error on Loading large text csv file to weka

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error on Loading large text csv file to weka

Daniel LIAO
Dear weka people,

I have encountered two problems when loading and filter large files (mainly strings): 

1. I can't load amazon_baby.csv in Explorer and reported an error message just saying "4 problem encountered on line: 34", I have no idea where went wrong. 

2. I am able to load and filter with StringToWordVector (on text attribute) through Explorer on dataset people_wiki.csv, but it takes a few minutes to load and process. Though weka completed without any error message, I didn't get any filtered result. Was it because the file is too large? I wonder is there a way to quickly load and filter, like doing it instance by instance in Weka?   

thanks in advance, 

Sincerely,

Daniel

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Re: error on Loading large text csv file to weka

Archie R

Hi Daniel

It's probably because of all the "" on that line:

"Lamaze Peekaboo, I Love You","we just got this book for our one-year-old and she loves it.  It\'s so nice that she can\'t bite chunks out of it like she can a board book or rip it like a paper one.  She can chew on it, pull on it, and carry it all over the house!  She loves the little flaps that open and is learning simple words like ""daddy,"" ""mommy,"" ""puppy,"" etc.  We love it.",5

I don't know how weka csv parsing works but this is likely tripping it up.    Usually there's a setting to indicate that you're doing quoting,  but if you don't want to deal with that you can probably strip most of the "" out of there since you probably don't need them.    To get a feel for how things work, try loading that one line on its own and mess around with it till you get through all the error messages.

Hope this helps,
Archie





On Sat, Dec 3, 2016 at 4:43 PM, Daniel LIAO <[hidden email]> wrote:
Dear weka people,

I have encountered two problems when loading and filter large files (mainly strings): 

1. I can't load amazon_baby.csv in Explorer and reported an error message just saying "4 problem encountered on line: 34", I have no idea where went wrong. 

2. I am able to load and filter with StringToWordVector (on text attribute) through Explorer on dataset people_wiki.csv, but it takes a few minutes to load and process. Though weka completed without any error message, I didn't get any filtered result. Was it because the file is too large? I wonder is there a way to quickly load and filter, like doing it instance by instance in Weka?   

thanks in advance, 

Sincerely,

Daniel

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Re: error on Loading large text csv file to weka

Peter Reutemann
> It's probably because of all the "" on that line:
>
> "Lamaze Peekaboo, I Love You","we just got this book for our one-year-old
> and she loves it.  It\'s so nice that she can\'t bite chunks out of it like
> she can a board book or rip it like a paper one.  She can chew on it, pull
> on it, and carry it all over the house!  She loves the little flaps that
> open and is learning simple words like ""daddy,"" ""mommy,"" ""puppy,"" etc.
> We love it.",5
>
> I don't know how weka csv parsing works but this is likely tripping it up.
> Usually there's a setting to indicate that you're doing quoting,  but if you
> don't want to deal with that you can probably strip most of the "" out of
> there since you probably don't need them.    To get a feel for how things
> work, try loading that one line on its own and mess around with it till you
> get through all the error messages.

Weka uses a backslash for escaping double quotes within text. In the
past, it couldn't handle the more common technique of doubling up
quotes within cells (used by LibreOffice, Excel, etc).

I loaded the CSV files using the Spreadsheet file viewer in ADAMS and
saved them as ARFF files:
- amazon_baby.arff:
  https://drive.google.com/open?id=0BxP96UNgPQUvRFhwWEgyQ21ySGM
- people_wiki.arff
  https://drive.google.com/open?id=0BxP96UNgPQUvcDIwQkQ2Uk9zUUk

Let me know when you've downloaded them.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/
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Re: error on Loading large text csv file to weka

Daniel LIAO
In reply to this post by Daniel LIAO
Thank you for your help! 

I have downloaded both arff files, and they are loaded perfectly. However, StringToWordVector still won't work, as  different instances caused errors for this filter. 

I tried to use Pyscript to replace some symbols like "+" to see whether this is a cause, the script works in the pyScripting console but it won't stop executing inside KnowledgeFlow's PyScriptExecutor. 

Are you able to make StringToWordVector Filter work for the 'review' column of amazon_baby dataset? 

Does weka has an easy-to-use filter to help replace symbols in string? 

