Treatment Emergent info for Adverse Event must be present A treatment-emergent flag should be included in SUPPAE according to SDTM IG v3.1.2 #8.4.3 3.1.2 3.1.3 3.2 AE SUPPAE SD1321 No Treatment Emergent info for Adverse Event - SUPPAE QVAL does not have an entry AETRTEM in ValueList ]]> Value for --TOX must be provided, when --TOXGR is populated A value for a Toxicity (--TOX) variable should be provided, when a Toxicity Grade (--TOXGR) variable value is populated and greater than 0 3.1.2 3.1.3 3.2 AE MH CE EG LB PC PP 0 :) let $toxvalue := $record/odm:ItemData[@ItemOID=$toxoid]/@Value where number($toxgrvalue) and not($toxvalue) return Missing value for {data($toxname)}, when {data($toxgrname)} is populated with a value >0, value={data($toxgrvalue)} ]]> Value for -DECOD must come from the MedDRA dictionary Value for the Dictionary-Derived Term (-DECOD) variable must be populated using a Preferred Term of the MedDRA dictionary of a version specified in the define.xml (Case-insensitive) 3.1.2 3.1.3 3.2 AE MH CE CG0379 Value '{data($decodvalue)}' for {data($decodname)} was not found in the MedDRA dictionary ]]> Value for --BODSYS must come from the MedDRA dictionary Value for Body System or Organ Class (--BODSYS) variable must be populated using a System Organ Class of the MedDRA dictionary of a version specified in the define.xml (case-insensitive) 3.1.2 3.1.3 3.2 AE MH CE CG0385 Value '{data($bodsysvalue)}' for {data($bodsysname)} was not found in the MedDRA dictionary ]]> Value for --PTCD must come from the MedDRA dictionary Value for Preferred Term Code (--PTCD) variable must be populated using a Preferred Term Code of the MedDRA dictionary of a version specified in the define.xml 3.1.3 3.2 AE MH CE Value '{data($ptcdvalue)}' for {data($ptcdname)} was not found in the MedDRA dictionary ]]> Value for --LLT must come from the MedDRA dictionary Value for Lowest Level Term (--LLT) variable must be populated using a Lowest Level Term of the MedDRA dictionary of a version specified in the define.xml (case-insensitive) 3.1.3 3.2 AE MH CE CG0377 Value '{data($lltvalue)}' for {data($lltname)} was not found in the MedDRA dictionary ]]> Value for --HLT must come from the MedDRA dictionary Value for High Level Term (--HLT) variable must be populated using a High Level Term of the MedDRA dictionary of a version specified in the define.xml (case-insensitive) 3.1.3 3.2 AE MH CE CG0381 Value '{data($hltvalue)}' for {data($hltname)} was not found in the MedDRA dictionary ]]> Value for --HLTCD must come from the MedDRA dictionary Value for High Level Term Code (--HLTCD) variable must be populated using a High Level Term Code of the MedDRA dictionary of a version specified in the define.xml. 3.1.3 3.2 AE MH CE CG0382 Value '{data($hltcdvalue)}' for {data($hltcdname)} was not found in the MedDRA dictionary ]]> Value for --HLGT must be in MedDRA dictionary Value for High Level Group Term (--HLGT) variable must be populated using a High Level Group Term of the MedDRA dictionary of a version specified in the define.xml (Case-insensitive) 3.1.3 3.2 AE MH CE Value '{data($hlgtvalue)}' for {data($hlgtname)} is not found in the MedDRA dictionary (case-insensitive) ]]> Value for --HLGTCD must come from the MedDRA dictionary Value for High Level Group Term Code (--HLGTCD) variable must be populated using a High Level Group Term Code of the MedDRA dictionary of a version specified in the define.xml 3.1.3 3.2 AE MH CE CG0384 Value '{data($hlgtcdvalue)}' for {data($hlgtcdname)} was not found in the MedDRA dictionary ]]> Value for --BDSYCD must be from the MedDRA dictionary Value for Body System or Organ Class Code (--BDSYCD) variable should be populated using a System Organ Class Code of the MedDRA dictionary of a version specified in the define.xml 3.1.3 3.2 AE MH CE CG0386 Value '{data($bdsycdvalue)}' for {data($bdsycdname)} was not found in the MedDRA dictionary ]]> Value for --SOC must be from the MedDRA dictionary - Value for System Organ Class (--SOC) variable must be populated using a System Organ Class of the MedDRA dictionary of a version specified in the define.xml (case-insensitive) 3.1.3 3.2 AE MH CE CG0436 Value '{data($socvalue)}' for {data($socname)} was not found in the MedDRA dictionary ]]> DS dataset must be included Disposition (DS) dataset should be included in every submission 3.1.2 3.1.3 3.2 DS Document {data($dsdatasetname)} could not be found in collection/folder {data($base)} ]]> AE dataset must be included Adverse Events (AE) dataset should be included in every submission 3.1.2 3.1.3 3.2 AE Document {data($aedatasetname)} could not be found in collection {data($base)} ]]> LB dataset must be included Lab Test Results (LB) dataset should be included in every submission 3.1.2 3.1.3 3.2 LB Document {data($lbdatasetname)} could not be found in collection {data($base)} ]]> VS dataset must be included Vital Signs (VS) dataset should be included in every submission 3.1.2 3.1.3 3.2 VS Document {data($vsdatasetname)} could not be found in collection {data($base)} ]]> SE dataset must be included Subject Elements (SE) dataset should be included in every submission 3.1.2 3.1.3 3.2 SE Document {data($sedatasetname)} could not be found in collection {data($base)} ]]> AGE or AGETXT variable must be present At least one of Age (AGE) or Age Text (AGETXT) variables should be inculded into Demographics (DM) domain 3.1.3 3.2 DM Neither AGE nor AGETXT variables are present ]]> AGE or AGETXT variables values must be populated Value for Age (AGE) of Age Range (AGETXT) variables should be populated for all subjects with only exception for Screen Failures (ARMCD=SCRNFAIL) and Not Assigned (ARMCD=NOTASSGN) subjects 3.1.3 3.2 DM Neither of AGE or AGETXT variables values are populated ]]> AGE must be provided Age (AGE) variable values should be provided, when Date/Time of Birth (BRTHDTC) variable values are populated 3.1.2 3.1.3 3.2 DM AGE is not provided ]]> AGE and AGETXT variables values may not be both populated Age (AGE) and Age Range (AGETXT) variables should never both be populated for the same subject 3.1.3 3.2 DM Both AGE and AGETXT variables values are populated ]]> DTHDTC must be populated, when DTHFL is populated Date/Time of Death (DTHDTC) should be provided, when subject died (DTHFL=Y) 3.1.3 3.2 DM Missing value for DTHDTC, when DTHFL is populated ]]> ECSTDTC/EXSTDTC date may not be before RFXSTDTC Start Date/Time of Treatment (EXSTDTC) variable value must be greater than or equal to Date/Time of First Study Treatment (RFXSTDTC) 3.1.3 3.2 EX EC {data($usubjoid)} - {data($rfxstdtcoid)}):) (: create a temporary structure containing USUBJID and RFXSTDTC :) let $usubjidrfxstdtcpairs := ( for $record in doc($dmdataset)//odm:ItemGroupData let $usubjid := $record/odm:ItemData[@ItemOID=$usubjoiddm]/@Value let $rfxstdtc := $record/odm:ItemData[@ItemOID=$rfxstdtcoid]/@Value return ) (: get the OID of EXSTDTC or EGSTDTC :) let $stdtcname := concat($datasetname,'STDTC') let $stdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$stdtcname]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$datasetname and (@Name='EC' or @Name='EX')]/odm:ItemRef/@ItemOID return $a ) (: get the OID of USUBJID in EX or EC :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$datasetname]/odm:ItemRef/@ItemOID return $a ) (: get the EX and/or EC dataset :) (: 2020-08-14 :) let $ecexdataset := $definedoc//odm:ItemDef[@Name=$datasetname][@Name='EX' or @Name='EC'] let $datasetloc := ( if($defineversion='2.1') then $ecexdataset/def21:leaf/@xlink:href else $ecexdataset/def:leaf/@xlink:href ) let $ecexdoc := ( if($datasetloc) then doc(concat($base,$datasetloc)) else () ) (: now iterate over all records in EX or EC that have a --STDTC :) for $record in $ecexdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$stdtcoid]] (: get the value of --STDTC :) let $stdtcvalue := $record/odm:ItemData[@ItemOID=$stdtcoid]/@Value (: get the value of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $rfxstdtcvalue := $usubjidrfxstdtcpairs[@usubjid=$usubjidvalue]/@rfxstdtc let $recnum := $record/@data:ItemGroupDataSeq (: and compare with the value of RFXSTDTC in DM for the same USUBJID :) where $rfxstdtcvalue and xs:date($rfxstdtcvalue) > xs:date($stdtcvalue) (: and when the STDTC is before RFXSTDTC give an error :) return {data($stdtcname)} date '{data($stdtcvalue)}' is before RFXSTDTC '{data($rfxstdtcvalue)}' ]]> --TEST value must be consistent within --TESTCD All values of Name of Measurement, Test or Examination (--TEST) should be the same for a given value of Short Name of Measurement, Test or Examination (--TESTCD) 3.1.2 3.1.3 3.2 FINDINGS 1] (: start from the second one :) let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --TEST :) let $testvalue := $record/odm:ItemData[@ItemOID=$testoid]/@Value (: take the previous record in the same group, and take its --TEST value :) let $precrecord := $record/preceding-sibling::odm:ItemGroupData[1] (: as they come in descending order :) let $recnum2 := $precrecord/@data:ItemGroupDataSeq let $testvalue2 := $precrecord/odm:ItemData[@ItemOID=$testoid]/@Value (: when the value of--TEST in both records is different, report an error :) where not($testvalue2 = $testvalue) return Inconsistent value for {data($testname)} within {data($testcdname)}='{data($testcdvalue)}' in dataset {data($datasetname)}. Following values were found: record number {data($recnum2)}: {data($testname)}={data($testvalue2)} - record number {data($recnum)}: {data($testname)}={data($testvalue)} ]]> --TEST value must be consistent within --TESTCD All values of Name of Measurement, Test or Examination (--TEST) should be the same for a given value of Short Name of Measurement, Test or Examination (--TESTCD) 3.1.2 3.1.3 3.2 FINDINGS 1] (: start from the second one :) let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --TEST :) let $testvalue := $record/odm:ItemData[@ItemOID=$testoid]/@Value (: take the previous record in the same group, and take its --TEST value :) let $precrecord := $record/preceding-sibling::odm:ItemGroupData[1] (: as they come in descending order :) let $recnum2 := $precrecord/@data:ItemGroupDataSeq let $testvalue2 := $precrecord/odm:ItemData[@ItemOID=$testoid]/@Value (: when the value of--TEST in both records is different, report an error :) where not($testvalue2 = $testvalue) return Inconsistent value for {data($testname)} within {data($testcdname)}='{data($testcdvalue)}' in dataset {data($datasetname)}. Following values were found: record number {data($recnum2)}: {data($testname)}={data($testvalue2)} - record number {data($recnum)}: {data($testname)}={data($testvalue)} ]]> --TESTCD value must be consistent within --TEST All values of Short Name of Measurement, Test or Examination (--TESTCD) should be the same for a given value of Name of Measurement, Test or Examination (--TEST) 3.1.2 3.1.3 3.2 FINDINGS 1] (: start from the second one :) let $recnum := $record/@data:ItemGroupDataSeq let $testcdvalue := $record/odm:ItemData[@ItemOID=$testcdoid]/@Value (: take the previous record in the same group, and take its --TESTCD value :) let $precrecord := $record/preceding-sibling::odm:ItemGroupData[1] (: as they come in descending order :) let $recnum2 := $precrecord/@data:ItemGroupDataSeq let $testcdvalue2 := $precrecord/odm:ItemData[@ItemOID=$testcdoid]/@Value let $recnum2 := $precrecord/@data:ItemGroupDataSeq (: when the value of--TESTCD in both records is different, report an error :) where not($testcdvalue2 = $testcdvalue) return Inconsistent value for {data($testcdname)} within {data($testname)}='{data($testvalue)}' in dataset {data($datasetname)}. Following values were found: record number {data($recnum2)}: {data($testcdname)}={data($testcdvalue2)} - record number {data($recnum)}: {data($testcdname)}={data($testcdvalue)} ]]> --TESTCD value must be consistent within --TEST, single dataset or domain All values of Short Name of Measurement, Test or Examination (--TESTCD) should be the same for a given value of Name of Measurement, Test or Examination (--TEST) 3.1.2 3.1.3 3.2 FINDINGS 1] (: start from the second one :) let $recnum := $record/@data:ItemGroupDataSeq let $testcdvalue := $record/odm:ItemData[@ItemOID=$testcdoid]/@Value (: take the previous record in the same group, and take its --TESTCD value :) let $precrecord := $record/preceding-sibling::odm:ItemGroupData[1] (: as they come in descending order :) let $recnum2 := $precrecord/@data:ItemGroupDataSeq let $testcdvalue2 := $precrecord/odm:ItemData[@ItemOID=$testcdoid]/@Value let $recnum2 := $precrecord/@data:ItemGroupDataSeq (: when the value of--TESTCD in both records is different, report an error :) where not($testcdvalue2 = $testcdvalue) return Inconsistent value for {data($testcdname)} within {data($testname)}='{data($testvalue)}' in dataset {data($datasetname)}. Following values were found: record number {data($recnum2)}: {data($testcdname)}={data($testcdvalue2)} - record number {data($recnum)}: {data($testcdname)}={data($testcdvalue)} ]]> QLABEL value must be consistent within QNAM All values of Qualifier Variable Label (QLABEL) should be the same for a given value of Qualifier Variable Name (QNAM) 3.1.2 3.1.3 3.2 SUPPQUAL Inconsistent value for QLABEL within QNAM={data($uniqueqnam)} in dataset {data($datasetname)}. {data($uniqueqlabelvaluescount)} different combinations were found ]]> QNAM value must be consistent within QLABEL All values of Qualifier Variable Name (QNAM) should be the same for a given value of Qualifier Variable Label (QLABEL) 3.1.2 3.1.3 3.2 SUPPQUAL Inconsistent value for QNAM within QLABEL={data($uniqueqlabel)} in dataset {data($datasetname)}. {data($uniqueqnamvaluescount)} different combinations were found ]]> ARM value must be consistent A value for Description of Planned Arm (ARM) must have a unique value for Planned Arm Code (ARMCD) with the domain DM, TA, TV 3.1.2 3.1.3 3.2 DM TA TV Inconsistent value for ARM within ARMCD={data($uniquearmcd)} in dataset {data($datasetname)}. {data($uniquearmvaluescount)} different combinations were found ]]> ARMCD value must be consistent A value for Planned Arm Code (ARMCD) must have a unique value for Description of Planned Arm (ARM) with the domain within the domain DM, TA, TV 3.1.2 3.1.3 3.2 DM TA TV Inconsistent value for ARMCD within ARM={data($uniquearm)} in dataset {data($datasetname)}. {data($uniquearmcdvaluescount)} different combinations were found ]]> ELEMENT value may not be duplicate in TE The value of Element (Description of Element) variable must be unique within Trial Elements (TE) domain 3.1.2 3.1.3 3.2 TE $recnum] (: and compare the value of ELEMENT in the record with the original one :) let $recnum2 := $record2/@data:ItemGroupDataSeq let $elementvalue2 := $record2//odm:ItemData[@ItemOID=$elementoid]/@Value where $elementvalue=$elementvalue2 return Duplicate ELEMENT value: records {data($recnum)} and {data($recnum2)} have the same value for ELEMENT, value={data($elementvalue)} ]]> ETCD value may not be duplicate in TE The value of Element Code (ETCD) variable must be unique within Trial Elements (TE) domain 3.1.2 3.1.3 3.2 TE $recnum] (: and compare the value of ETCD in the record with the original one :) let $recnum2 := $record2/@data:ItemGroupDataSeq let $etcdvalue2 := $record2//odm:ItemData[@ItemOID=$etcdoid]/@Value where $etcdvalue=$etcdvalue2 return Duplicate ETCD value: records {data($recnum)} and {data($recnum2)} have the same value for ETCD, value={data($etcdvalue)} ]]> ETCD must be unique within ELEMENT Element Code (ETCD) must have a unique value for a given value of Description of Element (ELEMENT) within the domain 3.1.2 3.1.3 3.2 SE TA 1] let $etcdvalue2 := $record/odm:ItemData[@ItemOID=$etcdoid]/@Value (: if the ETCD value is different from that within the first record of the group, give an error :) let $recnum2 := $record/@data:ItemGroupDataSeq where $etcdvalue != $etcdvalue2 return Non-unique value for ETCD within ELEMENT '{data($elementvalue)}' in dataset {data($datasetname)}. Record {data($recnum2)} has ETCD value '{data($etcdvalue2)}' whereas record {data($recnum)} has ETCD value '{data($etcdvalue)}' ]]> ACTARM must be consistent in DM A value for Description of Actual Arm (ACTARM) must have a unique value for Actual Arm Code (ACTARMCD) with the domain 3.1.3 3.2 DM 1] let $actarmvalue2 := $record/odm:ItemData[@ItemOID=$actarmoid]/@Value (: if the ACTARM value is different from that within the first record of the group, give an error :) let $recnum2 := $record/@data:ItemGroupDataSeq where $actarmvalue != $actarmvalue2 return Non-unique value for ACTARM within ACTARMCD '{data($actarmcdvalue)}' in dataset {data($datasetname)}. Record {data($recnum2)} has ACTARM value '{data($actarmvalue2)}' whereas record {data($recnum)} has ACTARM value '{data($actarmvalue)}' ]]> ACTARMCD must be consistent in DM A value for Actual Arm Code (ACTARMCD) must have a unique value for Description of Actual Arm (ACTARM) with the domain 3.1.3 3.2 DM 1] let $actarmcdvalue2 := $record/odm:ItemData[@ItemOID=$actarmcdoid]/@Value (: if the ACTARMCD value is different from that within the first record of the group, give an error :) let $recnum2 := $record/@data:ItemGroupDataSeq where $actarmcdvalue != $actarmcdvalue2 return Non-unique value for ACTARMCD within ACTARM '{data($actarmvalue)}' in dataset {data($datasetname)}. Record {data($recnum2)} has ACTARMCD value '{data($actarmcdvalue2)}' whereas record {data($recnum)} has ACTARMCD value '{data($actarmcdvalue)}' ]]> AESER must be 'Y' when any of AESCAN, AESCONG, AESDISAB, AESDTH, AESHOSP, AESLIFE, AESMIE has value 'Y' Serious Event (AESER) variable value is expected to be 'Y', when either of Seriousness Criteria variables (AESCAN, AESCONG, AESDISAB, AESDTH, AESHOSP, AESLIFE, AESMIE) has value 'Y' 3.1.2 3.1.3 3.2 AE AESER is not 'Y', when any of AESCAN, AESCONG, AESDISAB, AESDTH, AESHOSP, AESLIFE, AESMIE equals 'Y', value found for AESER={data($aeservalue)} ]]> AESDTH must be 'Y', when AEOUT='FATAL' Results in Death (AEDTH) should equal 'Y', when Outcome of Adverse Event (AEOUT) is 'FATAL' 3.1.2 3.1.3 3.2 AE AESDTH is not 'Y', when AEOUT='FATAL', value for AESDTH found is '{data($aesdthvalue)}' ]]> TA dataset must be present Trial Arms (TA) dataset should be included in every submission 3.1.2 3.1.3 3.2 TA Dataset 'TA' could not be found in collection {data($base)} ]]> TE dataset must be present Trial Elements (TE) dataset should be included in every submission 3.1.2 3.1.3 3.2 TE Dataset 'TE' could not be found in collection {data($base)} ]]> Only one ADDON record is allowed in TS Trial Summary (TS) domain must contain only one record for 'ADDON' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple ADDON records in dataset TS, number of ADDON records found ={data($count)} ]]> Only one AGEMAX record is allowed in TS Trial Summary (TS) domain must contain only one record for 'AGEMAX' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple AGEMAX records in TS: number of AGEMAX records found={data($count)} ]]> Only one AGEMIN record is allowed in TS Trial Summary (TS) domain must contain only one record for 'AGEMIN' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple AGEMIN records in dataset TS: number of AGEMIN records found={data($count)} ]]> Only one LENGTH record is allowed in TS Trial Summary (TS) domain must contain only one record for 'LENGTH' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple LENGTH records in dataset TS: number of LENGTH records found={data($count)} ]]> Only one PLANSUB record is allowed in TS Trial Summary (TS) domain must contain only one record for 'PLANSUB' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple PLANSUB Records in dataset TS: number of PLANSUB records found={data($count)} ]]> Only one RANDOM record is allowed in TS Trial Summary (TS) domain must contain only one record for 'RANDOM' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple RANDOM Records in dataset TS: number of RANDOM records found={data($count)} ]]> Only one SEXPOP record is allowed in TS Trial Summary (TS) domain must contain only one record for 'SEXPOP' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple SEXPOP Records: number of SEXPOP records found={data($count)} ]]> TSVCDREF variable value must be 'SNOMED', when TSPARAMCD='INDIC' TSVCDREF variable value must be 'SNOMED', when TSPARAMCD='INDIC' 3.1.2 3.1.3 3.2 TS SD2240 Invalid TSVCDREF value '{data($tsvcdrefvalue)}' for Trial Summary Parameter TSPARMCD={data($tsparmcdvalue)} in dataset TS ]]> TSVAL/TSVALCD value must match for TRT TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS {data($tsval)} :) (: now invoke the web service to check whether it is a valid UNII, e.g.: https://dailymed.nlm.nih.gov/dailymed/services/v2/uniis.xml?unii_code=1X0094V6JV :) (: ONLY FOR TESTING :) (: let $tsvalcd := '1X0094V6JV' let $tsval := 'NAFARELINx' :) (: call the web service :) let $webservice := concat('https://dailymed.nlm.nih.gov/dailymed/services/v2/uniis.xml?unii_code=',$tsvalcd) let $webserviceresult := doc($webservice) (: this is a document with the structure /uniis/unii/unii_code and /uniis/unii/active_moiety - it these must match TSVALCD and TSVAL :) let $srscode := $webserviceresult/uniis/unii/unii_code let $srsname := $webserviceresult/uniis/unii/active_moiety where not($tsvalcd = $srscode and $tsval = $srsname) return TSVAL/TSVALCD value mismatch for TRT in dataset {data($tsdatasetname)}: TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS): values '{data($tsvalcd)}' and '{data($tsval)}' do not belong to the same SRS record ]]> Only one NARMS record is allowed in TS Trial Summary (TS) domain must contain only one record for 'NARMS' Parameter 3.1.2 3.1.3 3.2 TS 1 return Multiple NARMS records in dataset {data($tsdatasetname)}, number of NARMS records found={data($count)} ]]> --VAMTU must be populated, when --VAMT is populated Treatment Vehicle Amount Units (--VAMTU) should not be NULL, when Treatment Vehicle Amount (--VAMT) is populated 3.1.2 3.1.3 3.2 INTERVENTIONS Missing value for {data($vamtuname)}, when {data($vamtname)} is populated ]]> Every subject must have a baseline result All subjects should have at least one baseline observation (--BLFL = 'Y') in EG, LB, MB, MS, PC and VS domains, except for subjects who failed screening (ARMCD = 'SCRNFAIL') or were not fully assigned to an Arm (ARMCD = 'NOTASSGN') or were not treated (ACTARMCD = 'NOTTRT') 3.1.2 3.1.3 3.2 EG LB MB MS PC VS {data($domain)} - {data($blfloid)} :) (: iterate over all the randomized subjects and count the number of baseline flag records over all the datasets within that domain :) for $subject in $randomizedsubjects let $count := count( for $dataset in $datasetslocationsindomain let $c := doc($dataset)//odm:ItemGroupData[odm:ItemData[@ItemOID=$usubjidoid][@Value=$subject] and odm:ItemData[@ItemOID=$blfloid]]/@data:ItemGroupDataSeq return $c ) (: $count gives the number of records with a baseline flag for the subject :) where count($datasets) > 0 and $count = 0 (: no baseline record for this subject found in any of the datasets in this domain :) return No baseline result in Domain {data($domain)} for subject {data($subject)} ]]> Every subject must have a baseline result All subjects should have at least one baseline observation (--BLFL = 'Y') in EG, LB, MB, MS, PC and VS domains, except for subjects who failed screening (ARMCD = 'SCRNFAIL') or were not fully assigned to an Arm (ARMCD = 'NOTASSGN') or were not treated (ACTARMCD = 'NOTTRT') 3.1.2 3.1.3 3.2 EG LB MB MS PC VS {data($domain)} - {data($blfloid)} :) (: iterate over all the randomized subjects and count the number of baseline flag records over all the datasets within that domain :) for $subject in $randomizedsubjects (: $randomizedsubjects is a list of randomized subjects :) (: $count gives the number of records with a baseline flag for the subject :) let $count := count(doc(concat($base,$datasetlocation))//odm:ItemGroupData[odm:ItemData[@ItemOID=$usubjidoid and @Value=$subject] and odm:ItemData[@ItemOID=$blfloid and @Value='Y']]) where $count = 0 (: no baseline record for this subject found in any of the datasets in this domain :) return No baseline result in Dataset {data($domain)} for subject {data($subject)} ]]> --BLFL variable must be present in every custom Findings domain Baseline Flag (--BLFL) should be present in all custom Findings domains 3.1.2 3.1.3 3.2 FINDINGS No baseline variable {data($blflname)} in custom Findings dataset {data(name)} ]]> DSCAT must be populated Category for Disposition Event (DSCAT) should be populated DS 3.1.2 3.1.3 3.2 Missing value for DSCAT ]]> Character values may not have leading spaces Character values should not have leading space ' ' characters, or '.' as an entire value. The only exceptions are COVALn and TSVALn variables 3.1.2 3.1.3 3.2 ALL {data($charvaroids)} :) (: iterate over all data points that are not of type 'integer' or 'float' :) for $record in $datasetdoc//odm:ItemGroupData (: get the record number :) let $recnum := $record/@data:ItemGroupDataSeq for $datapoint in $record/odm:ItemData[functx:is-value-in-sequence(@ItemOID,$charvaroids)] (: get the name from the OID :) let $varname := $definedoc//odm:ItemDef[@OID=$datapoint/@ItemOID]/@Name (: get the value :) let $value := $datapoint/@Value (: when the first character is a space, or the whole value is '.' give an warning :) where $value = '.' or starts-with($value,' ') return Unexpected character value in non-numeric variable value {data($varname)}. Value '{data($value)}' was found ]]> --DY variable must be present, when --DTC variable is present Collection Study Day (--DY) variable should be included into dataset, when Collection Study Date/Time (--DTC) variable is present 3.1.2 3.1.3 3.2 ALL Collection Study Day {data(concat($name,'DY'))} variable must be included into dataset, when Collection Study Date/Time {data($dtcname)} variable is present in dataset {data($datasetname)} ]]> Value for --DECOD must be in correct case Case for the Dictionary-Derived Term (--DECOD) variable must be sentence case using a Preferred Term of the MedDRA dictionary of a version specified in the define.xml (case-sensitive) 3.1.2 3.1.3 3.2 AE MH CE Value '{data($decodvalue)}' for {data($decodname)} is in incorrect case from the MedDRA dictionary ]]> Value for --LLT must be in correct case Case for the Dictionary-Derived Term (--DECOD) variable must be sentence case using a Preferred Term of the MedDRA dictionary of a version specified in the define.xml (sase-sensitive) 3.1.3 3.2 AE MH CE Value '{data($lltvalue)}' for {data($lltname)} is in incorrect case from the MedDRA dictionary ]]> Value for --HLT must be in correct case Case for High Level Term (--HLT) variable must be sentence case using a High Level Term of the MedDRA dictionary of a version specified in the define.xml (case-sensitive) 3.1.3 3.2 AE MH CE Value '{data($hltvalue)}' for {data($hltname)} is in incorrect case from the MedDRA dictionary ]]> Value for --HLGT must be in correct case Case for High Level Group Term (--HLGT) variable must be sentence case using a High Level Group Term of the MedDRA dictionary of a version specified in the define.xml (case-sensitive) 3.1.3 3.2 AE MH CE Value '{data($hlgtvalue)}' for {data($hlgtname)} is in incorrect case from the MedDRA dictionary ]]> Value for --SOC must be in correct case - Case for System Organ Class (--SOC) variable must be sentence case using a System Organ Class of the MedDRA dictionary of a version specified in the define.xml (case-sensitive) 3.1.3 3.2 AE MH CE Value '{data($socvalue)}' for {data($socname)} is in incorrect case from the MedDRA dictionary ]]> Value for COUNTRY (DM) must be found in ISO 3166 Value for the Country (COUNTRY) variable must be populated using terms found in ISO 3166 3.1.2 3.1.3 3.2 DM Value for COUNTRY '{data($country)}' is not found in ISO 3166 ]]> DM dataset must be included Demographics (DM) dataset must be included in every submission 3.1.2 3.1.3 3.2 DM Document {data($dmdatasetname)} could not be found in collection {data($base)} ]]> TS dataset must be included Trial Summary (TS) dataset must be included in every submission 3.1.2 3.1.3 3.2 TS Document {data($tsdatasetname)} could not be found in collection {data($base)} ]]> FDA expects variable EPOCH Variables requested by FDA in policy documents should be included in the dataset. E.g., EPOCH 3.1.2 3.1.3 3.2 ALL FDA expected variable EPOCH is not found in dataset '{data($name)}' ]]> EX record may not be present, when subject is not assigned to an arm Subjects that have withdrawn from a trial before assignment to an Arm (ARMCD='NOTASSGN') should not have any Exposure records 3.1.2 3.1.3 3.2 EX DM 0 (: at least one EX record was found :) return {data($count)} EX records were found in EX dataset {data($exdatasetname)} for USUBJID={data($usubjidvalue)} although subject has not been assigned to an arm (ARMCD='NOTASSGN') in DM dataset {data($dmdatasetname)} ]]> Randomized subjects must at least have one Exposure record All Demographics (DM) subjects (USUBJID) participating in a study that includes investigational product should have at least one record in the Exposure (EX) domain, except for subjects who failed screening (ARMCD = 'SCRNFAIL') or were not fully assigned to an Arm (ARMCD = 'NOTASSGN') 3.1.2 3.1.3 3.2 EX DM No exposure records were found in dataset {data($exdatasetname)} for subject {data($usubjidvalue)} with assigned arm {data($arm)} ]]> Dataset may not be greater than 5 GB in size Large datasets should be split into smaller datasets no larger than 5 GB in size. 3.1.2 3.1.3 3.2 ALL (5*1024) return Size of file {$child} is larger than 1GB - file size found = {$size} MB ]]> ACTARM must be equal to ARM A value for an Actual Arm (ACTARM) variable is expected to be equal to a value of an Arm (ARM) variable 3.1.3 3.2 DM ACTARM, value='{data($actarmvalue)}' does not equal ARM, value='{data($armvalue)}' ]]> --STRESC value must be present for Baseline record A Standard Result value (--STRESC) is expected to be populated for Baseline records (--BLFL="Y") 3.1.2 3.1.3 3.2 FINDINGS Missing {data($strescname)}, when {data($blflname)} value={data($blflvalue)} is provided in dataset {data($datasetname)} ]]> --STRESC value must be present for Baseline record A Standard Result value (--STRESC) is expected to be populated for Baseline records (--BLFL="Y") 3.1.2 3.1.3 3.2 FINDINGS Missing {data($strescname)}, when {data($blflname)} value={data($blflvalue)} is provided in dataset {data($datasetname)} ]]> 'SCRNFAIL' subject must have a record in the IE domain - All subjects with Planned Arm Code (ARMCD) equals 'SCRNFAIL' should have records in the Inclusion/Exclusion Criteria Not Met (IE) domain IE DM 3.1.2 3.1.3 3.2 1 return No records for in IE dataset {data($iedatasetname)} for Screen Failure subject with USUBJID {data($dmusubjid)} ]]> --STRESC must be populated, when --STAT is null Character Result/Finding in Std Format (--STRESC) value should not be NULL, when Status Flag (--STAT) value is null 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($strescname)}, when {data($statname)}=null ]]> --STRESC must be populated, when --STAT is null