[jira] [Closed] (OPENNLP-1179) BRAT Annotator service Fails to start

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1179?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-1179.


> BRAT Annotator service Fails to start 
> --
>
> Key: OPENNLP-1179
> URL: https://issues.apache.org/jira/browse/OPENNLP-1179
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Applications
>Affects Versions: 1.8.4
> Environment: Linux (Centos)
>Reporter: Daniel Russ
> Fix For: 1.8.5
>
>
> me@machine$ brat-annotation-service
> Error: Could not find or load main class opennlp.bratann.NameFinderAnnService
> caused by:
> /usr/bin/java -Xmx1024m -cp 'lib/*' opennlp.bratann.NameFinderAnnService
> should be:
> VACMD -Xmx1024m -cp $(echo $OPENNLP_HOME/lib/*.jar | tr ' ' ':') 
> opennlp.bratann.NameFinderAnnService $@
> as is found in the opennlp script.  I thought this was fixed already, but 
> clearly was not.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Resolved] (OPENNLP-1179) BRAT Annotator service Fails to start

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1179?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ resolved OPENNLP-1179.
--
Resolution: Fixed

The startup file now uses "-cp ${OpenNLPHome}/lib/* which includes all the jars 
in the lib directory.  

> BRAT Annotator service Fails to start 
> --
>
> Key: OPENNLP-1179
> URL: https://issues.apache.org/jira/browse/OPENNLP-1179
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Applications
>Affects Versions: 1.8.4
> Environment: Linux (Centos)
>Reporter: Daniel Russ
> Fix For: 1.8.5
>
>
> me@machine$ brat-annotation-service
> Error: Could not find or load main class opennlp.bratann.NameFinderAnnService
> caused by:
> /usr/bin/java -Xmx1024m -cp 'lib/*' opennlp.bratann.NameFinderAnnService
> should be:
> VACMD -Xmx1024m -cp $(echo $OPENNLP_HOME/lib/*.jar | tr ' ' ':') 
> opennlp.bratann.NameFinderAnnService $@
> as is found in the opennlp script.  I thought this was fixed already, but 
> clearly was not.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Created] (OPENNLP-1179) BRAT Annotator service Fails to start

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1179:


 Summary: BRAT Annotator service Fails to start 
 Key: OPENNLP-1179
 URL: https://issues.apache.org/jira/browse/OPENNLP-1179
 Project: OpenNLP
  Issue Type: Bug
  Components: Applications
Affects Versions: 1.8.4
 Environment: Linux (Centos)
Reporter: Daniel Russ
 Fix For: 1.8.5


me@machine$ brat-annotation-service
Error: Could not find or load main class opennlp.bratann.NameFinderAnnService

caused by:
/usr/bin/java -Xmx1024m -cp 'lib/*' opennlp.bratann.NameFinderAnnService

should be:
VACMD -Xmx1024m -cp $(echo $OPENNLP_HOME/lib/*.jar | tr ' ' ':') 
opennlp.bratann.NameFinderAnnService $@

as is found in the opennlp script.  I thought this was fixed already, but 
clearly was not.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Closed] (OPENNLP-1172) Add Annotator notes to BratAnnotation

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1172?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-1172.

Resolution: Fixed

> Add Annotator notes to BratAnnotation
> -
>
> Key: OPENNLP-1172
> URL: https://issues.apache.org/jira/browse/OPENNLP-1172
> Project: OpenNLP
>  Issue Type: Improvement
>  Components: Formats
>Affects Versions: 1.8.3
>Reporter: Daniel Russ
>Assignee: Daniel Russ
>Priority: Minor
> Fix For: 1.8.4
>
>
> The Brat Annotator allows Annotators to add Notes to entites/relations.  The 
> BratAnnotation class should reflect it.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Created] (OPENNLP-1172) Add Annotator notes to BratAnnotation

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1172:


