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Merged
rich-iannone merged 19 commits into from
Jun 30, 2026
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docs: improve CDISC examples #406

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1fc2911
Add load_metadata_example() function
rich-iannone Jun 30, 2026
573f381
Update __init__.py
rich-iannone Jun 30, 2026
0f3dee7
Update test_metadata.py
rich-iannone Jun 30, 2026
9621417
Update __init__.py
rich-iannone Jun 30, 2026
4d57bce
Create datapackage.json
rich-iannone Jun 30, 2026
978846b
Create define.xml
rich-iannone Jun 30, 2026
c1b9405
Create dm.xpt
rich-iannone Jun 30, 2026
1f74f85
Create sdtm_ct.xml
rich-iannone Jun 30, 2026
dc1c431
Create table_schema.json
rich-iannone Jun 30, 2026
af9fc1e
Create weather_csvw.json
rich-iannone Jun 30, 2026
08aaaa4
Update 03-cdisc-validation.qmd
rich-iannone Jun 30, 2026
76d019a
Update _import.py
rich-iannone Jun 30, 2026
588be90
Update test_metadata.py
rich-iannone Jun 30, 2026
7261f9b
Add dependencies to `docs` group
rich-iannone Jun 30, 2026
b59eda9
Update 03-cdisc-validation.qmd
rich-iannone Jun 30, 2026
e2a5afb
Update 03-cdisc-validation.qmd
rich-iannone Jun 30, 2026
2f77942
Update 03-cdisc-validation.qmd
rich-iannone Jun 30, 2026
24c2a7c
Update 03-cdisc-validation.qmd
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Update 03-cdisc-validation.qmd
rich-iannone Jun 30, 2026
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2 changes: 2 additions & 0 deletions pointblank/__init__.py
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Expand Up @@ -76,6 +76,7 @@
import_metadata,
list_adam_datasets,
list_sdtm_domains,
load_metadata_example,
sdtm_to_metadata,
validate_adam,
validate_adam_structure,
Expand Down Expand Up @@ -190,6 +191,7 @@
"register_adapter",
# Metadata standards import/export
"import_metadata",
"load_metadata_example",
"export_metadata",
"MetadataImport",
"MetadataPackage",
Expand Down
68 changes: 68 additions & 0 deletions pointblank/data/metadata_examples/datapackage.json
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{
"name": "quarterly-sales",
"title": "Quarterly Sales Dataset",
"description": "Sales transactions for Q1 2024",
"resources": [
{
"name": "transactions",
"path": "transactions.csv",
"schema": {
"fields": [
{
"name": "transaction_id",
"type": "string",
"description": "Unique transaction identifier",
"constraints": {"required": true, "unique": true, "minLength": 5, "maxLength": 20}
},
{
"name": "customer_id",
"type": "string",
"description": "Customer account number",
"constraints": {"required": true, "minLength": 5, "maxLength": 20}
},
{
"name": "amount",
"type": "number",
"description": "Transaction amount in USD",
"constraints": {"required": true, "minimum": 0.01, "maximum": 99999.99}
},
{
"name": "quantity",
"type": "integer",
"description": "Number of items purchased",
"constraints": {"required": true, "minimum": 1, "maximum": 1000}
},
{
"name": "category",
"type": "string",
"description": "Product category",
"constraints": {
"required": true,
"enum": ["electronics", "clothing", "food", "home", "sports"]
}
},
{
"name": "sale_date",
"type": "date",
"description": "Date of sale",
"constraints": {"required": true}
},
{
"name": "discount_pct",
"type": "number",
"description": "Discount percentage applied",
"constraints": {"minimum": 0, "maximum": 50}
},
{
"name": "email",
"type": "string",
"description": "Customer email address",
"constraints": {"pattern": "^[^@]+@[^@]+\\.[^@]+$"}
}
],
"primaryKey": ["transaction_id"],
"missingValues": ["", "NA", "N/A"]
}
}
]
}
156 changes: 156 additions & 0 deletions pointblank/data/metadata_examples/define.xml
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<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v1.3"
xmlns:def="http://www.cdisc.org/ns/def/v2.0"
xmlns:xlink="http://www.w3.org/1999/xlink"
FileOID="DEF.XYZ789"
FileType="Snapshot"
CreationDateTime="2024-06-01T10:00:00"
ODMVersion="1.3.2">

