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Posted to user@uima.apache.org by Bonnie MacKellar <bk...@gmail.com> on 2016/07/06 00:41:14 UTC
missing Ruta annotations from uimaFit
I have a very lengthy Ruta script which annotates my files successfully. I
can see all the annotations in AnnotationBrowser and they are correct.
I want to get all the annotations in a Java program, so I can count
occurrences. I am using uimaFit. I am getting very odd results.
When I use CasDumpWriter, I see all my annotations, correctly written to
the dump file. Here is the code that does this
-------------------------------------------------------------------------------------------------------
AnalysisEngineDescription rutaEngineDesc =
AnalysisEngineFactory.createEngineDescription(RutaEngine.class,
RutaEngine.PARAM_MAIN_SCRIPT,
"ecClassifier",
RutaEngine.PARAM_SCRIPT_PATHS, new String[]
{"/home/bonnie/Research/eclipse-uima-projects/counttypes/src/main/ruta"},
RutaEngine.PARAM_DESCRIPTOR_PATHS, new String[]
{"/home/bonnie/Research/eclipse-uima-projects/counttypes/target/generated-sources/ruta/descriptor"},
RutaEngine.PARAM_ADDITIONAL_UIMAFIT_ENGINES,
"org.apache.uima.ruta.engine.PlainTextAnnotator");
AnalysisEngineDescription writerDesc =
AnalysisEngineFactory.createEngineDescription(CasDumpWriter.class,
CasDumpWriter.PARAM_OUTPUT_FILE, "dump2.txt");
AnalysisEngine rae = AnalysisEngineFactory.createEngine(rutaEngineDesc);
SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, writerDesc);
-----------------------------------------------------------------------------------------------------
However, when I try to do this myself, using iteratePipeline to iterate
through the JCas structures for each input file, many of the annotations
are missing. I have a suspicion that the missing annotations are ones that
annotate text for which there is another annotation. For example, text
will be annotated with Line, and with my own annotation. My code to print
the annotations is based on the code in CasDumpWriter.
-----------------------------------------------------------------------------------------------------
for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
rutaEngineDesc)) {
displayRutaResults(jcas);
public void displayRutaResults(JCas jcas)
{
System.out.println("in display ruta results");
FSIterator<Annotation> annotationIter =
jcas.getAnnotationIndex().iterator();
while (annotationIter.hasNext())
{
AnnotationFS annotation = annotationIter.next();
System.out.println(annotation.getType().getName());
System.out.println(annotation.getCoveredText());
System.out.println("------------------------------------------");
// System.out.println(annotation.toString());
}
}
------------------------------------------------------------------------------------------------
Why would this code produce different results than CasDumpWriter, which
uses almost exactly the same code? Is it something to do with using
runPipeline vs iteratePipeline? Should I write my code so it can be placed
inside runPipeline?
thanks so much!
Bonnie MacKellar
Re: missing Ruta annotations from uimaFit
Posted by Bonnie MacKellar <bk...@gmail.com>.
Hi,
Sure, but it will take a little while. I am slow with this stuff, and I
have a deadline. Thanks for all your help - I do have everything running
now.
Bonnie MacKellar
On Thu, Jul 7, 2016 at 2:50 PM, Richard Eckart de Castilho <re...@apache.org>
wrote:
> Dear Bonnie,
>
> > On 07.07.2016, at 18:58, Bonnie MacKellar <bk...@gmail.com> wrote:
> >
> > Only if I put the code in a class that is used in runPipeline do I get
> the
> > correct results. If you have any ideas about this, I would love to know.
>
> Can you produce a minimal example by which we could reproduce and
> investigate this?
>
> Cheers,
>
> -- Richard
>
Re: missing Ruta annotations from uimaFit
Posted by Richard Eckart de Castilho <re...@apache.org>.
Dear Bonnie,
> On 07.07.2016, at 18:58, Bonnie MacKellar <bk...@gmail.com> wrote:
>
> Only if I put the code in a class that is used in runPipeline do I get the
> correct results. If you have any ideas about this, I would love to know.
Can you produce a minimal example by which we could reproduce and
investigate this?