 Summary: Add Annotator notes to BratAnnotation
 Key: OPENNLP-1172
 URL: https://issues.apache.org/jira/browse/OPENNLP-1172
 Project: OpenNLP
  Issue Type: Improvement
  Components: Formats
Affects Versions: 1.8.3
Reporter: Daniel Russ
Priority: Minor
 Fix For: 1.8.4


The Brat Annotator allows Annotators to add Notes to entites/relations.  The 
BratAnnotation class should reflect it.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Commented] (OPENNLP-1158) The Brat Annotation Service does not serialize results appropriately

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-1158?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16261394#comment-16261394
 ] 

Daniel Russ commented on OPENNLP-1158:
--

Making the fields in opennlp.bratann.NameFinderResource$NameAnn public solves 
this problem.

> The Brat Annotation Service does not serialize results appropriately
> 
>
> Key: OPENNLP-1158
> URL: https://issues.apache.org/jira/browse/OPENNLP-1158
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Applications
>Affects Versions: 1.8.3
>Reporter: Daniel Russ
> Fix For: 1.8.4
>
>
> After starting up the BratAnnotatorService NameFinderAnnSerive, BRAT passes 
> text to the service, but it never returns.
>  curl -v   -H "Content-type: text/plain" -H "Accept: application/json" -X 
> POST -d "I am a fireman" localhost:8123/ner
> * About to connect() to localhost port 8123 (#0)
> *   Trying 127.0.0.1... connected
> * Connected to localhost (127.0.0.1) port 8123 (#0)
> > POST /ner HTTP/1.1
> > User-Agent: curl/7.19.7 (x86_64-redhat-linux-gnu) libcurl/7.19.7 NSS/3.27.1 
> > zlib/1.2.3 libidn/1.18 libssh2/1.4.2
> > Host: localhost:8123
> > Content-type: text/plain
> > Accept: application/json
> > Content-Length: 14
> > 
> < HTTP/1.1 400 Bad Request
> < Content-Type: text/plain
> < Date: Tue, 21 Nov 2017 19:43:15 GMT
> < Connection: close
> < Content-Length: 247
> < 
> * Closing connection #0
> No serializer found for class opennlp.bratann.NameFinderResource$NameAnn and 
> no properties discovered to create BeanSerializer (to avoid exception, 
> disable SerializationFeature.FAIL_ON_EMPTY_BEANS) (through reference chain: 
> java.util.HashMap["0"]



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Created] (OPENNLP-1158) The Brat Annotation Service does not serialize results appropriately

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1158:


 Summary: The Brat Annotation Service does not serialize results 
appropriately
 Key: OPENNLP-1158
 URL: https://issues.apache.org/jira/browse/OPENNLP-1158
 Project: OpenNLP
  Issue Type: Bug
  Components: Applications
Affects Versions: 1.8.3
Reporter: Daniel Russ
 Fix For: 1.8.4


After starting up the BratAnnotatorService NameFinderAnnSerive, BRAT passes 
text to the service, but it never returns.

 curl -v   -H "Content-type: text/plain" -H "Accept: application/json" -X POST 
-d "I am a fireman" localhost:8123/ner

* About to connect() to localhost port 8123 (#0)
*   Trying 127.0.0.1... connected
* Connected to localhost (127.0.0.1) port 8123 (#0)
> POST /ner HTTP/1.1
> User-Agent: curl/7.19.7 (x86_64-redhat-linux-gnu) libcurl/7.19.7 NSS/3.27.1 
> zlib/1.2.3 libidn/1.18 libssh2/1.4.2
> Host: localhost:8123
> Content-type: text/plain
> Accept: application/json
> Content-Length: 14
> 
< HTTP/1.1 400 Bad Request
< Content-Type: text/plain
< Date: Tue, 21 Nov 2017 19:43:15 GMT
< Connection: close
< Content-Length: 247
< 
* Closing connection #0
No serializer found for class opennlp.bratann.NameFinderResource$NameAnn and no 
properties discovered to create BeanSerializer (to avoid exception, disable 
SerializationFeature.FAIL_ON_EMPTY_BEANS) (through reference chain: 
java.util.HashMap["0"]



