edits.seer.internal.rules.SEER_IR09.xml Maven / Gradle / Ivy
<rule id="SEER_IR09" name="Site and Laterality not Consistent ICD-O-2 for Patient (SEER IR09)" tag="S032" java-path="lines" category="inter-record">
<expression><![CDATA[if (lines.size() < 2)
return true
for (line in lines)
if (!(Functions.matches(line.dateOfDiagnosisYear, /\d\d\d\d/)) || line.dateOfDiagnosisYear >= '2001' || line.dateOfDiagnosisYear == null)
return true
//Define the properties we want to report
//We don't always want to report laterality and ignoring properties doesn't work when forcing entity failures
Closure<String[]> getPropertiesToFail = { String site1, String site2 ->
if (!((List)Context.IR09_PAIRED_ORGAN_Table).contains(Functions.asInt(site1.substring(1,4))) && !((List)Context.IR09_PAIRED_ORGAN_Table).contains(Functions.asInt(site2.substring(1,4))))
return ['line.histologicTypeIcdO3', 'line.primarySite', 'line.behaviorCodeIcdO3', 'line.overRideSiteLatSeqno'] as String[]
else
return ['line.histologicTypeIcdO3', 'line.primarySite', 'line.behaviorCodeIcdO3', 'line.overRideSiteLatSeqno', 'line.laterality'] as String[]
}
int index1 = 0
while ( index1 < lines.size() ) {
Map line1 = lines.get(index1)
int index2 = index1 + 1
String site1 = line1.primarySite
String hist1 = line1.histologyIcdO2
String lat1 = line1.laterality
String behav1 = line1.behaviorIcdO2
//String yeardx1 = line1.dateOfDiagnosisYear
if (line1.overRideSiteLatSeqno != '1' && site1 != null && hist1 != null && behav1 != null &&
(site1.length() == 4) && (hist1.length() == 4)) {
while ( index2 < lines.size() ) {
Map line2 = lines.get(index2)
String site2 = line2.primarySite
String hist2 = line2.histologyIcdO2
String lat2 = line2.laterality
String behav2 = line2.behaviorIcdO2
//String yeardx2 = line2.dateOfDiagnosisYear
if (line2.overRideSiteLatSeqno != '1' && site2 != null && hist2 != null && behav2 != null &&
site2.length() == 4 && hist2.length() == 4) {
if ( hist2.startsWith(hist1.substring(0,3))
&& (behav1 == '3' && behav1 == behav2)
&&!(((List)Context.IR09_PAIRED_ORGAN_Table).contains(Functions.asInt(site1.substring(1,4)))
&& ((List)Context.IR09_PAIRED_ORGAN_Table).contains(Functions.asInt(site2.substring(1,4)))
&& lat1 != lat2 && lat1 != '9' && lat2 != '9' /*&& lat1 != '5' && lat2 != '5'*/)) {
if (( site1 ==~ /^C\d\d(8)$/ || site2 ==~ /^C\d\d(8)$/)
&& !(site1 ==~ /^C(168|538|718)$/) && !(site2 ==~ /^C(16|53|71)\d$/)
&& site2.startsWith(site1.substring(0,3))) {
Functions.forceFailureOnEntity(binding, line1, getPropertiesToFail(site1, site2))
Functions.forceFailureOnEntity(binding, line2, getPropertiesToFail(site1, site2))
return false
}
if (( site1 ==~ /^C\d\d[9]$/ || site2 ==~ /^C\d\d[9]$/)
&& site2.startsWith(site1.substring(0,3))) {
Functions.forceFailureOnEntity(binding, line1, getPropertiesToFail(site1, site2))
Functions.forceFailureOnEntity(binding, line2, getPropertiesToFail(site1, site2))
return false
}
if ( ((Map)Context.IR09_NOS_SPEC_Table).containsKey(site1)
&& ((List)((Map)Context.IR09_NOS_SPEC_Table).getOrDefault(site1, [])).contains(Functions.asInt(site2.substring(1,4)))) {
Functions.forceFailureOnEntity(binding, line1, getPropertiesToFail(site1, site2))
Functions.forceFailureOnEntity(binding, line2, getPropertiesToFail(site1, site2))
return false
}
if ( ((Map)Context.IR09_NOS_SPEC_Table).containsKey(site2)
&& ((List)((Map)Context.IR09_NOS_SPEC_Table).getOrDefault(site2, [])).contains(Functions.asInt(site1.substring(1,4)))) {
Functions.forceFailureOnEntity(binding, line1, getPropertiesToFail(site1, site2))
Functions.forceFailureOnEntity(binding, line2, getPropertiesToFail(site1, site2))
return false
}
/*
if ( yeardx1 >= '2007' && yeardx2 >= '2007') {
String site1Num = site1.substring(1,3)
String site2Num = site2.substring(1,3)
int yearDif = yeardx1 - yeardx2;
if (yearDif < 0)
yearDif = yearDif * (-1)
//Breast
if((site1Num >= '500' && site1Num >= '509') &&
(site2Num >= '500' && site2Num >= '509')) {
if (yearDif < 6) {
Functions.forceFailureOnEntity(binding, line1)
Functions.forceFailureOnEntity(binding, line2)
return false
}
}
//Colon
else if ((site1Num >= '180' && site1Num <= '189') &&
(site2Num >= '180' && site2Num <= '189')) {
if (yearDif < 2) {
Functions.forceFailureOnEntity(binding, line1)
Functions.forceFailureOnEntity(binding, line2)
return false
}
}
//Head and Neck
else if((site1Num < '149' || (site1Num >= '300' && site1Num <= '329')) &&
(site2Num < '149' || (site2Num >= '300' && site2Num <= '329'))) {
if (yearDif < 6) {
Functions.forceFailureOnEntity(binding, line1)
Functions.forceFailureOnEntity(binding, line2)
return false
}
}
}
*/
}
}
index2++
}
}
index1++
}
return true]]></expression>
<message>Site and Laterality Inter-Record Error</message>
<description><![CDATA[This edit is only executed if all records for the patient have a Year of Diagnosis [390] prior to 2001 and not blank.