Cheers,
-- Richard
Re: missing Ruta annotations from uimaFit
Posted by Richard Eckart de Castilho <re...@apache.org>.
On 07.07.2016, at 18:58, Bonnie MacKellar <bk...@gmail.com> wrote:
>
> In any case, I almost have all the results I need. I have one more task - I
> need to figure out how to obtain text that was annotated with one
> particular annotation and NO OTHER. I am thinking that selectCovered might
> do what I need, but I can't find many examples of how to use it.
Something like this should work
boolean isLonelyAnnotation(AnnotationFS aAnno) {
return JCasUtil.selectCovered(AnnotationFS.class, aAnno).isEmpty();
}
If you look for selectCovered in action, check out e.g.
https://github.com/apache/uima-uimafit/search?utf8=✓&q=selectCovered
https://github.com/dkpro/dkpro-core/search?utf8=✓&q=selectCovered
(Note that the uimaFIT repo on GitHub is NOT our main repo and we do
presently not accept pull requests coming through it).
Cheers,
-- Richard
Re: missing Ruta annotations from uimaFit
Posted by Bonnie MacKellar <bk...@gmail.com>.
Hi,
I fixed the problem by taking the same code and putting it in a class that
extends CasConsumer_ImplBase. This method is called from the class's
process method
private void processFeatureStructures(CAS aCAS) {
Iterator<AnnotationFS> annotationIterator =
aCAS.getAnnotationIndex().iterator();
while (annotationIterator.hasNext()) {
AnnotationFS annotation = annotationIterator.next();
try {
out.println("[" + annotation.getCoveredText() + "]");
Type type = annotation.getType();
String typeName = type.getName();
out.println("found annotation type " + typeName );
Integer count = typeCounts.get(typeName);
out.println("current count is " + count);
etc.
I then use this code
AnalysisEngineDescription myWriterDesc =
AnalysisEngineFactory.createEngineDescription(CountWriter.class,
CountWriter.PARAM_OUTPUT_FILE, "myOutput.txt");
SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, myWriterDesc);
to run it. And it works perfectly. All my annotations show up. Which is
great, because I now have my totals that I needed. But it isn't great,
because I cannot explain this. That worries me because it is hard to
develop complex systems when you don't understand the underlying model.
Also, this method does not work either, and I believe that it should
AnalysisEngine rae = AnalysisEngineFactory.createEngine(rutaEngineDesc);
JCas jCas = rae.newJCas();
jCas.setDocumentText(someText);
rae.process(jCas);
displayRutaResults(jCas);
In this case, the jCas contents were incorrect in the same way that they
were when I used
for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
rutaEngineDesc)) {
displayRutaResults(jcas);
Only if I put the code in a class that is used in runPipeline do I get the
correct results. If you have any ideas about this, I would love to know.
In any case, I almost have all the results I need. I have one more task - I
need to figure out how to obtain text that was annotated with one
particular annotation and NO OTHER. I am thinking that selectCovered might
do what I need, but I can't find many examples of how to use it.
thanks for your help,
Bonnie MacKellar
On Thu, Jul 7, 2016 at 4:48 AM, Peter Klügl <pe...@averbis.com>
wrote:
> Nope, that should not be a problem since the types are initialized in
> process()
>
>
> Am 07.07.2016 um 10:26 schrieb Richard Eckart de Castilho:
> > Hi,
> >
> > iteratePipeline and runPipeline should be mostly equivalent.
> > A difference occurs if you e.g. have a CAS multiplier within
> > an aggregate engine.
> >
> > runPipeline delegates the execution to the UIMA core and is able
> > to handle CAS multipliers.
> >
> > iteratePipeline (re)uses a single CAS instance which is passed
> > to the reader and all analysis engines in turn. It does not
> > support CAS multipliers.
> >
> > A user recently pointed out that uimaFIT 2.2.0 reintroduces a bug
> > in iteratePipeline - typeSystemInit() is not called [1].
> >
> > @Peter: could the missing call to typeSystemInit() be a problem for Ruta?
