Text Mining and Drools
by Daniel Souza
Hi Drools Team,
I'm interested in mix drools with text mining.
I have in mind the process to do it, e.g:
Step 1:
> Tokenization:
* divide text to separate in a vector of word tokens;
* eliminate signals and separete hyphens in two tokens.
Step 2:
> Filtering:
* With a list of most common words built, eliminate this common words in
the vector of word tokens;
* Assign a sub-vector of synonyms for each token, if possible.
Step 3:
> The interest knowledge for text mining. (It still a cloud in my mind).
*The problem:
What I want to do in this step is to match a TEXT A with TEXT B for protein
function annotation.*
--------------------------------------------------------------------------------------------
Suppose these four situations below:
sequence: >Contig737
hit1: Pre mRNA splicing factor cwf8
hit2: cell control protein cwf8
*Match: hit1: cwf8 <> hit2: cwf8*
It's important to note that the most uncommon word is most important to
consider as an entire match.
sequence: >Contig1170
hit1: splicing coactivator SRm300 like
hit2: pre mRNA splicing factor CWC21
*Match: hit1: splicing <> hit2: splicing*
In this case splicing could be relevant or not, it will depend of the
biologist knowledge.
sequence: >Contig1431
hit1: transcription factor HAP3
hit2: pre mRNA splicing factor ATP dependent RNA helicase PRP43
*Match: hit1: factor <> hit2: factor*
In this case factor is a common word and I should filter it too.
sequence: >Contig56
hit1: Phosphoribosylpyrophosphate synthetase
hit2: ribose phosphate pyrophosphokinase
*Match: hit1: Phosphoribosylpyrophosphate <> substring-hit2: phosphate*
In this case phosphate match as a substring of Phosphoribosylpyrophosphate.
This match is very relevant to consider as an entire match.
-------------------------------------------------------------
Now I'm thinking in how to evaluate tokens between hit1 and hit2.
What I did before is to match vector with less tokens inside a vector with
more tokens using no sensitive case. Each token was matched as an entire
string or sub-string.
I searched about text mining and biomedical field and there are confused
informations.
Something interesting that I found is the Soundex algorithm that have
another point to face similarities between two texts. Reading in somewhere
in the Drools docs Soundex can be used with drools by an external lib or
class.
I don't know if there is something implemented in Drools to handle text
inside rules.
What I think to do is to build a model that still in cloud to evaluate the
matching between hit1 and hit2. A model to score matches. The most relevant
word can have a high weight.
If someone has a suggestion it will be well appreciated.
Regards,
Daniel Souza
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12 years, 12 months
Why are indented keywords in template causing NPE or DecisionTableParseException?
by magnusv
Drools 5.5.0
Indenting the "template header" or "rule" keywords in a template file will
cause exceptions on expansion. I believe it might be related to this old
JIRA issue: https://issues.jboss.org/browse/JBRULES-2786
"DecisionTableParseException" and "NullPointerException" are thrown. See
example code and related stack traces below.
Is this a bug in drools or is the template formatting intended to be this
strict? Or am I doing something else wrong?
=====================
Indented template header:
" template header
age
type
log"
Gives the exception:
org.drools.template.parser.DecisionTableParseException: Missing header
at
org.drools.template.parser.DefaultTemplateContainer.parseTemplate(DefaultTemplateContainer.java:87)
at
org.drools.template.parser.DefaultTemplateContainer.<init>(DefaultTemplateContainer.java:47)
at
org.drools.decisiontable.ExternalSpreadsheetCompiler.compile(ExternalSpreadsheetCompiler.java:97)
=====================
Indented rule keyword:
" rule "Cheese fans_(a){row.rowNumber}"
when
Person(age == @{age})"
Gives the exception:
java.lang.NullPointerException
at
org.drools.template.parser.DefaultTemplateColumn.createCellCondition(DefaultTemplateColumn.java:67)
at
org.drools.template.parser.DefaultTemplateColumn.addCondition(DefaultTemplateColumn.java:90)
at
org.drools.template.parser.DefaultTemplateRuleBase.createColumnConditions(DefaultTemplateRuleBase.java:103)
at
org.drools.template.parser.DefaultTemplateRuleBase.createTemplateRule(DefaultTemplateRuleBase.java:96)
at
org.drools.template.parser.DefaultTemplateRuleBase.getDTRules(DefaultTemplateRuleBase.java:83)
at
org.drools.template.parser.DefaultTemplateRuleBase.<init>(DefaultTemplateRuleBase.java:62)
at
org.drools.template.parser.TemplateDataListener.<init>(TemplateDataListener.java:74)
at
org.drools.decisiontable.ExternalSpreadsheetCompiler.compile(ExternalSpreadsheetCompiler.java:99)
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12 years, 12 months
[planner] Looking for testimonials for Drools Planner
by Geoffrey De Smet
Hi Planner users,
I need your help :)
Lately, several people have been asking me for public testimonials for
Drools Planner.