Character Result/Finding in Std Format (--STRESC) value should not be NULL, when Status Flag (--STAT) value is null 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($strescname)}, when {data($statname)}=null ]]> --STRESN must be populated when standardized value is numeric Standardized Result in Numeric Format (--STRESN) variable value should be populated, when Standardized Result in Character Format (--STRESC) variable value represents a numeric value 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($stresnname)}, when {data($strescname)} value={data($strescvalue)} is provided and represents a numeric value in dataset {data($datasetname)} ]]> --STRESN must be populated when standardized value is numeric Standardized Result in Numeric Format (--STRESN) variable value should be populated, when Standardized Result in Character Format (--STRESC) variable value represents a numeric value 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($stresnname)}, when {data($strescname)} value={data($strescvalue)} is provided and represents a numeric value in dataset {data($datasetname)} ]]> --STRESN must be equal to --STRESC Standardized Result in Numeric Format (--STRESN) variable value should be populated, when Standardized Result in Character Format (--STRESC) variable value represents a numeric value 3.1.2 3.1.3 3.2 FINDINGS Value for {data($stresnname)} '{data($stresnvalue)}' does not equal value for {data($strescname)} '{data($strescvalue)}' ]]> --STRESN must be equal to --STRESC Standardized Result in Numeric Format (--STRESN) variable value should be populated, when Standardized Result in Character Format (--STRESC) variable value represents a numeric value 3.1.2 3.1.3 3.2 FINDINGS Value for {data($stresnname)} '{data($stresnvalue)}' does not equal value for {data($strescname)} '{data($strescvalue)}' ]]> --DTC or --DY must be populated Start Date/Time of Observation (--DTC) or Study Day of Observation (--DY) should be populated in the Findings observation class where data are usually collected at multiple study days. 3.1.2 3.1.3 3.2 FINDINGS Missing values for both {data($dtcname)} and {data($dyname)} variables ]]> --DTC or --DY must be populated Start Date/Time of Observation (--DTC) or Study Day of Observation (--DY) should be populated in the Findings observation class where data are usually collected at multiple study days. 3.1.2 3.1.3 3.2 FINDINGS Missing values for both {data($dtcname)} and {data($dyname)} variables ]]> Exposure end date may not be after the latest Disposition date End Date/Time of Treatment (EXENDTC) should be less than or equal to the Start Date/Time of the latest Disposition Event (DSSTDTC) 3.1.2 3.1.3 3.2 EX DS Exposure end date EXENDTC={data($exendtcvalue)} for USUBJID={data($exusubjidvalue)} is after last disposition date {data($latestdate)} ]]> --STDY may not be after --ENDY Study Day of Start of Event, Exposure or Observation (--STDY) must be less or equal to Study Day of End of Event, Exposure or Observation (--ENDY) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS number($endyvalue) return {data($stdyname)}={data($stdyvalue)} is after {data($endyname)}={data($endyvalue)} ]]> --STDY may not be after --ENDY Study Day of Start of Event, Exposure or Observation (--STDY) must be less or equal to Study Day of End of Event, Exposure or Observation (--ENDY) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS number($endyvalue) return {data($stdyname)}={data($stdyvalue)} is after {data($endyname)}={data($endyvalue)} ]]> 3.1.2 3.1.3 3.2 --STDTC may not be after --ENDTC Start Date/Time of Event, Exposure or Observation (--STDTC) must be less or equal to End Date/Time of Event, Exposure or Observation (--ENDTC) ALL xs:dateTime($endtctestvalue) return {data($stdtcname)}={data($stdtcvalue)} is after {data($endtcname)}={data($endtcvalue)} in dataset {data($datasetname)} ]]> 3.1.2 3.1.3 3.2 --STDTC may not be after --ENDTC Start Date/Time of Event, Exposure or Observation (--STDTC) must be less or equal to End Date/Time of Event, Exposure or Observation (--ENDTC) ALL xs:dateTime($endtctestvalue) return {data($stdtcname)}={data($stdtcvalue)} is after {data($endtcname)}={data($endtcvalue)} in dataset {data($datasetname)} ]]> --DTC may not be after --ENDTC Date/Time of Specimen Collection (--DTC) must be less or equal to End Date/Time of Specimen Collection (--ENDTC) 3.1.2 3.1.3 3.2 FINDINGS xs:dateTime($endtctestvalue) return {data($dtcname)}={data($dtcvalue)} is after {data($endtcname)}={data($endtcvalue)} in dataset {data($name)} ]]> --DTC may not be after --ENDTC Date/Time of Specimen Collection (--DTC) must be less or equal to End Date/Time of Specimen Collection (--ENDTC) 3.1.2 3.1.3 3.2 FINDINGS xs:dateTime($endtctestvalue) return {data($dtcname)}={data($dtcvalue)} is after {data($endtcname)}={data($endtcvalue)} in dataset {data($name)} ]]> RFSTDTC may not be after RFENDTC Subject Reference Start Date/Time (RFSTDTC) must be less than or equal to Subject Reference End Date/Time (RFENDTC) 3.1.2 3.1.3 3.2 DM xs:dateTime($endtctestvalue) return RFSTDTC={data($rfstdtcvalue)} is after RFENDTC={data($rfendtcvalue)} for subject with USUBJID={data($usubjidvalue)} ]]> --STDY variable must be present, when --STDTC variable is present Study Day of Start (--STDY) variable should be included into dataset, when Start Study Date/Time (--STDTC) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SV SE Missing {data($stdyname)} variable in dataset {data($datasetname)}, when {data($stdtcname)} variable is present ]]> --ENDY variable must be present, when --ENDTC variable is present Study Day of End (--ENDY) variable should be included into dataset, when End Study Date/Time (--ENDTC) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SV SE Missing {data($endyname)} variable in dataset {data($datasetname)}, when {data($endtcname)} variable is present ]]> AE start date may not be after the latest Disposition date Start Date/Time of Adverse Event (AESTDTC) should be less than or equal to the Start Date/Time of the latest Disposition Event (DSSTDTC) 3.1.2 3.1.3 3.2 AE AE start date, value={data($aestdtcvalue)} is after the latest Disposition date, value={data($latestdate)} ]]> --STDTC date may not be after RFPENDTC Start Date/Time (--STDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over all INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name='DM' or @Name='SE' or @Name='SV' or upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: we need the OID of USUBJID and of the --STDTC variable :) let $stdtcvarname := concat($domain,'STDTC') let $stdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$stdtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --STDTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$stdtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --STDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $stdtcvalue := $record/odm:ItemData[@ItemOID=$stdtcoid]/@Value (: get the value of RFPENDTC in DM :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $stdtctestvalue := (: only the year is given :) if(string-length($stdtcvalue) = 4) then concat($stdtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($stdtcvalue) = 7) then concat($stdtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($stdtcvalue) = 10) then concat($stdtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($stdtcvalue) = 11) then concat($stdtcvalue,'00:00:00') (: only hour is given :) else if(string-length($stdtcvalue) = 13) then concat($stdtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($stdtcvalue) = 16) then concat($stdtcvalue,':00') (: all ok anyway :) else ($stdtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $stdtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($stdtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($stdtcvarname)}={data($stdtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> --STDTC date may not be after RFPENDTC Start Date/Time (--STDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over the provided dataset in classes INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name=$datasetname][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: we need the OID of USUBJID and of the --STDTC variable :) let $stdtcvarname := concat($domain,'STDTC') let $stdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$stdtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --STDTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$stdtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --STDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $stdtcvalue := $record/odm:ItemData[@ItemOID=$stdtcoid]/@Value (: get the value of RFPENDTC in DM :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $stdtctestvalue := (: only the year is given :) if(string-length($stdtcvalue) = 4) then concat($stdtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($stdtcvalue) = 7) then concat($stdtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($stdtcvalue) = 10) then concat($stdtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($stdtcvalue) = 11) then concat($stdtcvalue,'00:00:00') (: only hour is given :) else if(string-length($stdtcvalue) = 13) then concat($stdtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($stdtcvalue) = 16) then concat($stdtcvalue,':00') (: all ok anyway :) else ($stdtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $stdtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($stdtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($stdtcvarname)}={data($stdtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> --DTC date may not be after RFPENDTC Start Date/Time (--STDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over all INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name='DM' or @Name='SE' or @Name='SV' or upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: we need the OID of USUBJID and of the --DTC variable :) let $dtcvarname := concat($domain,'DTC') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$dtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --DTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --STDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: get the value of RFPENDTC in DM :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $dtctestvalue := (: only the year is given :) if(string-length($dtcvalue) = 4) then concat($dtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($dtcvalue) = 7) then concat($dtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($dtcvalue) = 10) then concat($dtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($dtcvalue) = 11) then concat($dtcvalue,'00:00:00') (: only hour is given :) else if(string-length($dtcvalue) = 13) then concat($dtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($dtcvalue) = 16) then concat($dtcvalue,':00') (: all ok anyway :) else ($dtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $dtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($dtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($dtcvarname)}={data($dtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> --DTC date may not be after RFPENDTC Start Date/Time (--STDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over the provided dataset within INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name=$datasetname][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) (: we need the OID of USUBJID and of the --DTC variable :) let $dtcvarname := concat($domain,'DTC') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$dtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --DTC :) for $record in doc(concat($base,$datasetlocation))//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --STDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: get the value of RFPENDTC in DM :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $dtctestvalue := (: only the year is given :) if(string-length($dtcvalue) = 4) then concat($dtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($dtcvalue) = 7) then concat($dtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($dtcvalue) = 10) then concat($dtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($dtcvalue) = 11) then concat($dtcvalue,'00:00:00') (: only hour is given :) else if(string-length($dtcvalue) = 13) then concat($dtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($dtcvalue) = 16) then concat($dtcvalue,':00') (: all ok anyway :) else ($dtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $dtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($dtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($dtcvarname)}={data($dtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> --ENDTC date may not be after RFPENDTC End Date/Time (--ENDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over all INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name='DM' or @Name='SE' or @Name='SV' or upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: we need the OID of USUBJID and of the --ENDTC variable :) let $endtcvarname := concat($domain,'ENDTC') let $endtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$endtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --STDTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$endtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --ENDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $endtcvalue := $record/odm:ItemData[@ItemOID=$endtcoid]/@Value (: get the value of RFPENDTC in DM from the temporary structure :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $endtctestvalue := (: only the year is given :) if(string-length($endtcvalue) = 4) then concat($endtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($endtcvalue) = 7) then concat($endtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($endtcvalue) = 10) then concat($endtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($endtcvalue) = 11) then concat($endtcvalue,'00:00:00') (: only hour is given :) else if(string-length($endtcvalue) = 13) then concat($endtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($endtcvalue) = 16) then concat($endtcvalue,':00') (: all ok anyway :) else ($endtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $endtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($endtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($endtcvarname)}={data($endtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> --ENDTC date may not be after RFPENDTC End Date/Time (--ENDTC) variable value must be less than or equal to Date/Time of End of Participation (RFPENDTC) 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV ) (: iterate over the provided dataset in INTERVENTIONS, EVENTS, FINDINGS, DM, SE, SV datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name=$datasetname][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: we need the OID of USUBJID and of the --ENDTC variable :) let $endtcvarname := concat($domain,'ENDTC') let $endtcoid := ( for $a in $definedoc//odm:ItemDef[@Name=$endtcvarname]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --STDTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$endtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --ENDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $endtcvalue := $record/odm:ItemData[@ItemOID=$endtcoid]/@Value (: get the value of RFPENDTC in DM from the temporary structure :) let $rfpendtcvalue := $usubjidrfpendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $endtctestvalue := (: only the year is given :) if(string-length($endtcvalue) = 4) then concat($endtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($endtcvalue) = 7) then concat($endtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($endtcvalue) = 10) then concat($endtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($endtcvalue) = 11) then concat($endtcvalue,'00:00:00') (: only hour is given :) else if(string-length($endtcvalue) = 13) then concat($endtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($endtcvalue) = 16) then concat($endtcvalue,':00') (: all ok anyway :) else ($endtcvalue) (: and also for RFPENDTC :) let $rfpendtctestvalue := ( (: only the year is given :) if(string-length($rfpendtcvalue) = 4) then concat($rfpendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfpendtcvalue) = 7) then concat($rfpendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfpendtcvalue) = 10) then concat($rfpendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfpendtcvalue) = 11) then concat($rfpendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfpendtcvalue) = 13) then concat($rfpendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfpendtcvalue) = 16) then concat($rfpendtcvalue,':00') (: all ok anyway :) else ($rfpendtcvalue) ) (: compare both values :) (: RFPENDTC value must be equal or higher than STDTC - but first check whether it really is a datetime :) where $endtctestvalue castable as xs:dateTime and $rfpendtctestvalue castable as xs:dateTime and xs:dateTime($endtctestvalue) > xs:dateTime($rfpendtctestvalue) return {data($endtcvarname)}={data($endtcvalue)} is after RFPENDTC={data($rfpendtcvalue)} in dataset {data($name)} ]]> EXSTDTC date may not be after RFXENDTC Start Date/Time of Treatment (EXSTDTC) variable value must be less than or equal to Date/Time of Last Study Treatment (RFXENDTC) 3.1.3 3.2 EX ) (: iterate over all EX datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Domain='EX' or starts-with(@Name,'EX')] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) (: we need the OID of USUBJID and of the EXSTDTC variable :) let $exstdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='EXSTDTC']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --EXSTDTC :) for $record in doc(concat($base,$datasetlocation))//odm:ItemGroupData[odm:ItemData[@ItemOID=$exstdtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --ENDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $exstdtcvalue := $record/odm:ItemData[@ItemOID=$exstdtcoid]/@Value (: get the value of RFPENDTC in DM from the temporary structure :) let $rfxendtcvalue := $usubjidrfxendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $exstdtctestvalue := (: only the year is given :) if(string-length($exstdtcvalue) = 4) then concat($exstdtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($exstdtcvalue) = 7) then concat($exstdtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($exstdtcvalue) = 10) then concat($exstdtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($exstdtcvalue) = 11) then concat($exstdtcvalue,'00:00:00') (: only hour is given :) else if(string-length($exstdtcvalue) = 13) then concat($exstdtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($exstdtcvalue) = 16) then concat($exstdtcvalue,':00') (: all ok anyway :) else ($exstdtcvalue) (: and also for RFXENDTC :) let $rfxendtctestvalue := ( (: only the year is given :) if(string-length($rfxendtcvalue) = 4) then concat($rfxendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfxendtcvalue) = 7) then concat($rfxendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfxendtcvalue) = 10) then concat($rfxendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfxendtcvalue) = 11) then concat($rfxendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfxendtcvalue) = 13) then concat($rfxendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfxendtcvalue) = 16) then concat($rfxendtcvalue,':00') (: all ok anyway :) else ($rfxendtcvalue) ) (: compare both values :) (: RFXENDTC value must be equal or higher than EXSTDTC - but first check whether it really is a datetime :) where $exstdtctestvalue castable as xs:dateTime and $rfxendtctestvalue castable as xs:dateTime and xs:dateTime($exstdtctestvalue) > xs:dateTime($rfxendtctestvalue) return EXSTDTC={data($exstdtcvalue)} is after RFXENDTC={data($rfxendtcvalue)} in dataset {data($name)} ]]> EXENDTC date may not be after RFXENDTC End Date/Time of Treatment (EXENDTC) variable value must be less than or equal to Date/Time of Last Study Treatment (RFXENDTC) 3.1.3 3.2 EX ) (: iterate over all EX datasets :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Domain='EX' or starts-with(@Name,'EX')] (: get the dataset name :) let $name := $datasetdef/@Name let $domain := $datasetdef/@Domain (: get the datasetlocation :) let $datasetlocation := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) (: we need the OID of USUBJID and of the EXENDTC variable :) let $exendtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='EXENDTC']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: now iterate over all records that do have a value for --EXSTDTC :) for $record in doc(concat($base,$datasetlocation))//odm:ItemGroupData[odm:ItemData[@ItemOID=$exendtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of --ENDTC and of USUBJID :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $exendtcvalue := $record/odm:ItemData[@ItemOID=$exendtcoid]/@Value (: get the value of RFPENDTC in DM from the temporary structure :) let $rfxendtcvalue := $usubjidrfxendtcpairs[@usubjid=$usubjidvalue]/@rfpendtc (: take care of incomplete dates :) let $exendtctestvalue := (: only the year is given :) if(string-length($exendtcvalue) = 4) then concat($exendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($exendtcvalue) = 7) then concat($exendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($exendtcvalue) = 10) then concat($exendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($exendtcvalue) = 11) then concat($exendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($exendtcvalue) = 13) then concat($exendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($exendtcvalue) = 16) then concat($exendtcvalue,':00') (: all ok anyway :) else ($exendtcvalue) (: and also for RFXENDTC :) let $rfxendtctestvalue := ( (: only the year is given :) if(string-length($rfxendtcvalue) = 4) then concat($rfxendtcvalue,'-01-01T00:00:00') (: only the month is given :) else if(string-length($rfxendtcvalue) = 7) then concat($rfxendtcvalue,'-01T00:00:00') (: complete date is given but no time :) else if(string-length($rfxendtcvalue) = 10) then concat($rfxendtcvalue,'T00:00:00') (: T is given but no hours - might bei invalid anyway :) else if(string-length($rfxendtcvalue) = 11) then concat($rfxendtcvalue,'00:00:00') (: only hour is given :) else if(string-length($rfxendtcvalue) = 13) then concat($rfxendtcvalue,':00:00') (: hour and minutes are given, but no seconds :) else if(string-length($rfxendtcvalue) = 16) then concat($rfxendtcvalue,':00') (: all ok anyway :) else ($rfxendtcvalue) ) (: compare both values :) (: RFXENDTC value must be equal or higher than EXENDTC - but first check whether it really is a datetime :) where $exendtctestvalue castable as xs:dateTime and $rfxendtctestvalue castable as xs:dateTime and xs:dateTime($exendtctestvalue) > xs:dateTime($rfxendtctestvalue) return EXENDTC={data($exendtcvalue)} is after RFXENDTC={data($rfxendtcvalue)} in dataset {data($name)} ]]> RFXSTDTC date may not be after RFXENDTC Date/Time of First Study Treatment (RFXSTDTC) variable value must be less than or equal to Date/Time of Last Study Treatment (RFXENDTC) 3.1.3 3.2 DM xs:dateTime($rfxendtctestvalue) return RFXSTDTC={data($rfxstdtcvalue)} is after RFXENDTC={data($rfxendtcvalue)} in dataset DM ]]> Dataset must be defined in the define.xml Datasets included in study data must be described in the data definition document (define.xml) 3.1.2 3.1.3 3.2 ALL Dataset {data($filename)} is not present in define file {data($define)} ]]> Domain referenced in define.xml must be included in the submission Domains referenced in data definition document (define.xml) should be included in the submission 3.1.2 3.1.3 3.2 ALL Dataset {data($filename)} referenced in {$define} but dataset is missing in submission ]]> Variables included in the dataset must be defined in the define.xml Variables included in the dataset must be described in the data definition document (define.xml) 3.1.2 3.1.3 3.2 ALL Variable with OID {data($var)} in dataset {data($datasetname)} in the dataset {data($datasetname)} is not defined in the define.xml ]]> Variable datatype must match datatype in the define.xml Variable Data Types in the dataset must match the variable data types described in the data definition document (define.xml) 3.1.2 3.1.3 3.2 ALL Define.xml/dataset variable type mismatch - Data point with OID = {data($itemoid)} and name = {data($varname)} and value {data($itemvalue)} is expected to be of type {data($datatype)} ]]> Variable values must be found in the corresponding user-defined codelist Variable values should be populated with terms found in the user-defined codelist associated with the variable in define.xml 3.1.2 3.1.3 3.2 ALL 0]//odm:ItemGroupData let $recnum := $record/@data:ItemGroupDataSeq (: iterate over the coded variables :) for $codeditem in $record/odm:ItemData[functx:is-value-in-sequence(@ItemOID,$codedoids)] (: get the OID and value :) let $oid := $codeditem/@ItemOID let $value := $codeditem/@Value (: also get the variable name for reporting :) let $varname := $definedoc//odm:ItemDef[@OID=$oid]/@Name (: look up the allowed values for this coded item in the define.xml :) let $codelistoid := $definedoc//odm:ItemDef[@OID=$oid]/odm:CodeListRef/@CodeListOID (: P.S. exclude "ExternalCodeList" :) let $allowedvalues := $definedoc//odm:CodeList[not(odm:ExternalCodeList)][@OID=$codelistoid]/odm:*/@CodedValue (: the value must be one of the coded values :) where count($allowedvalues) > 0 and not(functx:is-value-in-sequence($value,$allowedvalues)) return Value for variable {data($varname)}: value '{data($value)}' not found in not found in user-defined codelist {data($codelistoid)} ]]> Variable values must be found in the corresponding user-defined codelist Variable values should be populated with terms found in the user-defined codelist associated with the variable in define.xml 3.1.2 3.1.3 3.2 ALL 0]//odm:ItemGroupData let $recnum := $record/@data:ItemGroupDataSeq (: iterate over the coded variables :) for $codeditem in $record/odm:ItemData[functx:is-value-in-sequence(@ItemOID,$codedoids)] (: get the OID and value :) let $oid := $codeditem/@ItemOID let $value := $codeditem/@Value (: also get the variable name for reporting :) let $varname := $definedoc//odm:ItemDef[@OID=$oid]/@Name (: look up the allowed values for this coded item in the define.xml :) let $codelistoid := $definedoc//odm:ItemDef[@OID=$oid]/odm:CodeListRef/@CodeListOID (: P.S. exclude "ExternalCodeList" :) let $allowedvalues := $definedoc//odm:CodeList[not(odm:ExternalCodeList)][@OID=$codelistoid]/odm:*/@CodedValue (: the value must be one of the coded values :) where count($allowedvalues) > 0 and not(functx:is-value-in-sequence($value,$allowedvalues)) return Value for variable {data($varname)}: value '{data($value)}' not found in not found in user-defined codelist {data($codelistoid)} ]]> Variable value must be found in user-defined codelist when value-level condition occurs Variable value must be populated with terms from user-defined value level codelist as specified in define.xml file 3.1.2 3.1.3 3.2 ALL {data($valuelistvars)} :) (: iterate over the variables (OIDs) that do have an attached ValueList :) for $valuelistvar in $valuelistvars (: get the Name of the variable :) let $valuelistvarname := $definedoc//odm:ItemDef[@OID=$valuelistvar]/@Name (: get the reference valuelist itself :) let $valuelistoid := ( if($defineversion = '2.1') then $definedoc//odm:ItemDef[@OID=$valuelistvar]/def21:ValueListRef/@ValueListOID else $definedoc//odm:ItemDef[@OID=$valuelistvar]/def:ValueListRef/@ValueListOID ) let $valuelist := ( if($defineversion = '2.1') then $definedoc//def21:ValueListDef[@OID=$valuelistoid] else $definedoc//def:ValueListDef[@OID=$valuelistoid] ) (: iterate over the ValueList ItemRefs :) for $valuelistitemref in $valuelist/odm:ItemRef (: get the OID :) let $valuelistitemoid := $valuelistitemref/@ItemOID (: get the WhereClause :) let $whereclauserefoid := ( if($defineversion = '2.1') then $valuelistitemref/def21:WhereClauseRef/@WhereClauseOID else $valuelistitemref/def:WhereClauseRef/@WhereClauseOID ) (: and the corresponding WhereClauseDef :) let $whereclausedef := ( if($defineversion = '2.1') then $definedoc//def21:WhereClauseDef[@OID=$whereclauserefoid] else $definedoc//def:WhereClauseDef[@OID=$whereclauserefoid] ) (: get the item it is about - we currently only support 1 item and only the "EQ" comparator, and only the case that it is about data in the same dataset (e.g. STRESU depends of TESTCD value) This covers 90% of the cases :) let $whereclauseaboutitemoid := ( if($defineversion = '2.1') then $whereclausedef/odm:RangeCheck/@def21:ItemOID else $whereclausedef/odm:RangeCheck/@def:ItemOID ) let $checkvalue := $whereclausedef/odm:RangeCheck/odm:CheckValue/text() (: return {data($whereclauseaboutitemoid)} - {data($checkvalue)} :) (: pick up the corresponding ItemDef - but only when it does have a connected codelist :) for $valuelistitemdefcoded in $definedoc//odm:ItemDef[@OID=$valuelistitemoid and odm:CodeListRef/@CodeListOID] (: get the codelist itself and its coded values :) let $valuelistcodelistoid := $valuelistitemdefcoded/odm:CodeListRef/@CodeListOID (: exclude ExternalCodeList :) let $valuelistcodelist := $definedoc//odm:CodeList[@OID=$valuelistcodelistoid and not(odm:ExternalCodeList)] let $valuelistcodelistname := $valuelistcodelist/@Name (: get the coded values :) let $valuelistcodedvalues := $valuelistcodelist/odm:*/@CodedValue (: get all the records in the dataset that are about the given valuelist variable :) (: return {data($valuelistvar)} - {data($whereclauseaboutitemoid)} - {data($checkvalue)} - {data($valuelistcodedvalues)} :) (: iterate over all the records where the WhereClause applies to, i.e. $whereclauseaboutitemoid = $checkvalue :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$whereclauseaboutitemoid and @Value=$checkvalue]] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of the dependent variable :) let $dependentvarvalue := $record/odm:ItemData[@ItemOID=$valuelistvar]/@Value (: the dependent variable value must be a value in the codelist :) where not(functx:is-value-in-sequence($dependentvarvalue,$valuelistcodedvalues)) return Variable {data($valuelistvarname)} valuelist value '{data($dependentvarvalue)}' is not found in user-defined codelist '{data($valuelistcodelistname)}'. One of [{data($valuelistcodedvalues)}] is expected ]]> Variable value may not be null when value-level mandatory condition occurs Variable value must be populated when value level attribute Mandatory='Yes' as specified in define.xml file 3.1.2 3.1.3 3.2 ALL {data($valuelistvars)} :) (: iterate over the variables (OIDs) that do have an attached ValueList :) for $valuelistvar in $valuelistvars (: get the Name of the variable :) let $valuelistvarname := $definedoc//odm:ItemDef[@OID=$valuelistvar]/@Name (: get the reference valuelist itself :) let $valuelistoid := ( if($defineversion = '2.1') then $definedoc//odm:ItemDef[@OID=$valuelistvar]/def21:ValueListRef/@ValueListOID else $definedoc//odm:ItemDef[@OID=$valuelistvar]/def:ValueListRef/@ValueListOID ) let $valuelist := ( if($defineversion = '2.1') then $definedoc//def21:ValueListDef[@OID=$valuelistoid] else $definedoc//def:ValueListDef[@OID=$valuelistoid] ) (: iterate over the ValueList ItemRefs that are "Mandatory" :) for $valuelistitemref in $valuelist/odm:ItemRef[@Mandatory='Yes'] (: get the OID :) let $valuelistitemoid := $valuelistitemref/@ItemOID (: get the WhereClause :) let $whereclauserefoid := ( if($defineversion = '2.1') then $valuelistitemref/def21:WhereClauseRef/@WhereClauseOID else $valuelistitemref/def:WhereClauseRef/@WhereClauseOID ) (: and the corresponding WhereClauseDef :) let $whereclausedef := ( if($defineversion = '2.1') then $definedoc//def21:WhereClauseDef[@OID=$whereclauserefoid] else $definedoc//def:WhereClauseDef[@OID=$whereclauserefoid] ) (: get the item it is about - we currently only support 1 item and only the "EQ" comparator, and only the case that it is about data in the same dataset (e.g. STRESU depends of TESTCD value) This covers 90% of the cases :) let $whereclauseaboutitemoid := ( if($defineversion = '2.1') then $whereclausedef/odm:RangeCheck/@def21:ItemOID else $whereclausedef/odm:RangeCheck/@def:ItemOID ) let $whereclauseaboutitemname := $definedoc//odm:ItemDef[@OID=$whereclauseaboutitemoid]/@Name let $checkvalue := $whereclausedef/odm:RangeCheck/odm:CheckValue/text() (: return {data($whereclauseaboutitemoid)} - {data($checkvalue)} :) (: pick up the corresponding ItemDef :) for $valuelistitemdefmandatory in $definedoc//odm:ItemDef[@OID=$valuelistitemoid] (: get all the records in the dataset that are about the given valuelist variable :) (: return {data($valuelistvar)} - {data($whereclauseaboutitemoid)} - {data($checkvalue)} - {data($valuelistcodedvalues)} :) (: iterate over all the records where the WhereClause applies to, i.e. $whereclauseaboutitemoid = $checkvalue :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$whereclauseaboutitemoid and @Value=$checkvalue]] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of the dependent variable :) let $dependentvarvalue := $record/odm:ItemData[@ItemOID=$valuelistvar]/@Value (: the dependent variable value may not be null as "Mandatory='Yes'" :) where not($dependentvarvalue) return Variable {data($valuelistvarname)} valuelist value '{data($dependentvarvalue)}' is found to be null although the item is valuelist-mandatory for {data($whereclauseaboutitemname)}='{data($checkvalue)}' ]]> Value level datatype must match the datatype described in define.xml - Variable datatype is not %Variable.