> >
> > Cheers,
> >
> > -- Richard
> >
> > [1] https://issues.apache.org/jira/browse/UIMA-4998
> >
> >> On 07.07.2016, at 09:17, Peter Klügl <pe...@averbis.com> wrote:
> >>
> >> Hi,
> >>
> >>
> >> I have no idea yet why the code with iteratePipeline does not work.
> >>
> >>
> >> Richard, do you have an idea?
> >>
> >>
> >> Are there any exceptions? Do you use the rae objects somewhere? Is your
> >> code hosted somewhere, e.g., on github? What do you mean by your own
> >> annotations? Annotations of an external type system or annotations added
> >> by another engine or reader?
> >>
> >>
> >> Best,
> >>
> >>
> >> Peter
> >>
> >>
> >> Am 06.07.2016 um 02:41 schrieb Bonnie MacKellar:
> >>> I have a very lengthy Ruta script which annotates my files
> successfully. I
> >>> can see all the annotations in AnnotationBrowser and they are correct.
> >>> I want to get all the annotations in a Java program, so I can count
> >>> occurrences. I am using uimaFit. I am getting very odd results.
> >>>
> >>> When I use CasDumpWriter, I see all my annotations, correctly written
> to
> >>> the dump file. Here is the code that does this
> >>>
> -------------------------------------------------------------------------------------------------------
> >>> AnalysisEngineDescription rutaEngineDesc =
> >>> AnalysisEngineFactory.createEngineDescription(RutaEngine.class,
> >>> RutaEngine.PARAM_MAIN_SCRIPT,
> >>> "ecClassifier",
> >>> RutaEngine.PARAM_SCRIPT_PATHS, new String[]
> >>>
> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/src/main/ruta"},
> >>> RutaEngine.PARAM_DESCRIPTOR_PATHS, new String[]
> >>>
> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/target/generated-sources/ruta/descriptor"},
> >>> RutaEngine.PARAM_ADDITIONAL_UIMAFIT_ENGINES,
> >>> "org.apache.uima.ruta.engine.PlainTextAnnotator");
> >>> AnalysisEngineDescription writerDesc =
> >>> AnalysisEngineFactory.createEngineDescription(CasDumpWriter.class,
> >>> CasDumpWriter.PARAM_OUTPUT_FILE, "dump2.txt");
> >>> AnalysisEngine rae =
> AnalysisEngineFactory.createEngine(rutaEngineDesc);
> >>> SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, writerDesc);
> >>>
> -----------------------------------------------------------------------------------------------------
> >>>
> >>> However, when I try to do this myself, using iteratePipeline to iterate
> >>> through the JCas structures for each input file, many of the
> annotations
> >>> are missing. I have a suspicion that the missing annotations are ones
> that
> >>> annotate text for which there is another annotation. For example,
> text
> >>> will be annotated with Line, and with my own annotation. My code to
> print
> >>> the annotations is based on the code in CasDumpWriter.
> >>>
> >>>
> -----------------------------------------------------------------------------------------------------
> >>>
> >>> for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
> >>> rutaEngineDesc)) {
> >>> displayRutaResults(jcas);
> >>>
> >>>
> >>> public void displayRutaResults(JCas jcas)
> >>> {
> >>> System.out.println("in display ruta results");
> >>>
> >>> FSIterator<Annotation> annotationIter =
> >>> jcas.getAnnotationIndex().iterator();
> >>> while (annotationIter.hasNext())
> >>> {
> >>> AnnotationFS annotation = annotationIter.next();
> >>> System.out.println(annotation.getType().getName());
> >>> System.out.println(annotation.getCoveredText());
> >>>
> >>> System.out.println("------------------------------------------");
> >>> // System.out.println(annotation.toString());
> >>> }
> >>> }
> >>>
> >>>
> ------------------------------------------------------------------------------------------------
> >>>
> >>> Why would this code produce different results than CasDumpWriter, which
> >>> uses almost exactly the same code? Is it something to do with using
> >>> runPipeline vs iteratePipeline? Should I write my code so it can be
> placed
> >>> inside runPipeline?
> >>>
> >>> thanks so much!
> >>> Bonnie MacKellar
> >>>
>
>
Re: missing Ruta annotations from uimaFit
Posted by Peter Klügl <pe...@averbis.com>.