<Study OID="STUDY.XYZ789">
<GlobalVariables>
<StudyName>XYZ789 Phase III</StudyName>
<StudyDescription>A randomized, double-blind, placebo-controlled study</StudyDescription>
<ProtocolName>XYZ789</ProtocolName>
</GlobalVariables>

<MetaDataVersion OID="MDV.XYZ789.001"
Name="Study XYZ789, Data Definitions"
def:DefineVersion="2.0.0"
def:StandardName="SDTM-IG"
def:StandardVersion="3.4">

<!-- Demographics Domain -->
<ItemGroupDef OID="IG.DM"
Name="DM"
Repeating="No"
IsReferenceData="No"
Purpose="Tabulation"
def:Structure="One record per subject"
def:Class="SPECIAL PURPOSE"
def:Label="Demographics">
<ItemRef ItemOID="IT.DM.STUDYID" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.DM.DOMAIN" OrderNumber="2" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.DM.USUBJID" OrderNumber="3" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.DM.SUBJID" OrderNumber="4" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.DM.RFSTDTC" OrderNumber="5" Mandatory="No" Role="Timing"/>
<ItemRef ItemOID="IT.DM.RFENDTC" OrderNumber="6" Mandatory="No" Role="Timing"/>
<ItemRef ItemOID="IT.DM.SITEID" OrderNumber="7" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.AGE" OrderNumber="8" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.AGEU" OrderNumber="9" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.SEX" OrderNumber="10" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.RACE" OrderNumber="11" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.ARMCD" OrderNumber="12" Mandatory="No" Role="Record Qualifier"/>
<ItemRef ItemOID="IT.DM.ARM" OrderNumber="13" Mandatory="No" Role="Record Qualifier"/>
</ItemGroupDef>

<!-- Adverse Events Domain -->
<ItemGroupDef OID="IG.AE"
Name="AE"
Repeating="Yes"
IsReferenceData="No"
Purpose="Tabulation"
def:Structure="One record per adverse event per subject"
def:Class="EVENTS"
def:Label="Adverse Events">
<ItemRef ItemOID="IT.AE.STUDYID" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.AE.DOMAIN" OrderNumber="2" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.AE.USUBJID" OrderNumber="3" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.AE.AESEQ" OrderNumber="4" Mandatory="Yes" Role="Identifier"/>
<ItemRef ItemOID="IT.AE.AETERM" OrderNumber="5" Mandatory="Yes" Role="Topic"/>
<ItemRef ItemOID="IT.AE.AEDECOD" OrderNumber="6" Mandatory="Yes" Role="Synonym Qualifier"/>
<ItemRef ItemOID="IT.AE.AESEV" OrderNumber="7" Mandatory="No" Role="Record Qualifier" def:CodeListOID="CL.SEVERITY"/>
<ItemRef ItemOID="IT.AE.AESER" OrderNumber="8" Mandatory="No" Role="Record Qualifier" def:CodeListOID="CL.NY"/>
<ItemRef ItemOID="IT.AE.AESTDTC" OrderNumber="9" Mandatory="No" Role="Timing"/>
<ItemRef ItemOID="IT.AE.AEENDTC" OrderNumber="10" Mandatory="No" Role="Timing"/>
</ItemGroupDef>