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Created] (OPENNLP-1133) The Gaussian smoother cannot be used

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1133:


 Summary: The Gaussian smoother cannot be used
 Key: OPENNLP-1133
 URL: https://issues.apache.org/jira/browse/OPENNLP-1133
 Project: OpenNLP
  Issue Type: Bug
  Components: Machine Learning
Affects Versions: 1.8.2
Reporter: Daniel Russ
 Fix For: 1.8.3


In the  GISTrainer, the variable useGaussianSmoothing cannot be set using the 
TrainingParameters



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Created] (OPENNLP-1116) Add Concatenate Stream method for Collections of streams

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1116:


 Summary: Add Concatenate Stream method for Collections of streams
 Key: OPENNLP-1116
 URL: https://issues.apache.org/jira/browse/OPENNLP-1116
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: 1.8.1
Reporter: Daniel Russ
Priority: Trivial
 Fix For: 1.8.2


Minor change to opennlp.tools.util.ObjectStreamUtls.  First change the 
signature of the createObjectStream(final ObjectStream... streams)  to 
concatenateObjectStream(final ObjectStream... streams), and add a method 
concatenateObjectStream(final Collection streams)

The reason behind this is that I often pull data from multiple files, whereas 
it is possible to create an array of ObjectStreams, it is easier to work with 
Lists.  Also, the name of the method is clearer.  It concatenates a list/array 
of ObjectStreams  as opposed the the createObjectStream(final Collection 
collection) which makes an obectstream of items in the collection.



--
This message was sent by Atlassian JIRA
(v6.4.14#64029)

[jira] [Closed] (OPENNLP-1077) Make BratNameSampleStream constructors public

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1077?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-1077.

Resolution: Fixed

> Make BratNameSampleStream constructors public
> -
>
> Key: OPENNLP-1077
> URL: https://issues.apache.org/jira/browse/OPENNLP-1077
> Project: OpenNLP
>  Issue Type: Improvement
>  Components: Formats
>Affects Versions: 1.8.0
>Reporter: Daniel Russ
> Fix For: 1.8.1
>
>
> Reading in Brat formatted data without using the CLI or the 
> BratAnnotationService is difficult because the Constructor is public and the 
> Factory requires the program to supply the command line argument as a 
> String[].  



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Closed] (OPENNLP-1079) Refactor BratNameSampleStream

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1079?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-1079.

Resolution: Fixed

> Refactor BratNameSampleStream
> -
>
> Key: OPENNLP-1079
> URL: https://issues.apache.org/jira/browse/OPENNLP-1079
> Project: OpenNLP
>  Issue Type: Improvement
>Reporter: Daniel Russ
>Priority: Minor
>
> Create a BratAnnotationParser that parses a BratDocument and creates a 
> List   The NameSampleStream,read() method would call this 
> directly.
> Consider Making the changes for the other formats as well.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Created] (OPENNLP-1079) Refactor BratNameSampleStream

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1079:


 Summary: Refactor BratNameSampleStream
 Key: OPENNLP-1079
 URL: https://issues.apache.org/jira/browse/OPENNLP-1079
 Project: OpenNLP
  Issue Type: Improvement
Reporter: Daniel Russ
Priority: Minor


Create a BratAnnotationParser that parses a BratDocument and creates a 
List   The NameSampleStream,read() method would call this directly.

Consider Making the changes for the other formats as well.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Created] (OPENNLP-1077) Make BratNameSampleStream constructors public

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1077:


 Summary: Make BratNameSampleStream constructors public
 Key: OPENNLP-1077
 URL: https://issues.apache.org/jira/browse/OPENNLP-1077
 Project: OpenNLP
  Issue Type: Improvement
  Components: Formats
Affects Versions: 1.8.0
Reporter: Daniel Russ
 Fix For: 1.8.1


Reading in Brat formatted data without using the CLI or the 
BratAnnotationService is difficult because the Constructor is public and the 
Factory requires the program to supply the command line argument as a String[]. 
 



