Examples · ODMXMLTools.jl

using ODMXMLTools;

path = joinpath(dirname(pathof(ODMXMLTools)), "..", "test")

Load ODM-XML

ODMXMLTools.jl doesn't check correctness of *.xml file.

using ODMXMLTools;

# Load XML file

odm = ODMXMLTools.importxml(joinpath(path, "test.xml"))

ODM root node

Then you can get MetaDataVersion list, Study list, ClinicalData list and other.

# Get metadata list
ODMXMLTools.metadatalist(odm)

4×3 DataFrame

Row	StudyOID	OID	Name
	String	String	String
1	TEMPLATE_ST_01	mvd_tpl_1	Tpl_Version_v1
2	ST_1_1	mdv_1	Version_v1
3	ST_2_1	mdv_1	Version_v1
4	ST_2_1	mdv_2	Version_v2

# Get study list
ODMXMLTools.studylist(odm)

3×1 DataFrame

Row	StudyOID
	String
1	TEMPLATE_ST_01
2	ST_1_1
3	ST_2_1

# Get clinical data list
ODMXMLTools.clinicaldatalist(odm)

3×2 DataFrame

Row	StudyOID	MetaDataVersionOID
	String	String
1	ST_1_1	mdv_1
2	ST_2_1	mdv_1
3	ST_2_1	mdv_2

Build metadata

# Build metadata
mdb = ODMXMLTools.buildmetadata(odm, "ST_2_1", "mdv_2")

Completed Study MetaData (18 elements), OID: mdv_2, Name: Version_v2

Find clinical data and get observation data

# Find clinical data
cdat = ODMXMLTools.findclinicaldata(odm, "ST_2_1", "mdv_2")

ClinicalData  ( StudyOID:ST_2_1))

# Get clinical data
ODMXMLTools.clinicaldatatable(cdat)

14×7 DataFrame

Row	SubjectKey	StudyEventOID	FormOID	ItemGroupOID	ItemGroupRepeatKey	ItemOID	Value
	String	String	String	String	String?	String	String
1	003	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_1	1
2	003	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_2	49
3	003	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_3	2
4	003	SE_VIZIT1	FORM_DEAN_1	AN_IG_2	missing	AN_1	170
5	003	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_1	119
6	003	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_2	85
7	003	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_3	63
8	004	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_1	2
9	004	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_2	52
10	004	SE_VIZIT1	FORM_DEAN_1	DE_IG_1	missing	DE_3	1
11	004	SE_VIZIT1	FORM_DEAN_1	AN_IG_2	missing	AN_1	170
12	004	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_1	120
13	004	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_2	85
14	004	SE_VIZIT1	FORM_VD_1	VIT_IG_1	missing	I_3	60

Get tables

# Find study
st1 =  ODMXMLTools.findstudy(odm, "ST_2_1")

Study  (OID:ST_2_1))

# Find element
ODMXMLTools.findelement(st1, :MetaDataVersion, "mdv_2")

MetaDataVersion  (OID:mdv_2))

# Event list
ODMXMLTools.eventlist(mdb)

1×4 DataFrame

Row	OID	Name	Repeating	Type
	String?	String?	String?	String?
1	SE_VIZIT1	Vizit 1	No	Scheduled

# Form list
ODMXMLTools.formlist(mdb)

2×3 DataFrame

Row	OID	Name	Repeating
	String?	String?	String?
1	FORM_DEAN_1	Demographic and antropometric	No
2	FORM_VD_1	Vital data	No

# ItemGroup list
ODMXMLTools.itemgrouplist(mdb)

3×3 DataFrame

Row	OID	Name	Repeating
	String?	String?	String?
1	DE_IG_1	Demographic	No
2	AN_IG_2	Antropometric	No
3	VIT_IG_1	Vital data	No

# Item list
ODMXMLTools.itemlist(mdb)

7×3 DataFrame

Row	OID	Name	DataType
	String?	String?	String?
1	DE_1	Sex	integer
2	I_3	HR	integer
3	DE_2	Age	integer
4	DE_3	Race	integer
5	AN_1	Height	integer
6	I_1	SAD	integer
7	I_2	DAD	integer

Also

# Subject data
ODMXMLTools.subjectdatatable(odm; attrs = [:SubjectKey, :StudySubjectID])

6×2 DataFrame

Row	SubjectKey	StudySubjectID
	String?	String?
1	001	missing
2	002	missing
3	001	missing
4	002	missing
5	003	missing
6	004	missing

# Study information
ODMXMLTools.studyinfo(odm)

--------------------------------------
Study OID: TEMPLATE_ST_01
StudyName: Template 1
StudyDescription: This is basic form template
ProtocolName: Template
MetaDataVersion:
    OID: mvd_tpl_1; Name: Tpl_Version_v1
--------------------------------------
Study OID: ST_1_1
StudyName: Study 1
StudyDescription: Study 1 Description
ProtocolName: Protocol Number
MetaDataVersion:
    OID: mdv_1; Name: Version_v1
--------------------------------------
Study OID: ST_2_1
StudyName: Study 2
StudyDescription: Study 2 Description
ProtocolName: Protocol Number Study 2
MetaDataVersion:
    OID: mdv_1; Name: Version_v1
    OID: mdv_2; Name: Version_v2
--------------------------------------

Validation

# Basic validation
ODMXMLTools.validateodm(odm)

ODMXML log: 0 item(s). Info = 0, Warnings = 0, Errors = 0, skipped 0 node(s).

# Data validation
ODMXMLTools.checkdatavalues(odm)

Any[]

SPSS features

# Value labesl
ODMXMLTools.spss_form_value_labels(mdb, "FORM_DEAN_1"; variable = :OID)

VALUE LABELS
DE_1
1 'Male'
2 'Female'/
DE_3
1 'Asian'
2 'Caucasian'.

# Variable labels
ODMXMLTools.spss_form_variable_labels(mdb, "FORM_DEAN_1"; variable = :SASFieldName)

VARIABLE LABELS
DE_1 'Sex'
DE_2 'Age'
DE_3 'Race'
AN_1 'Height'.

# Event value labels
ODMXMLTools.spss_events_value_labels(mdb; variable = "StudyEventOID", value = :OID, label = :Name)

VALUE LABELS
StudyEventOID
'SE_VIZIT1' 'Vizit 1'.