<!-- Variable Definitions -->
<ItemDef OID="IT.DM.STUDYID" Name="STUDYID" DataType="text" Length="20" def:Label="Study Identifier"/>
<ItemDef OID="IT.DM.DOMAIN" Name="DOMAIN" DataType="text" Length="2" def:Label="Domain Abbreviation"/>
<ItemDef OID="IT.DM.USUBJID" Name="USUBJID" DataType="text" Length="40" def:Label="Unique Subject Identifier"/>
<ItemDef OID="IT.DM.SUBJID" Name="SUBJID" DataType="text" Length="20" def:Label="Subject Identifier for the Study"/>
<ItemDef OID="IT.DM.RFSTDTC" Name="RFSTDTC" DataType="text" Length="20" def:Label="Subject Reference Start Date/Time"/>
<ItemDef OID="IT.DM.RFENDTC" Name="RFENDTC" DataType="text" Length="20" def:Label="Subject Reference End Date/Time"/>
<ItemDef OID="IT.DM.SITEID" Name="SITEID" DataType="text" Length="10" def:Label="Study Site Identifier"/>
<ItemDef OID="IT.DM.AGE" Name="AGE" DataType="integer" def:Label="Age"/>
<ItemDef OID="IT.DM.AGEU" Name="AGEU" DataType="text" Length="10" def:Label="Age Units"/>
<ItemDef OID="IT.DM.SEX" Name="SEX" DataType="text" Length="2" def:Label="Sex">
<def:CodeListRef CodeListOID="CL.SEX"/>
</ItemDef>
<ItemDef OID="IT.DM.RACE" Name="RACE" DataType="text" Length="60" def:Label="Race">
<def:CodeListRef CodeListOID="CL.RACE"/>
</ItemDef>
<ItemDef OID="IT.DM.ARMCD" Name="ARMCD" DataType="text" Length="20" def:Label="Planned Arm Code"/>
<ItemDef OID="IT.DM.ARM" Name="ARM" DataType="text" Length="200" def:Label="Description of Planned Arm"/>

<ItemDef OID="IT.AE.STUDYID" Name="STUDYID" DataType="text" Length="20" def:Label="Study Identifier"/>
<ItemDef OID="IT.AE.DOMAIN" Name="DOMAIN" DataType="text" Length="2" def:Label="Domain Abbreviation"/>
<ItemDef OID="IT.AE.USUBJID" Name="USUBJID" DataType="text" Length="40" def:Label="Unique Subject Identifier"/>
<ItemDef OID="IT.AE.AESEQ" Name="AESEQ" DataType="integer" def:Label="Sequence Number"/>
<ItemDef OID="IT.AE.AETERM" Name="AETERM" DataType="text" Length="200" def:Label="Reported Term for the Adverse Event"/>
<ItemDef OID="IT.AE.AEDECOD" Name="AEDECOD" DataType="text" Length="200" def:Label="Dictionary-Derived Term"/>
<ItemDef OID="IT.AE.AESEV" Name="AESEV" DataType="text" Length="12" def:Label="Severity/Intensity">
<def:CodeListRef CodeListOID="CL.SEVERITY"/>
</ItemDef>
<ItemDef OID="IT.AE.AESER" Name="AESER" DataType="text" Length="2" def:Label="Serious Event">
<def:CodeListRef CodeListOID="CL.NY"/>
</ItemDef>
<ItemDef OID="IT.AE.AESTDTC" Name="AESTDTC" DataType="text" Length="20" def:Label="Start Date/Time of Adverse Event"/>
<ItemDef OID="IT.AE.AEENDTC" Name="AEENDTC" DataType="text" Length="20" def:Label="End Date/Time of Adverse Event"/>

