<br> Nelson,<br><br> Can you provide details on which exact version of drools (5.0.1?) you are using and what is the error/stack trace you are receiving?<br><br> Thanks,<br> Edson<br><br><div class="gmail_quote">
2010/1/19 Axelrod, Nelson <span dir="ltr"><<a href="mailto:naxelrod@jcvi.org">naxelrod@jcvi.org</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I’ve encountered problems constructing nested Boolean
expressions in Drools 5.0 using the prefixOr syntax. We’re using
Drools to build a genome annotation system at the Venter Institute.
The following example rule assigns an annotation if there is
a blast hit to a gene GB|AAQ16631.1, or either a blast hit to gene GB|AAQ16631.1,
or to any gene within 500 bases of a gene with an HMM hit to TIGR00905.
I’ve left off some details to focus on how we are structuring the syntax
of our prefixOr and prefixAnd expressions.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The Drools parser throws errors when it encounters the 2<sup>nd</sup>
“blast_hit” statement in the example below. Our prefixOr and
prefixAnd expressions work as expected when we use similar syntax, at least
until we attempt to use nested or expressions.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal" style=""><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">rule</span></b><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> </span><span style="font-size: 10pt; font-family: "Courier New"; color: green;">"2645|lysine decarboxylase
CadA"</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">when</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> (</span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">or</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> (</span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">and</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> blast_hit
: BlastHit( hitId==</span><span style="font-size: 10pt; font-family: "Courier New"; color: green;">'GB|AAQ16631.1'</span><span style="font-size: 10pt; font-family: "Courier New"; color: black;">)</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> gene1
: Feature( featureId == blast_hit.queryId )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> (</span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">or</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> (</span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">and</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> blast_hit
: BlastHit( hitId==</span><span style="font-size: 10pt; font-family: "Courier New"; color: green;">'GB|AAQ16631.1'</span><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> gene1
: Feature( featureId == blast_hit.queryId )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> (</span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">and</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> hmm_hit1
: HmmHit( hitId==</span><span style="font-size: 10pt; font-family: "Courier New"; color: green;">'TIGR00905'</span><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> gene1
: Feature( featureId == hmm_hit1.queryId )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> gene2
: Feature( </span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">eval</span></b><span style="font-size: 10pt; font-family: "Courier New"; color: black;">(gene2.isWithin(gene1, 500)) )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> )</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">then</span></b><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> </span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> Annotation
a = </span><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">new</span></b><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> Annotation(</span><span style="font-size: 10pt; font-family: "Courier New"; color: green;">"lysine decarboxylase CadA"</span><span style="font-size: 10pt; font-family: "Courier New"; color: black;">);</span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt; font-family: "Courier New"; color: black;"> gene1.addAnnotation(a);</span><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal" style=""><b><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(150, 0, 0);">end</span></b><span style="font-size: 10pt; font-family: "Courier New";"></span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Any suggestions are much appreciated.</p>
<p class="MsoNormal">Thanks,</p>
<p class="MsoNormal">Nelson</p>
<p class="MsoNormal"> </p>
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<br></blockquote></div><br><br clear="all"><br>-- <br> Edson Tirelli<br> JBoss Drools Core Development<br> JBoss by Red Hat @ <a href="http://www.jboss.com">www.jboss.com</a><br>