Thanks again, 

Sincerely,

Daniel


> It's probably because of all the "" on that line:
>
> "Lamaze Peekaboo, I Love You","we just got this book for our one-year-old
> and she loves it.  It\'s so nice that she can\'t bite chunks out of it like
> she can a board book or rip it like a paper one.  She can chew on it, pull
> on it, and carry it all over the house!  She loves the little flaps that
> open and is learning simple words like ""daddy,"" ""mommy,"" ""puppy,"" etc.
> We love it.",5
>
> I don't know how weka csv parsing works but this is likely tripping it up.
> Usually there's a setting to indicate that you're doing quoting,  but if you
> don't want to deal with that you can probably strip most of the "" out of
> there since you probably don't need them.    To get a feel for how things
> work, try loading that one line on its own and mess around with it till you
> get through all the error messages.

Weka uses a backslash for escaping double quotes within text. In the
past, it couldn't handle the more common technique of doubling up
quotes within cells (used by LibreOffice, Excel, etc).

I loaded the CSV files using the Spreadsheet file viewer in ADAMS and
saved them as ARFF files:
- amazon_baby.arff:
  https://drive.google.com/open?id=0BxP96UNgPQUvRFhwWEgyQ21ySGM
- people_wiki.arff
  https://drive.google.com/open?id=0BxP96UNgPQUvcDIwQkQ2Uk9zUUk

Let me know when you've downloaded them.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/



2016-12-04 21:18 GMT+08:00 <[hidden email]>:
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Today's Topics:

   1. error on Loading large text csv file to weka (Daniel LIAO)
   2. Re: error on Loading large text csv file to weka (Archie Russell)
   3. Re: How to install Groovy to have access to Groovy console?
      (Mark Hall)
   4. Re: error on Loading large text csv file to weka (Peter Reutemann)
   5. Can we change the spliting criterion in classifiers (MAROU)


----------------------------------------------------------------------

Message: 1
Date: Sun, 4 Dec 2016 08:43:14 +0800
From: Daniel LIAO <[hidden email]>
To: [hidden email]
Subject: [Wekalist] error on Loading large text csv file to weka
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Dear weka people,

I have encountered two problems when loading and filter large files (mainly
strings):

1. I can't load amazon_baby.csv
<https://drive.google.com/open?id=0BwfMX-a2pWKsMkR4S3pqS3R1SGs> in Explorer
and reported an error message just saying "4 problem encountered on line:
34", I have no idea where went wrong.

2. I am able to load and filter with StringToWordVector (on text attribute)
through Explorer on dataset people_wiki.csv
<https://drive.google.com/open?id=0BwfMX-a2pWKsa3luLUZacHVCcVk>, but it
takes a few minutes to load and process. Though weka completed without any
error message, I didn't get any filtered result. Was it because the file is
too large? I wonder is there a way to quickly load and filter, like doing
it instance by instance in Weka?

thanks in advance,

Sincerely,

Daniel
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Message: 2
Date: Sat, 3 Dec 2016 20:47:48 -0800
From: Archie Russell <[hidden email]>
To: "Weka machine learning workbench list."
        <[hidden email]>
Subject: Re: [Wekalist] error on Loading large text csv file to weka
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hi Daniel

It's probably because of all the "" on that line:

"Lamaze Peekaboo, I Love You","we just got this book for our one-year-old
and she loves it.  It\'s so nice that she can\'t bite chunks out of it like
she can a board book or rip it like a paper one.  She can chew on it, pull
on it, and carry it all over the house!  She loves the little flaps that
open and is learning simple words like ""daddy,"" ""mommy,"" ""puppy,""
etc.  We love it.",5
I don't know how weka csv parsing works but this is likely tripping it up.
   Usually there's a setting to indicate that you're doing quoting,  but if
you don't want to deal with that you can probably strip most of the "" out
of there since you probably don't need them.    To get a feel for how
things work, try loading that one line on its own and mess around with it
till you get through all the error messages.