Nope, that should not be a problem since the types are initialized in
process()
Am 07.07.2016 um 10:26 schrieb Richard Eckart de Castilho:
> Hi,
>
> iteratePipeline and runPipeline should be mostly equivalent.
> A difference occurs if you e.g. have a CAS multiplier within
> an aggregate engine.
>
> runPipeline delegates the execution to the UIMA core and is able
> to handle CAS multipliers.
>
> iteratePipeline (re)uses a single CAS instance which is passed
> to the reader and all analysis engines in turn. It does not
> support CAS multipliers.
>
> A user recently pointed out that uimaFIT 2.2.0 reintroduces a bug
> in iteratePipeline - typeSystemInit() is not called [1].
>
> @Peter: could the missing call to typeSystemInit() be a problem for Ruta?
>
> Cheers,
>
> -- Richard
>
> [1] https://issues.apache.org/jira/browse/UIMA-4998
>
>> On 07.07.2016, at 09:17, Peter Kl�gl <pe...@averbis.com> wrote:
>>
>> Hi,
>>
>>
>> I have no idea yet why the code with iteratePipeline does not work.
>>
>>
>> Richard, do you have an idea?
>>
>>
>> Are there any exceptions? Do you use the rae objects somewhere? Is your
>> code hosted somewhere, e.g., on github? What do you mean by your own
>> annotations? Annotations of an external type system or annotations added
>> by another engine or reader?
>>
>>
>> Best,
>>
>>
>> Peter
>>
>>
>> Am 06.07.2016 um 02:41 schrieb Bonnie MacKellar:
>>> I have a very lengthy Ruta script which annotates my files successfully. I
>>> can see all the annotations in AnnotationBrowser and they are correct.
>>> I want to get all the annotations in a Java program, so I can count
>>> occurrences. I am using uimaFit. I am getting very odd results.
>>>
>>> When I use CasDumpWriter, I see all my annotations, correctly written to
>>> the dump file. Here is the code that does this
>>> -------------------------------------------------------------------------------------------------------
>>> AnalysisEngineDescription rutaEngineDesc =
>>> AnalysisEngineFactory.createEngineDescription(RutaEngine.class,
>>> RutaEngine.PARAM_MAIN_SCRIPT,
>>> "ecClassifier",
>>> RutaEngine.PARAM_SCRIPT_PATHS, new String[]
>>> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/src/main/ruta"},
>>> RutaEngine.PARAM_DESCRIPTOR_PATHS, new String[]
>>> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/target/generated-sources/ruta/descriptor"},
>>> RutaEngine.PARAM_ADDITIONAL_UIMAFIT_ENGINES,
>>> "org.apache.uima.ruta.engine.PlainTextAnnotator");
>>> AnalysisEngineDescription writerDesc =
>>> AnalysisEngineFactory.createEngineDescription(CasDumpWriter.class,
>>> CasDumpWriter.PARAM_OUTPUT_FILE, "dump2.txt");
>>> AnalysisEngine rae = AnalysisEngineFactory.createEngine(rutaEngineDesc);
>>> SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, writerDesc);
>>> -----------------------------------------------------------------------------------------------------
>>>
>>> However, when I try to do this myself, using iteratePipeline to iterate
>>> through the JCas structures for each input file, many of the annotations
>>> are missing. I have a suspicion that the missing annotations are ones that
>>> annotate text for which there is another annotation. For example, text
>>> will be annotated with Line, and with my own annotation. My code to print
>>> the annotations is based on the code in CasDumpWriter.
>>>
>>> -----------------------------------------------------------------------------------------------------
>>>
>>> for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
>>> rutaEngineDesc)) {
>>> displayRutaResults(jcas);
>>>
>>>
>>> public void displayRutaResults(JCas jcas)
>>> {
>>> System.out.println("in display ruta results");
>>>
>>> FSIterator<Annotation> annotationIter =
>>> jcas.getAnnotationIndex().iterator();
>>> while (annotationIter.hasNext())
>>> {
>>> AnnotationFS annotation = annotationIter.next();
>>> System.out.println(annotation.getType().getName());
>>> System.out.println(annotation.getCoveredText());
>>>
>>> System.out.println("------------------------------------------");
>>> // System.out.println(annotation.toString());
>>> }
>>> }
>>>
>>> ------------------------------------------------------------------------------------------------
>>>
>>> Why would this code produce different results than CasDumpWriter, which
>>> uses almost exactly the same code? Is it something to do with using
>>> runPipeline vs iteratePipeline? Should I write my code so it can be placed
>>> inside runPipeline?