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Closed] (OPENNLP-1056) DictionaryLemmatizer throws a NullPointerException

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-1056?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-1056.

Resolution: Fixed

> DictionaryLemmatizer throws a NullPointerException
> --
>
> Key: OPENNLP-1056
> URL: https://issues.apache.org/jira/browse/OPENNLP-1056
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Lemmatizer
>Affects Versions: 1.8.0
>Reporter: Daniel Russ
>  Labels: easyfix
> Fix For: 1.8.0
>
>
> If the word/POS combination are not found in the dictionary, the Lemmatizer 
> throws a NPE.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Created] (OPENNLP-1056) DictionaryLemmatizer throws a NullPointerException

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-1056:


 Summary: DictionaryLemmatizer throws a NullPointerException
 Key: OPENNLP-1056
 URL: https://issues.apache.org/jira/browse/OPENNLP-1056
 Project: OpenNLP
  Issue Type: Bug
  Components: Lemmatizer
Affects Versions: 1.8.0
Reporter: Daniel Russ
 Fix For: 1.8.0


If the word/POS combination are not found in the dictionary, the Lemmatizer 
throws a NPE.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Closed] (OPENNLP-987) TrainerFactory.getEventTrainer() does not take a TrainingParameter

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-987?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ closed OPENNLP-987.
---
Resolution: Duplicate

Already fixed.  Not in the released version yet.

> TrainerFactory.getEventTrainer() does not take a TrainingParameter
> --
>
> Key: OPENNLP-987
> URL: https://issues.apache.org/jira/browse/OPENNLP-987
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Affects Versions: 1.7.2
>Reporter: Daniel Russ
>Priority: Minor
> Fix For: 1.8.0
>
>
> When creating a trainer, the client creates a TrainingParameter object.  
> Unfortunately, the TrainerFactory does not use it.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Created] (OPENNLP-987) TrainerFactory.getEventTrainer() does not take a TrainingParameter

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-987:
---

 Summary: TrainerFactory.getEventTrainer() does not take a 
TrainingParameter
 Key: OPENNLP-987
 URL: https://issues.apache.org/jira/browse/OPENNLP-987
 Project: OpenNLP
  Issue Type: Bug
  Components: Machine Learning
Affects Versions: 1.7.2
Reporter: Daniel Russ
Priority: Minor
 Fix For: 1.8.0


When creating a trainer, the client creates a TrainingParameter object.  
Unfortunately, the TrainerFactory does not use it.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Resolved] (OPENNLP-981) Training EventStream Hash was removed from event trainer

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-981?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ resolved OPENNLP-981.
-
Resolution: Fixed

Also added a test in PerceptronPrepAttachTest.java to check that the reportMap 
contained the hash.

> Training EventStream Hash was removed from event trainer
> 
>
> Key: OPENNLP-981
> URL: https://issues.apache.org/jira/browse/OPENNLP-981
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Affects Versions: 1.7.2
>Reporter: Daniel Russ
>Priority: Minor
> Fix For: 1.8.0
>
>




--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Created] (OPENNLP-981) Training EventStream Hash was removed from event trainer

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-981:
---

 Summary: Training EventStream Hash was removed from event trainer
 Key: OPENNLP-981
 URL: https://issues.apache.org/jira/browse/OPENNLP-981
 Project: OpenNLP
  Issue Type: Bug
  Components: Machine Learning
Affects Versions: 1.7.2
Reporter: Daniel Russ
Priority: Minor
 Fix For: 1.8.0






--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Resolved] (OPENNLP-977) TrainerFactory uses Deprecated methods

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-977?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ resolved OPENNLP-977.
-
Resolution: Fixed

