edits.seer.internal.rules.SEER_IR09_3.xml Maven / Gradle / Ivy
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Java implemenation of the SEER edits.
<rule id="SEER_IR09_3" name="Site and Laterality ICD-O-3 not Consistent for Patient (SEER IR09_3)" tag="S033" java-path="lines" category="inter-record">
<expression><![CDATA[if (lines.size() < 2)
return true
for (line in lines)
if (line.histologicTypeIcdO3 == 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.histologicTypeIcdO3
String behav1 = line1.behaviorCodeIcdO3
String lat1 = line1.laterality
if (line1.overRideSiteLatSeqno != '1' && site1 != null && behav1 != null &&
site1.length() == 4 && hist1.length() == 4 && hist1 < '9590') {
while ( index2 < lines.size() ) {
Map line2 = lines.get(index2)
String site2 = line2.primarySite
String hist2 = line2.histologicTypeIcdO3
String behav2 = line2.behaviorCodeIcdO3
String lat2 = line2.laterality
if (line2.overRideSiteLatSeqno != '1' && site2 != null && hist2 != null && behav2 != null &&
site2.length() == 4 && hist2.length() == 4 && hist2 < '9590') {
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')) {
Integer year1 = Functions.asInt(line1.dateOfDiagnosisYear) ?: 9999
Integer month1 = Functions.asInt(line1.dateOfDiagnosisMonth) ?: 99
Integer day1 = Functions.asInt(line1.dateOfDiagnosisDay) ?: 99
Integer year2 = Functions.asInt(line2.dateOfDiagnosisYear) ?: 9999
Integer month2 = Functions.asInt(line2.dateOfDiagnosisMonth) ?: 99
Integer day2 = Functions.asInt(line2.dateOfDiagnosisDay) ?: 99
boolean fiveYearsApart = !((((Integer)((Closure)Context.compareDate).call(year1 +5, month1, day1, year2, month2, day2)) >= 0) && (((Integer)((Closure)Context.compareDate).call(year1 -5, month1, day1, year2, month2, day2)) <= 0))
boolean oneYearApart = !((((Integer)((Closure)Context.compareDate).call(year1 + 1, month1, day1, year2, month2, day2)) >= 0) && (((Integer)((Closure)Context.compareDate).call(year1 - 1, month1, day1, year2, month2, day2)) <= 0))
boolean siteExceptionBreast = (site1 ==~ /^C50\d$/ && site2 ==~ /^C50\d$/ && fiveYearsApart)
boolean siteExceptionColon = (site1 ==~ /^C18[0-8]$/ && site2 ==~ /^C18[0-8]$/ && oneYearApart)
boolean siteExceptionHeadNeck = (site1 ==~ /^C(0\d\d|1[0-3]\d|14[0-8]|3[012]\d)$/ && site2 ==~ /^C(0\d\d|1[0-3]\d|14[0-8]|3[012]\d)$/ && fiveYearsApart)
if (!((siteExceptionBreast || siteExceptionColon || siteExceptionHeadNeck) && (year1 > 2006 || year2 > 2006))) {
if (( site1 ==~ /^C\d\d(8)$/ || site2 ==~ /^C\d\d(8)$/)
&& !(site1 ==~ /^C(168|538|718)$/) && !(site2 ==~ /^C(16|53|71)\d$/)
&& !(site2 ==~ /^C(168|538|718)$/) && !(site1 ==~ /^C(16|53|71)\d$/)
&& 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\d9$/ || site2 ==~ /^C\d\d9$/)
&& 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
}
}
}
}
index2++
}
}
index1++
}
return true]]></expression>
<message>Site and Laterality ICD-O-3 Inter-Record Error</message>
<description><![CDATA[IR09 is performed only for invasive diagnoses (Behavior Code ICD-O-3 = 3) and histologies (Histologic Type ICD-O-3) less than 9590.
This edit compares records for a patient that have the same three-digit histology 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 of 5 (paired site, midline) or 9 (paired site, but no information concerning laterality).