Hope this helps,
Archie





On Sat, Dec 3, 2016 at 4:43 PM, Daniel LIAO <[hidden email]>
wrote:

> Dear weka people,
>
> I have encountered two problems when loading and filter large files
> (mainly strings):
>
> 1. I can't load amazon_baby.csv
> <https://drive.google.com/open?id=0BwfMX-a2pWKsMkR4S3pqS3R1SGs> in
> Explorer and reported an error message just saying "4 problem encountered
> on line: 34", I have no idea where went wrong.
>
> 2. I am able to load and filter with StringToWordVector (on text
> attribute) through Explorer on dataset people_wiki.csv
> <https://drive.google.com/open?id=0BwfMX-a2pWKsa3luLUZacHVCcVk>, but it
> takes a few minutes to load and process. Though weka completed without any
> error message, I didn't get any filtered result. Was it because the file is
> too large? I wonder is there a way to quickly load and filter, like doing
> it instance by instance in Weka?
>
> thanks in advance,
>
> Sincerely,
>
> Daniel
>
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> List info and subscription status: https://list.waikato.ac.nz/
> mailman/listinfo/wekalist
> List etiquette: http://www.cs.waikato.ac.nz/~
> ml/weka/mailinglist_etiquette.html
>
>
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------------------------------

Message: 3
Date: Sun, 04 Dec 2016 21:01:49 +1300
From: Mark Hall <[hidden email]>
To: "Weka machine learning workbench list."
        <[hidden email]>
Subject: Re: [Wekalist] How to install Groovy to have access to Groovy
        console?
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

The groovy console appears for me in 3.8.0. It was not appearing in the nightly snapshot versions of Weka and I have just committed a fix that rectifies this. There is also a new version of the kfGroovy package available, and this is also needed if you are using a snapshot version of Weka.



Cheers,

Mark.





From: <[hidden email]> on behalf of Daniel LIAO <[hidden email]>
Reply-To: "Weka machine learning workbench list." <[hidden email]>
Date: Sunday, 4 December 2016 at 11:17 AM
To: "Weka machine learning workbench list." <[hidden email]>
Subject: [Wekalist] How to install Groovy to have access to Groovy console?



Dear Weka people,



I have installed kfgroovy and is able to access groovy scripting as a component of KnowledgeFlow, but I could not find Groovy console in the menu where Jython console is placed.



However, I didn't find anything else with a name 'groovy' in package manager. So, what should I do to install groovy console?



Also, there seems to be very few examples on coding weka in groovy console, where can I find more examples?



Thanks in advance,



Sincerely,



Daniel

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Message: 4
Date: Sun, 4 Dec 2016 22:19:39 +1300
From: Peter Reutemann <[hidden email]>
To: "Weka machine learning workbench list."
        <[hidden email]>
Subject: Re: [Wekalist] error on Loading large text csv file to weka
Message-ID:
        <CAHoQ12JW+xsDcO5RnDiYxSRx=WMzeVhY2o9z=2XS=[hidden email]>
Content-Type: text/plain; charset=UTF-8

> It's probably because of all the "" on that line:
>
> "Lamaze Peekaboo, I Love You","we just got this book for our one-year-old
> and she loves it.  It\'s so nice that she can\'t bite chunks out of it like
> she can a board book or rip it like a paper one.  She can chew on it, pull
> on it, and carry it all over the house!  She loves the little flaps that
> open and is learning simple words like ""daddy,"" ""mommy,"" ""puppy,"" etc.
> We love it.",5
>
> I don't know how weka csv parsing works but this is likely tripping it up.
> Usually there's a setting to indicate that you're doing quoting,  but if you
> don't want to deal with that you can probably strip most of the "" out of
> there since you probably don't need them.    To get a feel for how things
> work, try loading that one line on its own and mess around with it till you
> get through all the error messages.

Weka uses a backslash for escaping double quotes within text. In the
past, it couldn't handle the more common technique of doubling up
quotes within cells (used by LibreOffice, Excel, etc).

I loaded the CSV files using the Spreadsheet file viewer in ADAMS and
saved them as ARFF files:
- amazon_baby.arff:
  https://drive.google.com/open?id=0BxP96UNgPQUvRFhwWEgyQ21ySGM
- people_wiki.arff
  https://drive.google.com/open?id=0BxP96UNgPQUvcDIwQkQ2Uk9zUUk

Let me know when you've downloaded them.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/


------------------------------

Message: 5
Date: Sun, 4 Dec 2016 04:47:04 -0700 (MST)
From: MAROU <[hidden email]>
To: [hidden email]
Subject: [Wekalist] Can we change the spliting criterion in
        classifiers
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Hi weka team,

I have a question and i hope that you help me :)

Can we change the spliting criterion like the gain ratio in J48 by another
measure like correlation ?

in fact i want to test a new measure in some classifiers like J48, random
forest... to see his performance.