@Clause.DataType% when value-level condition occurs 3.1.2 3.1.3 3.2 ALL {data($valuelistvars)} :) (: iterate over the variables (OIDs) that do have an attached ValueList :) for $valuelistvar in $valuelistvars (: get the Name of the variable :) let $valuelistvarname := $definedoc//odm:ItemDef[@OID=$valuelistvar]/@Name (: get the reference valuelist itself :) let $valuelistoid := ( if($defineversion = '2.1') then $definedoc//odm:ItemDef[@OID=$valuelistvar]/def21:ValueListRef/@ValueListOID else $definedoc//odm:ItemDef[@OID=$valuelistvar]/def:ValueListRef/@ValueListOID ) let $valuelist := ( if($defineversion = '2.1') then $definedoc//def21:ValueListDef[@OID=$valuelistoid] else $definedoc//def:ValueListDef[@OID=$valuelistoid] ) (: iterate over the ValueList ItemRefs :) for $valuelistitemref in $valuelist/odm:ItemRef[@Mandatory='Yes'] (: get the OID :) let $valuelistitemoid := $valuelistitemref/@ItemOID (: get the WhereClause :) let $whereclauserefoid := ( if($defineversion = '2.1') then $valuelistitemref/def21:WhereClauseRef/@WhereClauseOID else $valuelistitemref/def:WhereClauseRef/@WhereClauseOID ) (: and the corresponding WhereClauseDef :) let $whereclausedef := ( if($defineversion = '2.1') then $definedoc//def21:WhereClauseDef[@OID=$whereclauserefoid] else $definedoc//def:WhereClauseDef[@OID=$whereclauserefoid] ) (: get the item it is about - we currently only support 1 item and only the "EQ" comparator, and only the case that it is about data in the same dataset (e.g. STRESU depends of TESTCD value) This covers 90% of the cases :) let $whereclauseaboutitemoid := ( if($defineversion = '2.1') then $whereclausedef/odm:RangeCheck/@def21:ItemOID else $whereclausedef/odm:RangeCheck/@def:ItemOID ) let $whereclauseaboutitemname := $definedoc//odm:ItemDef[@OID=$whereclauseaboutitemoid]/@Name let $checkvalue := $whereclausedef/odm:RangeCheck/odm:CheckValue/text() (: return {data($whereclauseaboutitemoid)} - {data($checkvalue)} :) (: pick up the corresponding ItemDef :) for $valuelistitemdef in $definedoc//odm:ItemDef[@OID=$valuelistitemoid] (: get the datatype :) let $datatype := $valuelistitemdef/@DataType (: get all the records in the dataset that are about the given valuelist variable :) (: return {data($valuelistvar)} - {data($whereclauseaboutitemoid)} - {data($checkvalue)} - {data($valuelistcodedvalues)} :) (: iterate over all the records where the WhereClause applies to, i.e. $whereclauseaboutitemoid = $checkvalue :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$whereclauseaboutitemoid and @Value=$checkvalue]] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of the dependent variable :) let $itemvalue := $record/odm:ItemData[@ItemOID=$valuelistvar]/@Value (: the value must be according to the datatype :) (: define.xml allows following datatypes: text, integer, float, datetime, date, time, partialDate, partialTime, partialDatetime, incompleteDatetime, durationDatetime :) (: P.S. in case 'datetime' is expected but a correct date is provided, that is also ok :) let $isValidDataTypeValue := if ($datatype = 'text') then 'true' (: everything is text ... :) else if($datatype = 'integer' and $itemvalue castable as xs:integer) then 'true' else if($datatype = 'float' and $itemvalue castable as xs:double) then 'true' else if($datatype = 'datetime' and $itemvalue castable as xs:dateTime) then 'true' else if($datatype = 'date' and $itemvalue castable as xs:date or $itemvalue castable as xs:date) then 'true' else if($datatype = 'time' and $itemvalue castable as xs:time) then 'true' (: use function for partialDate :) else if($datatype = 'partialDate' and functx:isPartialDate($itemvalue)) then 'true' (: use function for partialTime :) else if($datatype = 'partialTime' and functx:isPartialTime($itemvalue)) then 'true' (: use function for partialDateTime :) else if($datatype = 'partialDateTime' and functx:isPartialDatetime($itemvalue)) then 'true' (: TODO: write function for incompleteDatetime :) else if($datatype = 'durationDatetime' and $itemvalue castable as xs:duration) then 'true' (: TODO: write function for other form of durationDatetime ("from-to" format) :) else 'false' (: when the value does not match the datatype, give an error :) where $isValidDataTypeValue = 'false' return Variable {data($valuelistvarname)} valuelist value '{data($itemvalue)}' is compatible with its data type '{data($datatype)}' ]]> Value level length must not exceed the length as specified define.xml Variable value is longer than defined max length %Variable.@Clause.Length% when value-level condition occurs 3.1.2 3.1.3 3.2 ALL {data($valuelistvars)} :) (: iterate over the variables (OIDs) that do have an attached ValueList :) for $valuelistvar in $valuelistvars (: get the Name of the variable :) let $valuelistvarname := $definedoc//odm:ItemDef[@OID=$valuelistvar]/@Name (: get the reference valuelist itself :) let $valuelistoid := ( if($defineversion = '2.1') then $definedoc//odm:ItemDef[@OID=$valuelistvar]/def21:ValueListRef/@ValueListOID else $definedoc//odm:ItemDef[@OID=$valuelistvar]/def:ValueListRef/@ValueListOID ) let $valuelist := ( if($defineversion = '2.1') then $definedoc//def21:ValueListDef[@OID=$valuelistoid] else $definedoc//def:ValueListDef[@OID=$valuelistoid] ) (: iterate over the ValueList ItemRefs :) for $valuelistitemref in $valuelist/odm:ItemRef[@Mandatory='Yes'] (: get the OID :) let $valuelistitemoid := $valuelistitemref/@ItemOID (: get the WhereClause :) let $whereclauserefoid := ( if($defineversion = '2.1') then $valuelistitemref/def21:WhereClauseRef/@WhereClauseOID else $valuelistitemref/def:WhereClauseRef/@WhereClauseOID ) (: and the corresponding WhereClauseDef :) let $whereclausedef := ( if($defineversion = '2.1') then $definedoc//def21:WhereClauseDef[@OID=$whereclauserefoid] else $definedoc//def:WhereClauseDef[@OID=$whereclauserefoid] ) (: get the item it is about - we currently only support 1 item and only the "EQ" comparator, and only the case that it is about data in the same dataset (e.g. STRESU depends of TESTCD value) This covers 90% of the cases :) let $whereclauseaboutitemoid := ( if($defineversion = '2.1') then $whereclausedef/odm:RangeCheck/@def21:ItemOID else $whereclausedef/odm:RangeCheck/@def:ItemOID ) let $whereclauseaboutitemname := $definedoc//odm:ItemDef[@OID=$whereclauseaboutitemoid]/@Name let $checkvalue := $whereclausedef/odm:RangeCheck/odm:CheckValue/text() (: return {data($whereclauseaboutitemoid)} - {data($checkvalue)} :) (: pick up the corresponding ItemDef :) for $valuelistitemdef in $definedoc//odm:ItemDef[@OID=$valuelistitemoid] (: get the maximal length :) let $maxlength := $valuelistitemdef/@Length (: get all the records in the dataset that are about the given valuelist variable :) (: return {data($valuelistvar)} - {data($whereclauseaboutitemoid)} - {data($checkvalue)} - {data($valuelistcodedvalues)} :) (: iterate over all the records where the WhereClause applies to, i.e. $whereclauseaboutitemoid = $checkvalue :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$whereclauseaboutitemoid and @Value=$checkvalue]] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of the dependent variable :) let $itemvalue := $record/odm:ItemData[@ItemOID=$valuelistvar]/@Value (: and get its length :) let $valuelength := string-length($itemvalue) (: real length should be less or equal than the maximum lenth :) where $valuelength > $maxlength return Variable {data($valuelistvarname)} valuelist value '{data($itemvalue)}' is longer than the allowed maximal length {data($maxlength)} ]]> The value for Study Day must not be negative for Exposure treatments - Study Day variables (*DY) value should not be negative in Exposure (EX) datasets 3.1.2 3.1.3 3.2 EX Value of {data($varname)} is not allowed to be negative in dataset {data($name)}. A value of {data($dyvalue)} was found ]]> Time Point Reference must be provided, when Reference Time Point is used Time Point Reference (--TPTREF) variable values should be provided, when Date/Time of Reference Time Point (--RFTDTC) variable values are populated 3.1.2 3.1.3 3.2 EX BG LB CL PC EG VS {data($tptrefname)} is not populated although {data($rftdtcname)} is populated ]]> An End Time-Point value must be populated One End Time-Point variable is expected to be populated when an event or an intervention occurred. (E.g., End Date/Time of Event or Intervention (--ENDTC), or End Relative to Reference Period (--ENRF), or End Relative to Reference Period (--ENRTPT) should not be missing, or Occurrence (--OCCUR) = 'N' or Completion Status (--STAT) != '') or Duration (--DUR) != '') 3.1.2 3.1.3 3.2 EVENTS INTERVENTIONS {data($endtcoid)} - {data($enrfoid)} - {data($enrtptoid)} :) (: and the OIDs of --STAT and --OCCUR and --DUR :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $occuroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'OCCUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $duroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: return {data($statoid)} - {data($occuroid)} :) (: now iterate over all the records in the dataset for which --OCCUR is NOT 'N' or --STAT is null or empty or --DUR is null or empty :) for $record in $datasetdoc//odm:ItemGroupData[not(odm:ItemData[@ItemOID=$statoid]) or not(odm:ItemData[@ItemOID=$duroid]) or odm:ItemData[@ItemOID=$occuroid]/@Value='N' ] let $recnum := $record/@data:ItemGroupDataSeq (: one of --ENDTC, --ENRF or --ENRTPT must be populated - if none of them is, give warning :) where not($record/odm:ItemData[@ItemOID=$endtcoid]/@Value) and not($record/odm:ItemData[@ItemOID=$enrfoid]/@Value) and not($record/odm:ItemData[@ItemOID=$enrtptoid]/@Value) return One of the End Time-Point variables {data($endtcname)}, {data($enrfname)} or {data($enrtptname)} must be populated ]]> An End Time-Point value must be populated One End Time-Point variable is expected to be populated when an event or an intervention occurred. (E.g., End Date/Time of Event or Intervention (--ENDTC), or End Relative to Reference Period (--ENRF), or End Relative to Reference Period (--ENRTPT) should not be missing, or Occurrence (--OCCUR) = 'N' or Completion Status (--STAT) != '') or Duration (--DUR) != '') 3.1.2 3.1.3 3.2 EVENTS INTERVENTIONS {data($endtcoid)} - {data($enrfoid)} - {data($enrtptoid)} :) (: and the OIDs of --STAT and --OCCUR and --DUR :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $occuroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'OCCUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $duroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: return {data($statoid)} - {data($occuroid)} :) (: now iterate over all the records in the dataset for which --OCCUR is NOT 'N' or --STAT is null or empty or --DUR is null or empty :) for $record in $datasetdoc//odm:ItemGroupData[not(odm:ItemData[@ItemOID=$statoid]) or not(odm:ItemData[@ItemOID=$duroid]) or odm:ItemData[@ItemOID=$occuroid]/@Value='N' ] let $recnum := $record/@data:ItemGroupDataSeq (: one of --ENDTC, --ENRF or --ENRTPT must be populated - if none of them is, give warning :) where not($record/odm:ItemData[@ItemOID=$endtcoid]/@Value) and not($record/odm:ItemData[@ItemOID=$enrfoid]/@Value) and not($record/odm:ItemData[@ItemOID=$enrtptoid]/@Value) return One of the End Time-Point variables {data($endtcname)}, {data($enrfname)} or {data($enrtptname)} must be populated ]]> Start Time-Point value must be populated One of Start Time-Point variables values is expected to be populated when an event an intervention occurred. (E.g., one of Start Date/Time of Event or Intervention (--STDTC), Start Relative to Reference Period (--STRF), and Start Relative to Reference Period (--STRTPT) variables values should not be missing, or Occurrence (--OCCUR) variable value should be 'N') 3.1.2 3.1.3 3.2 EVENTS INTERVENTIONS {data($stdtcoid)} - {data($strfoid)} - {data($strtptoid)} :) (: and the OIDs of --STAT and --OCCUR :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $occuroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'OCCUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: return {data($statoid)} - {data($occuroid)} :) (: now iterate over all the records in the dataset for which --OCCUR is NOT 'N' :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$occuroid]/@Value='N'] let $recnum := $record/@data:ItemGroupDataSeq (: one of --STDTC, --STENRF or -STRTPT must be populated - if none of them is, give warning :) where not($record/odm:ItemData[@ItemOID=$stdtcoid]/@Value) and not($record/odm:ItemData[@ItemOID=$strfoid]/@Value) and not($record/odm:ItemData[@ItemOID=$strtptoid]/@Value) return One of the End Time-Point variables {data($stdtcname)}, {data($strfname)} or {data($strtptname)} must be populated ]]> A Start Time-Point must be populated One of Start Time-Point variables values is expected to be populated when an event an intervention occurred. (E.g., one of Start Date/Time of Event or Intervention (--STDTC), Start Relative to Reference Period (--STRF), and Start Relative to Reference Period (--STRTPT) variables values should not be missing, or Occurrence (--OCCUR) variable value should be 'N') 3.1.2 3.1.3 3.2 EVENTS INTERVENTIONS {data($stdtcoid)} - {data($strfoid)} - {data($strtptoid)} :) (: and the OIDs of --STAT and --OCCUR :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $occuroid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'OCCUR')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: return {data($statoid)} - {data($occuroid)} :) (: now iterate over all the records in the dataset for which --OCCUR is NOT 'N' :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$occuroid]/@Value='N'] let $recnum := $record/@data:ItemGroupDataSeq (: one of --STDTC, --STENRF or -STRTPT must be populated - if none of them is, give warning :) where not($record/odm:ItemData[@ItemOID=$stdtcoid]/@Value) and not($record/odm:ItemData[@ItemOID=$strfoid]/@Value) and not($record/odm:ItemData[@ItemOID=$strtptoid]/@Value) return One of the Start Time-Point variables {data($stdtcname)}, {data($strfname)} or {data($strtptname)} must be populated ]]> --DTC must be provided, when --ENDTC is provided Date/Time of Collection (--DTC) should not be NULL, when End Date/Time of Observation (--ENDTC) is not NULL 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($dtcname)}, when {data($endtcname)} is provided, value={data($endtcvalue)} ]]> --DTC must be provided, when --ENDTC is provided Date/Time of Collection (--DTC) should not be NULL, when End Date/Time of Observation (--ENDTC) is not NULL 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($dtcname)}, when {data($endtcname)} is provided, value={data($endtcvalue)} ]]> One of --STDTC, --DTC or --STDY must be populated in DS At least one value of three variables Start Date/Time (--STDTC), Collection Date/Time (--DTC) or Start Study Day (--STDY) should be populated 3.1.2 3.1.3 3.2 DS Neither DSSDTDTC nor DSSTDY nor DSDTC are populated in dataset {data($dsdatasetname)} ]]> RFXENDTC must be provided, when RFXSTDTC is provided Value for Date/Time of Last Study Treatment (RFXENDTC) variable must be populated, when Date/Time of First Study Treatment (RFXSTDTC) variable value is provided 3.1.3 3.2 DM RFXENDTC is not populated although RFXSTDTC is populated ]]> RFSTDTC must be provided for a randomized subject Subject Reference Start Date/Time (RFSTDTC) should be populated for all randomized subjects, those where Planned Arm Code (ARMCD) is not equal to 'SCRNFAIL' or 'NOTASSGN' 3.1.3 3.2 DM RFSTDTC is not provided for a randomized subject with USUBJID={data($usubjidvalue)} ]]> Value of --DUR, --ELTM, --EVLINT must conform to the ISO 8601 'duration' international standard Value of Duration, Elapsed Time, and Interval variables (--DUR, --ELTM, --EVLINT) must conform to the ISO 8601 international standard 3.1.2 3.1.3 3.2 ALL {data($durname)} - {data($eltmname)} - {data($evlintname)} :) (: iterate over all records that have either a value for --DUR, --ELTM or --EVLINT :) for $record in doc($datasetlocation)[$duroid or $eltmoid or $evlintoid]//odm:ItemGroupData (: get the record number :) let $recnum := $record/@data:ItemGroupDataSeq (: iterate over all the datapoints --DUR, --ELTM, --EVLINT :) let $durdatapoints := $record/odm:ItemData[@ItemOID=$duroid or @ItemOID=$eltmoid or @ItemOID=$evlintoid] for $datapoint in $durdatapoints (: get the value :) let $value := $datapoint/@Value (: we need the name of the datapoint in the define.xml for reporting :) let $itemoid := $datapoint/@ItemOID let $itemname := $definedoc//odm:ItemDef[@OID=$itemoid]/@Name (: the value must be a valid ISO-8601 "duration" :) (: IMPORTANT: PnW and -PnW are rejected as valid ISO-8601 durations, so we need to take care of that :) (: TODO: check the "n" is an integer :) where not($value castable as xs:duration) and not((starts-with($value,'P') or starts-with($value,'-P')) and ends-with($value,'W')) return Invalid (non-ISO8601 duration) value='{data($value)}' ]]> Value for --STNRHI may not be less than value for --STNRLO Reference Range Upper Limit-Std Units (--STNRHI) value must be greater than or equal to Reference Range Lower Limit-Std Units (--STNRLO) value 3.1.2 3.1.3 3.2 FINDINGS Value for {data($stnrihname)}, value={data($stnrhivalue)} is less than value for {data($stnrloname)}, value={data($stnrlovalue)} ]]> Value for --STNRHI may not be less than value for --STNRLO Reference Range Upper Limit-Std Units (--STNRHI) value must be greater than or equal to Reference Range Lower Limit-Std Units (--STNRLO) value 3.1.2 3.1.3 3.2 FINDINGS Value for {data($stnrihname)}, value={data($stnrhivalue)} is less than value for {data($stnrloname)}, value={data($stnrlovalue)} ]]> Value for –DOSE may not be negative Non-missing Dose (--DOSE) value must be greater than or equal to 0 INTERVENTIONS 3.1.2 3.1.3 3.2 = 0 :) where $dosevalue and number($dosevalue) < 0 return Negative value for {data($dosename)} in dataset {data($datasetname)}: {data($dosevalue)} was found ]]> Value for –DOSE may not be negative Non-missing Dose (--DOSE) value must be greater than or equal to 0 3.1.2 3.1.3 3.2 INTERVENTIONS = 0 :) where $dosevalue and number($dosevalue) < 0 return Negative value for {data($dosename)} in dataset {data($datasetname)}: {data($dosevalue)} was found ]]> Value for --DUR may not be negative Non-missing Duration of Event, Exposure or Observation (--DUR) value must be greater than or equal to 0 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TE SE SV = 0 :) where $durvalue and starts-with($durvalue,'-') (: a --DUR value is present and it is a -P so negative value :) return Negative value for {data($durname)} in dataset {data($datasetname)}: {data($durvalue)} was found ]]> Value for --DUR may not be negative Non-missing Duration of Event, Exposure or Observation (--DUR) value must be greater than or equal to 0 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TE SE SV = 0 :) where $durvalue and starts-with($durvalue,'-') (: a --DUR value is present and it is a -P so negative value :) return Negative value for {data($durname)} in dataset {data($datasetname)}: {data($durvalue)} was found ]]> The value for AGE may not be negative The value of Age (AGE) cannot be less than 0 3.1.2 3.1.3 3.2 DM = 0 :) where $agevalue and number($agevalue) < 0 return Negative value for AGE in DM dataset {data($dmdatasetname)}: {data($agevalue)} was found ]]> Only ASCII characters in variables are allowed Variables value must not include non-ASCII or non-printable characters (outside of 32-126 ASCII code range), limited to variables which values may be converted into new variable name or label (--TEST, --TESTCD, --PARM, --PARMCD, QLABEL, QNAM) 3.1.2 3.1.3 3.2 ALL 0, the all the characters must be ASCII - see e.g. https://stackoverflow.com/questions/51521676/use-xpath-to-check-if-a-string-has-only-ascii-characters :) where string-length($varvalue) > 0 and not(matches($varvalue,'^[ -~\n\t]+$')) return Variable value '{data($varvalue)}' contains non-ASCII characters ]]> Value for --STRESC may not be populated, when --STAT is 'NOT DONE' Status (--STAT) should be NULL, when Standardized Result in Character Format (--STRESC ) is provided 3.1.2 3.1.3 3.2 SC BW BG FW LB DD CL MI MA OM PM PC PP TF EG VS Status {data($statname)} should be NULL, when Result or Finding in Original Units ({data($strescname)}) is provided ]]> Value for --ORRES may not be populated, when --STAT is 'NOT DONE' Value of Original Result (--ORRES) variable is expected to be missing, when observation was not performed (Status (--STAT) is 'NOT DONE') 3.1.2 3.1.3 3.2 FINDINGS {data($orresname)} value is populated (value={data($orresvalue)}), when {data($orresname)} is 'NOT DONE' ]]> Value for --ORRES may not be populated, when --STAT is 'NOT DONE' Value of Original Result (--ORRES) variable is expected to be missing, when observation was not performed (Status (--STAT) is 'NOT DONE') 3.1.2 3.1.3 3.2 FINDINGS {data($orresname)} value is populated (value={data($orresvalue)}), when {data($orresname)} is 'NOT DONE' ]]> Value for --REASND must be present, when --STAT is 'NOT DONE' Value of Reason Not Done (--REASND) variable should be populated, when Status (--STAT) variable value is 'NOT DONE' 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Missing value for {data($reasndname)} when {data($statname)}={data($statvalue)} in dataset {data($datasetname)} ]]> Value for --REASND must be present, when --STAT is 'NOT DONE' Value of Reason Not Done (--REASND) variable should be populated, when Status (--STAT) variable value is 'NOT DONE' 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Missing value for {data($reasndname)} when {data($statname)}={data($statvalue)} in dataset {data($datasetname)} ]]> One of --STDTC, --STRF or --STRTPT must be populated, when --ENDTC, --ENRF or --ENRTPT is provided Start Date/Time of Observation (--STDTC), Start Relative to Reference Period (--STRF) or Start Relative to Reference Time Point (--STRTPT) should not be NULL, when End Date/Time of Observation (--ENDTC), End Relative to Reference Period (--ENRF) or End Relative to Reference Time Period (--ENRTPT) is not NULL 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS SE SV Missing values for {data(concat($name,'STDTC'))}, {data(concat($name,'STRF'))} and {data(concat($name,'STRTPT'))}, when one of {data(concat($name,'ENDTC'))}, {data(concat($name,'ENRF'))} or {data(concat($name,'ENRTPT'))} is provided in dataset {data($name)} ]]> One of --STDTC, --STRF or --STRTPT must be populated, when --ENDTC, --ENRF or --ENRTPT is provided Start Date/Time of Observation (--STDTC), Start Relative to Reference Period (--STRF) or Start Relative to Reference Time Point (--STRTPT) should not be NULL, when End Date/Time of Observation (--ENDTC), End Relative to Reference Period (--ENRF) or End Relative to Reference Time Period (--ENRTPT) is not NULL 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS SE SV Missing values for {data(concat($name,'STDTC'))}, {data(concat($name,'STRF'))} and {data(concat($name,'STRTPT'))}, when one of {data(concat($name,'ENDTC'))}, {data(concat($name,'ENRF'))} or {data(concat($name,'ENRTPT'))} is provided in dataset {data($name)} ]]> --STTPT must be populated, when --STRTPT is populated Start Reference Time Point (--STTPT) must not be NULL, when Start Relative to Reference Time Point (--STRTPT) is provided 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SV SE Missing value for {data($sttptname)}, when {data($strtptname)} is populated, value = {data($strtptvalue)} ]]> --STTPT must be populated, when --STRTPT is populated Start Reference Time Point (--STTPT) must not be NULL, when Start Relative to Reference Time Point (--STRTPT) is provided 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SV SE Missing value for {data($sttptname)}, when {data($strtptname)} is populated, value = {data($strtptvalue)} ]]> --ENTPT must be populated, when --ENRTPT is populated End Reference Time Point (--ENTPT) must not be NULL, when End Relative to Reference Time Point (--ENRTPT) is provided 3.1.2 3.1.3 3.2 ALL Missing value for {data($entptname)}, when {data($enrtptname)} is populated, value = {data($enrtptvalue)} ]]> --ENTPT must be populated, when --ENRTPT is populated End Reference Time Point (--ENTPT) must not be NULL, when End Relative to Reference Time Point (--ENRTPT) is provided 3.1.2 3.1.3 3.2 ALL Missing value for {data($entptname)}, when {data($enrtptname)} is populated, value = {data($enrtptvalue)} ]]> AGEU must be provided, when AGE is provided Age Units (AGEU) should be provided, when Age (AGE) is populated 3.1.2 DM Missing value for AGEU, when AGE is provided ]]> AGE must be provided, when AGEU is provided Age (AGE) should be provided, when Age Units (AGEU) are populated 3.1.2 DM Missing value for AGE, when AGEU is provided ]]> AGETXT must be provided in number-number format Age Range (AGETXT) variable values should be populated with 'number-number' format 3.1.2 3.2 DM Invalid value for AGETXT. '{data($agetxtvalue)}' was found ]]> Study Day variables (*DY) value may not equal 0 Study Day variables (*DY) value should not equal 0 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV Value of Study Day {data($dyname)} variable equals 0 ]]> Study Day variables (*DY) value may not equal 0 Study Day variables (*DY) value should not equal 0 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS DM SE SV Value of Study Day {data($dyname)} variable equals 0 ]]> --DY variable value must be correctly calculated Collection Study Day (--DY) variable value should be populated as defined by CDISC standards: --DY = (date portion of --DTC) - (date portion of RFSTDTC) +1 if --DTC is on or after RFSTDTC; --DY = (date portion of --DTC) - (date portion of RFSTDTC) if --DTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS ) (: iterate over all other provided datasets within INTERVENTIONS, EVENTS, FINDINGS :) for $dataset in $definedoc//odm:ItemGroupDef[not(@Name='DM')][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] let $name := $dataset/@Name let $dsname := ( if($defineversion = '2.1') then $dataset/def21:leaf/@xlink:href else $dataset/def:leaf/@xlink:href ) let $datasetdoc := ( if($dsname) then doc(concat($base,$dsname)) else () ) (: Get the OIDs of the --DY and --DTC variables :) let $dyoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DY') and string-length(@Name)=4]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dyname := concat($name,'DY') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DTC') and string-length(@Name)=5]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dtcname := $definedoc//odm:ItemDef[@OID=$dtcoid]/@Name (: and the OID of the USUBJID variable (might be different from the one in DM) :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]] let $recnum := $record/@data:ItemGroupDataSeq (: get the USUBJID value :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: get the --DTC value :) let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: and check whether it is a complete date - i.e. string-length at least 10 :) let $iscompletedtcvalue := string-length($dtcvalue) >= 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: keeping worst case scenario into account that there are two records for the same USUBJID in DM - take the first :) (: let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value :) (: replacement 2020-08-08: more efficient :) let $rfstdtcvalue := $usubjidrfstdtcpairs[@usubjid=$usubjidvalue]/@rfstdtc (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: now calculate the DY value but only when RFSTDTC and DTC have a complete date part :) let $dycalculated := ( if ($iscompleterfstdtcvalue and $iscompletedtcvalue) then (: if there is one, we must strip off the time part :) let $dtcvalueshort := substring($dtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $dycalc := ( if($dtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($dtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $dycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $dycalculatedfda := ( if($dycalculated >= 0) then $dycalculated + 1 else ( $dycalculated ) ) (: before comparing, check that the DY value is really an integer :) where $dyvalue castable as xs:integer and $dycalculatedfda and $dyvalue and not($dycalculatedfda = $dyvalue) return Invalid value for {data($dyname)}, calculated value={data($dycalculatedfda)}, provided value={data($dyvalue)}, in dataset {data($name)} ]]> --DY variable value must be correctly calculated Collection Study Day (--DY) variable value should be populated as defined by CDISC standards: --DY = (date portion of --DTC) - (date portion of RFSTDTC) +1 if --DTC is on or after RFSTDTC; --DY = (date portion of --DTC) - (date portion of RFSTDTC) if --DTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS ) (: iterate over all other provided datasets within INTERVENTIONS, EVENTS, FINDINGS :) for $dataset in $definedoc//odm:ItemGroupDef[@Name=$datasetname][not(@Name='DM')][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] let $name := $dataset/@Name let $dsname := ( if($defineversion = '2.1') then $dataset/def21:leaf/@xlink:href else $dataset/def:leaf/@xlink:href ) let $datasetdoc := ( if($dsname) then doc(concat($base,$dsname)) else () ) (: Get the OIDs of the --DY and --DTC variables :) let $dyoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DY') and string-length(@Name)=4]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dyname := concat($name,'DY') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DTC') and string-length(@Name)=5]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dtcname := $definedoc//odm:ItemDef[@OID=$dtcoid]/@Name (: and the OID of the USUBJID variable (might be different from the one in DM) :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]] let $recnum := $record/@data:ItemGroupDataSeq (: get the USUBJID value :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: get the --DTC value :) let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: and check whether it is a complete date - i.e. string-length at least 10 :) let $iscompletedtcvalue := string-length($dtcvalue) >= 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: keeping worst case scenario into account that there are two records for the same USUBJID in DM - take the first :) (: let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value :) (: replacement 2020-08-08: more efficient :) let $rfstdtcvalue := $usubjidrfstdtcpairs[@usubjid=$usubjidvalue]/@rfstdtc (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: now calculate the DY value but only when RFSTDTC and DTC have a complete date part :) let $dycalculated := ( if ($iscompleterfstdtcvalue and $iscompletedtcvalue) then (: if there is one, we must strip off the time part :) let $dtcvalueshort := substring($dtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $dycalc := ( if($dtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($dtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $dycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $dycalculatedfda := ( if($dycalculated >= 0) then $dycalculated + 1 else ( $dycalculated ) ) (: before comparing, check that the DY value is really an integer :) where $dyvalue castable as xs:integer and $dycalculatedfda and $dyvalue and not($dycalculatedfda = $dyvalue) return Invalid value for {data($dyname)}, calculated value={data($dycalculatedfda)}, provided value={data($dyvalue)}, in dataset {data($name)} ]]> --DY variable value must be populated Collection Study Day (--DY) variable value should be populated, when Collection Study Date/Time (--DTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS = 10 return $record/odm:ItemData[@ItemOID=$dmusubjidoid]/@Value ) (: iterate over all other datasets in INTERVENTIONS, EVENTS, FINDINGS :) for $dataset in $definedoc//odm:ItemGroupDef[upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] let $name := $dataset/@Name let $datasetname := ( if($defineversion = '2.1') then $dataset/def21:leaf/@xlink:href else $dataset/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetname) then doc(concat($base,$datasetname)) else () ) (: Get the OIDs of the --DY and --DTC variables :) let $dyoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DY') and string-length(@Name)=4]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dyname := concat($name,'DY') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DTC') and string-length(@Name)=5]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dtcname := $definedoc//odm:ItemDef[@OID=$dtcoid]/@Name (: and the OID of the USUBJID variable (might be different from the one in DM) :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) (: iterate over all records but only when --DY and --DTC have been defined :) for $record in $datasetdoc[$dtcoid and $dyoid]//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]] let $recnum := $record/@data:ItemGroupDataSeq (: get the USUBJID value :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: get the --DTC value :) let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: and check whether it is a complete date - i.e. string-length at least 10 :) let $iscompletedtcvalue := string-length($dtcvalue) >= 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: and check whether also RFSTDTC is complete :) let $hascompleterfstdtcvalue := functx:is-value-in-sequence($usubjidvalue,$usubjidcompleterfstdtc) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: when RFSTDTC and xxDTC are complete, there MUST be a xxDY value :) where $iscompletedtcvalue and $hascompleterfstdtcvalue and not($dyvalue) return {data($dyname)} is absent although both {data($dtcname)} (value={data($dtcvalue)}) and RFSTDTC contain complete dates ]]> --DY variable value must be populated Collection Study Day (--DY) variable value should be populated, when Collection Study Date/Time (--DTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS = 10 return $record/odm:ItemData[@ItemOID=$dmusubjidoid]/@Value ) (: iterate over all provided datasets in INTERVENTIONS, EVENTS, FINDINGS :) for $dataset in $definedoc//odm:ItemGroupDef[@Name=$datasetname][upper-case(@def:Class)='INTERVENTIONS' or upper-case(@def:Class)='EVENTS' or upper-case(@def:Class)='FINDINGS' or upper-case(./def21:Class/@Name)='INTERVENTIONS' or upper-case(./def21:Class/@Name)='EVENTS' or upper-case(./def21:Class/@Name)='FINDINGS'] let $name := $dataset/@Name let $datasetname := ( if($defineversion = '2.1') then $dataset/def21:leaf/@xlink:href else $dataset/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetname) then doc(concat($base,$datasetname)) else () ) (: Get the OIDs of the --DY and --DTC variables :) let $dyoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DY') and string-length(@Name)=4]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dyname := concat($name,'DY') let $dtcoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'DTC') and string-length(@Name)=5]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) let $dtcname := $definedoc//odm:ItemDef[@OID=$dtcoid]/@Name (: and the OID of the USUBJID variable (might be different from the one in DM) :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$name]/odm:ItemRef/@ItemOID return $a ) (: iterate over all records but only when --DY and --DTC have been defined :) for $record in $datasetdoc[$dtcoid and $dyoid]//odm:ItemGroupData[odm:ItemData[@ItemOID=$dtcoid]] let $recnum := $record/@data:ItemGroupDataSeq (: get the USUBJID value :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: get the --DTC value :) let $dtcvalue := $record/odm:ItemData[@ItemOID=$dtcoid]/@Value (: and check whether it is a complete date - i.e. string-length at least 10 :) let $iscompletedtcvalue := string-length($dtcvalue) >= 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: and check whether also RFSTDTC is complete :) let $hascompleterfstdtcvalue := functx:is-value-in-sequence($usubjidvalue,$usubjidcompleterfstdtc) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: when RFSTDTC and xxDTC are complete, there MUST be a xxDY value :) where $iscompletedtcvalue and $hascompleterfstdtcvalue and not($dyvalue) return {data($dyname)} is absent although both {data($dtcname)} (value={data($dtcvalue)}) and RFSTDTC contain complete dates ]]> --DY variable value may not be imputed --DY variable may be only populated, when both Collection Study Date/Time (--DTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO SE SV = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: keeping worst case scenario into account that there are two records for the same USUBJID in DM - take the first :) (: let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value :) (: and check whether also RFSTDTC is complete :) let $hascompleterfstdtcvalue := functx:is-value-in-sequence($usubjidvalue,$usubjidincompleterfstdtc) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: when one of RFSTDTC and xxDTC is not complete, there may NOT be a xxDY value :) where (not($iscompletedtcvalue) or $hascompleterfstdtcvalue) and $dyvalue return {data($dyname)} is imputed (value={data($dyvalue)}) although one of {data($dtcname)} (value={data($dtcvalue)}) or RFSTDTC is not a complete date ]]> --DY variable value may not be imputed --DY variable may be only populated, when both Collection Study Date/Time (--DTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO SE SV = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: keeping worst case scenario into account that there are two records for the same USUBJID in DM - take the first :) (: let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value :) (: and check whether also RFSTDTC is complete :) let $hasincompleterfstdtcvalue := functx:is-value-in-sequence($usubjidvalue,$usubjidincompleterfstdtc) let $dyvalue := $record/odm:ItemData[@ItemOID=$dyoid]/@Value (: when one of RFSTDTC and xxDTC is not complete, there may NOT be a xxDY value :) where (not($iscompletedtcvalue) or $hasincompleterfstdtcvalue) and $dyvalue return {data($dyname)} is imputed (value={data($dyvalue)}) although one of {data($dtcname)} (value={data($dtcvalue)}) or RFSTDTC is not a complete date ]]> --TPTREF must be provided, when --ELTM is provided Time Point Reference (--TPTREF) should not be NULL, when Planned Elapsed Time from Time Point Ref (--ELTM) is populated 3.1.2 3.1.3 3.2 ALL Missing value for {data($tptrefname)} when {data($eltmname)} is populated, value={data($eltmvalue)} ]]> --TPTREF must be provided, when --ELTM is provided Time Point Reference (--TPTREF) should not be NULL, when Planned Elapsed Time from Time Point Ref (--ELTM) is populated 3.1.2 3.1.3 3.2 ALL Missing value for {data($tptrefname)} when {data($eltmname)} is populated, value={data($eltmvalue)} ]]> EPOCH value must match an entry in TA Epoch (EPOCH) values in all datasets should match entries in the Trial Arms (TA) dataset 3.1.2 3.1.3 3.2 ALL Invalid EPOCH. Value for EPOCH={data($epochvalue)} in dataset {data($datasetname)} was not found in the TA dataset {data($tadatasetname)} ]]> EPOCH value must match an entry in TA Epoch (EPOCH) values in all datasets should match entries in the Trial Arms (TA) dataset 3.1.2 3.1.3 3.2 ALL Invalid EPOCH. Value for EPOCH={data($epochvalue)} in dataset {data($datasetname)} was not found in the TA dataset {data($tadatasetname)} ]]> Variable appearing in dataset must be in the SDTM model Only variables listed in SDTM model should appear in a dataset. New sponsor defined variables must not be added, and existing variables must not be renamed or modified 3.2 ALL Variable {data($var)} is not in the SDTM model (v.1.4) for domain {data($domaincode)} ]]> Variable appearing in dataset must be in the SDTM model Only variables listed in SDTM model should appear in a dataset. New sponsor defined variables must not be added, and existing variables must not be renamed or modified 3.2 ALL Variable {data($var)} is not in the SDTM model (v.1.4) for domain {data($domaincode)} ]]> Permissible variable with missing value for all records is not allowed Permissible variable whould not be present in domain, when the variable has missing value for all records in the dataset 3.1.2 3.1.3 3.2 ALL Permissible variable {data($variablename)} has no values for all records in dataset {data($datasetname)} ]]> Permissible variable with missing value for all records is not allowed Permissible variable whould not be present in domain, when the variable has missing value for all records in the dataset 3.1.2 3.1.3 3.2 ALL Permissible variable {data($variablename)} has no values for all records in dataset {data($datasetname)} ]]> SDTM Expected variables must be included in datasets When no data has been collected for an expected variable, however, a null column must still be included in the dataset, and a comment must be included in the define.xml to state that data was not collected 3.1.2 3.1.3 3.2 ALL {data($expectedvaroids)} :) (: check whether each of the expected variables is at least defined in the define.xml - which does mean that there is a column for it, empty or not :) for $oid in $expectedvaroids let $varname := $definedoc//odm:ItemDef[@OID=$oid]/@Name (: needed for reporting :) let $expectedpresent := $datasetdef/odm:ItemRef[@ItemOID=$oid] (: a boolean :) where not($expectedpresent) (: expected variable is not present :) return Expected variable {data($varname)} was not found in dataset {data($name)} for domain {data($domain)} ]]> SDTM Expected variables must be included in datasets When no data has been collected for an expected variable, however, a null column must still be included in the dataset, and a comment must be included in the define.xml to state that data was not collected 3.1.2 3.1.3 3.2 ALL {data($expectedvaroids)} :) (: check whether each of the expected variables is at least defined in the define.xml - which does mean that there is a column for it, empty or not :) for $oid in $expectedvaroids let $varname := $definedoc//odm:ItemDef[@OID=$oid]/@Name (: needed for reporting :) let $expectedpresent := $datasetdef/odm:ItemRef[@ItemOID=$oid] (: a boolean :) where not($expectedpresent) (: expected variable is not present :) return Expected variable {data($varname)} was not found in dataset {data($name)} for domain {data($domain)} ]]> Split datasets must not have name of original domain Split datasets must not have name of original domain. E.g., lbhm.xpt is a valid name, when lb.xpt is not a valid dataset name for split domain. 3.1.2 3.1.3 3.2 INTERVENTIONS FINDINGS EVENTS 1 and not(string-length(substring-before($filename,'.')) > 2) (: filenames should have >2 characters before the dot :) return Split dataset {data($name)} has a file name '{data($filename)}' that is typical for non-split datasets ]]> RELTYPE may oly be 'ONE' or 'MANY' Relationship Type (RELTYPE) variable values should be populated with terms 'ONE', 'MANY', when Related Records (RELREC) dataset is used to identify relationships between datasets 3.1.2 3.1.3 3.2 RELREC Invalid value for RELTYPE variable: only 'ONE' or 'MANY' is allowed. The value '{data($value)}'was found ]]> Coded and Decoded values must have the same NCI Code in CDISC CT Paired variables TEST/TESTCD must be populated using terms with the same Codelist Code value in CDISC control terminology. There is one-to-one relationship between paired variable values defined in CDISC control terminology by Codelist Code value 3.1.2 3.1.3 3.2 ALL {data($testcdncivalue)} - {data($testncivalue)} :) (: if there is an NCI value for the TESTCD, then the NCI value for the TEST must be identical :) where $testcdncivalue and not($testcdncivalue=$testncivalue) return The Coded value '{data($testcdvalue)}' with NCI code '{data($testcdncivalue)}' and Decode value '{data($testvalue)}' with NCI code '{data($testcdncivalue)}' do not have the same NCI code ]]> Coded and Decoded values must have the same NCI Code in CDISC CT Paired variables TEST/TESTCD must be populated using terms with the same Codelist Code value in CDISC control terminology. There is one-to-one relationship between paired variable values defined in CDISC control terminology by Codelist Code value 3.1.2 3.1.3 3.2 ALL {data($testcdncivalue)} - {data($testncivalue)} :) (: if there is an NCI value for the TESTCD, then the NCI value for the TEST must be identical :) where $testcdncivalue and not($testcdncivalue=$testncivalue) return The Coded value '{data($testcdvalue)}' with NCI code '{data($testcdncivalue)}' and Decode value '{data($testvalue)}' with NCI code '{data($testcdncivalue)}' do not have the same NCI code ]]> --RFTDTC may not be populated when --TPTREF is not populated --RFTDTC may not be populated when --TPTREF is not populated 3.1.2 3.1.3 3.2 ALL {data($rftdtcdname)} is populated but {$tptrefname} is not populated ]]> --RFTDTC may not be populated when --TPTREF is not populated --RFTDTC may not be populated when --TPTREF is not populated 3.1.2 3.1.3 3.2 ALL {data($rftdtcdname)} is populated but {$tptrefname} is not populated ]]> Values for --CAT and --SCAT may not be identical Values of Category (--CAT) and Subcategory (--SCAT) variables should not be identical 3.1.2 3.1.3 3.2 ALL {data($scatname)} value '{data($catvalue)}' is identical to {data($catname)} value '{data($scatvalue)}' ]]> Values for --CAT and --SCAT may not be identical Values of Category (--CAT) and Subcategory (--SCAT) variables should not be identical 3.1.2 3.1.3 3.2 ALL {data($scatname)} value '{data($catvalue)}' is identical to {data($catname)} value '{data($scatvalue)}' ]]> Variables marked as Required may not have a null value Required variables (where Core attribute is 'Req') cannot be NULL for any records 3.1.2 3.1.3 3.2 ALL {data($query)} :) (: Execute the RESTful web service query and get the value for "core" :) let $core := doc($query)//Response/text() (: iterate over each dataset record :) for $record in $datasetdoc//odm:ItemGroupData[@ItemGroupOID=$itemgroupoid] (: get the record number :) let $recnum := $record/@data:ItemGroupDataSeq (: data point is absent in this record, althout "core" is "Req" :) where $core='Req' and empty($record/odm:ItemData[@ItemOID=$itemrefoid]) return No data found for required variable {data($itemname)} in record number {data($recnum)} in dataset {data($datasetname)} ]]> Values for --SEQ variable may not be duplicate within USUBJID/POOLID The value of Sequence Number (--SEQ) variable must be unique for each record within a domain and within each Unique Subject Identifier (USUBJID) or Pool Identifier (POOLID) variables value when they are present in the domain 3.1.2 3.1.3 3.2 ALL 1 return The record with USUBJID = {data($usubjid)} and {data($seqname)} is not unique in the dataset {data($itemgroupname)}. The following records have the same combination of USUBJID and {data($seqname)}: records number {data($recnums)} ]]> Values for --SEQ variable may not be duplicate within USUBJID/POOLID The value of Sequence Number (--SEQ) variable must be unique for each record within a domain and within each Unique Subject Identifier (USUBJID) or Pool Identifier (POOLID) variables value when they are present in the domain 3.1.2 3.1.3 3.2 ALL 1 return The record with USUBJID = {data($usubjid)} and {data($seqname)} is not unique in the dataset {data($itemgroupname)}. The following records have the same combination of USUBJID and {data($seqname)}: records number {data($recnums)} ]]> Subject must be present in DM domain All Subjects (USUBJID) must be present in Demographics (DM) domain 3.1.2 3.1.3 3.2 ALL USUBJID {data($value)} in dataset {data($datasetname)} could not be found in DM dataset ]]> Subject must be present in DM domain All Subjects (USUBJID) must be present in Demographics (DM) domain 3.1.2 3.1.3 3.2 ALL USUBJID {data($value)} in dataset {data($datasetname)} could not be found in DM dataset ]]> VISIT/VISITNUM values must match TV domain data Combination of Visit Name (VISIT) and Visit Number (VISITNUM) in subject-level domains should match that in the TV domain with the exception of Unscheduled and Unplanned visits 3.1.2 3.1.3 3.2 ALL VISIT={data($visitvalue)}, VISITUM={data($visitnumvalue)} in dataset {data($datasetname)} does not match TV domain data in dataset TV ]]> VISIT/VISITNUM values must match TV domain data Combination of Visit Name (VISIT) and Visit Number (VISITNUM) in subject-level domains should match that in the TV domain with the exception of Unscheduled and Unplanned visits 3.1.2 3.1.3 3.2 ALL VISIT={data($visitvalue)}, VISITUM={data($visitnumvalue)} in dataset {data($datasetname)} does not match TV domain data in dataset TV ]]> VISITNUM/VISIT/VISITDY values must match TV domain data The combination of Visit Number (VISITNUM), Visit Name (VISIT), and Planned Study Day of Visit (VISITDY) values should match entries in the Trial Visits (TV) dataset, when they are planned visits (SVUPDES = NULL) 3.1.2 3.1.3 3.2 SV VISITNUM/VISIT/VISITDY values in SV do not match TV domain data, SV VISITNUM='{data($svvisitnumvalue)}', VISIT='{data($svvisitvalue)}', VISITDY='{data($svvisitdyvalue)}' ]]> USUBJID/VISIT/VISITNUM values must match SV domain data All Unique Subject Identifier (USUBJID) + Visit Name (VISIT) + Visit Number (VISITNUM) combination values in data should be present in the Subject Visits (SV) domain. There is an exception for records, where Status (--STAT) variable value is populated. E.g., --STAT = 'NOT DONE' 3.1.2 3.1.3 3.2 ALL ) (: return {$svtriples} :) (: iterate over all other datasets except for SV :) for $datasetdef in $definedoc//odm:ItemGroupDef[not(@Name='SV')] (: get the dataset name :) let $name := $datasetdef/@Name (: also here, we need the OIDs of USUBJID, VISIT and VISITNUM . these can be different from those in SV :) let $usubjudoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $visitoid := ( for $a in $definedoc//odm:ItemDef[@Name='VISIT']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $visitnumoid := ( for $a in $definedoc//odm:ItemDef[@Name='VISITNUM']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: and, not to forget, the OID of the --STAT variable :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: get the location of the dataset :) let $datasetloc := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) (: and the document itself :) let $datasetdoc := ( if($datasetloc) then doc(concat($base,$datasetloc)) else () ) (: iterate over all the records in the dataset, but only if USUBJID, VISIT and VISITNUM have been defined for the dataset, AND there is a value for all three of them :) for $record in $datasetdoc[$usubjudoid and $visitoid and $visitnumoid]//odm:ItemGroupData[odm:ItemData[@ItemOID=$usubjudoid]/@Value and odm:ItemData[@ItemOID=$visitoid]/@Value and odm:ItemData[@ItemOID=$visitnumoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the values of USUBJID, VISIT and VISITNUM :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjudoid]/@Value let $visitvalue := $record/odm:ItemData[@ItemOID=$visitoid]/@Value let $visitnumvalue := $record/odm:ItemData[@ItemOID=$visitnumoid]/@Value let $statvalue := $record/odm:ItemData[@ItemOID=$statoid]/@Value (: this triple must also appear in the list of triples :) let $count := count($svtriples[@usubjid=$usubjidvalue and @visit=$visitvalue and @visitnum=$visitnumvalue]) (: there must be at least one such record in SV, except for when --STAT is populated :) where $count = 0 and not($statvalue) return The value of USUBJID='{data($usubjidvalue)}', VISIT='{data($visitvalue)}', VISITNUM='{data($visitnumvalue)}' in dataset '{data($name)}' could not be found in the SV dataset ]]> USUBJID/VISIT/VISITNUM values must match SV domain data All Unique Subject Identifier (USUBJID) + Visit Name (VISIT) + Visit Number (VISITNUM) combination values in data should be present in the Subject Visits (SV) domain. There is an exception for records, where Status (--STAT) variable value is populated. E.g., --STAT = 'NOT DONE' 3.1.2 3.1.3 3.2 ALL ) (: return {$svtriples} :) (: iterate over all other provided datasets except for SV :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name=$datasetname][not(@Name='SV')] (: get the dataset name :) let $name := $datasetdef/@Name (: also here, we need the OIDs of USUBJID, VISIT and VISITNUM . these can be different from those in SV :) let $usubjudoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $visitoid := ( for $a in $definedoc//odm:ItemDef[@Name='VISIT']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $visitnumoid := ( for $a in $definedoc//odm:ItemDef[@Name='VISITNUM']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: and, not to forget, the OID of the --STAT variable :) let $statoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STAT')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: get the location of the dataset :) let $datasetloc := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) (: and the document itself :) let $datasetdoc := ( if($datasetloc) then doc(concat($base,$datasetloc)) else () ) (: iterate over all the records in the dataset, but only if USUBJID, VISIT and VISITNUM have been defined for the dataset, AND there is a value for all three of them :) for $record in $datasetdoc[$usubjudoid and $visitoid and $visitnumoid]//odm:ItemGroupData[odm:ItemData[@ItemOID=$usubjudoid]/@Value and odm:ItemData[@ItemOID=$visitoid]/@Value and odm:ItemData[@ItemOID=$visitnumoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the values of USUBJID, VISIT and VISITNUM :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjudoid]/@Value let $visitvalue := $record/odm:ItemData[@ItemOID=$visitoid]/@Value let $visitnumvalue := $record/odm:ItemData[@ItemOID=$visitnumoid]/@Value let $statvalue := $record/odm:ItemData[@ItemOID=$statoid]/@Value (: this triple must also appear in the list of triples :) let $count := count($svtriples[@usubjid=$usubjidvalue and @visit=$visitvalue and @visitnum=$visitnumvalue]) (: there must be at least one such record in SV, except for when --STAT is populated :) where $count = 0 and not($statvalue) return The value of USUBJID='{data($usubjidvalue)}', VISIT='{data($visitvalue)}', VISITNUM='{data($visitnumvalue)}' in dataset '{data($name)}' could not be found in the SV dataset ]]> Inconsistent Value for VISIT must be consistent within VISITNUM in SV and TV All values of Visit Name (VISIT) should be the same for a given value of Visit Number (VISITNUM) in domains TV and SV 3.1.2 3.1.3 3.2 SV TV Inconsistent value for VISIT within VISITNUM={data($uniquevisitnum)} in dataset {data($datasetname)}. {data($uniquevisitvaluescount)} different combinations were found ]]> Values for VISITNUM must be consistent within VISIT All values of Visit Number (VISITNUM) should be the same for a given value of Visit Name (VISIT) 3.1.2 3.1.3 3.2 SV TV Inconsistent value for VISITNUM within VISIT={data($uniquevisit)} in dataset {data($datasetname)}. {data($uniquevisitnumvaluescount)} different combinations were found ]]> AESER must be 'Y', when AESOD equals 'Y' Serious Event (AESER) variable value is expected to be 'Y', when Occurred with Overdose (AESOD) variable value equals 'Y' 3.1.2 3.1.3 3.2 AE AESER is not 'Y', when AESOD equals 'Y', value found for AESER={data($aeservalue)} ]]> At least one qualifier must be set to 'Y', when AE is Serious When Serious Event (AESER) variable value is 'Y', then at least one of seriousness criteria variables is expected to have value 'Y' (Involves Cancer (AESCAN), Congenital Anomaly or Birth Defect (AESCONG), Persist or Signif Disability/Incapacity (AESDISAB), Results in Death (AESDTH), Requires or Prolongs Hospitalization (AESHOSP), Is Life Threatening (AESLIFE), or Other Medicaly Important Serious Event (AESMIE)) 3.1.2 3.1.3 3.2 AE No qualifiers set to 'Y', when AE is Serious in dataset {data($datasetname)} ]]> Details info for AESMIE Adverse Event must be provided in SUPPAE domain When a description of Other Medically Important Serious Adverse Events category is collected on a CRF, sponsors should place the description in the SUPPAE dataset using the standard supplemental qualifier name code AESOSP 3.2 AE No record with IDVAR=AESOSP could be found in SUPPAE or SUPPAE is missing ]]> --ENRTPT must be populated, when --ENTPT is populated - End Relative to Reference Time Point (--ENRTPT) must be populated when End Reference Time Point (--ENTPT) is populated 3.1.2 3.1.3 3.2 ALL Missing value for {data($enrtptname)}, when {data($entptname)} is populated, value = {data($entptvalue)} ]]> --ENRTPT must be populated, when --ENTPT is populated - End Relative to Reference Time Point (--ENRTPT) must be populated when End Reference Time Point (--ENTPT) is populated 3.1.2 3.1.3 3.2 ALL Missing value for {data($enrtptname)}, when {data($entptname)} is populated, value = {data($entptvalue)} ]]> --ENTPT variable must be present, when --ENRTPT variable is present End Reference Time Point (--ENTPT) variable must be included into the domain, when End Relative to Reference Time Point (--ENRTPT) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE Missing {data($entptname)} variable, when {data($enrtptname)} variable is present ]]> Value for --DECOD must be consistent within --PTCD All values of Dictionary-Derived Term (--DECOD) should be the same for a given value of Preferred Term Code (--PTCD) 3.1.2 3.1.3 3.2 EVENTS 1] (: start from the second one :) let $recnum2 := $record/@data:ItemGroupDataSeq (: as we grouped, the value of PTCD is the same, but we need to check on -DECOD :) let $decod2 := $record/odm:ItemData[@ItemOID=$decodoid]/@Value (: return {data($ptcd)} - {data($decod)} - {data($decod2)} :) (: the two -DECOD values must be identical, as they have the same value for -PTCD :) where not($decod1 = $decod2) return Inconsistent value for {data($decodname)} within {data($ptcdname)}: Record {data($recnum2)} has {data($decodname)}={data($decod2)} whereas recordnumber={data($recnum1)} has {data($decodname)}={data($decod1)} for the same value of {data($ptcdname)}={data($ptcd)} ]]> Value for --PTCD must be consistent within --DECOD All values of Preferred Term Code (--PTCD) should be the same for a given value of Dictionary-Derived Term (--DECOD) 3.1.2 3.1.3 3.2 EVENTS 1] (: start from the second one :) let $recnum2 := $record/@data:ItemGroupDataSeq (: as we grouped, the value of PTCD is the same, but we need to check on -DECOD :) let $ptcd2 := $record/odm:ItemData[@ItemOID=$ptcdoid]/@Value (: the two -PTCD values must be identical, as they have the same value for -DECOD :) where not($ptcd1 = $ptcd2) return Inconsistent value for {data($ptcdname)} within {data($decodname)}: Record {data($recnum2)} has {data($ptcdname)}={data($ptcd2)} whereas recordnumber={data($recnum1)} has {data($ptcdname)}={data($ptcd1)} for the same value of {data($decodname)}={data($decod)} ]]> --DECOD must be populated, when --PTCD is populated Dictionary-Derived Term (--DECOD) should be populated when Preferred Term Code (--PTCD) is populated 3.1.2 3.1.3 3.2 EVENTS Missing value for {data($decodname)} with {data($ptcdname)}='{data($decod)}' is populated ]]> --REASND may not be present in dataset when --PRESP not present in dataset then (Interventions, Events, except for DS,DV,EX) Reason Not Done (--REASND) variable should not be present in the domain, when the Pre-specified (--PRESP) variable is missing 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS CG0053 {data($reasndname)} is present although {data($prespname)} is absent ]]> --STAT may not present in dataset when --PRESP not present in dataset then (Interventions,Events, except for DS,DV,EX) Completion Status (--STAT) variable should not be present in the domain, when the Pre-specified (--PRESP) variable is missing 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS CG0056 {data($statname)} is present although {data($prespname)} is absent ]]> --ENRTPT variable must be present, when --ENTPT variable is present End Reference to Reference Time Point (--ENRTPT) variable must be included into the domain, when End Relative