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.
The 2007 Multiple Primary Rules that incorporate extended timing rules apply only to tumors diagnosed in 2007 and later. Therefore a date test for exemption should only be applied to tumors diagnosed on or after 2007, and only for breast, colon, and head and neck cancers. (See Table 3 for site-specific groups and timing rules.) If there were multiple tumors with diagnosis dates prior to 2007, they should be reviewed.
If there were multiple tumors with diagnosis in 2007 or later, review should be based on the site-specific timing rules. For example: 2 breast cancers diagnosed 2 years apart (2007 and 2009) should be reviewed because breast cancers diagnosed less than 5 years apart are to be abstracted only once, whereas 2 colon cancers diagnosed 2 years apart should not be reviewed because colon cancers diagnosed more than one year apart are abstracted separately.
If there were multiple tumors that span January 1, 2007: If the absolute value of any of the time differences is within the site-specific timing rule, the tumors should be reviewed. For example: two breast cancers diagnosed in 2001 and 2007 should not be reviewed. Two colon cancers diagnosed in December 2006 and March 2007 should be reviewed. If there were breast cancers diagnosed in 2001, 2003, and 2007, they should all be reviewed because 2001 and 2003 will have to be reviewed and if 2003 is determined to be a primary, then 2003 and 2007 will have to be reviewed.
To calculate time differences when one or both records have a partial diagnosis date:
If the diagnosis date in one record has more information than the diagnosis date in the other record, set the missing portion of the partial date to the known portion of the other date. For example, if the first diagnosis date is 200605__ and the second date is 20071020, set the first diagnosis date to 20060520 before calculating whether the second tumor was diagnosed more than 1 year (or 5 years) after the first. If the first date is 200512__ and the second is 2008____, set the value of the second date to 200812__.
For patients whose records have been previously reviewed (Over-ride Site/Lat/SeqNo = 1), no further checking is done.
If one record contains an NOS site code, the records require review as follows: if the site code in one of the records appears in the left column of Table 1 then the site in the other record must not occur in the same line on the right side of the table.
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
* AA represents any two-digit number except 16, 53, 71 (that is, site exceptions = C168, C538, C718)
** BB represents any two-digit number and x represents any one-digit number
Table 2
C079 C080 C081 C090 C091 C099 C301 C310 C312 C341 C342 C343
C344 C345 C346 C347 C348 C349 C384 C400 C401 C402 C403 C441
C442 C443 C445 C446 C447 C471 C472 C491 C492 C500 C501 C502
C503 C504 C505 C506 C507 C508 C509 C569 C570 C620 C621 C622
C623 C624 C625 C626 C627 C628 C629 C630 C631 C649 C659 C669
C690 C691 C692 C693 C694 C695 C696 C697 C698 C699 C740 C741
C742 C743 C744 C745 C746 C747 C748 C749 C754
Table 3
Group Primary Site Review Not Required
Breast C500-C509 Diagnosed more than 5 years apart
Colon C180-C188 Diagnosed more than 1 years apart
Head and Neck C000-C148, C300-C329 Diagnosed more than 5 years apart]]></description>
<history>
<event version="SE12-002-04" user="murphyr" date="2010-07-29">Fixed an issue where edit 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="SE15-014-01" user="kirbyk" date="2015-06-25" ref="67202">Changed the error reporting to not always report laterality.</event>
<event version="SE15-014-03" user="kirbyk" date="2015-09-17" ref="67211">Fixed the reported properties to include the entity prefix.</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>
<event version="SE21-021-04" user="kirbyk" date="2021-05-20" ref="68647">Updating edit to match the NPCR logic.</event>
<event version="SE21-021-08" user="beverung" date="2021-08-06" ref="68700">Fix date exemption logic.</event>
<event version="SE22-022-01" user="beverung" date="2022-01-24" ref="68782">Update edit to use compareDate context entry.</event>
</history>
</rule>