This edit compares records for a patient that have the same three-digit malignant Histology (92-00) ICD-O-2 [420] code. The records are not compared if both are paired organs (see Table 2), their lateralities are not the same, and neither has a Laterality [410] of '9' (Paired site, but no information concerning laterality; midline tumor).
For the records that are compared, there must be no ambiguity of primary site between specified and NOS. That is, if the site code in one of the records appears in the left column of Table 1 below then the site in the other record must not occur in the same line on the right side of the table.
For patients whose records have been previously reviewed (Site/Histology/Laterality/Sequence Number Interrecord Review = 1), no further checking is done.
Table 1
NOS Specified
CAA8 CAAx
CBB9 CBBx
C260 C150-C259, C480-C488
C268 C150-C259, C480-C488
C269 C150-C259, C480-C488
C390 C300-C349, C384
C398 C300-C349, C380-C388
C399 C300-C349, C384
C579 C510-C578, C589
C639 C600-C638
C689 C649-C688
C758 C379, C739-C749
C759 C379, C739-C749
(Where AA represents any two-digit number except 16, 53, 71; BB represents any two-digit number and x represents any one-digit number.)
Table 2
Paired organs:
C079 Parotid gland
C080 Submandibular gland
C081 Sublingual gland
C090 Tonsillar fossa
C091 Tonsillar pillar
C099 Tonsil, NOS
C301 Middle ear
C310 Maxillary sinus
C312 Frontal sinus
C341-C349 Lung
C384 Pleura
C400 Long bones of upper limb, scapula
C401 Short bones of upper limb
C402 Long bones of lower limb
C403 Short bones of lower limb
C441 Skin of eyelid
C442 Skin of external ear
C443 Skin of other and unpecified parts of the face
(midline code '9')
C445 Skin of trunk (midline code '9')
C446 Skin of arm and shoulder
C447 Skin of lower limb and hip
C471 Upper limb and shoulder
C472 Lower limb and shoulder
C491 Connective, subcutaneous, and other soft tissues of upper
limb and shoulder
C492 Connective, subcutaneous, and other soft tissues of lower
limb and hip
C500-C509 Breast
C569 Ovary
C570 Fallopian tube
C620-C629 Testis
C630 Epididymis
C631 Spermatic cord
C649 Kidney, NOS
C659 Renal pelvis
C669 Ureter
C690-C699 Eye
C740-C749 Adrenal glands
C754 Carotid body]]></description>
<history>
<event version="SE11-001-01" user="greend" date="1985-12-29">The site field is now a three digit field. The override switch, SITE-LAT-OVERRIDE-SW, is used to specify reviewed cases. The check on laterality is now done only for paired sites.</event>
<event version="SE11-001-04" user="greend" date="1988-05-25">The list of paired organs was updated. The list of exclusion sites was updated.</event>
<event version="SE11-001-07" user="greend" date="1991-09-15">Conversion of morphology and topography codes from ICD-O-1 to ICD-O-2.</event>
<event version="SE11-001-17" user="greend" date="2003-04-14">Edit modified to only compare cases for a person where all records occur before 2001.</event>
<event version="SE12-002-01" user="murphyr" date="2009-12-22">Edit now skipped if year of diagnosis is blank.</event>
<event version="SE12-002-04" user="murphyr" date="2010-07-29">Fixed issue where we compared laterality to an int when it's a character.</event>
<event version="SE14-011-04" user="depryf" date="2014-04-21" ref="67077">Now reporting all the tumors when this edit fails.</event>
<event version="SE15-013-01" user="kirbyk" date="2015-01-26" ref="67112">Reports only the two tumors that fail the edit.</event>
<event version="SE15-014-03" user="kirbyk" date="2015-09-17" ref="67213">Changed the error reporting to not always report laterality.</event>
<event version="SE16-016-08" user="depryf" date="2017-11-22" ref="67674">Edit syntax updated to allow pre-compilation optimization; no change in behavior.</event>
<event version="SE18-020-01" user="depryf" date="2020-02-04" ref="68281">Changed property names to align with NAACCR XML IDs.</event>
</history>
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