So if you're a Planner user, would like to say a few words about it by
responding to this mail?
Say what you want.
It's extra nice if you can mention the benefits, project status
(development/production), country and/or company,
but that's optional (as it might be too sensitive to mention that).
Thanks in advance,
Geoffrey De Smet
12 years, 12 months
Drools 5.4 Jitting Error
by gboro54
I just updated to Drools 5.4 and I am not getting the following error on all
my map accessors:
10:41:12,997 ERROR [stderr] (Thread-169) Exception in thread "Thread-169"
java.lang.RuntimeException: Exception jitting: feeKeys[1] == null
10:41:12,998 ERROR [stderr] (Thread-169) at
org.drools.rule.constraint.MvelConstraint.executeJitting(MvelConstraint.java:219)
10:41:12,999 ERROR [stderr] (Thread-169) at
org.drools.rule.constraint.MvelConstraint.access$000(MvelConstraint.java:41)
10:41:13,000 ERROR [stderr] (Thread-169) at
org.drools.rule.constraint.MvelConstraint$1.run(MvelConstraint.java:201)
10:41:13,000 ERROR [stderr] (Thread-169) at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
10:41:13,001 ERROR [stderr] (Thread-169) at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
10:41:13,002 ERROR [stderr] (Thread-169) at
java.lang.Thread.run(Thread.java:662)
10:41:13,002 ERROR [stderr] (Thread-169) Caused by: java.lang.VerifyError:
(class: ConditionEvaluator51817e9f4a7542c5b295be7d674f854c, method: evaluate
signature:
(Ljava/lang/Object;Lorg/drools/common/InternalWorkingMemory;Lorg/drools/reteoo/LeftTuple;)Z)
Expecting to find object/array on stack
10:41:13,004 ERROR [stderr] (Thread-169) at
java.lang.Class.getDeclaredConstructors0(Native Method)
10:41:13,004 ERROR [stderr] (Thread-169) at
java.lang.Class.privateGetDeclaredConstructors(Class.java:2389)
10:41:13,005 ERROR [stderr] (Thread-169) at
java.lang.Class.getConstructor0(Class.java:2699)
10:41:13,005 ERROR [stderr] (Thread-169) at
java.lang.Class.getConstructor(Class.java:1657)
10:41:13,006 ERROR [stderr] (Thread-169) at
org.drools.rule.builder.dialect.asm.ClassGenerator.newInstance(ClassGenerator.java:173)
10:41:13,006 ERROR [stderr] (Thread-169) at
org.drools.rule.constraint.ASMConditionEvaluatorJitter.jitEvaluator(ASMConditionEvaluatorJitter.java:53)
10:41:13,007 ERROR [stderr] (Thread-169) at
org.drools.rule.constraint.MvelConstraint.executeJitting(MvelConstraint.java:217)
10:41:13,008 ERROR [stderr] (Thread-169) ... 5 more
Could anyone indicate how to fix this?
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13 years
Using Guvnor with Seam
by rjr201
Hi,
I'm very interested in using Drools Guvnor with Seam and was hoping someone
here may have some experience of doing this.
I've currently got Seam 2.3 working fine with Guvnor 5.3. My question is, is
it possible to get Seam 2.3 working with Guvnor 5.5? Or is it necessary to
move onto Seam 3 in order to do this?
>From my understanding, the drools libraries that come with Seam 2.3 aren't
compatible with versions of Guvnor later than 5.3. I've experimented with
replacing Seam's drools libraries with the latest drools libraries (as used
by Guvnor 5.5) but then Seam complains, as it requires the older drools
libraries for some of it's internal workings.
Any advice/experience with this would be greatly appreciated.
Rich.
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13 years
Collecting items in a List
by devan.vanreenen＠gmail.com
Hi there,
I have checked existing posts and able to find problems which are similar to
mine but not exactly.