Time Point (--ENTPT) variable is present 3.1.2 3.1.3 3.2 ALL Missing {data($enrtptname)} variable, when {data($entptname)} variable is present ]]> --STRTPT must be populated, when --STTPT is populated Start Relative to Reference Time Point (--STRTPT) must be populated when Start Reference Time Point (--STTPT) is populated 3.1.2 3.1.3 3.2 ALL No value for {data($strtptname)} was found although there is a value for {data($sttptname)}={data($sttptvalue)} ]]> Value for --STTPT value must be consistent within --STDTC and USUBJID Start Reference Time Point (--STTPT) value must be consistent for all records with same Subject (USUBJID) and Start Date/Time (--STDTC) values 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS {data($usubjidoid)} - {data($sttptoid)} - {data($stdtcoid)} :) (: group the records by USUBJID and --STDTC - all the records in each group will have the same value for USUBJID and --STDTC:) let $orderedrecords := ( for $record in $datasetdoc//odm:ItemGroupData group by $b := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value, $c := $record/odm:ItemData[@ItemOID=$stdtcoid]/@Value return element group { $record } ) (: Each group now has the same value for USUBJID and --STDTC - iterate over all the groups what DO have a value for USUBJID, --STTPT and --STDTC:) for $group in $orderedrecords[$usubjidoid and $stdtcoid and $sttptoid] (: get the values of USUBJID and --STDTC :) let $usubjid := $group/odm:ItemGroupData[1]/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $stdtc := $group/odm:ItemGroupData[1]/odm:ItemData[@ItemOID=$stdtcoid]/@Value (: and the value of --STTPT and then record number:) let $sttpt1 := $group/odm:ItemGroupData[1]/odm:ItemData[@ItemOID=$sttptoid]/@Value let $recnum1 := $group/odm:ItemGroupData[1]/@data:ItemGroupDataSeq (: now iterate over all other records in the same group: the value of --STTPT should be the same as in the first record in the group :) for $record in $group/odm:ItemGroupData[position()>1] (: get the value of --STTPT and the record number :) let $sttpt2 := $record/odm:ItemData[@ItemOID=$sttptoid]/@Value let $recnum2 := $record/@data:ItemGroupDataSeq (: the two --STTPT values must be equal :) where not($sttpt1 = $sttpt2) return Inconsistent value for {data($sttptname)}: Record {data($recnum2)} has {data($sttptname)}={data($sttpt2)} whereas recordnumber={data($recnum1)} has {data($sttptname)}={data($sttpt1)} for the same value of USUBJID='{data($usubjid)}' and {data($stdtcname)}='{data($stdtc)}' ]]> --STRTPT variable must be present, when --STTPT variable is present Start Relative to Reference Time Point (--STRTPT) variable must be included into the domain, when Start Relative Time Point (--STTPT) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE CG0060 {data($strtptname)} is not present although {data($sttptname)} is present ]]> --STTPT variable must be present, when --STRTPT variable is present Start Reference Time Point (--STTPT) variable must be included into the domain, when Start Relative to Reference Time Point (--STRTPT) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE CG0061 {data($sttptname)} is not present although {data($strtptname)} is present ]]> EPOCH value must be provided, when DSCAT is 'DISPOSITION EVENT' Epoch (EPOCH) variable should be provided, when Category for Disposition Event (DSCAT) equals 'DISPOSITION EVENT' 3.1.2 3.1.3 3.2 DS Missing EPOCH value, although DSCAT is 'DISPOSITION EVENT' ]]> DSDECOD must be 'COMPLETED', when DSTERM='COMPLETED' When Reported Term for the Disposition Event (DSTERM) is 'COMPLETED', Standardized Disposition Term (DSDECOD) should have the same value 'COMPLETED' 3.1.2 3.1.3 3.2 DS Value for DSDECOD='{data($dsdecod)}' must be 'COMPLETED', as DSTERM='COMPLETED' ]]> DSDECOD must be the same as DSTERM, when DSCAT='PROTOCOL MILESTONE' Reported Term for the Disposition Event (DSTERM) and Standardized Disposition Term (DSDECOD) should contain the same value, when Category for Disposition Event (DSCAT) is 'PROTOCOL MILESTONE' DS 3.1.2 3.1.3 3.2 Value for DSDECOD='{data($dsdecod)}' is not equal to value for DSTERM='{data($dsterm)}', as DSCAT='PROTOCOL MILESTONE' ]]> 'DEATH' record for subject msut be present in DS domain when SSSTRESC='DEAD' All subjects who have Death records (SSSTRESC = 'DEAD') in Survival Status (SS) domain should also have death records (DSDECOD='DEATH') in Disposition (DS) domain 3.2 SS DS No record was found in DS with DSDECOD='DEATH' for the record in dataset {data($ssname)} with SSSTRESC='DEAD' for subject with USUBJID='{data($ssusubjid)}' ]]> --STDTC may not be before RFICDTC 'All records in Disposition Event (DS) and Protocol Diviation (DV) domains should have Start Date/Time of Event (--STDTC) equal or after subject's Date/Time of Informed Consent (RFICDTC) in Demographics (DM) domain 3.1.3 3.2 DS DV ) (: get the DS and DV dataset :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name='DS' or @Domain='DS' or @Name='DV' or @Domain='DV'] let $name := $datasetdef/@Name (: get the location and the dataset document itself :) let $datasetloc := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetloc) then doc(concat($base,$datasetloc)) else () ) (: get the OID of USUBJID and --STDTC :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $stdtcoid := ( for $a in $definedoc//odm:ItemDef[ends-with(@Name,'STDTC')]/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: and the full name of --STDTC :) let $stdtcname := $definedoc//odm:ItemDef[@OID=$stdtcoid]/@Name (: iterate over all the records that do have a value for --STDTC :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$stdtcoid]/@Value] let $recnum := $record/@data:ItemGroupDataSeq (: get the values of USUBJID and -STDTC :) let $usubjid := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $stdtc := $record/odm:ItemData[@ItemOID=$stdtcoid]/@Value (: and look them up in the DM-USUBJID-RFICDTC structure, retrieving the value for RFICDTC for the given subject :) let $rficdtc := $rficdtcpairs[@usubjid=$usubjid]/@rficdtc (: -DTC must be after RFICDTC - but first need to check for the correct datatype :) where $rficdtc castable as xs:dateTime and $stdtc castable as xs:dateTime and xs:dateTime($stdtc) < xs:dateTime($rficdtc) return {data($stdtcname)}={data($stdtc)} is before DM.RFICDTC={data($rficdtc)} in dataset {data($name)} ]]> DSSTDTC for DEATH record must be the same as DM.DTHDTC DEATH records (DSDECOD='DEATH') in Disposition (DS) domain should have Start Date of Event (DSDTDTC) equals to subject's Date/Time of Death (DTHDTC) populated in Demographics (DM) domain. Subject's Date/Time of Death info should be consistent across all domain 3.1.3 3.2 DS ) (: get the DS dataset(s) :) for $datasetdef in $definedoc//odm:ItemGroupDef[@Name='DS' or @Domain='DS'] let $name := $datasetdef/@Name (: get the location and the dataset document itself :) let $datasetloc := ( if($defineversion = '2.1') then $datasetdef/def21:leaf/@xlink:href else $datasetdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetloc) then doc(concat($base,$datasetloc)) else () ) (: get the OID of USUBJID, DSDECOD, DSDTDTC :) let $usubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $dsdecodoid := ( for $a in $definedoc//odm:ItemDef[@Name='DSDECOD']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) let $dsstdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='DSSTDTC']/@OID where $a = $datasetdef/odm:ItemRef/@ItemOID return $a ) (: iterate over all the records that for which DSDECOD='DEATH' :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dsdecodoid and @Value='DEATH']] let $recnum := $record/@data:ItemGroupDataSeq (: get the values of USUBJID and DSDTDTC :) let $usubjid := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value let $dsstdtc := $record/odm:ItemData[@ItemOID=$dsstdtcoid]/@Value (: and look them up in the DM-USUBJID- structure, retrieving the value for DTHDTC for the given subject :) let $dthdtc := $dthdtcpairs[@usubjid=$usubjid]/@dthdtc (: DTHDTC from DM and DSSTDTC from DS must be equal :) where not($dsstdtc = $dthdtc) return DSSTDTC value '{data($dsstdtc)}' does not correspond to DM.DTHDTC='{data($dthdtc)}' for USUBJID={data($usubjid)} ]]> Subjects with DSDECOD='PROTOCOL VIOLATION' in DS must have records in DV Subjects who has DSDECOD='PROTOCOL VIOLATION' records in Disposition (DS) domain should have supportive records with details in Protocol Deviations (DV) domain 3.1.2 3.1.3 3.2 DS No record was found in DV for subject with USUBJID='{data($dsusubjid)}' although there is a record in DS with DSDECOD='PROTOCOL DEVIATION' ]]> --CAT value may not be redundant with other variable values Value of Category (--CAT) should not be identical to that in Domain Abbreviation (DOMAIN); Reported Term (--TERM); Name of Measurement, Test, or Examination (--TESTCD); Name of Treatment (--TRT); Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TI The value of {data($catname)} is redundant. It is equal to one of DOMAIN, --TERM, --TESTCD, --TRT, --BODSYS ]]> --CAT value may not be redundant with other variable values Value of Category (--CAT) should not be identical to that in Domain Abbreviation (DOMAIN); Reported Term (--TERM); Name of Measurement, Test, or Examination (--TESTCD); Name of Treatment (--TRT); Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TI The value of {data($catname)} is redundant. It is equal to one of DOMAIN, --TERM, --TESTCD, --TRT, --BODSYS ]]> MHENDTC date may not be after RFSTDTC - The medical history dataset includes the subject's prior history at the start of the trial. End Date/Time of Medical History Event (MHENDTC) should be before Subject Reference Start Date/Time (RFSTDTC) 3.2 MH CG0078 RFSTDTC :) where $rfstdtc castable as xs:date and $mhendtccomplete castable as xs:date and not(xs:date($mhendtccomplete) <= xs:date($rfstdtc)) return MHENDTC={data($mhendtc)} is after or on RFSTDTC={data($rfstdtc)} ]]> MHSTDTC date may not be after RFSTDTC The medical history dataset includes the subject's prior history at the start of the trial. Start Date/Time of Medical History Event (MHSTDTC) should be before Subject Reference Start Date/Time (RFSTDTC) 3.1.2 3.1.3 3.2 MH CG0079 RFSTDTC :) where $rfstdtc castable as xs:date and $mhstdtccomplete castable as xs:date and not(xs:date($mhstdtccomplete) <= xs:date($rfstdtc)) return MHSTDTC={data($mhstdtc)} is after or on RFSTDTC={data($rfstdtc)} ]]> --STAT must be equal to 'NOT DONE', when --PRESP='Y' and --OCCUR is NULL When no response is provided for Occurrence (--OCCUR) for a pre-specified Intervention or Event (--PRESP = 'Y'), then Status (--STAT) should be set to 'NOT DONE' 3.1.3 3.2 EVENTS INTERVENTIONS SD0042 Invalid value for {data($statname)}='{data($stat)}' for {data($prespname)}='Y' and {data($occurname)}=null. Value for {data($statname)} expected is 'NOT DONE' ]]> --STAT must be equal to 'NOT DONE', when --PRESP='Y' and --OCCUR is NULL When no response is provided for Occurrence (--OCCUR) for a pre-specified Intervention or Event (--PRESP = 'Y'), then Status (--STAT) should be set to 'NOT DONE' 3.1.3 3.2 EVENTS INTERVENTIONS SD0042 Invalid value for {data($statname)}='{data($stat)}' for {data($prespname)}='Y' and {data($occurname)}=null. Value for {data($statname)} expected is 'NOT DONE' ]]> --BODSYS must be populated when --BDSYCD is populated Body System or Organ Class (--BODSYS) must be populated when Body System or Organ Class Code (--BDSYCD) is populated 3.1.2 3.1.3 3.2 AE MH CE CG0082 Null value found for {data($bodsysname)} where {data($bdsycdname)}='{data($bdsycd)}' ]]> --BODSYS must be populated when --BDSYCD is populated Body System or Organ Class (--BODSYS) must be populated when Body System or Organ Class Code (--BDSYCD) is populated 3.1.2 3.1.3 3.2 AE MH CE CG0082 Null value found for {data($bodsysname)} where {data($bdsycdname)}='{data($bdsycd)}' ]]> Value for --BODSYS must be consistent within --BDSYCD All values of Body System or Organ Class (--BODSYS) should be the same for a given value of Body System or Organ Class Code (--BDSYCD) 3.1.2 3.1.3 3.2 AE MH CE CG0083 {data($bodsys)} - {data($bodsys)} :) (: iterate over all other records in the same group, they have the same value for --BDSYCD, and must also have the same value for --BODSYS :) for $record in $group/odm:ItemGroupData[position()>1] let $recnum2 := $record/@data:ItemGroupDataSeq (: get the value of --BODSYS :) let $bodsys2 := $record/odm:ItemData[@ItemOID=$bodsysoid]/@Value (: the two --BODSYS values must be equal, except when they are null :) where $bdsycd!='' and $bodsys1!='' and $bodsys2!='' and not($bodsys1 = $bodsys2) return Combination of {data($bdsycdname)} and {data($bodsysname)} in dataset {data($datasetname)} is inconsistent: record {data($recnum1)}: {data($bdsycdname)}='{data($bdsycd)}' - {data($bodsysname)}='{data($bodsys1)}', record {data($recnum2)}: {data($bdsycdname)}='{data($bdsycd)}' - {data($bodsysname)}='{data($bodsys2)}', , ]]> Value for --BDSYCD must be consistent within --BODSYS - All values of Body System or Organ Class Code (--BDSYCD) should be the same for a given value of Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 AE MH CE CG0083 {data($bodsys)} - {data($bdsycd)} :) (: iterate over all other records in the same group, they have the same value for --BODSYS, and must also have the same value for --BDSYCD :) for $record in $group/odm:ItemGroupData[position()>1] let $recnum2 := $record/@data:ItemGroupDataSeq (: get the value of --BDSYCD :) let $bdsycd2 := $record/odm:ItemData[@ItemOID=$bdsycdoid]/@Value (: the two --BDSYCD values must be equal, except when they are null :) where $bodsys!='' and $bdsycd1 != '' and $bdsycd2 != '' and not($bdsycd1 = $bdsycd2) return Combination of {data($bdsycdname)} and {data($bodsysname)} in dataset {data($datasetname)} is inconsistent: record {data($recnum1)}: {data($bdsycdname)}='{data($bdsycd1)}' - {data($bodsysname)}='{data($bodsys)}', record {data($recnum2)}: {data($bdsycdname)}='{data($bdsycd2)}' - {data($bodsysname)}='{data($bodsys)}', , ]]> Value for --BDSYCD must be consistent within --BODSYS - All values of Body System or Organ Class Code (--BDSYCD) should be the same for a given value of Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 AE MH CE CG0083 {data($bodsys)} - {data($bdsycd)} :) (: iterate over all other records in the same group, they have the same value for --BODSYS, and must also have the same value for --BDSYCD :) for $record in $group/odm:ItemGroupData[position()>1] let $recnum2 := $record/@data:ItemGroupDataSeq (: get the value of --BDSYCD :) let $bdsycd2 := $record/odm:ItemData[@ItemOID=$bdsycdoid]/@Value (: the two --BDSYCD values must be equal, except when they are null :) where $bodsys!='' and $bdsycd1 != '' and $bdsycd2 != '' and not($bdsycd1 = $bdsycd2) return Combination of {data($bdsycdname)} and {data($bodsysname)} in dataset {data($datasetname)} is inconsistent: record {data($recnum1)}: {data($bdsycdname)}='{data($bdsycd1)}' - {data($bodsysname)}='{data($bodsys)}', record {data($recnum2)}: {data($bdsycdname)}='{data($bdsycd2)}' - {data($bodsysname)}='{data($bodsys)}', , ]]> --TOX variable may not be present when --TOXGR variable is missing Toxicity (--TOX) variable should not be present in the domain, when the Toxicity Grade (--TOXGR) variable is missing 3.1.2 3.1.3 3.2 LB AE SD1280 {data($toxname)} is present, although {data($toxgrname)} is absent in dataset {data($name)} ]]> --OCCUR may only be populated, when --PRESP = 'Y' Occurrence (--OCCUR) may only be populated, when a given Intervention or Event has been pre-specified (--PRESP = 'Y') 3.1.3 3.2 INTERVENTIONS EVENTS 0 return {data($occurname)} is populated, value={data($occur)} although {data($prespname)} is not populated or absent ]]> --OCCUR variable may not be present when --PRESP variable is missing Occurrence (--OCCUR) variable should not be present in the domain, when the Pre-specified (--PRESP) variable is missing 3.1.2 3.1.3 3.2 EVENTS INTERVENTIONS CG0088 Variable {data($occurname)} is present in dataset {data($name)} although {data($prespname)} is not present in the dataset ]]> --TPTREF must be present in the dataset when --RFTDTC present Time Point Reference (--TPTREF) variable must be included into the domain, when Date/Time of Reference Point (--RFTDTC) variable is present 3.1.2 3.1.3 3.2 ALL CG0090 Variable {data($rftdtcname)} is present in dataset {data($name)} but {data($tptrefname)} is not present in the dataset ]]> Value for --TPT must be provided, when --TPTNUM is provided Planned Time Point Name (--TPT) should not be NULL, when Planned Time Point Number (--TPTNUM) is populated 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO Variable {data($tptname)} is not populated although variable {data($tptnumname)} is populated, value={data($tptnum)} ]]> Value for --TPT must be provided, when --TPTNUM is provided Planned Time Point Name (--TPT) should not be NULL, when Planned Time Point Number (--TPTNUM) is populated 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO Variable {data($tptname)} is not populated although variable {data($tptnumname)} is populated, value={data($tptnum)} ]]> --TPT variable must be present, when --TPTNUM variable is present Planned Time Point Name (--TPT) variable must be included into the domain, when Planned Time Point Number (--TPTNUM) variable is present 3.1.2 3.1.3 3.2 ALL CG0091 Variable {data($tptnumname)} is present in dataset {data($name)} but {data($tptname)} is not present in the dataset ]]> --TPTREF variable must be present in dataset, when --ELTM variable is present Time Point Reference (--TPTREF) variable must be included into the domain, when Planned Elapsed Time from Time Point Ref (--ELTM) variable is present 3.1.2 3.1.3 3.2 ALL CG0092 Variable {data($eltmname)} is present in dataset {data($name)} but {data($tptrefname)} is not present in the dataset ]]> When --ELTM, --TPTNUM, and --TPT is not present in the dataset then --TPTREF may not be present in the dataset Time Point Reference (--TPTREF) variable should not be present in the domain, when the Planned Elapsed Time from Time Point Ref (--ELTM) variable, Planned Time Point Number (--TPTNUM) variable, and Planned Time Point (--TPT) variable are missing 3.1.2 3.1.3 3.2 ALL CG0093 Variable {data($tptrefname)} is present in dataset {data($name)} although {data($eltmname)}, {data($tptnumname)} and {data($tptname)} are not present in the dataset ]]> --STAT must be populated, when --REASND is populated Completion Status (--STAT) should be set to 'NOT DONE', when Reason Not Done (--REASND) is populated 3.1.2 3.1.3 3.2 ALL Missing or invalid value for {data($statname)} when {data($reasndname)} is provided - {data($reasndname)}={data($reasndvalue)} - {data($statname)}={data($statvalue)} in dataset {data($datasetname)} ]]> --STAT must be populated, when --REASND is populated Completion Status (--STAT) should be set to 'NOT DONE', when Reason Not Done (--REASND) is populated 3.1.2 3.1.3 3.2 ALL Missing or invalid value for {data($statname)} when {data($reasndname)} is provided - {data($reasndname)}={data($reasndvalue)} - {data($statname)}={data($statvalue)} in dataset {data($datasetname)} ]]> --LAT variable may not be present when --LOC variable is missing Laterality (--LAT) variable should not be present in the domain, when the Location (--LOC) variable is missing 3.1.3 3.2 MI MO TU VS FA SR EX EC PR CG0095 Variable {data($locname)} is absent in dataset {data($name)} but {data($latname)} is present in the dataset ]]> ECDOSE must be greater than 0 when ECOCCUR does not equal 'N' and ECDOSTXT is null ECDOSE must not be set to zero (0) as an alternative method for indicating doses not taken, not given, or missed 3.2 EC CG0100 0 :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: get the EC dataset(s) definition :) for $itemgroupdef in $definedoc//odm:ItemGroupDef[@Domain='EC' or starts-with(@Name,'EC')] let $name := $itemgroupdef/@Name (: get the dataset itself :) let $datasetlocation := ( if($defineversion = '2.1') then $itemgroupdef/def21:leaf/@xlink:href else $itemgroupdef/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetlocation) then doc(concat($base,$datasetlocation)) else () ) (: get the OID of ECOCCUR, ECDOSTXT and ECDOSE :) let $ecoccuroid := ( for $a in $definedoc//odm:ItemDef[@Name='ECOCCUR']/@OID where $a = $itemgroupdef/odm:ItemRef/@ItemOID return $a ) let $ecdostxtoid := ( for $a in $definedoc//odm:ItemDef[@Name='ECDOSTXT']/@OID where $a = $itemgroupdef/odm:ItemRef/@ItemOID return $a ) (: :) let $ecdoseoid := ( for $a in $definedoc//odm:ItemDef[@Name='ECDOSE']/@OID where $a = $itemgroupdef/odm:ItemRef/@ItemOID return $a ) (: get all the records in the dataset for which ECOCCUR != 'N' and ECDOSTXT is null :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$ecoccuroid and @Value!='N'] and not(odm:ItemData[@ItemOID=$ecdostxtoid])] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of ECDOSE (as text) :) let $dose := $record/odm:ItemData[@ItemOID=$ecdoseoid]/@Value (: ECDOSE > 0 :) where $dose castable as xs:double and xs:double($dose)<0 return ECDOSE is not a number or is a non-positive number where ECOCCUR != 'N' and ECDOSTXT is null. The value found for ECDOSE is '{data($dose)}' ]]> When ECOCCUR = 'N' then ECDOSE = null ECDOSE must either be null when ECOCCUR equals 'N', or ECDOSE must be greater than 0. ECDOSE would be greater than 0 (when ECOCCUR equals N) for records that represent specific dose amounts that are not taken, not given, or missed 3.2 CG0101 EC ECDOSE={data($dose)} is expected to be null as ECOCCUR='N' ]]> When EXTRT = 'PLACEBO' then EXDOSE = 0 Doses of placebo should be represented by EXTRT = 'PLACEBO' and EXDOSE = 0 (indicating 0 mg of active ingredient was taken or administered) 3.1.2 3.1.3 3.2 EX CG0102 {data($extrtoid)} :) (: get all the records in the dataset for which EXTRT='PLACEBO' :) for $record in $datasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$extrtoid and @Value='PLACEBO']] let $recnum := $record/@data:ItemGroupDataSeq (: get the value of EXDOSE (as text) :) let $exdose := $record/odm:ItemData[@ItemOID=$exdoseoid]/@Value (: When EXTRT = 'PLACEBO' then EXDOSE = 0 :) where $exdose castable as xs:double and xs:double($exdose)!= 0 return EXDOSE={data($exdose)} is expected to be 0 as EXTRT='PLACEBO' ]]> When EXTRTV = null then EXVAMTU = null When EXTRTV = null then EXVAMTU must be null 3.1.2 3.1.3 3.2 INTERVENTIONS CG0108 EXVAMTU={data($exvamtu)} but was expected to be null as EXTRTV is null ]]> When EXTRTV = null then EXVAMTU = null When EXTRTV = null then EXVAMTU must be null 3.1.2 3.1.3 3.2 INTERVENTIONS CG0108 EXVAMTU={data($exvamtu)} but was expected to be null as EXTRTV is null ]]> Only one of Dose (--DOSE) or Dose Description (--DOSTXT) variables must be populated on the same record Only one of Dose (--DOSE) or Dose Description (--DOSTXT) variables must be populated on the same record 3.1.2 3.1.3 3.2 INTERVENTIONS CG0110 Both {data($dosename)} and {data($dostxtname)} are populated ]]> Only one of Dose (--DOSE) or Dose Description (--DOSTXT) variables must be populated on the same record Only one of Dose (--DOSE) or Dose Description (--DOSTXT) variables must be populated on the same record 3.1.2 3.1.3 3.2 INTERVENTIONS CG0110 Both {data($dosename)} and {data($dostxtname)} are populated ]]> When --DOSE != null or --DOSTOT != null or --DOSTXT != null then --DOSU may not be null Dose Units (--DOSU) must be populated, when Dose per Administration (--DOSE), Dose Description (--DOSTXT) or Total Daily Dose (--DOSTOT) is provided 3.1.2 3.1.3 3.2 INTERVENTIONS CG0114 {data($dosuname)} is not populated although one of {data($dosename)}, {data($dostxtname)} or {data($dostotname)} is populated ]]> When --DOSE != null or --DOSTOT != null or --DOSTXT != null then --DOSU must be != null Dose Units (--DOSU) must be populated, when Dose per Administration (--DOSE), Dose Description (--DOSTXT) or Total Daily Dose (--DOSTOT) is provided 3.1.2 3.1.3 3.2 INTERVENTIONS CG0114 {data($dosuname)} is not populated although one of {data($dosename)}, {data($dostxtname)} or {data($dostotname)} is populated ]]> Portion or Totality (--PORTOT) variable may not be present, when the Location (--LOC) variable is missing Portion or Totality (--PORTOT) variable should not be present in the domain, when the Location (--LOC) variable is missing 3.1.3 3.2 INTERVENTIONS FINDINGS CG0115 {data($portotname)} is present although {data($locname)} is present in dataset {data($name)} ]]> Directionality (--DIR) variable may not be present, when the Location (--LOC) variable is missing Directionality (--DIR) variable should not be present in the domain, when the Location (--LOC) variable is missing 3.1.3 3.2 INTERVENTIONS FINDINGS CG0116 {data($dirname)} is present although {data($locname)} is present in dataset {data($name)} ]]> When ACTARM is not in TA.ARM, then ACTARM must be one of 'Screen Failure', 'Not Assigned', 'Not Treated', or 'Unplanned Treatment' - 'Description of Actual Arm (ACTARM) values should match entries in the Trial Arms (TA) dataset, except for subjects who failed screening ('Screen Failure'), or were not fully assigned to an Arm ('Not Assigned'), or randomized, but not treated ('Not Treated') or received non-planned treatment ('Unplanned Treatment') 3.1.3 3.2 DM CG0117 Invalid value for ACTARM, value={data($actarmvalue)} in dataset {data($datasetname)} ]]> Screen failure subjects, if submitted, must be in DM, with ARMCD = 'SCRNFAIL' and ARM = 'Screen Failure' The combination of Description of Planned Arm (ARM) and Planned Arm Code (ARMCD) values must match entries in the Trial Arms (TA) dataset, except for subjects who failed screening (ARMCD = 'SCRNFAIL') or were not fully assigned to an Arm (ARMCD = 'NOTASSGN') 3.1.2 3.1.3 3.2 DM CG0128 Invalid value for ARMCD, value='{data($armcdvalue)}' is not found in TA and is not one of('SCRNFAIL', 'NOTASSGN') ]]> Subjects withdrawn before arm assignment, if not screen failures, must have ARMCD ='NOTASSGN' and ARM = 'Not Assigned' in DM Subjects withdrawn from a trial before assignment to an Arm, if they are not screen failures, should have ARMCD ='NOTASSGN' and ARM = 'Not Assigned' 3.1.2 3.1.3 3.2 DM CG0128 Invalid value for ARM, value='{data($armvalue)}' is not found in TA and is not one of('Screen Failure', 'Not Assigned') ]]> ACTARMCD may be no more than 20 characters The value of Actual Arm Code (ACTARMCD) may be no more than 20 characters in length 3.1.3 3.2 DM CG0123 20 return Invalid value for ACTARMCD in dataset {data($datasetname)}, it's length is more than 20 characters, value='{data($actarmcdvalue)}' ]]> When ACTARMCD not in ('SCRNFAIL', 'NOTASSGN', 'NOTTRT', 'UNPLAN') then ACTARMCD must be in TA.ARMCD Actual Arm Code (ACTARMCD) values should match entries in the Trial Arms (TA) dataset, except for subjects who failed screening ('SCRNFAIL'), or were not fully assigned to an Arm ('NOTASSGN'), or randomized but not treated ('NOTTRT'), or received non-planned treatment ('UNPLAN') 3.1.3 3.2 DM CG0125 Invalid value for ACTARMCD, value={data($actarmcdvalue)} in dataset DM is not one of ('SCRNFAIL', 'NOTASSGN', 'NOTTRT', 'UNPLAN') and is not found in TA.ARMCD - {data($armcdsequence)} ]]> When ARMCD not in ('SCRNFAIL', 'NOTASSGN') then ARMCD must be in TA.ARMCD Planned Arm Code (ARMCD) values should match entries in the Trial Arms (TA) dataset, except for subjects who failed screening (ARMCD = 'SCRNFAIL') or were not fully assigned to an Arm (ARMCD = 'NOTASSGN') 3.1.2 3.1.3 3.2 DM CG0126 Invalid value for ARMCD, value={data($armcdvalue)} in dataset DM is not one of ('SCRNFAIL', 'NOTASSGN') and is not found in TA.ARMCD ]]> ARM must equal 'Screen Failure', when ARMCD is 'SCRNFAIL', and vice versa Description of Arm (ARM) must equal 'Screen Failure', when Arm Code (ARMCD) is 'SCRNFAIL', and vice versa 3.1.2 3.1.3 3.2 DM TA CG0127 Invalid value for ACTARMCD, value='{data($actarmcdvalue)}' is expected to be equal to the value of ARMCD='{data($armcdvalue)}' ]]> ACTARMCD is expected to be equal to a ARMCD A value for an Actual Arm Code (ACTARMCD) variable is expected to be equal to a value of an Arm Code (ARMCD) variable 3.1.3 3.2 DM Invalid value for ARMCD, value='{data($armcdvalue)}', expected value='{data($actarmcdvalue)}' ]]> ARM must be 'Not Assigned', when ARMCD is 'NOTASSGN', and vice versa Description of Arm (ARM) must equal 'Not Assigned', when Arm Code (ARMCD) is 'NOTASSGN', and vice versa 3.1.2 3.1.3 3.2 DM TA ARM is not 'Not Assigned', when ARMCD equals 'NOTASSGN', or vice versa. ARMCD={data($armcdvalue)} with ARM={data($armvalue)} was found ]]> DTHFL must be 'Y' when SS.SSSTRESC = 'DEAD' DTHFL must equal 'Y' when there is a record in the Subject Status (SS) domain with SSSTRESC = 'DEAD' 3.2 SS DM CG0132 A record (record number={data($recnumss)}) for USUBJID='{data($ssusubjid)}' has been found for which SSSTRESC='DEAD' but the value of DTHFL='{data($dthfl)}' in DM is not 'Y' ]]> DTHFL must be 'Y' when there is a SS.STRESC='DEAD' for the subject DTHFL must equal 'Y' when there is a record in the Subject Status (SS) domain with SSSTRESC = 'DEAD' 3.2 DD DM CG0133 A record for USUBJID='{data($subject)}' has been found in the DD dataset but the value of DTHFL='{data($dthfl)}' in DM is not 'Y' ]]> DTHFL must be 'Y' when there is a record in AE with AEOUT = 'FATAL' DTHFL must equal 'Y' when there is a record in the Adverse Events (AE) domain with AEOUT = 'FATAL' 3.1.3 3.2 AE DM CG0134 A record for USUBJID='{data($usubjid)}' (record number {data($recnum)}) has been found in the AE dataset with AEOUT='FATAL' but the value of DTHFL='{data($dthfl)}' in DM is not 'Y' ]]> DTHFL must be 'Y' when there is a record AE with AESDTH = 'Y' DTHFL must equal 'Y' when there is a record in the Adverse Events (AE) domain with AESDTH = 'Y' 3.1.3 3.2 AE DM CG0135 A record for USUBJID='{data($usubjid)}' (record number {data($recnum)}) has been found in the AE dataset with AESDTH='Y' but the value of DTHFL='{data($dthfl)}' in DM is not 'Y' ]]> DTHFL must be 'Y' when there is a record in DS with DSDECOD = 'DEATH' DTHFL must equal 'Y' when there is a record in the Disposition (DS) domain with DSDECOD = 'DEATH' 3.1.3 3.2 DS DM CG0136 A record for USUBJID='{data($usubjid)}' (record number {data($recnum)}) has been found in the DS dataset with DSDECOD='DEATH' but the value of DTHFL='{data($dthfl)}' in DM is not 'Y' ]]> RFENDTC must be populated, unless ARMCD = 'SCRNFAIL' or ARMCD = 'NOTASSGN' Subject Reference End Date/Time (RFENDTC) must be populated for all randomized subjects, that have Planned Arm Code (ARMCD) not equal to 'SCRNFAIL' or 'NOTASSGN' 3.1.2 3.1.3 3.2 DM CG0142 RFENDTC=null for ACTARM='{data($actarmvalue)}'. RFENDTC is required to be populated for all randomized subjects. ]]> All subjects must have an Informed Consent record in the Disposition domain All subjects must have an Informed Consent record is DS 3.1.2 3.1.3 3.2 DS DM CG0143 No informed consent record (DSTERM='INFORMED CONSENT OBTAINED') in DS could be found for subject {data($dmusubjid)} ]]> When ACTARM in ('Screen Failure' 'Not Assigned' 'Not Treated') then RFSTDTC must be null RFSTDTC must be null when actual arm indicates that the subject is a screen failure ('Screen Failure'), was not assigned to an arm ('Not Assigned'), or was not treated ('NOTTRT'). This rule applies to studies where RFSTDTC is associated with a treatment date 3.1.3 3.2 DM CG0145 RFSTDTC='{data($rfstdtcvalue)}' expected to be null for ACTARM='{data($actarmvalue)}' ]]> RFSTDTC must be populated for all subjects, those where ARMCD is not equal to 'SCRNFAIL' or 'NOTASSGN' Subject Reference Start Date/Time (RFSTDTC) should be populated for all randomized subjects, those where Planned Arm Code (ARMCD) is not equal to 'SCRNFAIL' or 'NOTASSGN' 3.1.2 3.1.3 3.2 DM CG0146 RFSTDTC expected to be not null for ACTARM='{data($actarmvalue)}' ]]> The value of Set Code (SETCD) may not be more than 8 characters in length The value of Set Code (SETCD) should be no more than 8 characters in length 3.1.2 3.1.3 3.2 DM CG0149 8 return SETCD='{data($setcdvalue)}' has more than 8 characters ]]> SUBJID must be unique for each subject in the study The value of Subject Identifier for the Study (SUBJID) variable must be unique for each subject within the study - DM 3.1.2 3.1.3 3.2 DM FDAC048 $recnum][odm:ItemData[@ItemOID=$subjidoid][@Value=$subjidvalue]]) where $count > 0 return Duplicate value of SUBJID={data($subjidvalue)} - {data($count)} in dataset {data($datasetname)} ]]> USUBJID must be unique for each subject The value of Unique Subject Identifier (USUBJID) variable must be unique for each subject across all trials in the submission 3.1.2 3.1.3 3.2 DM FDAC048 $recnum][odm:ItemData[@ItemOID=$usubjidoid][@Value=$usubjidvalue]]) where $count > 0 return Duplicate value of SUBJID={data($usubjidvalue)} - {data($count)} in dataset {data($datasetname)} ]]> When ETCD = 'UNPLAN' then ELEMENT must be null Description of Element (ELEMENT) should be NULL, when subject's experience for a particular period of time is represented as an unplanned Element, where Element Code (ETCD) is equal to 'UNPLAN' 3.1.2 3.1.3 3.2 SE CG0152 Invalid value for ELEMENT={data($element)}, null was expected for ETCD='UNPLAN' ]]> ARMCD may be no more than 20 characters The value of Planned Arm Code (ARMCD) should be no more than 20 characters in length 3.1.2 3.1.3 3.2 DM TA TV CG0153 20 return Invalid value for ARMCD={data($armcdvalue)} in dataset {data($datasetname)} - it has more than 20 characters ]]> ELEMENT must be unique for a given ETCD Description of Element (ELEMENT) must have a unique value for a given value of Element Code (ETCD) within the domain 3.1.2 3.1.3 3.2 SE TA CG0154 $recnum][odm:ItemData[@ItemOID=$etcdoid] and odm:ItemData[@ItemOID=$elementoid] and odm:ItemData[@ItemOID=$etcdoid]/@Value=$etcdvalue] let $recnum2 := $record2/@data:ItemGroupDataSeq (: and again, get the values of ETCD and ELEMENT :) let $etcdvalue2 := $record2/odm:ItemData[@ItemOID=$etcdoid]/@Value (: should be identical to $etcdvalue :) let $elementvalue2 := $record2/odm:ItemData[@ItemOID=$elementoid]/@Value (: ELEMENT must be equal to ELEMENT of the the earlier record :) where not($elementvalue=$elementvalue2) return Non-unique combination for ELEMENT and ETCD. Record {data($recnum)} has ETCD='{data($etcdvalue)}' and and ELEMENT='{data($elementvalue)}' whereas record {data($recnum2)} has ETCD='{data($etcdvalue2)}' and has ELEMENT='{data($elementvalue2)}' in dataset {data($name)} ]]> RDOMAIN must be populated when IDVAR is populated Value of Related Domain Abbreviation (RDOMAIN) variable must be populated, when value of Identifying Variable (IDVAR) variable is populated 3.1.2 3.1.3 3.2 CO CG0166 IDVARVAL={data($idvarval)} but RDOMAIN=null ]]> CODTC must be NULL when RDOMAIN, IDVAR and IDVARVAL are populated The value of Date/Time of Comment (CODTC) should be NULL, when comments are related to a specific parent record or group of parent records in a domain (RDOMAIN, IDVAR and IDVARVAL are populated) 3.1.2 3.1.3 3.2 CO CG0168 IDVAR={data($idvar)} but a value for CODTC={data($codtc)} was found ]]> SSDTC must be greater than or equal to DTHDTC when SSSTRESC is 'DEAD' Subject Status Date/Time of Assessment (SSDTC) must be greater than or equal to Date/Time of Death (DTHDTC) when the subject's status is 'DEAD' SS 3.2 CG0171 = DM.DTHDTC :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: Get the DM dataset :) let $dmitemgroupdef := $definedoc//odm:ItemGroupDef[@Name='DM'] (: and the location of the DM dataset :) let $dmdatasetlocation := ( if($defineversion = '2.1') then $dmitemgroupdef/def21:leaf/@xlink:href else $dmitemgroupdef/def:leaf/@xlink:href ) let $dmdatasetdoc := doc(concat($base,$dmdatasetlocation)) (: Get the SS (Subject Status) dataset and its location :) let $ssitemgroupdef := $definedoc//odm:ItemGroupDef[@Name='SS'] let $ssdatasetlocation := ( if($defineversion = '2.1') then $ssitemgroupdef/def21:leaf/@xlink:href else $ssitemgroupdef/def:leaf/@xlink:href ) let $ssdatasetdoc := ( if($ssdatasetlocation) then doc(concat($base,$ssdatasetlocation)) else () ) (: we need the OID of DTHDTC and of USUBJID in DM :) let $dmdthdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='DTHDTC']/@OID where $a = $dmitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $dmusubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $dmitemgroupdef/odm:ItemRef/@ItemOID return $a ) (: we need the OID of SSSTRESC, SSDTC and of USUBJID in SS :) let $ssusubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $ssstresc := ( for $a in $definedoc//odm:ItemDef[@Name='SSSTRESC']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $ssdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='SSDTC']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) (: iterate over all records in SS for which SSSTRESC='DEAD' :) for $record in $ssdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$ssstresc and @Value='DEAD']] let $recnumss := $record/@data:ItemGroupDataSeq (: get the value of USUBJID for this record :) let $ssusubjid := $record/odm:ItemData[@ItemOID=$ssusubjidoid]/@Value (: get the value of SSDTC for this record :) let $ssdtc := $record/odm:ItemData[@ItemOID=$ssdtcoid]/@Value (: get the DM record for this subject :) let $dmrecord := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$ssusubjid]] let $dmrecnum := $dmrecord/@data:ItemGroupDataSeq (: get the value of DTHDTC :) let $dthdtc := $dmrecord/odm:ItemData[@ItemOID=$dmdthdtcoid]/@Value (: SSDTC >= DM.DTHDTC :) where $ssdtc castable as xs:date and $dthdtc castable as xs:date and not(xs:date($ssdtc) >= xs:date($dthdtc)) return SSDTC={data($ssdtc)} is not before or equal to DM.DTHDTC={data($dthdtc)} for SSSTRESC='DEAD' ]]> SSDTC must be greater than or equal to DSSTDTC when SSSTRESC = 'DEAD' Subject Status Date/Time of Assessment (SSDTC) must be greater than or equal to Start Date/Time of Disposition Event (DSSTDTC) when the subject's status is 'DEAD' 3.2 SS CG0172 = DS.DSSTDTC :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; declare namespace functx = "http://www.functx.com"; (: sorting function - also sorts dates :) declare function functx:sort ( $seq as item()* ) as item()* { for $item in $seq order by $item return $item } ; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: Get the DS dataset :) let $dsitemgroupdef := $definedoc//odm:ItemGroupDef[@Name='DS'] (: and the location of the DS dataset :) let $dsdatasetlocation := ( if($defineversion = '2.1') then $dsitemgroupdef/def21:leaf/@xlink:href else $dsitemgroupdef/def:leaf/@xlink:href ) let $dsdatasetdoc := doc(concat($base,$dsdatasetlocation)) (: Get the SS (Subject Status) dataset and its location :) let $ssitemgroupdef := $definedoc//odm:ItemGroupDef[@Name='SS'] let $ssdatasetlocation := ( if($defineversion = '2.1') then $ssitemgroupdef/def21:leaf/@xlink:href else $ssitemgroupdef/def:leaf/@xlink:href ) let $ssdatasetdoc := ( if($ssdatasetlocation) then doc(concat($base,$ssdatasetlocation)) else () ) (: we need the OID of DSSTDTC and of USUBJID in DS :) let $dsstdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='DSSTDTC']/@OID where $a = $dsitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $dsusubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $dsitemgroupdef/odm:ItemRef/@ItemOID return $a ) (: we need the OID of SSSTRESC, SSDTC and of USUBJID in SS :) let $ssusubjidoid := ( for $a in $definedoc//odm:ItemDef[@Name='USUBJID']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $ssstresc := ( for $a in $definedoc//odm:ItemDef[@Name='SSSTRESC']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) let $ssdtcoid := ( for $a in $definedoc//odm:ItemDef[@Name='SSDTC']/@OID where $a = $ssitemgroupdef/odm:ItemRef/@ItemOID return $a ) (: iterate over all records in SS for which SSSTRESC='DEAD' :) for $record in $ssdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$ssstresc and @Value='DEAD']] let $recnumss := $record/@data:ItemGroupDataSeq (: get the value of USUBJID for this record :) let $ssusubjid := $record/odm:ItemData[@ItemOID=$ssusubjidoid]/@Value (: get the value of SSDTC for this record :) let $ssdtc := $record/odm:ItemData[@ItemOID=$ssdtcoid]/@Value (: get all the DSSTDTC values for this subject :) let $dsstdtcvalues := $dsdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dsusubjidoid and @Value=$ssusubjid]]/odm:ItemData[@ItemOID=$dsstdtcoid]/@Value (: sort the DSSTDTC values and take the latest one :) let $latestdsstdtc := functx:sort($dsstdtcvalues)[last()] (: SSDTC >= DS.DSSTDTC :) where $ssdtc castable as xs:date and $latestdsstdtc castable as xs:date and not(xs:date($ssdtc) >= xs:date($latestdsstdtc)) return SSDTC={data($ssdtc)} is not before or equal to latest DSSTDTC={data($ssdtc)} for SSSTRESC='DEAD' ]]> When IECAT = 'EXCLUSION' then IEORRES must be 'Y' I/E Criterion Original Result (IEORRES) must equal 'Y', when Inclusion/Exclusion Category (IECAT) is 'EXCLUSION' 3.1.2 3.1.3 3.2 IE CG0175 For IECAT='EXCLUSION', IEORRES must be 'Y' but {data($ieorresvalue)} was found ]]> When IECAT = 'INCLUSION' then IEORRES must be 'N' I/E Criterion Original Result (IEORRES) must equal 'N', when Inclusion/Exclusion Category (IECAT) is 'INCLUSION' 3.1.2 3.1.3 3.2 IE CG0176 For IECAT='INCLUSION', IEORRES must be 'N' but {data($ieorresvalue)} was found ]]> IESTRESC and IEORRES must have the same value I/E Criterion Original Result (IEORRES) and I/E Criterion Result in Std Format (IESTRESC) should have the same value 3.1.2 3.1.3 3.2 IE CG0177 Mismatch between IEORRES and IESTRESC values for USUBJID={data($usubjid)}. IEORRES={data($ieorres)}, whereas IESTRESC={data($iestresc)} ]]> Combination of IETESTCD, IETEST, and IECAT values must match entries in TI The combination of IETESTCD, IETEST, and IECAT values must match entries in the Trial Inclusion/Exclusion Criteria (TI) dataset 3.1.2 3.1.3 3.2 IE CG0178 ) (: get the OID of IETESTCD, IETEST and IECAT in the IE dataset :) let $ietestcdoid := ( for $a in $definedoc//odm:ItemDef[@Name='IETESTCD']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='IE']/odm:ItemRef/@ItemOID return $a ) let $ietestoid := ( for $a in $definedoc//odm:ItemDef[@Name='IETEST']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='IE']/odm:ItemRef/@ItemOID return $a ) let $iecatoid := ( for $a in $definedoc//odm:ItemDef[@Name='IECAT']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='IE']/odm:ItemRef/@ItemOID return $a ) (: iterate over all the records in the IE dataset :) for $record in $iedatasetdoc//odm:ItemGroupData let $recnum := $record/@data:ItemGroupDataSeq (: get the value of ITESTCD, IETEST and IECAT in IE :) let $ietestcd := $record/odm:ItemData[@ItemOID=$ietestcdoid]/@Value let $ietest := $record/odm:ItemData[@ItemOID=$ietestoid]/@Value let $iecat := $record/odm:ItemData[@ItemOID=$iecatoid]/@Value (: match with the values in the temporary structure :) let $count := count ($titriples/record[@titestcd=$ietestcd and @titest=$ietest and @ticat=$iecat]) (: there must be a match :) where $count = 0 return The combination IETESTCD='{data($ietestcd)}', IETEST='{data($ietest)}' and IECAT='{data($iecat)}' cannot be found in the TI dataset ]]> A value for IETESTCD must be present in TI A value for Inclusion/Exclusion Criterion Short Name (IETESTCD) must be present the Trial Inclusion/Exclusion Criteria (TI) domain 3.1.2 3.1.3 3.2 IE CG0179 Value of IE.IETESTCD={data($ieietestcd)} cannot be found in the TI dataset ]]> LBTOXGR must be a numeric value when a numeric scale is used When a numeric scale is used (Grade 1, Grade 2, etc.), LBTOXGR should only contain the number 3.1.2 3.1.3 3.2 LB CG0185 0 return Value of LBTOXGR={data($lbtoxgr)} represents a numeric scale but is not a complete number ]]> MB dataset must be included, when an MS dataset is present Microbiology Specimen (MB) dataset should be included, when a Microbiology Susceptibility Test (MS) dataset is present 3.1.2 3.1.3 3.2 MB MS Document {data($mbdatasetname)} for domain MB could not be found in collection {data($base)} although document {data($msdatasetname)} is present ]]> When MBTESTCD = 'ORGANISM' then MBRESCAT may not be null MBRESCAT is expected to be populated in all records where a microorganism has been identified (MBTESTCD = 'ORGANISM'), excluding records where MBSTRESC equals 'NO GROWTH' or MBMETHOD equals 'GRAM STAIN'. 3.1.2 3.1.3 3.2 MB CG0193 MBTESTCD='ORGANISM' but MBRESCAT=null ]]> When IDVARVAL = null and USUBJID = null then the value of IDVAR may not be '--SEQ' When the RELREC dataset is used to identify relationships between datasets (in which case USUBJID and IDVARVAL are left null), instead of relating individual records, --SEQ cannot be used for IDVAR because --SEQ only has meaning within a subject within a dataset, not across datasets 3.1.2 3.1.3 3.2 RELREC CG0201 IDVAR={data($idvar)} is not allowed as USUBJID=null and IDVARVAL=null ]]> IDVARVAL value may not be populated, when RELTYPE values is populated Variable Value (IDVARVAL) variable value should not be populated, when Relationship Type (RELTYPE) variable value is populated 3.1.2 3.1.3 3.2 RELREC IDVARVAL value is populated (value={data($idvarvalvalue)}, when RELTYPE values is populated (value={data($reltypevalue)}) ]]> USUBJID value may not be populated, when RELTYPE values is populated Unique Subject Identifier (USUBJID) variable value should not be populated, when Relationship Type (RELTYPE) variable value is populated in RELREC 3.1.2 3.1.3 3.2 RELREC USUBJID value is populated (value={data($usubjidvalue)}), when RELTYPE values is populated (value={data($reltypevalue)}) in dataset {data($relrecdatasetname)} ]]> When QORIG = 'ASSIGNED' then QEVAL may not be null For subjective data (when QORIG='ASSIGNED'), QEVAL should be populated and the value should reflect the role of the person or institution assigning the value 3.1.2 3.1.3 3.2 SUPPQUAL CG0202 QEVAL may not be null when QORIG='ASSIGNED' ]]> IDVAR and IDVARVAL may not populated for DM supplemental qualifiers Both Identifying Variable (IDVAR) and Identifying Variable Value (IDVARVAL) should not be populated, when relating information to the Demographics (DM) domain 3.1.2 3.1.3 3.2 SUPPQUAL Unexpected value for IDVAR/IDVARVAL: IDVAR and/or IDVARVAL are populated although RDOMAIN=DM in dataset {data($datasetname)} ]]> IDVAR value must be provided, when RDOMAIN value is provided Value of Identifying Variable (IDVAR) variable must be populated, when Related Domain Abbreviation (RDOMAIN) variable value is provided, with the only exception of 'DM' value for RDOMAIN 3.1.2 3.1.3 3.2 RELREC SUPPQUAL Missing IDVAR value, when RDOMAIN value is provided, RDOMAIN={data($rdomainvalue)} ]]> TAETORD may not be populated, when ETCD = 'UNPLAN' Planned Order of Elements within Arm (TAETORD) should be NULL, when subject's experience for a particular period of time is represented as an unplanned Element (ETCD = 'UNPLAN') 3.1.2 3.1.3 3.2 SE 0 return TAETORD is populated, value={data($taetordvalue)} with ETCD='UNPLAN' in dataset SE ]]> When SEUPDES = null then ETCD may not be 'UNPLAN' 3.1.2 3.1.3 3.2 SE CG0210 ETCD='UNPLAN' for SEUPDES=null ]]> When ETCD='UNPLAN', SEUPDES may not be null 3.1.2 3.1.3 3.2 SE CG0211 Missing value for SEUPDES, when ETCD='UNPLAN' ]]> VISITNUM value must match TV domain data Visit Number (VISITNUM) values should match entries in the Trial Visits (TV) dataset, when they are planned visits (SVUPDES = NULL) 3.1.2 3.1.3 3.2 SV VISITNUM value={data($svvisitnumvalue)} in SV does not match TV domain data ]]> VISITDY may not be populated for an unplanned visit Planned Study Day of Visit (VISITDY) should equal NULL for unplanned visits, where Description of Unplanned Visit (SVUPDES) is populated 3.1.2 3.1.3 3.2 SV VISITDY is populated for unplanned visit, value for VISITDY={data($visitdyvalue)} in dataset SE ]]> At least one timing variable must be present in the dataset All domains based on the general observation classes (Interventions, Events, Findings) should have at least one Timing variable present, except for: IE, SC 3.1.2 3.1.3 3.2 INTERVENTIONS FINDINGS EVENTS CG0219 {data($timingvarsdomain)} :) (: create a list of the variables for this dataset :) let $datasetvars := ( for $a in $itemgroupdef/odm:ItemRef/@ItemOID return $definedoc//odm:ItemDef[@OID=$a]/@Name ) (: return {data($datasetvars)} :) (: count the number of variables in the intersection of allowed timing variables and the variables in this dataset :) let $intersection := distinct-values($timingvarsdomain[.=$datasetvars]) (: return {data($intersection)} :) let $count := count($intersection) (: if the count of items in the intersection = 0, there is no timing variable in the dataset :) where $count=0 return No timing variables have been defined in dataset {data($name)} ]]> --STDY variable value must be populated when --STDTC and DM.RFSTDTC are provided Study Day of Start (--STDY) variable value should be populated, when Start Study Date (--STDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: keeping the worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: STDY MUST be populated when the variable is in the dataset and when both RFSTDTC AND STDTC are complete dates :) where $stdyoid and $iscompletestdtcdate and $iscompleterfstdtcdate and not($stdyvalue) return {data($stdyname)} variable is not populated although both {data($stdtcname)} (value={data($stdtcvalue)}) and RFSTDTC (value={data($rfstdtcvalue)}) are complete dates ]]> --STDY variable value must be populated when --STDTC and DM.RFSTDTC are provided Study Day of Start (--STDY) variable value should be populated, when Start Study Date (--STDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: keeping the worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first :) let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: STDY MUST be populated when the variable is in the dataset and when both RFSTDTC AND STDTC are complete dates :) where $stdyoid and $iscompletestdtcdate and $iscompleterfstdtcdate and not($stdyvalue) return {data($stdyname)} variable is not populated although both {data($stdtcname)} (value={data($stdtcvalue)}) and RFSTDTC (value={data($rfstdtcvalue)}) are complete dates ]]> --STDY must be correctly calculated Study Day of Start (--STDY) variable value should be populated as defined by CDISC standards: --STDY = (date portion of --STDTC) - (date portion of RFSTDTC) +1 if --STDTC is on or after RFSTDTC; --STDY = (date portion of --STDTC) - (date portion of RFSTDTC) if --STDTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: taking the worst case scenario into account that there is more than one record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := doc($dmdatasetlocation)//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: now calculate the DY value but only when RFSTDTC and STDTC have a complete date part :) let $stdycalculated := ( if ($iscompleterfstdtcvalue and $iscompletestdtcvalue) then (: if there is one, we must strip off the time part :) let $stdtcvalueshort := substring($stdtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $stdycalc := ( if($stdtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($stdtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $stdycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $stdycalculatedfda := ( if($stdycalculated >= 0) then $stdycalculated + 1 else ( $stdycalculated ) ) (: before comparing, also check whether the value is really an integer :) where $stdyvalue castable as xs:integer and $stdycalculatedfda and $stdyvalue and not($stdycalculatedfda = $stdyvalue) return Invalid value for {data($stdyname)}, calculated value={data($stdycalculatedfda)}, observed value={data($stdyvalue)}, in dataset {data($name)} ]]> --STDY must be correctly calculated Study Day of Start (--STDY) variable value should be populated as defined by CDISC standards: --STDY = (date portion of --STDTC) - (date portion of RFSTDTC) +1 if --STDTC is on or after RFSTDTC; --STDY = (date portion of --STDTC) - (date portion of RFSTDTC) if --STDTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: taking the worst case scenario into account that there is more than one record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: now calculate the DY value but only when RFSTDTC and STDTC have a complete date part :) let $stdycalculated := ( if ($iscompleterfstdtcvalue and $iscompletestdtcvalue) then (: if there is one, we must strip off the time part :) let $stdtcvalueshort := substring($stdtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $stdycalc := ( if($stdtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($stdtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $stdycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $stdycalculatedfda := ( if($stdycalculated >= 0) then $stdycalculated + 1 else ( $stdycalculated ) ) (: before comparing, also check whether the value is really an integer :) where $stdyvalue castable as xs:integer and $stdycalculatedfda and $stdyvalue and not($stdycalculatedfda = $stdyvalue) return Invalid value for {data($stdyname)}, calculated value={data($stdycalculatedfda)}, observed value={data($stdyvalue)}, in dataset {data($name)} ]]> STDY variable value may not be imputed Study Day of Start (--STDY) variable value may not be imputed. It may be only populated, when both Start Study Date/Time (--STDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part. 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking the worst case scenario into account that there is more than one record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: STDY may NOT be populated when of RFSTDTC or STDTC is an incomplete date :) where $stdyoid and (not($iscompletestdtcdate) or not($iscompleterfstdtcdate)) and $stdyvalue return {data($stdyname)} variable value {data($stdyvalue)} is imputed although one of {data($stdtcname)} (value={data($stdtcvalue)}) or RFSTDTC (value={data($rfstdtcvalue)}) is not a complete date ]]> STDY variable value may not be imputed Study Day of Start (--STDY) variable value may not be imputed. It may be only populated, when both Start Study Date/Time (--STDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part. 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking the worst case scenario into account that there is more than one record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $stdyvalue := $record/odm:ItemData[@ItemOID=$stdyoid]/@Value (: STDY may NOT be populated when of RFSTDTC or STDTC is an incomplete date :) where $stdyoid and (not($iscompletestdtcdate) or not($iscompleterfstdtcdate)) and $stdyvalue return {data($stdyname)} variable value {data($stdyvalue)} is imputed although one of {data($stdtcname)} (value={data($stdtcvalue)}) or RFSTDTC (value={data($rfstdtcvalue)}) is not a complete date ]]> --ENDY variable value must be populated when --ENDTC and DM.RFSTDTC are provided Study Day of End (--ENDY) variable value should be populated, when End Study Date/Time (--ENDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking the worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: ENDY MUST be populated when the variable is in the dataset and when both ENSTDTC AND ENDTC are complete dates :) where $endyoid and $iscompleteendtcdate and $iscompleterfstdtcdate and not($endyvalue) return {data($endyname)} variable is not populated although both {data($endtcname)} (value={data($endtcvalue)}) and RFSTDTC (value={data($rfstdtcvalue)}) are complete dates ]]> --ENDY variable value must be populated when --ENDTC and DM.RFSTDTC are provided Study Day of End (--ENDY) variable value should be populated, when End Study Date/Time (--ENDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking the worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: ENDY MUST be populated when the variable is in the dataset and when both ENSTDTC AND ENDTC are complete dates :) where $endyoid and $iscompleteendtcdate and $iscompleterfstdtcdate and not($endyvalue) return {data($endyname)} variable is not populated although both {data($endtcname)} (value={data($endtcvalue)}) and RFSTDTC (value={data($rfstdtcvalue)}) are complete dates ]]> --ENDY must be correctly calculated Study Day of End (--ENDY) variable value should be populated as defined by CDISC standards: --ENDY = (date portion of --STDTC) - (date portion of RFSTDTC) +1 if --ENDTC is on or after RFSTDTC; --ENTDY = (date portion of --ENDTC) - (date portion of RFSTDTC) if --ENDTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: taking worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: now calculate the DY value but only when RFSTDTC and ENDTC have a complete date part :) let $endycalculated := ( if ($iscompleterfstdtcvalue and $iscompletestdtcvalue) then (: if there is one, we must strip off the time part :) let $endtcvalueshort := substring($endtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $endycalc := ( if($endtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($endtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $endycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $endycalculatedfda := ( if($endycalculated >= 0) then $endycalculated + 1 else ( $endycalculated ) ) (: before comparing, check that the ENDY value is really an integer :) where $endyvalue castable as xs:integer and $endycalculatedfda and $endyvalue and not($endycalculatedfda = $endyvalue) return Invalid value for {data($endyname)}, calculated value={data($endycalculatedfda)}, observed value={data($endyvalue)}, in dataset {data($datasetname)} ]]> --ENDY must be correctly calculated Study Day of End (--ENDY) variable value should be populated as defined by CDISC standards: --ENDY = (date portion of --STDTC) - (date portion of RFSTDTC) +1 if --ENDTC is on or after RFSTDTC; --ENTDY = (date portion of --ENDTC) - (date portion of RFSTDTC) if --ENDTC precedes RFSTDTC 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: look up the record in the DM dataset and get the RFSTDTC :) (: taking worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether also RFSTDTC is complete :) let $iscompleterfstdtcvalue := string-length($rfstdtcvalue) >= 10 (: boolean :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: now calculate the DY value but only when RFSTDTC and ENDTC have a complete date part :) let $endycalculated := ( if ($iscompleterfstdtcvalue and $iscompletestdtcvalue) then (: if there is one, we must strip off the time part :) let $endtcvalueshort := substring($endtcvalue,1,10) let $rfstdtcvalueshort := substring($rfstdtcvalue,1,10) let $endycalc := ( if($endtcvalueshort castable as xs:date and $rfstdtcvalueshort castable as xs:date) then days-from-duration(xs:date($endtcvalueshort)-xs:date($rfstdtcvalueshort)) else() ) return $endycalc else () (: one or both dates are not complete dates :) ) (: for the FDA there is no day 0, DY can only be <0 or >0, first day is day 1 :) let $endycalculatedfda := ( if($endycalculated >= 0) then $endycalculated + 1 else ( $endycalculated ) ) (: before comparing, check that the ENDY value is really an integer :) where $endyvalue castable as xs:integer and $endycalculatedfda and $endyvalue and not($endycalculatedfda = $endyvalue) return Invalid value for {data($endyname)}, calculated value={data($endycalculatedfda)}, observed value={data($endyvalue)}, in dataset {data($datasetname)} ]]> --ENDY variable value may not be imputed Study Day of End (--ENDY) variable value should be not be imputed. It may be only populated, when both End Study Date/Time (--ENDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: ENDY may NOT be populated when of RFSTDTC or ENDTC is an incomplete date :) where $endyoid and (not($iscompletestdtcdate) or not($iscompleterfstdtcdate)) and $endyvalue return {data($endyname)} variable value {data($endyvalue)} is imputed although one of {data($endtcname)} (value={data($endtcvalue)}) or RFSTDTC (value={data($rfstdtcvalue)}) is not a complete date ]]> --ENDY variable value may not be imputed--ENDY variable value may not be imputed Study Day of End (--ENDY) variable value should be not be imputed. It may be only populated, when both End Study Date/Time (--ENDTC) and Subject Reference Start Date/Time (RFSTDTC) variables values are provided, and both of them include complete date part 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV = 10 (: boolean :) (: get the USUBJID and get the corresponding RFSTDTC in the DM dataset :) let $usubjidvalue := $record/odm:ItemData[@ItemOID=$usubjidoid]/@Value (: taking worst case scenario into account that there is more than 1 record for a USUBJID in DM - take the first one :) let $rfstdtcvalue := $dmdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$dmusubjidoid and @Value=$usubjidvalue]][1]/odm:ItemData[@ItemOID=$rfstdtcoid]/@Value (: and check whether RFSTDTC is a complete date :) let $iscompleterfstdtcdate := string-length($rfstdtcvalue) >= 10 (: Get the value of the STDY variable (if any) :) let $endyvalue := $record/odm:ItemData[@ItemOID=$endyoid]/@Value (: ENDY may NOT be populated when of RFSTDTC or ENDTC is an incomplete date :) where $endyoid and (not($iscompletestdtcdate) or not($iscompleterfstdtcdate)) and $endyvalue return {data($endyname)} variable value {data($endyvalue)} is imputed although one of {data($endtcname)} (value={data($endtcvalue)}) or RFSTDTC (value={data($rfstdtcvalue)}) is not a complete date ]]> Value for --STRF may not be populated, when RFSTDTC is NULL Start Relative to Reference Period (--STRF) should not be populated for subjects with missing value for Reference Start Date/Time (RFSTDTC) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV Value for {data($strfname)} is populated(value={data($strfvalue)}), when RFSTDTC is NULL in dataset {data($datasetname)} ]]> Value for --STRF may not be populated, when RFSTDTC is NULL Start Relative to Reference Period (--STRF) should not be populated for subjects with missing value for Reference Start Date/Time (RFSTDTC) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV Value for {data($strfname)} is populated(value={data($strfvalue)}), when RFSTDTC is NULL in dataset {data($datasetname)} ]]> Value for --ENRF may not be populated, when RFSTDTC is NULL End Relative to Reference Period (--ENRF) should not be populated for subjects with missing value for Reference End Date/Time (RFENDTC) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV Value for {data($enrfname)} is