> TrainerFactory uses Deprecated methods
> --
>
> Key: OPENNLP-977
> URL: https://issues.apache.org/jira/browse/OPENNLP-977
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Affects Versions: 1.7.2
>Reporter: Daniel Russ
>Priority: Minor
> Fix For: 1.8.0
>
>
> getEventTrainer/getEventModelSequenceTrainer use maps instead of Training 
> Parameters.  Also EventModelSequenceTrainer uses maps instead of 
> TrainingParameters.  This is not an outward facing interface to most users.  
> All init(Map,Map) methods should be deprecated 
> in favor of init(TraingParameters, Map



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Commented] (OPENNLP-974) DataIndexer Param can't be set to a class name

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-974?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15854581#comment-15854581
 ] 

Daniel Russ commented on OPENNLP-974:
-

this may have been addressed in OpenNLP-977

> DataIndexer Param can't be set to a class name
> --
>
> Key: OPENNLP-974
> URL: https://issues.apache.org/jira/browse/OPENNLP-974
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Affects Versions: 1.7.2
>Reporter: Joern Kottmann
>Priority: Minor
> Fix For: 1.7.3
>
>
> The DataIndexer factory is capable of loading a DataIndexer by its class 
> name. The TrainerFactory validation method rejects that as invalid. The 
> validation should be updated to allow this.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Resolved] (OPENNLP-971) Remove static training methods from GIS

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-971?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ resolved OPENNLP-971.
-
   Resolution: Won't Fix
Fix Version/s: (was: 1.7.3)

Since the class was deprecated, and all functionality of GIS was moved to 
GISTrainer.  This fix is no longer needed

> Remove static training methods from GIS
> ---
>
> Key: OPENNLP-971
> URL: https://issues.apache.org/jira/browse/OPENNLP-971
> Project: OpenNLP
>  Issue Type: Improvement
>  Components: Machine Learning
>Affects Versions: 1.7.1
>Reporter: Daniel Russ
>Priority: Minor
>
> The pluggable TrainingParameters has been implemented.  There is no reason to 
> call the static train methods on GIS.  They should be Deprecated in 1.7.3, 
> and removed in a later version.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

[jira] [Updated] (OPENNLP-929) GIS not indexing

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-929?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ updated OPENNLP-929:

Attachment: GisIndexTest.java

> GIS not indexing
> 
>
> Key: OPENNLP-929
> URL: https://issues.apache.org/jira/browse/OPENNLP-929
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Reporter: Daniel Russ
> Attachments: GisIndexTest.java
>
>
> If the user calls the GIS.train(ObjectStream) methods, the trainer is 
> not indexing.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Commented] (OPENNLP-929) GIS not indexing

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-929?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15815589#comment-15815589
 ] 

Daniel Russ commented on OPENNLP-929:
-

I am not sure why this was not caught by any of the JUnit tests.  I have 
attached a JUnit test that fails

> GIS not indexing
> 
>
> Key: OPENNLP-929
> URL: https://issues.apache.org/jira/browse/OPENNLP-929
> Project: OpenNLP
>  Issue Type: Bug
>  Components: Machine Learning
>Reporter: Daniel Russ
>
> If the user calls the GIS.train(ObjectStream) methods, the trainer is 
> not indexing.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Created] (OPENNLP-929) GIS not indexing

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-929:
---

 Summary: GIS not indexing
 Key: OPENNLP-929
 URL: https://issues.apache.org/jira/browse/OPENNLP-929
 Project: OpenNLP
  Issue Type: Bug
  Components: Machine Learning
Reporter: Daniel Russ


If the user calls the GIS.train(ObjectStream) methods, the trainer is 
not indexing.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Created] (OPENNLP-927) Merge TrainingParameters and PluggableParameters