I have an Alert object as per below, several alert instances may have the
same caseNumber
I am trying to collect all the Alert instances that have the same
caseNumber, the rule is below, the rule below collects the items correctly
but the execution happens for each Alert object inserted into the knowledge
session. How can I get around this?
public class Alert {
int caseNumber;
short alertNo;
public int getCaseNumber() {
return caseNumber;
}
public void setCaseNumber(int caseNumber) {
this.caseNumber = caseNumber;
}
public short getAlertNo() {
return alertNo;
}
public void setAlertNo(short alertNo) {
this.alertNo = alertNo;
}
@Override
public String toString() {
return "Alert [caseNumber=" + caseNumber + ", alertNo=" + alertNo + "]";
}
}
rule 'Collect Alerts for a specific case'
dialect 'java'
when
Alert( $caseNumber : caseNumber)
$list : List( ) from collect($alertalert : Alert( caseNumber ==
$caseNumber))
then
for(Object a : $list){
System.out.println(a);
}
end
I insert 5 alert objects as per below
Alert alert1 = new Alert();
alert1.setAlertNo((short)1);
alert1.setCaseNumber(830826);
Alert alert4 = new Alert();
alert4.setAlertNo((short)4);
alert4.setCaseNumber(830826);
Alert alert7 = new Alert();
alert7.setAlertNo((short)7);
alert7.setCaseNumber(830826);
Alert alert3 = new Alert();
alert3.setAlertNo((short)3);
alert3.setCaseNumber(820424);
Alert alert5 = new Alert();
alert5.setAlertNo((short)5);
alert5.setCaseNumber(820424);
I would like the output to be as follows
Alert [caseNumber=820424, alertNo=3]
Alert [caseNumber=820424, alertNo=5]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=1]
but instead the output is
Alert [caseNumber=820424, alertNo=5]
Alert [caseNumber=820424, alertNo=5]
Alert [caseNumber=820424, alertNo=3]
Alert [caseNumber=820424, alertNo=5]
Alert [caseNumber=820424, alertNo=3]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=1]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=1]
Alert [caseNumber=830826, alertNo=7]
Alert [caseNumber=830826, alertNo=4]
Alert [caseNumber=830826, alertNo=1]
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13 years
Unknown execution error: jitting
by David R Robison
I have a rule that runs fine when I execute it inside Guvnor in a Test
Scenario but when I run it in production I get the following error.
Exception in thread "Thread-24" java.lang.RuntimeException: Exception
jitting: $incidentRoutingIncreasing.isIncreasing &&
$sign.routeMileMarker > routeMileMarker ||
!$incidentRoutingIncreasing.isIncreasing && $sign.routeMileMarker <
routeMileMarker
at
org.drools.rule.constraint.MvelConstraint.executeJitting(MvelConstraint.java:219)
at
org.drools.rule.constraint.MvelConstraint.access$000(MvelConstraint.java:41)
at
org.drools.rule.constraint.MvelConstraint$1.run(MvelConstraint.java:201)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.VerifyError: (class:
ConditionEvaluatorebdfa6ebae044e95bc706dfcd6f5654a, method: evaluate
signature:
(Ljava/lang/Object;Lorg/drools/common/InternalWorkingMemory;Lorg/drools/reteoo/LeftTuple;)Z)
Expecting to find integer on stack
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2404)
at java.lang.Class.getConstructor0(Class.java:2714)
at java.lang.Class.getConstructor(Class.java:1674)
at
org.drools.rule.builder.dialect.asm.ClassGenerator.newInstance(ClassGenerator.java:173)
at
org.drools.rule.constraint.ASMConditionEvaluatorJitter.jitEvaluator(ASMConditionEvaluatorJitter.java:53)
at
org.drools.rule.constraint.MvelConstraint.executeJitting(MvelConstraint.java:217)
... 5 more
The rule does seem to fire. Any idea what it is trying to tell me or any
hints on how to debug this?
TNX David
--
David R Robison
Open Roads Consulting, Inc.
103 Watson Road, Chesapeake, VA 23320
phone: (757) 546-3401
e-mail: drrobison(a)openroadsconsulting.com
web: http://openroadsconsulting.com
blog: http://therobe.blogspot.com
book: http://www.xulonpress.com/bookstore/bookdetail.php?PB_ISBN=9781597816526
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13 years
drools-expert: Log atomic assertions !?
by bholzer
Is wonder how to log atomic assertions (i.e. the results of the Rete-Nodes -
visits ) ?
I tried the three Debug*EventListeners, but they're too coarse-grained.
As a workaround, I patched org.drools.reteoo.AlphaNode.assertObject(...) as
follows:
public void assertObject(...) {
final AlphaMemory memory = (AlphaMemory)
workingMemory.getNodeMemory( this );
boolean allowed = this.constraint.isAllowed(factHandle,
workingMemory, memory.context );
*log("Eval of " + this.constraint + " on " + factHandle.getObject()
+ ":" + allowed);*
if ( allowed ) {
this.sink.propagateAssertObject(factHandle, context,
workingMemory);
}
}
Is there a better way to archieve my goal ?
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13 years