populated(value={data($enrfvalue)}), when RFENDTC is NULL in dataset {data($name)} ]]> Value for --ENRF may not be populated, when RFENDTC is NULL End Relative to Reference Period (--ENRF) should not be populated for subjects with missing value for Reference End Date/Time (RFENDTC) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS SE SV Value for {data($enrfname)} is populated(value={data($enrfvalue)}), when RFENDTC is NULL in dataset {data($name)} ]]> Value of *DTC variable must be a valid ISO 8601 date/datime value Value of Dates/Time variables (*DTC) must conform to the ISO 8601 date/datetime international standard 3.1.2 3.1.3 3.2 ALL invalid ISO-8601 value for variable {data($itemname)} value = {data($value)} in dataset {data($itemgroupdefname)} ]]> Value of *DTC variable must be a valid ISO 8601 date/datime value Value of Dates/Time variables (*DTC) must conform to the ISO 8601 date/datetime international standard 3.1.2 3.1.3 3.2 ALL Invalid ISO-8601 value for variable {data($itemname)} value = {data($value)} in dataset {data($itemgroupdefname)} ]]> Value for --TPT must be consistent within --TPTNUM All values of Planned Time Point Name (--TPT) variable should be the same for a given value of Planned Time Point Number (--TPTNUM) variable 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Inconsistent value for {data($tptname)} within {data($tptnumname)} in dataset {data($datasetname)}. {data($uniquetptvaluescount)} different {data($tptname)} values were found for {data($tptnumname)}={data($tptnumuniquevalue)} ]]> Value for --TPT must be consistent within --TPTNUM All values of Planned Time Point Name (--TPT) variable should be the same for a given value of Planned Time Point Number (--TPTNUM) variable 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Inconsistent value for {data($tptname)} within {data($tptnumname)} in dataset {data($datasetname)}. {data($uniquetptvaluescount)} different {data($tptname)} values were found for {data($tptnumname)}={data($tptnumuniquevalue)} ]]> Value for --TPTNUM must be consistent within --TPT All values of Planned Time Point Number (--TPTNUM) variable should be the same for a given value of Planned Time Point Name (--TPT) variable 3.1.2 3.1.3 3.2 INTERVENTIONS FINDING EVENTS 1 (: take missing values into account :) return Inconsistent value for {data($tptnumname)} within {data($tptname)} in dataset {data($datasetname)}. {data($uniquetptnumvaluescount)} different {data($tptnumname)} values were found for {data($tptname)}={data($tptuniquevalue)} ]]> Value for --TPTNUM must be consistent within --TPT All values of Planned Time Point Number (--TPTNUM) variable should be the same for a given value of Planned Time Point Name (--TPT) variable 3.1.2 3.1.3 3.2 INTERVENTIONS FINDING EVENTS 1 (: take missing values into account :) return Inconsistent value for {data($tptnumname)} within {data($tptname)} in dataset {data($datasetname)}. {data($uniquetptnumvaluescount)} different {data($tptnumname)} values were found for {data($tptname)}={data($tptuniquevalue)} ]]> Value for --TPT must be consistent within --ELTM All values of Planned Elapsed Time (--ELTM) variable should be the same for a given value of Planned Time Point Name (--TPT) variable 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Inconsistent value for {data($eltmname)} within {data($tptname)} in dataset {data($datasetname)}. {data($uniqueeltmvaluescount)} different {data($eltmname)} values were found for {data($tptname)}={data($tptuniquevalue)} ]]> Value for --TPT must be consistent within --ELTM All values of Planned Elapsed Time (--ELTM) variable should be the same for a given value of Planned Time Point Name (--TPT) variable 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Inconsistent value for {data($eltmname)} within {data($tptname)} in dataset {data($datasetname)}. {data($uniqueeltmvaluescount)} different {data($eltmname)} values were found for {data($tptname)}={data($tptuniquevalue)} ]]> The value of Element Code (ETCD) may not be more than 8 characters in length The value of Element Code (ETCD) may not be more than 8 characters in length 3.1.2 3.1.3 3.2 SE 8 return Invalid value for ETCD in SE dataset {data($sedatasetname)} - Value {data($etcdvalue)} has more than 8 characters ]]> TAETORD must be unique within ARMCD Order of Element within Arm (TAETORD) must have a unique value for a given value of Planned Arm Code (ARMCD) within the domain 3.1.2 3.1.3 3.2 TA $recnum] let $recnumnext := $nextrecord/@data:ItemGroupDataSeq (: and look for duplicate values :) let $taarmcdvaluenext := $nextrecord/odm:ItemData[@ItemOID=$taarmcdoid]/@Value let $tataetordvaluenext := $nextrecord/odm:ItemData[@ItemOID=$tataetordoid]/@Value where $taarmcdvalue = $taarmcdvaluenext and $tataetordvalue = $tataetordvaluenext return Non-unique value for TAETORD within ARMCD. Records {data($recnum)} and {data($recnumnext)} have the same value for ARMCD={data($taarmcdvalue)} and TAETORD={data($tataetordvalue)} in TA dataset {data($tadatasetname)} ]]> TAETORD must be an integer Planned Order of Element within Arm (TAETORD) variable value must be an integer 3.1.2 3.1.3 3.2 TA CG0248 TAETORD={data($taetord)} must be an integer ]]> When TIVERS present in dataset then IETESTCD must be unique within TIVERS A value of Incl/Excl Criterion Short Name (IETESTCD) must be unique within a version of inclusion/exclusion criteria (TIVERS) 3.1.2 3.1.3 3.2 TI CG0255 Records {data($recnum)} and {data($recnumnext)} have the same value for IETESTCD='{data($ietestcd)}' and TIVERS={data($tivers)} ]]> Value for --PARMCD variable may not be longer than 8 characters The value of Parameter Short Name (--PARMCD) variables should be no more than 8 characters in length 3.1.2 3.1.3 3.2 TS 8 return The value for TSPARMCD in dataset {data($datasetname)} has more than 8 characters: '{data($testvalue)}' was found ]]> The value in TSPARM may not be longer than 40 characters The value of Parameter (--PARM) variable should be no more than 40 characters in length 3.1.2 3.1.3 3.2 TS 40 characters. The rule is a relict of the ancient XPT format. :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; declare namespace xs="http://www.w3.org/2001/XMLSchema"; declare namespace functx = "http://www.functx.com"; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: iterate over all TS datasets (there should be only one) :) for $itemgroup in $definedoc//odm:ItemGroupDef[@Name='TS'] (: Get the OID for the TSPARM variable :) let $testoid := ( for $a in $definedoc//odm:ItemDef[@Name='TSPARM']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='TS']/odm:ItemRef/@ItemOID return $a ) (: we of course only look into datasets where there really is a --TEST :) let $datasetname := ( if($defineversion = '2.1') then $itemgroup/def21:leaf/@xlink:href else $itemgroup/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetname) then doc(concat($base,$datasetname)) else() ) (: iterate over all the records within the TS dataset :) for $record in $datasetdoc//odm:ItemGroupData (: get the record number :) let $recnum := $record/@data:ItemGroupDataSeq (: and get the value of the TSPARM variable :) let $testvalue := $record/odm:ItemData[@ItemOID=$testoid]/@Value (: when it has more than 40 characters, give an error :) where string-length($testvalue) > 40 return The value for TSPARM in dataset {data($datasetname)} has more than 40 characters: '{data($testvalue)}' was found ]]> TSVALNF must be populated when TSVAL is missing Value for Parameter Null Flavor (TSVALNF) variable must be populated, when Parameter Value (TSVAL) variable value is missing 3.1.3 3.2 TS Missing TSVALNF value ]]> TSVAL may only be null when TSVALNF is populated Value for Parameter Value (TSVAL) variable must be populated. TSVAL can only be null when Parameter Null Flavor (TSVALNF) variable value is populated 3.1.3 3.2 TS Missing TSVAL value ]]> Value for TSVALCD must be consistent within TSVAL - When TSVAL != null and TSVALCD != null then TSVALCD and TSVAL have a one-to-one relationship. When TSVAL != null and TSVALCD != null then TSVALCD and TSVAL have a one-to-one relationship 3.1.3 3.2 TS CG0265 Inconsistent value for TSVAL within TSVALCD in dataset {data($datasetname)}. {data($uniquetsvalvaluescount)} different TSVAL values were found for TSVALCD={data($tsvalcduniquevalue)} ]]> CURTRT: TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS) CURTRT: TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS TSVAL/TSVALCD value mismatch for CURTRT, TSVALCD={data($tsvalcdvalue)}, TSVAL={data($tsvalvalue)} - NLM webservice provides active moeity={data($activemoiety)} ]]> COMPTRT: TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS) COMPTRT: TSVAL and TSVALCD values must be populated from the same name record in FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS TSVAL/TSVALCD value mismatch for COMPTRT, TSVALCD={data($tsvalcdvalue)}, TSVAL={data($tsvalvalue)} - NLM webservice provides active moeity={data($activemoiety)} ]]> PCLAS: TSVAL and TSVALCD values must be populated from the same record in NDF-RT PCLAS: TSVAL and TSVALCD values must be populated from the same record in NDF-RT 3.1.2 3.1.3 3.2 TS Invalid TSVAL value='{data($tsvalvalue)}' for PCLAS with TSVALCD={data($tsvalcdvalue)} - value from NLM web service found='{data($conceptName)}' ]]> When TSVCDVER is populated then TSVCDREF must be populated The Name of the Reference Terminology (TSVCDREF) must be populated when the Version of the Reference Terminology (TSVCDVER) is populated 3.1.2 3.1.3 3.2 TS CG0266 TSVCDVER='{data($tsvcdver)}' but TSVCDREF=null ]]> TSSEQ variable value must be unique within TSPARMCD The value of Sequence Number (--SEQ) variable must be unique for each record within a domain and within each Unique Subject Identifier (USUBJID) or Pool Identifier (POOLID) variables value when they are present in the domain 3.1.2 3.1.3 3.2 TS $recnum] :) let $count := count($tsdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$tsseq and @Value=$seqvalue] and odm:ItemData[@ItemOID=$tsparmcd and @Value=$parmcdvalue]]) where $count > 1 return Non-unique value for TSSEQ variable within TSPARMCD - combination of TSSEQ={data($seqvalue)} and TSPARMCD={data($parmcdvalue)} occurs {data($count)} times ]]> TSVAL for ADDON record must be 'Y' or 'N' TSVAL for ADDON record must be 'Y' or 'N' 3.1.2 3.1.3 3.2 TS CG0269 TSVAL='{data($tsval)}' for TSPARMCD='ADDON' is expected to be in ('N','Y') ]]> TSVAL value must be either ISO 8601 duration format or null, when TSPARMCD='AGEMAX' TSVAL value must be either ISO 8601 duration format for time period (e.g. P80Y) or null, when TSPARMCD='AGEMAX' 3.1.2 3.1.3 3.2 TS Invalid (non-ISO8601 duration) TSVAL value='{data($tsvalvalue)}' for AGEMAX in dataset TS ]]> TSVAL for RANDOM record must be 'Y' or 'N'. TSVAL for RANDOM record must be 'Y' or 'N'. 3.1.2 3.1.3 3.2 TS TSVAL='{data($tsval)}' for TSPARMCD='RANDOM' is expected to be in ('N','Y') ]]> When a record exists where TSPARMCD = 'HLTSUBJI' and TSVAL = 'Y' then for TSPARMCD = 'TDIGRP', TSVAL must be null When the study population is healthy subjects (TSPARMCD = 'HLTSUBJI' and TSVAL = 'Y'), the Diagnosis Group parameter should be provided with a null Parameter Value (TSVAL should be null when TSPARMCD = 'TDIGRP') 3.1.3 3.2 TS CG0272 TSVAL='{data($tdigrpvalue)}' for TSPARMCD='TDIGRP' is expected to be null as a record with TSPARMCD='HLTSUBJI and TSVAL='Y' exists ]]> TDIGRP record must be populated in TS, when HLTSUBJI = 'N' TDIGRP record must be populated in TS, when HLTSUBJI = 'N' - 'Diagnosis Group' (TDIGRP) record must be populated in Trial Summay (TS) domain, when study population is unhealthy subjects (HLTSUBJI = 'N'). It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.3 3.2 TS Missing TDIGRP Trial Summary Parameter in dataset TS ]]> When a record exists where TSPARMCD = 'ADDON' and TSVAL = 'Y' then for TSPARMCD = 'CURTRT', TSVAL must be populated When test product is added to existing treatment (TSPARMCD = 'ADDON' and TSVAL = 'Y'), the Current Therapy or Treatment parameter should be provided with Parameter Value populated (TSVAL should not be null when TSPARMCD = 'CURTRT') 3.1.3 3.2 TS CG0275 Null value for TSVAL for TSPARMCD='CURTRT' found although a record with TSPARMCD='ADDON and TSVAL='Y' exists ]]> When a record exists where TSPARMCD = 'STYPE' and TSVAL = 'INTERVENTIONAL' then for TSPARMCD = 'TRT', TSVAL must be populated When the study type is interventional (TSPARMCD = 'STYPE' and TSVAL = 'INTERVENTIONAL'), the Investigational Therapy or Treatment parameter should be provided with Parameter Value populated (TSVAL should not be null when TSPARMCD = 'TRT') TS 3.1.3 3.2 CG0276 Null value for TSVAL for TSPARMCD='TRT' found although a record with TSPARMCD='STYPE and TSVAL='INTERVENTIONAL' exists ]]> INTMODEL record must be present when STYPE='INTERVENTIONAL' 'Intervention Model' (INTMODEL) record must be populated in Trial Summay (TS) domain, when study type is 'INTERVENTIONAL'. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.3 3.2 TS Missing INTMODEL Trial Summary Parameter: No populated TSPARMCD=INTMODEL record was found although a record with TSPARMCD=STYPE and TSVAL=INTERVENTIONAL is present ]]> INTTYPE record must be present when STYPE='INTERVENTIONAL' 'Intervention Type' (INTTYPE) record must be populated in Trial Summay (TS) domain, when study type is 'INTERVENTIONAL'. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.3 3.2 TS Missing INTTYPE Trial Summary Parameter: No populated TSPARMCD=INTTYPE record was found although a record with TSPARMCD=STYPE and TSVAL=INTERVENTIONAL is present ]]> PCLAS must be populated when STYPE='INTERVENTIONAL' When the study type is interventional (TSPARMCD = 'STYPE' and TSVAL = 'INTERVENTIONAL'), the Pharmacologic Class parameter should be provided with Parameter Value populated (TSVAL should not be null when TSPARMCD = 'PCLAS') 3.1.3 3.2 TS Missing PCLAS Trial Summary Parameter, although there is a record with TSPARMCD=STYPE and TSVAL=INTERVENTIONAL ]]> TSVAL must be between 0 and 1, when TSPARMCD = 'RANDQT' For the trial summary parameter Randomization Quotient (TSPARMCD = 'RANDQT'), the value must always be a number between 0 and 1, with some cases where the ratio might be equal to 1 3.1.2 3.1.3 3.2 TS CG0280 0 and TSVAL <= 1 :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; declare namespace xs="http://www.w3.org/2001/XMLSchema"; declare namespace functx = "http://www.functx.com"; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: iterate over all TS datasets (there should be only one) :) for $itemgroup in $definedoc//odm:ItemGroupDef[@Name='TS'] (: Get the OID for the TSVAL and TSPARMCD variables :) let $tsvaloid := ( for $a in $definedoc//odm:ItemDef[@Name='TSVAL']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='TS']/odm:ItemRef/@ItemOID return $a ) let $tsparmcdoid := ( for $a in $definedoc//odm:ItemDef[@Name='TSPARMCD']/@OID where $a = $definedoc//odm:ItemGroupDef[@Name='TS']/odm:ItemRef/@ItemOID return $a ) (: get the dataset :) let $tsdatasetname := ( if($defineversion = '2.1') then $itemgroup/def21:leaf/@xlink:href else $itemgroup/def:leaf/@xlink:href ) let $tsdatasetdoc := ( if($tsdatasetname) then doc(concat($base,$tsdatasetname)) else () ) (: look for a record with TSPARMCD='RANDQT' - we assume there is only 1 :) for $randqtrecord in $tsdatasetdoc//odm:ItemGroupData[odm:ItemData[@ItemOID=$tsparmcdoid and @Value='RANDQT']] let $recnum := $randqtrecord/@data:ItemGroupDataSeq (: get the value of TSVAL in this record (if any) :) let $tsval := $randqtrecord/odm:ItemData[@ItemOID=$tsvaloid]/@Value (: TSVAL != null then TSVAL > 0 and TSVAL <= 1 :) where $tsval and not($tsval castable as xs:double and xs:double($tsval) > 0 and xs:double($tsval) <=1 ) return TSVAL={data($tsval)} whereas a number >0 and <=1 was expected ]]> TSVAL for ADAPT record must be 'Y' or 'N' TSVAL for ADAPT record must be 'Y' or 'N'. 3.1.2 3.1.3 3.2 TS CG0282 TSVAL='{data($tsval)}' for TSPARMCD='ADAPT' is expected to be in ('N','Y') ]]> TSVAL variable value must be in ISO 8601 format, when TSPARMCD='DCUTDTC' TSVAL variable value must be in ISO 8601 format, when TSPARMCD='DCUTDTC' 3.1.2 3.1.3 3.2 TS Invalid TSVAL value for DCUTDTC: value={data($tsvalvalue)} is not a valid ISO-8601 date ]]> TSVAL variable value must be numeric, when TSPARMCD='NARMS' TSVAL variable value must be numeric, when TSPARMCD='NARMS' 3.1.2 3.1.3 3.2 TS -1) return Invalid TSVAL value for NARMS. A non-negative integer is expected, value found={data($tsvalvalue)} ]]> TSVAL variable value must be in ISO 8601 date format, when TSPARMCD='SSTDTC' TSVAL variable value must be in ISO 8601 date format, when TSPARMCD='SSTDTC' 3.1.2 3.1.3 3.2 TS Invalid TSVAL value {data($ssdtcval)} for Trial Summary Parameter SSTDTC Trial Summary Parameter TS ]]> TSVAL variable value must be in ISO 8601 date format, when TSPARMCD='SETDTC' TSVAL variable value must be in ISO 8601 date format, when TSPARMCD='SETDTC' 3.1.2 3.1.3 3.2 TS Invalid TSVAL value {data($sedtcval)} for Trial Summary Parameter SETDTC in dataset TS ]]> INDIC Trial Summary Parameter must be present 'Trial Indication' (INDIC) record must be populated in Trial Summary (TS) domain, when study type is 'INTERVENTIONAL'. It is required for SDTM IG v3.1.2 data and all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing INDIC Trial Summary Parameter in dataset TS: No populated TSPARMCD=INDIC record was found although a record with TSPARMCD=STYPE and TSVAL=INTERVENTIONAL is present ]]> ADDON Trial Summary Parameter must be present - Added on to Existing Treatments' (ADDON) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing ADDON Trial Summary Parameter in dataset TS ]]> AGEMAX Trial Summary Parameter must be present 'Planned Maximum Age of Subjects' (AGEMAX) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing AGEMAX Trial Summary Parameter in dataset TS ]]> AGEMIN Trial Summary Parameter must be present 'Planned Minimum Age of Subject' (AGEMIN) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing AGEMIN Trial Summary Parameter in dataset TS ]]> LENGTH Trial Summary Parameter must be present 'Trial Length' (LENGTH) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing LENGTH Trial Summary Parameter in dataset TS ]]> PLANSUB Trial Summary Parameter must be present 'Planned Number of Subjects' (PLANSUB) record must be populated in Trial Summary (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing PLANSUB Trial Summary Parameter in dataset TS ]]> RANDOM Trial Summary Parameter must be present - 'Trial is Randomized' (RANDOM) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing RANDOM Trial Summary Parameter in dataset TS ]]> SEXPOP Trial Summary Parameter must be present - 'Sex of Participants' (SEXPOP) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing SEXPOP Trial Summary Parameter in dataset TS ]]> TBLIND Trial Summary Parameter must be present 'Trial Blinding Schema' (TBLIND) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TBLIND Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> TCNTRL Trial Summary Parameter must be present 'Control Type' (TCNTRL) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TCNTRL Trial Summary Parameter in dataset TS ]]> TINDTP record must be present in TS when STYPE='INTERVENTIONAL' 'Trial Indication Type' (TINDTP) record must be populated in Trial Summay (TS) domain, when study type is 'INTERVENTIONAL'. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TINDTP Trial Summary Parameter in dataset TS ]]> TITLE Trial Summary Parameter must be present 'Trial Title' (TITLE) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TITLE Trial Summary Parameter in dataset TS ]]> TPHASE Trial Summary Parameter must be present 'Trial Phase Classification' (TPHASE) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TPHASE Trial Summary Parameter in dataset TS ]]> TTYPE Trial Summary Parameter must be present 'Trial Type (TTYPE) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TTYPE Trial Summary Parameter in dataset TS ]]> CURTRT Trial Summary Parameter must be present - 'Current Therapy or Treatment' (CURTRT) record must be populated in Trial Summay (TS) domain, when ADDON is 'Y'. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing CURTRT Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> OBJPRIM Trial Summary Parameter must be present 'Trial Primary Objective' (OBJPRIM) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing OBJPRIM Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> SPONSOR Trial Summary Parameter must be present 'Clinical Study Sponsor' (SPONSOR) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing SPONSOR Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> TRT Trial Summary Parameter must be present Registry Identifier' (REGID) record may be populated in Trial Summary (TS) domain. It is expected for SDTM IG v3.1.2 data and all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing TRT Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> REGID Trial Summary Parameter must be present 'Registry Identifier' (REGID) record may be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing REGID Trial Summary Parameter in dataset TS ]]> OUTMSPRI Trial Summary Parameter must be present 'Primary Outcome Measure' (OUTMSPRI) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing OUTMSPRI Trial Summary Parameter ]]> FCNTRY Trial Summary Parameter must be present 'Planned Country of Investigational Sites' (FCNTRY) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing FCNTRY Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> ADAPT Trial Summary Parameter must be present 'Adaptive Design' (ADAPT) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing ADAPT Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> DCUTDTC Trial Summary Parameter must be present 'Data Cutoff Date' (DCUTDTC) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing DCUTDTC Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> DCUTDESC Trial Summary Parameter must be present 'Data Cutoff Description' (DCUTDESC) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing DCUTDESC Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> NARMS Trial Summary Parameter must be present 'Planned Number of Arms' (NARMS) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing NARMS Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> STYPE Trial Summary Parameter must be present 'Study Type' (STYPE) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing STYPE Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> SSTDTC Trial Summary Parameter must be present 'Study Start Date' (SSTDTC) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing SSTDTC Trial Summary Parameter in dataset {data($tsdatasetname)} ]]> SENDTC Trial Summary Parameter must be present 'Study End Date' (SENDTC) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing SENDTC Trial Summary Parameter in dataset TS ]]> ACTSUB Trial Summary Parameter must be present - 'Actual Number of Subjects' (ACTSUB) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing ACTSUB Trial Summary Parameter in dataset TS ]]> HLTSUBJI Trial Summary Parameter must be present 'Healthy Subject Indicator' (HLTSUBJI) record must be populated in Trial Summay (TS) domain. It is expected for SDTM IG v3.1.2 data and required for data in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing HLTSUBJI Trial Summary Parameter in dataset TS ]]> TSVAL may not be populated with a value from the ISO 21090 null flavor codelist TSVAL should not be populated with a value from the ISO 21090 null flavor codelist, or synonyms of the values. The TSVALNF variable should be used to capture these values, not TSVAL 3.1.2 3.1.3 3.2 TS CG0291 As TSVALNF=null, TSVAL={data($tsval)} is not allowed to come out of the list of ISO-21090 null flavors ({data($nfvalues)} ]]> Value for --PARM must be consistent within --PARMCD All values of a Parameter (--PARM) variables should be the same for a given value of a Parameter Short Name (--PARMCD) variables - TS domain 3.1.2 3.1.3 3.2 TS $recnum][odm:ItemData[@ItemOID=$tsparmcdoid and @Value=$tsparmcdvalue1]] let $recnum2 := $record2/@data:ItemGroupDataSeq (: let $tsparmcdvalue2 := $record/odm:ItemData[@ItemOID=$tsparmcdoid]/@Value :) let $tsparmvalue2 := $record2/odm:ItemData[@ItemOID=$tsparmoid]/@Value (: and compare the values - both must be equal :) where not($tsparmvalue1=$tsparmvalue2) return Inconsistent value for --PARM within --PARMCD: both records {data($recnum)} and {data($recnum2)} have --PARMCD='{data($tsparmcdvalue1)}' but the values for --PARM '{data($tsparmvalue1)}' and '{data($tsparmvalue2)}' are different ]]> Value for --PARMCD must be consistent within --PARM All values of a Parameter Short Name (--PARMCD) variables should be the same for a given value of a Parameter (--PARM) variables 3.1.2 3.1.3 3.2 TS $recnum][odm:ItemData[@ItemOID=$tsparmoid and @Value=$tsparmvalue1]] let $recnum2 := $record2/@data:ItemGroupDataSeq let $tsparmcdvalue2 := $record2/odm:ItemData[@ItemOID=$tsparmcdoid]/@Value (: and compare the values - both must be equal :) where not($tsparmcdvalue1=$tsparmcdvalue2) return Inconsistent value for --PARMCD within --PARM: both records {data($recnum)} and {data($recnum2)} have --PARM='{data($tsparmvalue1)}' but the values for --PARMCD '{data($tsparmcdvalue1)}' and '{data($tsparmcdvalue2)}' are different ]]> RDOMAIN must correspond to a domain defined in the submission Related Domain Abbreviation (RDOMAIN) must have a valid value of Domains included in the study data 3.1.2 3.1.3 3.2 CO RELREC SUPPQUAL Invalid value for RDOMAIN='{data($rdomainvalue)}' in dataset {data($datasetname)} - domain {data($rdomainvalue)} was not found in the define.xml file {data($define)} ]]> DOMAIN value length must be 2, except for AP, RELREC The value of DOMAIN should be no more than 2 characters in length, excluding Associated Persons domains 3.1.2 3.1.3 3.2 ALL CG0308 The value for DOMAIN in the dataset does not consist of exactly 2 characters: DOMAIN='{data($domainvalue)}' was found ]]> DOMAIN value length must be 2, except for AP, RELREC The value of DOMAIN should be no more than 2 characters in length, excluding Associated Persons domains ALL 3.1.2 3.1.3 3.2 CG0308 The value for DOMAIN in the dataset does not consist of exactly 2 characters: DOMAIN='{data($domainvalue)}' was found ]]> Either one of USUBJID or POOLID must be populated Either Unique Subject Identifier (Missing or redundant values for USUBJID and POOLIDUSUBJID) or Pool Identifier (POOLID) variables values and only one must be populated 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS 0 and string-length($usubjid) > 0) then Both USUBJID and POOLID in dataset {data($name)} are populated (: case that neither USUBJID nor POOLID are populated :) else if (not($usubjid) and not($poolid)) then Both USUBJID and POOLID in dataset {data($name)} are populated else () ) (: return the dynamically generated message (which can be null) :) return $message ]]> Either one of USUBJID or POOLID must be populated Either Unique Subject Identifier (Missing or redundant values for USUBJID and POOLIDUSUBJID) or Pool Identifier (POOLID) variables values and only one must be populated 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS 0 and string-length($usubjid) > 0) then Both USUBJID and POOLID in dataset {data($name)} are populated (: case that neither USUBJID nor POOLID are populated :) else if (not($usubjid) and not($poolid)) then Both USUBJID and POOLID in dataset {data($name)} are populated else () ) (: return the dynamically generated message (which can be null) :) return $message ]]> PC dataset must be included when PP dataset is present Pharmacokinetic Concentrations (PC) dataset should be included, when a Pharmacokinetic Parameters(PP) dataset is present 3.1.2 3.1.3 3.2 PP PC CG0318 The PP dataset is present in the study but the PC dataset is not present in study ]]> The combination of ELEMENT, TESTRL TEENRL, and TEDUR must be unique for each ETCD The combination of Description of Element (ELEMENT), Rule for Start of Element (TESTRL), Rule for End of Element (TEENRL), and Planned Duration of Element (TEDUR) should be unique for each Element Code (ETCD) 3.1.2 3.1.3 3.2 TE 1] (: and get the value :) let $element2 := $record/odm:ItemData[@ItemOID=$elementoid]/@Value let $testrl2 := $record/odm:ItemData[@ItemOID=$testrloid]/@Value let $teenrl2 := $record/odm:ItemData[@ItemOID=$teenrloid]/@Value let $tedur2 := $record/odm:ItemData[@ItemOID=$teduroid]/@Value let $recnum2 := $record/@data:ItemGroupDataSeq (: the values for ELEMENT, TESTRL, TEENRL, and TEDUR must be the same as in the first record :) where (not($element=$element2) or not($testrl=$testrl2) or not($teenrl=$teenrl2) or not($tedur=$tedur2)) return Records {data($recnum)} and {data($recnum2)} with ETCD='{data($etcd)}' do not have the same combination of ELEMENT, TESTRL, TEENRL, and TEDUR ]]> At least one of TEENRL or TEDUR must be populated At least one of Rule for End of Element (TEENRL) or Planned Duration of Element (TEDUR) should be populated in TE 3.1.2 3.1.3 3.2 TE Missing values for TEENRL and TEDUR ]]> Variable must be ordered in the domain as by CDISC Standards Order of variables should be as specified by CDISC standard 3.1.2 3.1.3 3.2 ALL {data($datasetname)} - domain {data($domaincode)}: Invalid order of variables in define.xml - found: {data($vararray)} - expected: {data($standardvars)} ]]> SCAT may not have the same value as DOMAIN, -TERM, -TESTCD, -TRT or BODSYS Value of Subcategory (--SCAT) should not be identical to that in Domain Abbreviation (DOMAIN); Reported Term (--TERM); Name of Measurement, Test, or Examination (--TESTCD); Name of Treatment (--TRT); Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TI Redundancy in paired variables values for {data($scatname)} with value={data($scatvalue)}. ]]> SCAT may not have the same value as DOMAIN, -TERM, -TESTCD, -TRT or BODSYS Value of Subcategory (--SCAT) should not be identical to that in Domain Abbreviation (DOMAIN); Reported Term (--TERM); Name of Measurement, Test, or Examination (--TESTCD); Name of Treatment (--TRT); Body System or Organ Class (--BODSYS) 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS TI Redundancy in paired variables values for {data($scatname)} with value={data($scatvalue)}. ]]> The value of --TESTCD must be different from 'OTHER' Test Code variables (--TESTCD) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 FINDINGS CG0341 Value of {data($testcdname)}='{data($testcd)}' is not allowed to be equal to 'OTHER' ]]> The value of --TESTCD must be different from 'OTHER' Test Code variables (--TESTCD) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 FINDINGS CG0341 Value of {data($testcdname)}='{data($testcd)}' is not allowed to be equal to 'OTHER' ]]> --TRT is not allowed to have the value 'OTHER' Test Code variables (--TESTCD) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 INTERVENTIONS CG0342 Value of {data($trtname)}='{data($trt)}' is not allowed to be equal to 'OTHER' ]]> --TRT is not allowed to have the value 'OTHER' Test Code variables (--TESTCD) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 INTERVENTIONS CG0342 Value of {data($trtname)}='{data($trt)}' is not allowed to be equal to 'OTHER' ]]> The value of --TERM must be different from 'OTHER' Reported Term variables (--TERM) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 EVENTS CG0343 Value of {data($termname)}='{data($term)}' is not allowed to be equal to 'OTHER' ]]> The value of --TERM must be different from 'OTHER' Reported Term variables (--TERM) should not be populated with values of 'OTHER' 3.1.2 3.1.3 3.2 EVENTS CG0343 Value of {data($termname)}='{data($term)}' is not allowed to be equal to 'OTHER' ]]> The value of --TESTCD must be different from 'MULTIPLE' Test Code variables (--TESTCD) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 FINDINGS CG0344 Value of {data($testcdname)}='{data($testcd)}' is not allowed to be equal to 'MULTIPLE' ]]> The value of --TESTCD must be different from 'MULTIPLE' Test Code variables (--TESTCD) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 FINDINGS CG0344 Value of {data($testcdname)}='{data($testcd)}' is not allowed to be equal to 'MULTIPLE' ]]> The value of --TRT must be different from 'MULTIPLE' Name of Treatment variables (--TRT) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 INTERVENTIONS CG0345 Value of {data($trtname)}='{data($trt)}' is not allowed to be equal to 'MULTIPLE' ]]> The value of --TRT must be different from 'MULTIPLE' Name of Treatment variables (--TRT) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 INTERVENTIONS CG0345 Value of {data($trtname)}='{data($trt)}' is not allowed to be equal to 'MULTIPLE' ]]> The value of --TERM must be different from 'MULTIPLE' Reported Term variables (--TERM) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 EVENTS CG0346 Value of {data($termname)}='{data($term)}' is not allowed to be equal to 'MULTIPLE' ]]> The value of --TERM must be different from 'MULTIPLE' Reported Term variables (--TERM) should not be populated with values of 'MULTIPLE' 3.1.2 3.1.3 3.2 EVENTS CG0346 Value of {data($termname)}='{data($term)}' is not allowed to be equal to 'MULTIPLE' ]]> --ORRES must be provided, when --ORRESU is provided Result or Finding in Original Units (--ORRES) should not be NULL, when Original Units (--ORRESU) is provided 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($orresname)}, when {data($orresuname)}, value={data($orresuvalue)} is provided in dataset {data($datasetname)} ]]> --ORRES must be provided, when --ORRESU is provided Result or Finding in Original Units (--ORRES) should not be NULL, when Original Units (--ORRESU) is provided 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($orresname)}, when {data($orresuname)}, value={data($orresuvalue)} is provided in dataset {data($datasetname)} ]]> --ORRES must be populated, when --STAT or --DRVFL is not populated Status (--STAT) should be set to 'NOT DONE' or Derived Flag (--DRVFL) should have a value of 'Y', when Result or Finding in Original Units (--ORRES) is NULL 3.1.2 3.1.3 3.2 FINDINGS Status {data($statname)} should be set to 'NOT DONE' or Derived Flag {data($drvflname)} should have a value of 'Y', when Result or Finding in Original Units {data($orresname)} is NULL ]]> --ORRES must be populated, when --STAT or --DRVFL is not populated Status (--STAT) should be set to 'NOT DONE' or Derived Flag (--DRVFL) should have a value of 'Y', when Result or Finding in Original Units (--ORRES) is NULL 3.1.2 3.1.3 3.2 FINDINGS Status {data($statname)} should be set to 'NOT DONE' or Derived Flag {data($drvflname)} should have a value of 'Y', when Result or Finding in Original Units {data($orresname)} is NULL ]]> When --DRVFL = 'Y' then --ORRES must be null Character Result/Finding in Original Units (--ORRES) value should be NULL, when Derived Flag (--DRVFL) value is 'Y' 3.1.2 3.1.3 3.2 FINDINGS 0 return Value of {data($orresname)} must be null when {data($drvflname)}='Y'. The value found for {data($orresname)}='{data($orres)}' ]]> When --DRVFL = 'Y' then --ORRES must be null Character Result/Finding in Original Units (--ORRES) value should be NULL, when Derived Flag (--DRVFL) value is 'Y' 3.1.2 3.1.3 3.2 FINDINGS 0 return Value of {data($orresname)} must be null when {data($drvflname)}='Y'. The value found for {data($orresname)}='{data($orres)}' ]]> When --DRVFL = 'Y' then --STRESC must be populated Character Result/Finding in Std Format (--STRESC) value should not be NULL, when Derived Flag (--DRVFL) value is 'Y' 3.1.2 3.1.3 3.2 FINDINGS Value of {data($strescname)} may not be null when {data($drvflname)}='Y' ]]> When --DRVFL = 'Y' then --STRESC must be populated Character Result/Finding in Std Format (--STRESC) value should not be NULL, when Derived Flag (--DRVFL) value is 'Y' 3.1.2 3.1.3 3.2 FINDINGS Value of {data($strescname)} may not be null when {data($drvflname)}='Y' ]]> IDVAR must be a valid variable name of the referenced domain Identifying Variable (IDVAR) must have a valid value of variables from a referenced Domain 3.1.2 3.1.3 3.2 RELREC SUPPQUAL CO Variable '{data($idvarvalue)}' was not found in the parent dataset of the referenced domain RDOMAIN='{data($rdomain)}' ]]> Referenced record must be an existing record Reference record defined by Related Domain Abbreviation (RDOMAIN), Unique Subject Identifier (USUBJID), Identifying Variable (IDVAR) and Identifying Variable Value (IDVARVAL) must exist in the target Domain 3.1.2 3.1.3 3.2 CO RELREC SUPPQUAL dataset={data($name)} - RDOMAIN={data($rdomainval)} - IDVAR={data($idvarvalue)} - IDVARVAL={data($idvarvalvalue)} - count={data($parentrecordcountsummed)} :) where $parentrecordcountsummed = 0 (: parent no records found at all :) return Invalid referenced record - Dataset={data($name)}: no parent records found in RDOMAIN={data($rdomainval)} for USUBJID={data($usubjidvalue)} ]]> Value for --TESTCD variable may not be longer than 8 characters The value of a Short Name of Measurement, Test or Examination (--TESTCD) variable should be limited to 8 characters, cannot start with a number, and cannot contain characters other than letters in upper case, numbers, or underscores 3.1.2 3.1.3 3.2 FINDINGS 8 or functx:is-value-in-sequence($firstchar,$numbers) or not(matches($value,'[A-Z_][A-Z0-9_]*')) return Invalid value for Short Name of Measurement, Test or Examination (--TESTCD) variable: it should be limited to 8 characters, cannot start with a number, and cannot contain characters other than letters in upper case, numbers, or underscores. Value '{data($value)}' was found for variable {data($testname)} in dataset {data($datasetname)}. ]]> Value for --TESTCD variable may not be longer than 8 characters The value of a Short Name of Measurement, Test or Examination (--TESTCD) variable should be limited to 8 characters, cannot start with a number, and cannot contain characters other than letters in upper case, numbers, or underscores 3.1.2 3.1.3 3.2 FINDINGS 8 or functx:is-value-in-sequence($firstchar,$numbers) or not(matches($value,'[A-Z_][A-Z0-9_]*')) return Invalid value for Short Name of Measurement, Test or Examination (--TESTCD) variable: it should be limited to 8 characters, cannot start with a number, and cannot contain characters other than letters in upper case, numbers, or underscores. Value '{data($value)}' was found for variable {data($testname)} in dataset {data($datasetname)}. ]]> TDSTOFF must be either 0 or a positive ISO 8601 Duration format Offset from the Anchor (TDSTOFF) variable value must be either 0, ISO 8601 format for duration (e.g. P80Y), or null 3.1.2 3.1.3 3.2 TD CG0376 TDSTOFF must either be '0' or a non-negative duration. TDSTOFF='{data($tdstoff)}' was found ]]> --LLT must be a valid MedDRA lowest level term Value for Lowest Level Term Code (--LLTCD) variable must be populated using a Lowest Level Term Code of the MedDRA dictionary of a version specified in the define.xml 3.1.3 3.2 AE MH CE CG0377 Value '{data($lltvalue)}' for {data($lltname)} was not found in the MedDRA dictionary ]]> --STRESC must be provided, when --ORRES is provided Character Result/Finding in Std Units (--STRESC) must be populated, when Result or Finding in Original Units (--ORRES) is provided 3.1.2 3.1.3 3.2 FINDINGS FDAC171 Missing value for {data($strescname)}, when {data($orresname)} is provided, {data($orresname)}='{data($orresvalue)}' is provided in dataset {data($datasetname)} ]]> --STRESC must be provided, when --ORRES is provided Character Result/Finding in Std Units (--STRESC) must be populated, when Result or Finding in Original Units (--ORRES) is provided 3.1.2 3.1.3 3.2 FINDINGS FDAC171 Missing value for {data($strescname)}, when {data($orresname)} is provided, {data($orresname)}='{data($orresvalue)}' is provided in dataset {data($datasetname)} ]]> The value of --TEST may not be more than 40 characters The value of Name of Measurement, Test or Examination (--TEST) should be no more than 40 characters in length 3.1.2 3.1.3 3.2 FINDINGS 40 characters. The rule is a relict of the ancient XPT format. ALSO:IETEST is an exception: may be up to 200 characters :) xquery version "3.0"; declare namespace def = "http://www.cdisc.org/ns/def/v2.0"; declare namespace def21 = "http://www.cdisc.org/ns/def/v2.1"; declare namespace odm="http://www.cdisc.org/ns/odm/v1.3"; declare namespace data="http://www.cdisc.org/ns/Dataset-XML/v1.0"; declare namespace xlink="http://www.w3.org/1999/xlink"; declare namespace xs="http://www.w3.org/2001/XMLSchema"; declare namespace functx = "http://www.functx.com"; (: "declare variable ... external" allows to pass $base and $define from an external programm :) declare variable $base external; declare variable $define external; declare variable $defineversion external; (: let $base := '/db/fda_submissions/cdisc01/' :) (: let $define := 'define2-0-0-example-sdtm.xml' :) let $definedoc := doc(concat($base,$define)) (: iterate over all datasets and variables in the define.xml :) for $itemgroup in $definedoc//odm:ItemGroupDef let $itemgroupdefname := $itemgroup/@Name (: Get the @Domain value when present, otherwise the @Name value - this is for allowing 'splitted' domains, e.g. @Name=QSCG @Domain=QS :) let $datasetname := $itemgroup/@Name let $domain := ( if($itemgroup/@Domain != '') then $itemgroup/@Domain else $itemgroup/@Name ) (: The --TEST variable is the concatenation of the domain code and 'TEST' :) let $testvar := concat($domain,'TEST') (: Get the OID for the --TEST variable :) let $testoid := ( for $a in $definedoc//odm:ItemDef[@Name=$testvar]/@OID where $a = $definedoc//odm:ItemGroupDef[@Name=$datasetname]/odm:ItemRef/@ItemOID return $a ) (: we of course only look into datasets where there really is a --TEST :) let $datasetname := ( if($defineversion = '2.1') then $itemgroup/def21:leaf/@xlink:href else $itemgroup/def:leaf/@xlink:href ) let $datasetdoc := ( if($datasetname) then doc(concat($base,$datasetname)) else () ) (: iterate over all the records where there is a --TEST variable :) for $record in $datasetdoc//odm:ItemGroupData (: get the record number :) let $recnum := $record/@data:ItemGroupDataSeq (: and get the value of the --TEST variable :) let $testvalue := $record/odm:ItemData[@ItemOID=$testoid]/@Value (: when it has more than 40 characters, give an error. Attention: IETEST is an exception (may be up to 200 characters) :) where string-length($testvalue) > 40 and not($testvar='IETEST') return The value for {data($testvar)} has more than 40 characters: '{data($testvalue)}' was found ]]> EX dataset must be present Exposure (EX) dataset should be included in every submission 3.1.2 3.1.3 3.2 EX EX document {data($exdatasetlocation)} could not be found in collection {data($base)} ]]> Domain tables must have at least one record Domain table should have at least one record 3.1.2 3.1.3 3.2 ALL {$numrecords} found in dataset: {data($datasetname)} ]]> Domain tables must have at least one record Domain table should have at least one record 3.1.2 3.1.3 3.2 ALL {$numrecords} found in dataset: {data($datasetname)} ]]> Study Identifier (STUDYID) values must match the STUDYID in Demographics (DM) domain Study Identifier (STUDYID) values must match the STUDYID in Demographics (DM) domain 3.1.2 3.1.3 3.2 ALL STUDYID {data($d/@Value)} in dataset {data($dataset)} does not match the STUDYID {data($dmstudyid)} in the DM dataset ]]> VISITNUM must be unique for each subject in SV The value of Visit Number (VISITNUM) variable should be unique for each record within a subject - Dataset SV 3.1.2 3.1.3 3.2 SV 1 return Non-unique combination of USUBID and VISITNUM in dataset SV - combination of USUBJID={data($usubjidvalue)} and VISITNUM={data($visitnumvalue)} occurrs {data($count)} times ]]> There may be only one record per IDVAR, IDVARVAL, and QNAM value per subject All SUPPQUAL Domains records are associated with a single parent record and must have a unique combination of Study Identifier (STUDYID), Unique Subject Identifier (USUBJID), Identifying Variable (IDVAR), Identifying Variable Value (IDVARVAL) and Qualifier Variable Name (QNAM) variable value. For all SUPPQUAL domain record all The QNAM variable should be unique for each parent record 3.1.2 3.1.3 3.2 SUPPQUAL CG0411 1 return The combination of USUBJID={data($usubjidvalue)}, IDVAR={data($idvar)}, IDVARVAL={data($idvarval)} and QNAM={data($qnam)} is not unique ]]> Every treated subject must have at least one DS record All Demographics (DM) subjects (USUBJID) should have at least one record in the Disposition (DS) domain with only possible exceptions to Screen Failures (ARMCD='SCRNFAIL') and Not Assigned Treatment (ARMCD='NOTASSGN') subjects 3.1.2 3.1.3 3.2 DS DM No disposition records were found in dataset {data($dsdatasetname)} for subject {data($usubjidvalue)} with assigned arm {data($arm)} ]]> Value for DOMAIN variable must be consistent Domain Abbreviation (DOMAIN) variable should be consistent with the name of the dataset 3.1.2 3.1.3 3.2 ALL 1 return Inconsistent Domain Abbreviation (DOMAIN) variable value in dataset {data($datasetname)}. Following values were found: {data($distinctdomainvalues)} ]]> Value for DOMAIN variable must be consistent Domain Abbreviation (DOMAIN) variable should be consistent with the name of the dataset 3.1.2 3.1.3 3.2 ALL 1 return Inconsistent Domain Abbreviation (DOMAIN) variable value in dataset {data($datasetname)}. Following values were found: {data($distinctdomainvalues)} ]]> ETCD values must be registered in TA except for unplanned Element Code (ETCD) values should match entries in the Trial Elements (TE) dataset, except for unplanned Element (ETCD = 'UNPLAN') 3.1.2 3.1.3 3.2 SE TA Invalid ETCD: Element Code ETCD={data($etcdvalue)} in dataset {data($datasetlocation)} was not found in TE dataset {data($tedatasetlocation)} ]]> ETCD/ELEMENT combinations must match entries in TE The combination of Element Code (ETCD) and Description of Element (ELEMENT) values should match entries in the Trial Elements (TE) dataset, except for unplanned Element (ETCD = 'UNPLAN') - dataset SE,TA 3.1.2 3.1.3 3.2 SE TA Invalid ETCD/ELEMENT in dataset {data($datasetname)}. The combination of Element Code ETCD={data($etcdvalue)} and Description of Element ELEMENT={data($elementvalue)} was not found in the TE dataset {data($tedatasetname)} ]]> Screen failures and untreated subjects may not have a value for the ARMCD variable - Records for subjects who failed a screening or were not assigned to study treatment (ARMCD is 'SCRNFAIL' or 'NOTASSGN') should not be included in the Trial Arms (TA) or Trial Visits (TV) datasets 3.1.2 3.1.3 3.2 TA TV Unexpected value for ARMCD={data($armcdvalue)} in dataset {data($itemgroupdefname)} - 'SCRNFAIL' and 'NOTASSGN' are not allowed to appear in TA nor TV ]]> QLABEL may not have more than 40 characters Qualifier Variable Label (QLABEL) value may have up to 40 characters 3.1.2 3.1.3 3.2 ALL 40 return Invalid value for QLABEL in dataset {data($datasetname)} - Label={data($qlabelvalue)} has more than 40 characters ]]> QNAM may not have more than 8 characters The value of Qualifier Variable Name (QNAM) should be limited to 8 characters, cannot start with a number, and cannot contain characters other than letters in upper case, numbers, or underscores 3.1.2 3.1.3 3.2 SUPPQUAL 8 or not(matches($qnamvalue,'[A-Z_][A-Z0-9_]*')) return Invalid value for QNAM in dataset {data($datasetname)} - Label={data($qnamvalue)} has more than 8 characters or starts with a number or contains characters other than letters in upper case, numbers, or underscores ]]> TAETORD must be registered in TA Order of Element within Arm (TAETORD) values for all datasets should match entries in the Trial Arms (TA) dataset 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO SE Invalid TAETORD in {data($name)} in dataset {data($datasetname)}. TAETORD={data($taetord)} was not found in dataset {data($tadatasetname)} ]]> TAETORD must be registered in TA - Order of Element within Arm (TAETORD) values for all datasets should match entries in the Trial Arms (TA) dataset Order of Element within Arm (TAETORD) values for all datasets should match entries in the Trial Arms (TA) dataset 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS CO SE Invalid TAETORD in {data($name)} in dataset {data($datasetname)}. TAETORD={data($taetord)} was not found in dataset {data($tadatasetname)} ]]> RELTYPE must be null when IDVAR is populated with a --SEQ Relationship Type (RELTYPE) in RELREC must be NULL, when Identifying Variable (IDVAR) is populated with a --SEQ value 3.1.2 3.1.3 3.2 RELREC 0 return Invalid value for RELTYPE variable. Non-null value={data($relvalue)} was found though identifying variable is {data($idvarvalue)} ]]> --STRF Time point for non-occurred event or intervention may not be provided Value of Start Relative to Reference Period (--STRF) should not be populated, when an event or intervention is marked as not occurred 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS Value of Start Relative to Reference Period ({data($strfname)} should not be populated for non-occurred event or intervation is provided, with value of {data($occurname)}={data($occurvalue)} ]]> --STRF Time point for non-occurred event or intervention may not be provided Value of Start Relative to Reference Period (--STRF) should not be populated, when an event or intervention is marked as not occurred 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS Value of Start Relative to Reference Period ({data($strfname)} should not be populated for non-occurred event or intervation is provided, with value of {data($occurname)}={data($occurvalue)} ]]> --ENRF Time point for non-occurred event or intervention may not be provided Value of End Relative to Reference Period (--ENRF) should not be populated, when an event or intervention is marked as not occurred 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS Value of End Relative to Reference Period ({data($enrfname)} should not be populated for non-occurred event or intervation is provided, with value of {data($occurname)}={data($occurvalue)} ]]> --ENRF Time point for non-occurred event or intervention may not be provided Value of End Relative to Reference Period (--ENRF) should not be populated, when an event or intervention is marked as not occurred 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS Value of End Relative to Reference Period ({data($enrfname)} should not be populated for non-occurred event or intervation is provided, with value of {data($occurname)}={data($occurvalue)} ]]> --TRTV must be populated, when --VAMT is not NULL Treatment Vehicle (--TRTV) should be provided, when Treatment Vehicle Amount (--VAMT) is specified 3.1.2 3.1.3 3.2 INTERVENTIONS Missing value for {data($trtvname)}, when {data($vamtname)} is not NULL ]]> --TRTV must be populated, when --VAMT is not NULL Treatment Vehicle (--TRTV) should be provided, when Treatment Vehicle Amount (--VAMT) is specified 3.1.2 3.1.3 3.2 INTERVENTIONS Missing value for {data($trtvname)}, when {data($vamtname)} is not NULL ]]> --STRESC must be populated, when --STRESU is provided Character Result/Finding in Std Units (--STRESC) should not be NULL, when Standard Units (--STRESU) is provided 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($strescname)}, when {data($stresuname)} is provided, value={data($stresuvalue)} is provided in dataset {data($datasetname)} ]]> --STRESC must be populated, when --STRESU is provided Character Result/Finding in Std Units (--STRESC) should not be NULL, when Standard Units (--STRESU) is provided 3.1.2 3.1.3 3.2 FINDINGS Missing value for {data($strescname)}, when {data($stresuname)} is provided, value={data($stresuvalue)} is provided in dataset {data($datasetname)} ]]> --STRESC must be populated, when --RESCAT is populated Character Result/Finding in Std Units (--STRESC) should be provided, when Result Category (--RESCAT) is specified 3.1.2 3.1.3 3.2 FINDINGS Missing {data($strescname)}, when {data($rescatname)} value={data($rescatvalue)} is provided in dataset {data($datasetname)} ]]> --STRESC must be populated, when --RESCAT is populated Character Result/Finding in Std Units (--STRESC) should be provided, when Result Category (--RESCAT) is specified 3.1.2 3.1.3 3.2 FINDINGS Missing {data($strescname)}, when {data($rescatname)} value={data($rescatvalue)} is provided in dataset {data($datasetname)} ]]> --TOXGR must be populated when --TOX is populated Toxicity Grade (--TOXGR) should be provided, when Toxicity (--TOX) is populated 3.1.2 3.1.3 3.2 AE MH CE EG LB PC PP Missing value for {data($toxgrname)}, when {data($toxname)} is populated, value={data($toxvalue)} ]]> --TOXGR must be populated when --TOX is populated Toxicity Grade (--TOXGR) should be provided, when Toxicity (--TOX) is populated 3.1.2 3.1.3 3.2 AE MH CE EG LB PC PP Missing value for {data($toxgrname)}, when {data($toxname)} is populated, value={data($toxvalue)} ]]> --CAT value must be populated, when --SCAT value is populated Value for Category (--CAT) variable should be populated, when value for Subcategory (--SCAT) variable is populated 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Missing {data($catname)} value, when {data($scatname)} value is populated ]]> --CAT value must be populated, when --SCAT value is populated Value for Category (--CAT) variable should be populated, when value for Subcategory (--SCAT) variable is populated 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Missing {data($catname)} value, when {data($scatname)} value is populated ]]> --CAT variable must be present, when --SCAT variable is present Category (--CAT) variable should be included into dataset, when Subcategory (--SCAT) variable is present 3.1.2 3.1.3 3.2 INTERVENTIONS EVENTS FINDINGS Missing {data($catname)} variable, when {data($scatname)} variable is present ]]> AGEU must be populated, when AGE or AGETXT is populated Age Units (AGEU) variable values must be provided, when Age (AGE) or Age Range (AGETXT) variables values are populated 3.1.3 3.2 DM CG0432 AGEU=null, although AGE or AGETXT is populated ]]> One of AGE or AGETXT must be populated, when AGEU is provided Either of Age (AGE) or Age Range (AGETXT) variable values should be provided, when Age Units (AGEU) are populated 3.1.3 3.2 DM Missing values for both AGE and AGETXT, when AGEU is provided ]]> DTHFL must be populated, when DTHDTC is populated Subject Death Flag (DTHFL) value must equal 'Y', when Date/Time of Death (DTHDTC) is provided 3.1.3 3.2 DM Missing value for DTHFL, when DTHDTC is populated ]]> Value for --SOCCD must be in MedDRA dictionary Value for System Organ Class Code (--SOCCD) variable must be populated using a System Organ Class Code of the MedDRA dictionary of a version specified in the define.xml 3.1.3 3.2 AE MH CE Value '{data($soccdvalue)}' for {data($soccdname)} was not found in the MedDRA dictionary ]]> TSVAL value for AGEMIN must be in ISO 8601 'duration' formal or null TSVAL value must be either ISO 8601 format for time period (e.g. P80Y) or null, when TSPARMCD='AGEMIN' 3.1.2 3.1.3 3.2 TS Invalid (non-ISO8601) TSVAL value={data($tsvalvalue)} for AGEMIN in dataset TS ]]> TSVAL value for LENGTH must be in ISO 8601 'duration' formal or null TSVAL value must be either ISO 8601 format for time period (e.g. P80Y) or null, when TSPARMCD='LENGTH' 3.1.2 3.1.3 3.2 TS Invalid (non-ISO8601) TSVAL value={data($tsvalvalue)} for LENGTH in dataset TS ]]> TSVAL value for PLANSUB record must be numeric TSVAL for PLANSUB record must be numeric 3.1.2 3.1.3 3.2 TS Invalid TSVAL value for PLANSUB, value={data($tsvalvalue)} in dataset TS ]]> STOPRULE Trial Summary Parameter must be present 'Study Stop Rules' (STOPRULE) record may be populated in Trial Summay (TS) domain. It is permissible for SDTM IG v3.1.2 data and in all more recent SDTM versions 3.1.2 3.1.3 3.2 TS Missing STOPRULE Trial Summary Parameter in dataset TS ]]> TSVAL value for CURTRT must be from FDA-SRS TSVAL for CURTRT record must be a valid preferred term from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVAL value={data($tsvalvalue)} for CURTRT in dataset TS ]]> Invalid TSVALCD value for CURTRT TSVALCD for CURTRT record must be a valid unique ingredient identifier from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVALCD value={data($tsvalcdvalue)} for CURTRT ]]> TSVCDREF variable value must be 'UNII', when TSPARMCD='CURTRT' TSVCDREF variable value must be 'UNII', when TSPARMCD='CURTRT' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value={data($tsvcdrefvalue)} for CURTRT in dataset TS. The value must be 'UNII' ]]> TSVCDREF value for TRT must be 'UNII' TSVCDREF variable value must be 'UNII', when TSPARMCD='TRT' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value for TRT: TSVCDREF variable value must be 'UNII', when TSPARMCD='TRT', value found is '{data($tsvcdref)}' ]]> TSVCDREF value for COMPTRT must be 'UNII' TSVCDREF variable value must be 'UNII', when TSPARMCD='COMPTRT' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value={data($tsvcdrefvalue)} for COMPTRT. The value must be 'UNII' ]]> TSVAL value for COMPTRT must be from FDA-SRS TSVAL for COMPTRT record must be a valid preferred term from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVAL value={data($tsvalvalue)} for COMPTRT in dataset TS ]]> TSVALCD value for COMPTRT must be from FDA-SRS TSVALCD for COMPTRT record must be a valid unique ingredient identifier from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVALCD value={data($tsvalcdvalue)} for COMPTRT in dataset TS ]]> TSVALCD for INDIC record must be a valid concept id from SNOMED CT TSVALCD for INDIC record must be a valid concept ID from SNOMED CT 3.1.2 3.1.3 3.2 TS Invalid TSVALCD, value={data($tsvalcdvalue)} for INDIC is not a valid SNOMED-CT code in dataset TS ]]> TSVALCD for TDIGRP record must be a valid concept id from SNOMED CT TSVALCD for TDIGRP record must be a valid concept ID from SNOMED CT 3.1.2 3.1.3 3.2 TS Invalid TSVALCD, value={data($tsvalcdvalue)} for TDIGRP is not a valid SNOMED-CT code in dataset TS ]]> TSVAL value for TRT must be from FDA-SRS TSVAL for TRT record must be a valid preferred term from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVAL value for TRT in dataset {data($tsdatasetname)}: TSVAL for TRT record must be a valid preferred term from FDA Substance Registration System (SRS): value '{data($tsval)}' is not a valid preferred term identifier from SRS ]]> TSVALCD value for TRT must be from FDA-SRS TSVALCD for TRT record must be a valid unique ingredient identifier from FDA Substance Registration System (SRS) 3.1.2 3.1.3 3.2 TS Invalid TSVALCD value for TRT in dataset {data($tsdatasetname)}: TSVALCD for TRT record must be a valid unique ingredient identifier from FDA Substance Registration System (SRS): value '{data($tsval)}' is not a valid unique ingredient identifier from SRS ]]> TSVAL value for PCLAS must be from NDF-RT TSVAL for PCLAS record must be a valid term from NDF-RT 3.1.2 3.1.3 3.2 TS Invalid TSVAL value for PCLASS in dataset {data($tsdatasetname)}: TSVAL for TSPARMCD=PCLAS record must be a valid a valid term from NDF-RT: value '{data($tsval)}' was found ]]> TSVALCD value for PCLAS must be from NDF-RT - TSVALCD for PCLAS record must be a valid code from NDF-RT TSVALCD for PCLAS record must be a valid code from NDF-RT 3.1.2 3.1.3 3.2 TS Invalid TSVALCD value={data($tsvalcdvalue)} for PCLAS ]]> TSVCDREF value for PCLAS must be 'NDF-RT' TSVCDREF variable value must be 'NDF-RT', when TSPARMCD='PCLAS' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value={data($tsvcdrefvalue)} for PCLAS. The value must be 'NDF-RT' ]]> TSVCDREF variable value must be "ISO 3166", when TSPARMCD='FCNTRY' TSVCDREF variable value must be "ISO 3166", when TSPARMCD='FCNTRY' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value={data($tsvcdrefvalue)} for FCNTRY. The value must be 'ISO 3166' ]]> TSVAL value for ACTSUB must be numeric TSVAL variable value must be numeric, when TSPARMCD='ACTSUB' 3.1.2 3.1.3 3.2 TS Invalid TSVAL value {data($actsubval)} for Trial Summary Parameter ACTSUB in dataset {data($tsdatasetname)} ]]> TSVCDREF variable value must be "SNOMED", when TSPARAMCD='INDIC' TSVCDREF variable value must be "SNOMED", when TSPARAMCD='INDIC' 3.1.2 3.1.3 3.2 TS Invalid TSVCDREF value={data($tsvcdrefvalue)} for INDIC. The value must be 'SNOMED' ]]> ECDOSTXT may not be null when ECDOSE is null and ECOCCUR does not equal 'N' Dose Description (ECDOSTXT) should be populated when Dose (ECDOSE) is null (and ECOCCUR does not equal 'N') 3.2 EC ECDOSTXT must be populated when ECDOSE=null ]]> SDTM Required variables must always be included Variables described in SDTM as Required must be included in the dataset 3.1.2 3.1.3 3.2 ALL No data found for required variable {data($varname)} in record number {data($recnum)} in dataset {data($datasetname)} ]]> SDTM Required variables must always be included Variables described in SDTM as Required must be included in the dataset 3.1.2 3.1.3 3.2 ALL No data found for required variable {data($varname)} in record number {data($recnum)} in dataset {data($datasetname)} ]]> Value for --TPTNUM must be provided, when value for --TPT is provided Planned Time Point Number (--TPTNUM) variable must be included into the domain, when Planned Time Point Name (--TPT) variable is present 3.1.2 3.1.3 3.2 ALL Planned Time Point Number {data($tptnumname)} may not be NULL, when Planned Time Point Name {data($tptname)} is populated, value = {data($tptvalue)} ]]> Value for --TPTNUM must be provided, when value for --TPT is provided Planned Time Point Number (--TPTNUM) variable must be included into the domain, when Planned Time Point Name (--TPT) variable is present 3.1.2 3.1.3 3.2 ALL Planned Time Point Number {data($tptnumname)} may not be NULL, when Planned Time Point Name {data($tptname)} is populated, value = {data($tptvalue)} ]]> --TPTNUM variable must be present, when --TPT variable is present Planned Time Point Number (--TPTNUM) variable must be included into the domain, when Planned Time Point Name (--TPT) variable is present 3.1.2 3.1.3 3.2 ALL CG0468 Variable {data($tptname)} is present in dataset {data($name)} but {data($tptnumname)} is not present in the dataset ]]>