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-927:
---

 Summary: Merge TrainingParameters and PluggableParameters
 Key: OPENNLP-927
 URL: https://issues.apache.org/jira/browse/OPENNLP-927
 Project: OpenNLP
  Issue Type: New Feature
  Components: Machine Learning
Affects Versions: 1.7.0
Reporter: Daniel Russ
Priority: Minor


The PluggableParameters class was added to pull out the 
get(Int/String/Boolean)Parameters() methods from the AbstractTrainer.  Merge 
the functionality of the PluggableParameters into the TrainingParameters.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Created] (OPENNLP-900) DictionaryLemmatizer dictionary and LemmatizerME training format different

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-900:
---

 Summary: DictionaryLemmatizer dictionary and LemmatizerME training 
format different
 Key: OPENNLP-900
 URL: https://issues.apache.org/jira/browse/OPENNLP-900
 Project: OpenNLP
  Issue Type: Bug
  Components: Lemmatizer
Affects Versions: 1.6.0, 1.7.0
Reporter: Daniel Russ
Priority: Minor
 Fix For: 1.7.0


The LemmatizerME training data has a format of word\tpos\tlemma.
The DictionaryLemmatizer format is word\tlemma\tpos.

Can we make them the same.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Commented] (OPENNLP-880) Refactor the GIS trainer integration

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-880?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15768423#comment-15768423
 ] 

Daniel Russ commented on OPENNLP-880:
-

Pull request made.

> Refactor the GIS trainer integration
> 
>
> Key: OPENNLP-880
> URL: https://issues.apache.org/jira/browse/OPENNLP-880
> Project: OpenNLP
>  Issue Type: Improvement
>Reporter: Joern Kottmann
>Priority: Minor
> Attachments: patch.txt
>
>
> The GIS code was never reshaped to fit properly into the new Training API. 
> There are a couple of issues e.g. not using parameters which should be fixed.
> TODO: Update this description and list the changes 



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Updated] (OPENNLP-880) Refactor the GIS trainer integration

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-880?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ updated OPENNLP-880:

Attachment: patch.txt

> Refactor the GIS trainer integration
> 
>
> Key: OPENNLP-880
> URL: https://issues.apache.org/jira/browse/OPENNLP-880
> Project: OpenNLP
>  Issue Type: Improvement
>Reporter: Joern Kottmann
>Priority: Minor
> Attachments: patch.txt
>
>
> The GIS code was never reshaped to fit properly into the new Training API. 
> There are a couple of issues e.g. not using parameters which should be fixed.
> TODO: Update this description and list the changes 



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Commented] (OPENNLP-870) Please Make ContextGenerator a Generic Type

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-870?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15595197#comment-15595197
 ] 

Daniel Russ commented on OPENNLP-870:
-

/** Here is a Patch **/

diff --git 
a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/BasicContextGenerator.java
 
b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/BasicContextGenerator.java
index 1175ecc..ec90d60 100644
--- 
a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/BasicContextGenerator.java
+++ 
b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/BasicContextGenerator.java
@@ -29,7 +29,7 @@ package opennlp.tools.ml.maxent;
  * cp_1 cp_2 ... cp_n
  * 
  */
-public class BasicContextGenerator implements ContextGenerator {
+public class BasicContextGenerator implements ContextGenerator {
 
   private String separator = " ";
 
@@ -42,8 +42,7 @@ public class BasicContextGenerator implements 
ContextGenerator {
   /**
* Builds up the list of contextual predicates given a String.
*/
-  public String[] getContext(Object o) {
-String s = (String) o;
+  public String[] getContext(String s) {
 return (String[]) s.split(separator);
   }
 
diff --git 
a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/ContextGenerator.java 
b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/ContextGenerator.java
index 0582323..fa92846 100644
--- a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/ContextGenerator.java
+++ b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/ContextGenerator.java
@@ -22,11 +22,11 @@ package opennlp.tools.ml.maxent;
 /**
  * Generate contexts for maxent decisions.
  */
-public interface ContextGenerator {
+public interface ContextGenerator {
 
