkdatavalues(odm::ODMRoot)

Check all data values in all ClinicalData sections.

spss_form_variable_labels(mdb, form; variable = :OID, labels = :Name, source = :attr, lang = nothing)

SPSS command to set variable labels:

VARIABLE LABELS variable 'labels'.

variable - varable names attribute, OID by default.

labels - labels names attribute, Name by default.

If source == :Question - try to get description from TranslatedText of Question element, if there is no Question element - get from attribute labels.

If source == :Description - try to get description from TranslatedText of Description element.

spss_form_variable_labels(mdb, form, `pairs`; kwargs...)

SPSS command to set variable labels.

Append pair vector pairs at the end.

spss_form_value_labels(mdb, form; variable = :OID)

SPSS command to set value labels.

variable - varable names attribute, OID by default.

spss_events_value_labels(mdb; variable = "StudyEventOID", value::Symbol = :OID, label::Symbol = :Name)

Labels for event values.

attribute(n::AbstractODMNode, attr::Symbol, str::Bool = false)

Return attribute value. If str is true - always return String.

content(n::AbstractODMNode)

Return node content.

hasattribute(n::AbstractODMNode, attr::Symbol)

Return true if node have attribute attr.

name(n::ODMNode)

Return name of ODM node.

sortelements!(node::AbstractODMNode, rec::Bool = true)

Try to sort node elements as in Specification for the Operational Data Model (ODM).

rec - recursive.

writenode(io::IO, node::AbstractODMNode)

Write XML node into IO.

oclformdetailslist(md::AbstractODMNode)

Openclinica form information (md - MetaDataVersion element).

countelements(n::AbstractODMNode, nname::Symbol)

Count elements by node name nname.

findelementbyattr(el::AbstractVector{<:AbstractODMNode}, nname::Symbol, attr::Symbol, value::AbstractString)

Find first element by node name nname with attribute attr equal value.

buildelementsdata(stmd::AbstractODMNode)

Build elements data.

Base.findall(n::AbstractODMNode, nname::Symbol)

Find all elements indexes by node name nname.

findfirst(n::AbstractODMNode, nname::Symbol, oid::AbstractString)

Find first index of element.