<!-- Code Lists -->
<CodeList OID="CL.SEX" Name="Sex" DataType="text" def:Extensible="No">
<CodeListItem CodedValue="M">
<Decode><TranslatedText xml:lang="en">Male</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="F">
<Decode><TranslatedText xml:lang="en">Female</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="U">
<Decode><TranslatedText xml:lang="en">Unknown</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<CodeList OID="CL.RACE" Name="Race" DataType="text" def:Extensible="Yes">
<CodeListItem CodedValue="WHITE">
<Decode><TranslatedText xml:lang="en">White</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="BLACK OR AFRICAN AMERICAN">
<Decode><TranslatedText xml:lang="en">Black or African American</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="ASIAN">
<Decode><TranslatedText xml:lang="en">Asian</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="AMERICAN INDIAN OR ALASKA NATIVE">
<Decode><TranslatedText xml:lang="en">American Indian or Alaska Native</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER">
<Decode><TranslatedText xml:lang="en">Native Hawaiian or Other Pacific Islander</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<CodeList OID="CL.SEVERITY" Name="Severity" DataType="text" def:Extensible="No">
<CodeListItem CodedValue="MILD">
<Decode><TranslatedText xml:lang="en">Mild</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="MODERATE">
<Decode><TranslatedText xml:lang="en">Moderate</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="SEVERE">
<Decode><TranslatedText xml:lang="en">Severe</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<CodeList OID="CL.NY" Name="No Yes Response" DataType="text" def:Extensible="No">
<CodeListItem CodedValue="N">
<Decode><TranslatedText xml:lang="en">No</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="Y">
<Decode><TranslatedText xml:lang="en">Yes</TranslatedText></Decode>
</CodeListItem>
</CodeList>

</MetaDataVersion>
</Study>
</ODM>
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119 changes: 119 additions & 0 deletions pointblank/data/metadata_examples/sdtm_ct.xml
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<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v1.3"
xmlns:nciodm="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC"
FileOID="CT.SDTM.2024-03-29"
FileType="Snapshot"
CreationDateTime="2024-03-29T00:00:00"
ODMVersion="1.3.2">

<Study OID="CT.SDTM">
<GlobalVariables>
<StudyName>CDISC SDTM Controlled Terminology</StudyName>
<StudyDescription>CDISC Submission Value-Level Terminology, 2024-03-29</StudyDescription>
<ProtocolName>SDTM Terminology</ProtocolName>
</GlobalVariables>

<MetaDataVersion OID="MDV.CT.SDTM.2024-03-29" Name="CDISC SDTM CT 2024-03-29">

<!-- Sex Codelist (C66731) -->
<CodeList OID="CL.C66731.SEX" Name="Sex" DataType="text"
nciodm:CodeListExtensible="No"
nciodm:CDISCSubmissionValue="SEX">
<nciodm:CDISCSynonym>Sex</nciodm:CDISCSynonym>
<nciodm:CDISCDefinition>Sex of the subject.</nciodm:CDISCDefinition>
<CodeListItem CodedValue="F" nciodm:ExtCodeID="C16576">
<Decode><TranslatedText xml:lang="en">Female</TranslatedText></Decode>
<nciodm:CDISCSynonym>Female</nciodm:CDISCSynonym>
<nciodm:CDISCDefinition>A person who belongs to the sex that normally produces ova.</nciodm:CDISCDefinition>
</CodeListItem>
<CodeListItem CodedValue="M" nciodm:ExtCodeID="C20197">
<Decode><TranslatedText xml:lang="en">Male</TranslatedText></Decode>
<nciodm:CDISCSynonym>Male</nciodm:CDISCSynonym>
<nciodm:CDISCDefinition>A person who belongs to the sex that normally produces sperm.</nciodm:CDISCDefinition>
</CodeListItem>
<CodeListItem CodedValue="U" nciodm:ExtCodeID="C17998">
<Decode><TranslatedText xml:lang="en">Unknown</TranslatedText></Decode>
<nciodm:CDISCSynonym>Unknown</nciodm:CDISCSynonym>
<nciodm:CDISCDefinition>Not known, not observed, not recorded, or refused.</nciodm:CDISCDefinition>
</CodeListItem>
<CodeListItem CodedValue="UNDIFFERENTIATED" nciodm:ExtCodeID="C45908">
<Decode><TranslatedText xml:lang="en">Undifferentiated</TranslatedText></Decode>
<nciodm:CDISCSynonym>Undifferentiated</nciodm:CDISCSynonym>
<nciodm:CDISCDefinition>Sex could not be determined.</nciodm:CDISCDefinition>
</CodeListItem>
</CodeList>