   /**
* Builds up the list of contextual predicates given an Object.
*/
-  public String[] getContext(Object o);
+  public String[] getContext(T o);
 
 }
diff --git 
a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/RealBasicEventStream.java 
b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/RealBasicEventStream.java
index 97ff167..682185a 100644
--- 
a/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/RealBasicEventStream.java
+++ 
b/opennlp-tools/src/main/java/opennlp/tools/ml/maxent/RealBasicEventStream.java
@@ -26,7 +26,7 @@ import opennlp.tools.ml.model.RealValueFileEventStream;
 import opennlp.tools.util.ObjectStream;
 
 public class RealBasicEventStream implements ObjectStream {
-  ContextGenerator cg = new BasicContextGenerator();
+  ContextGenerator cg = new BasicContextGenerator();
   ObjectStream ds;
 
   public RealBasicEventStream(ObjectStream ds) {


> Please Make ContextGenerator a Generic Type
> ---
>
> Key: OPENNLP-870
> URL: https://issues.apache.org/jira/browse/OPENNLP-870
> Project: OpenNLP
>  Issue Type: Improvement
>  Components: Machine Learning
>Reporter: Daniel Russ
>Priority: Minor
>   Original Estimate: 24h
>  Remaining Estimate: 24h
>
> public interface ContextGenerator {
>   /**
>* Builds up the list of contextual predicates given an Object.
>*/
>   public String[] getContext(T o);
> }
> If this is a generic method, it makes writing ContextGenerators easier to 
> debug at compile time.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Updated] (OPENNLP-786) Depricate EventStream

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-786?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ updated OPENNLP-786:

Description: GIS No longer  accepts an EventStream in GIS.trainModel(...).  
There is no need for the EventStream class anymore.  There are 2 
AbstractEventStream classes.  opennlp.tools.ml.model.AbstractEventStream and 
opennlp.tools.utils.EventStream. Remove or Deprecate 
opennlp.tools.ml.model.AbstractEventStream to avoid confusion.  (was: GIS No 
longer  accepts an EventStream in GIS.trainModel(...).  )

 Depricate EventStream
 -

 Key: OPENNLP-786
 URL: https://issues.apache.org/jira/browse/OPENNLP-786
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: 1.6.0
Reporter: Daniel Russ
 Fix For: 1.6.0


 GIS No longer  accepts an EventStream in GIS.trainModel(...).  There is no 
 need for the EventStream class anymore.  There are 2 AbstractEventStream 
 classes.  opennlp.tools.ml.model.AbstractEventStream and 
 opennlp.tools.utils.EventStream. Remove or Deprecate 
 opennlp.tools.ml.model.AbstractEventStream to avoid confusion.



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Updated] (OPENNLP-759) Speed up GIS training by saving Executor in the GISTrainer

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-759?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ updated OPENNLP-759:

Attachment: GISTrainer.patch

Sorry for the early problems.  I used svn diff  GISTrainer.patch to create 
this patch.  I hope it works.  Thank you. Dan

 Speed up GIS training by saving Executor in the GISTrainer
 --

 Key: OPENNLP-759
 URL: https://issues.apache.org/jira/browse/OPENNLP-759
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: maxent-3.0.3
Reporter: Daniel Russ
Assignee: Joern Kottmann
Priority: Minor
  Labels: Patch
 Attachments: GISTrainer.patch


 In GISTrainer.nextIteration(double) an ExecutorService is created and 
 shutdown.  I don't see a reason to create a ExecutorService for each 
 iteration.  
 If you create the ExecutorService in the TrainModels(int, dataindexer, Prior, 
 int, int) method you can save it as a field in GISTrainer or pass it as an 
 argument to findParameters(int, double).
 To test it out, I made a MyGIS and MyGISTrainer classes with the fixes.  
 There was a 5% speedup with 100 my dataset and 100 iterations of GIS.
 I would be happy to share the code with you.  (I can not share my data 
 though, sorry data-use agreements).