>>>
>>> thanks so much!
>>> Bonnie MacKellar
>>>
Re: missing Ruta annotations from uimaFit
Posted by Richard Eckart de Castilho <re...@apache.org>.
Hi,
iteratePipeline and runPipeline should be mostly equivalent.
A difference occurs if you e.g. have a CAS multiplier within
an aggregate engine.
runPipeline delegates the execution to the UIMA core and is able
to handle CAS multipliers.
iteratePipeline (re)uses a single CAS instance which is passed
to the reader and all analysis engines in turn. It does not
support CAS multipliers.
A user recently pointed out that uimaFIT 2.2.0 reintroduces a bug
in iteratePipeline - typeSystemInit() is not called [1].
@Peter: could the missing call to typeSystemInit() be a problem for Ruta?
Cheers,
-- Richard
[1] https://issues.apache.org/jira/browse/UIMA-4998
> On 07.07.2016, at 09:17, Peter Klügl <pe...@averbis.com> wrote:
>
> Hi,
>
>
> I have no idea yet why the code with iteratePipeline does not work.
>
>
> Richard, do you have an idea?
>
>
> Are there any exceptions? Do you use the rae objects somewhere? Is your
> code hosted somewhere, e.g., on github? What do you mean by your own
> annotations? Annotations of an external type system or annotations added
> by another engine or reader?
>
>
> Best,
>
>
> Peter
>
>
> Am 06.07.2016 um 02:41 schrieb Bonnie MacKellar:
>> I have a very lengthy Ruta script which annotates my files successfully. I
>> can see all the annotations in AnnotationBrowser and they are correct.
>> I want to get all the annotations in a Java program, so I can count
>> occurrences. I am using uimaFit. I am getting very odd results.
>>
>> When I use CasDumpWriter, I see all my annotations, correctly written to
>> the dump file. Here is the code that does this
>> -------------------------------------------------------------------------------------------------------
>> AnalysisEngineDescription rutaEngineDesc =
>> AnalysisEngineFactory.createEngineDescription(RutaEngine.class,
>> RutaEngine.PARAM_MAIN_SCRIPT,
>> "ecClassifier",
>> RutaEngine.PARAM_SCRIPT_PATHS, new String[]
>> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/src/main/ruta"},
>> RutaEngine.PARAM_DESCRIPTOR_PATHS, new String[]
>> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/target/generated-sources/ruta/descriptor"},
>> RutaEngine.PARAM_ADDITIONAL_UIMAFIT_ENGINES,
>> "org.apache.uima.ruta.engine.PlainTextAnnotator");
>> AnalysisEngineDescription writerDesc =
>> AnalysisEngineFactory.createEngineDescription(CasDumpWriter.class,
>> CasDumpWriter.PARAM_OUTPUT_FILE, "dump2.txt");
>> AnalysisEngine rae = AnalysisEngineFactory.createEngine(rutaEngineDesc);
>> SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, writerDesc);
>> -----------------------------------------------------------------------------------------------------
>>
>> However, when I try to do this myself, using iteratePipeline to iterate
>> through the JCas structures for each input file, many of the annotations
>> are missing. I have a suspicion that the missing annotations are ones that
>> annotate text for which there is another annotation. For example, text
>> will be annotated with Line, and with my own annotation. My code to print
>> the annotations is based on the code in CasDumpWriter.