<!-- Severity (C66769) -->
<CodeList OID="CL.C66769.SEVERITY" Name="Severity/Intensity Scale for Adverse Events"
DataType="text"
nciodm:CodeListExtensible="No"
nciodm:CDISCSubmissionValue="AESEV">
<nciodm:CDISCSynonym>Severity/Intensity Scale for Adverse Events</nciodm:CDISCSynonym>
<CodeListItem CodedValue="MILD" nciodm:ExtCodeID="C41338">
<Decode><TranslatedText xml:lang="en">Mild</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="MODERATE" nciodm:ExtCodeID="C41339">
<Decode><TranslatedText xml:lang="en">Moderate</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="SEVERE" nciodm:ExtCodeID="C41340">
<Decode><TranslatedText xml:lang="en">Severe</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<!-- No Yes (C66742) -->
<CodeList OID="CL.C66742.NY" Name="No Yes Response" DataType="text"
nciodm:CodeListExtensible="No"
nciodm:CDISCSubmissionValue="NY">
<CodeListItem CodedValue="N" nciodm:ExtCodeID="C49487">
<Decode><TranslatedText xml:lang="en">No</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="Y" nciodm:ExtCodeID="C49488">
<Decode><TranslatedText xml:lang="en">Yes</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<!-- Race (C74457) -->
<CodeList OID="CL.C74457.RACE" Name="Race" DataType="text"
nciodm:CodeListExtensible="Yes"
nciodm:CDISCSubmissionValue="RACE">
<CodeListItem CodedValue="AMERICAN INDIAN OR ALASKA NATIVE" nciodm:ExtCodeID="C41259">
<Decode><TranslatedText xml:lang="en">American Indian or Alaska Native</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="ASIAN" nciodm:ExtCodeID="C41260">
<Decode><TranslatedText xml:lang="en">Asian</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="BLACK OR AFRICAN AMERICAN" nciodm:ExtCodeID="C16352">
<Decode><TranslatedText xml:lang="en">Black or African American</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER" nciodm:ExtCodeID="C41219">
<Decode><TranslatedText xml:lang="en">Native Hawaiian or Other Pacific Islander</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="WHITE" nciodm:ExtCodeID="C41261">
<Decode><TranslatedText xml:lang="en">White</TranslatedText></Decode>
</CodeListItem>
</CodeList>

<!-- Route of Administration (C66729) - extensible example -->
<CodeList OID="CL.C66729.ROUTE" Name="Route of Administration" DataType="text"
nciodm:CodeListExtensible="Yes"
nciodm:CDISCSubmissionValue="ROUTE">
<CodeListItem CodedValue="ORAL" nciodm:ExtCodeID="C38288">
<Decode><TranslatedText xml:lang="en">Oral</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="INTRAVENOUS" nciodm:ExtCodeID="C38276">
<Decode><TranslatedText xml:lang="en">Intravenous</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="SUBCUTANEOUS" nciodm:ExtCodeID="C38299">
<Decode><TranslatedText xml:lang="en">Subcutaneous</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="TOPICAL" nciodm:ExtCodeID="C38304">
<Decode><TranslatedText xml:lang="en">Topical</TranslatedText></Decode>
</CodeListItem>
<CodeListItem CodedValue="INTRAMUSCULAR" nciodm:ExtCodeID="C28161">
<Decode><TranslatedText xml:lang="en">Intramuscular</TranslatedText></Decode>
</CodeListItem>
</CodeList>

</MetaDataVersion>
</Study>
</ODM>
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