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Updated] (OPENNLP-759) Speed up GIS training by saving Executor in the GISTrainer

[Daniel Russ (JIRA)]

 [ 
https://issues.apache.org/jira/browse/OPENNLP-759?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Daniel Russ updated OPENNLP-759:

Attachment: (was: GISTrainer.patch)

 Speed up GIS training by saving Executor in the GISTrainer
 --

 Key: OPENNLP-759
 URL: https://issues.apache.org/jira/browse/OPENNLP-759
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: maxent-3.0.3
Reporter: Daniel Russ
Assignee: Joern Kottmann
Priority: Minor
  Labels: Patch
 Attachments: GISTrainer.patch


 In GISTrainer.nextIteration(double) an ExecutorService is created and 
 shutdown.  I don't see a reason to create a ExecutorService for each 
 iteration.  
 If you create the ExecutorService in the TrainModels(int, dataindexer, Prior, 
 int, int) method you can save it as a field in GISTrainer or pass it as an 
 argument to findParameters(int, double).
 To test it out, I made a MyGIS and MyGISTrainer classes with the fixes.  
 There was a 5% speedup with 100 my dataset and 100 iterations of GIS.
 I would be happy to share the code with you.  (I can not share my data 
 though, sorry data-use agreements).



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Commented] (OPENNLP-759) Speed up GIS training by saving Executor in the GISTrainer

[Daniel Russ (JIRA)]

[ 
https://issues.apache.org/jira/browse/OPENNLP-759?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=14347201#comment-14347201
 ] 

Daniel Russ commented on OPENNLP-759:
-

Added the file GISTrainer.patch.  This is my first patch file.  If it is not 
formatted properly, let me know and I can either give you the new code or you 
could give me a hand making the patch.

 Speed up GIS training by saving Executor in the GISTrainer
 --

 Key: OPENNLP-759
 URL: https://issues.apache.org/jira/browse/OPENNLP-759
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: maxent-3.0.3
Reporter: Daniel Russ
Priority: Minor
 Attachments: GISTrainer.patch


 In GISTrainer.nextIteration(double) an ExecutorService is created and 
 shutdown.  I don't see a reason to create a ExecutorService for each 
 iteration.  
 If you create the ExecutorService in the TrainModels(int, dataindexer, Prior, 
 int, int) method you can save it as a field in GISTrainer or pass it as an 
 argument to findParameters(int, double).
 To test it out, I made a MyGIS and MyGISTrainer classes with the fixes.  
 There was a 5% speedup with 100 my dataset and 100 iterations of GIS.
 I would be happy to share the code with you.  (I can not share my data 
 though, sorry data-use agreements).



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)

[jira] [Created] (OPENNLP-759) Speed up GIS training by saving Executor in the GISTrainer

[Daniel Russ (JIRA)]

Daniel Russ created OPENNLP-759:
---

 Summary: Speed up GIS training by saving Executor in the GISTrainer
 Key: OPENNLP-759
 URL: https://issues.apache.org/jira/browse/OPENNLP-759
 Project: OpenNLP
  Issue Type: Improvement
  Components: Machine Learning
Affects Versions: maxent-3.0.3
Reporter: Daniel Russ
Priority: Minor


In GISTrainer.nextIteration(double) an ExecutorService is created and shutdown. 
 I don't see a reason to create a ExecutorService for each iteration.  

If you create the ExecutorService in the TrainModels(int, dataindexer, Prior, 
int, int) method you can save it as a field in GISTrainer or pass it as an 
argument to findParameters(int, double).

To test it out, I made a MyGIS and MyGISTrainer classes with the fixes.  There 
was a 5% speedup with 100 my dataset and 100 iterations of GIS.

I would be happy to share the code with you.  (I can not share my data though, 
sorry data-use agreements).



--
This message was sent by Atlassian JIRA
(v6.3.4#6332)