>>
>> -----------------------------------------------------------------------------------------------------
>>
>> for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
>> rutaEngineDesc)) {
>> displayRutaResults(jcas);
>>
>>
>> public void displayRutaResults(JCas jcas)
>> {
>> System.out.println("in display ruta results");
>>
>> FSIterator<Annotation> annotationIter =
>> jcas.getAnnotationIndex().iterator();
>> while (annotationIter.hasNext())
>> {
>> AnnotationFS annotation = annotationIter.next();
>> System.out.println(annotation.getType().getName());
>> System.out.println(annotation.getCoveredText());
>>
>> System.out.println("------------------------------------------");
>> // System.out.println(annotation.toString());
>> }
>> }
>>
>> ------------------------------------------------------------------------------------------------
>>
>> Why would this code produce different results than CasDumpWriter, which
>> uses almost exactly the same code? Is it something to do with using
>> runPipeline vs iteratePipeline? Should I write my code so it can be placed
>> inside runPipeline?
>>
>> thanks so much!
>> Bonnie MacKellar
>>
>
Re: missing Ruta annotations from uimaFit
Posted by Peter Klügl <pe...@averbis.com>.
Hi,
I have no idea yet why the code with iteratePipeline does not work.
Richard, do you have an idea?
Are there any exceptions? Do you use the rae objects somewhere? Is your
code hosted somewhere, e.g., on github? What do you mean by your own
annotations? Annotations of an external type system or annotations added
by another engine or reader?
Best,
Peter
Am 06.07.2016 um 02:41 schrieb Bonnie MacKellar:
> I have a very lengthy Ruta script which annotates my files successfully. I
> can see all the annotations in AnnotationBrowser and they are correct.
> I want to get all the annotations in a Java program, so I can count
> occurrences. I am using uimaFit. I am getting very odd results.
>
> When I use CasDumpWriter, I see all my annotations, correctly written to
> the dump file. Here is the code that does this
> -------------------------------------------------------------------------------------------------------
> AnalysisEngineDescription rutaEngineDesc =
> AnalysisEngineFactory.createEngineDescription(RutaEngine.class,
> RutaEngine.PARAM_MAIN_SCRIPT,
> "ecClassifier",
> RutaEngine.PARAM_SCRIPT_PATHS, new String[]
> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/src/main/ruta"},
> RutaEngine.PARAM_DESCRIPTOR_PATHS, new String[]
> {"/home/bonnie/Research/eclipse-uima-projects/counttypes/target/generated-sources/ruta/descriptor"},
> RutaEngine.PARAM_ADDITIONAL_UIMAFIT_ENGINES,
> "org.apache.uima.ruta.engine.PlainTextAnnotator");
> AnalysisEngineDescription writerDesc =
> AnalysisEngineFactory.createEngineDescription(CasDumpWriter.class,
> CasDumpWriter.PARAM_OUTPUT_FILE, "dump2.txt");
> AnalysisEngine rae = AnalysisEngineFactory.createEngine(rutaEngineDesc);
> SimplePipeline.runPipeline(readerDesc, rutaEngineDesc, writerDesc);
> -----------------------------------------------------------------------------------------------------
>
> However, when I try to do this myself, using iteratePipeline to iterate
> through the JCas structures for each input file, many of the annotations
> are missing. I have a suspicion that the missing annotations are ones that
> annotate text for which there is another annotation. For example, text
> will be annotated with Line, and with my own annotation. My code to print
> the annotations is based on the code in CasDumpWriter.
>
> -----------------------------------------------------------------------------------------------------
>
> for (JCas jcas : SimplePipeline.iteratePipeline(readerDesc,
> rutaEngineDesc)) {
> displayRutaResults(jcas);
>
>
> public void displayRutaResults(JCas jcas)
> {
> System.out.println("in display ruta results");
>
> FSIterator<Annotation> annotationIter =
> jcas.getAnnotationIndex().iterator();
> while (annotationIter.hasNext())
> {
> AnnotationFS annotation = annotationIter.next();
> System.out.println(annotation.getType().getName());
> System.out.println(annotation.getCoveredText());
>
> System.out.println("------------------------------------------");
> // System.out.println(annotation.toString());
> }
> }
>
> ------------------------------------------------------------------------------------------------
>
> Why would this code produce different results than CasDumpWriter, which
> uses almost exactly the same code? Is it something to do with using
> runPipeline vs iteratePipeline? Should I write my code so it can be placed
> inside runPipeline?
>
> thanks so much!
> Bonnie MacKellar
>