Thank you in advance



--
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Re: error on Loading large text csv file to weka

Peter Reutemann
> I have downloaded both arff files, and they are loaded perfectly. However,
> StringToWordVector still won't work, as  different instances caused errors
> for this filter.

Always post the full stacktrace, not just parts.

> I tried to use Pyscript to replace some symbols like "+" to see whether this
> is a cause, the script works in the pyScripting console but it won't stop
> executing inside KnowledgeFlow's PyScriptExecutor.
>
> Are you able to make StringToWordVector Filter work for the 'review' column
> of amazon_baby dataset?

Using the default settings, but operating only on the "review"
attribute, I get this:

java.lang.ArrayIndexOutOfBoundsException: 3
    at weka.core.DictionaryBuilder.processInstance(DictionaryBuilder.java:1608)
    at weka.filters.unsupervised.attribute.StringToWordVector.batchFinished(StringToWordVector.java:687)

After a bit of digging in the code, turns out that the
DictionaryBuilder might assume a nominal class, but your rating class
is numeric.
I turned on "doNotOperateOnPerClassBasis" and it worked fine.

> Does weka has an easy-to-use filter to help replace symbols in string?

Use the stopwords handler option of the filter, in conjunction with
RegExpFromFile (and define your regular expressions in that file).

NB: I'm using a pre 3.9.0 version, so your mileage may vary.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/
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Re: error on Loading large text csv file to weka

Eibe Frank-2
Administrator

> On 5/12/2016, at 6:27 PM, Peter Reutemann <[hidden email]> wrote:
>
> Using the default settings, but operating only on the "review"
> attribute, I get this:
>
> java.lang.ArrayIndexOutOfBoundsException: 3
>    at weka.core.DictionaryBuilder.processInstance(DictionaryBuilder.java:1608)
>    at weka.filters.unsupervised.attribute.StringToWordVector.batchFinished(StringToWordVector.java:687)
>
> After a bit of digging in the code, turns out that the
> DictionaryBuilder might assume a nominal class, but your rating class
> is numeric.
> I turned on "doNotOperateOnPerClassBasis" and it worked fine.

I’ve just checked in a fix for this. Thanks for the bug report.

Cheers,
Eibe

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Re: error on Loading large text csv file to weka

David Sant
In reply to this post by Peter Reutemann
error on Loading large text csv file to weka

I have encountered a problem when I try to load and filter this large csv
(mainly strings):

I can't load globalterrorismdb_0718dist.csv Global Terrorism Database from
https://www.kaggle.com/START-UMD/gtd in Explorer and reported an error
message just saying "135 problem encountered on line: 7", I have no idea
where went wrong.


thanks in advance,

Sincerely,

David




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Re: error on Loading large text csv file to weka

Peter Reutemann
> error on Loading large text csv file to weka
>
> I have encountered a problem when I try to load and filter this large csv
> (mainly strings):
>
> I can't load globalterrorismdb_0718dist.csv Global Terrorism Database from
> https://www.kaggle.com/START-UMD/gtd in Explorer and reported an error
> message just saying "135 problem encountered on line: 7", I have no idea
> where went wrong.

My guess is, that the CSVLoader cannot handle the double quotes in the
citations (column "scite1") correctly.

The CSV reader in ADAMS, which is independent of Weka, loads the data
just fine. With its Spreadsheet file reader tool, you can load the CSV
file and then save it as ARFF for further processing within Weka. Just
download the "adams-ml-app-snapshot-bin.zip" snapshot from the ADAMS
snapshot download page
(https://adams.cms.waikato.ac.nz/download/snapshot/).

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/
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Re: error on Loading large text csv file to weka

David Sant
Dear Peter,

First of all thanks for your support, unfortunately I followed your steps to
load the globalterrorismdb_0718dist.csv and Spreadsheet file viewer gave me
the following error:

<http://weka.8497.n7.nabble.com/file/t6717/SPREADSHEET.jpg>

Please could you help me with this problem.
Thanks in advance for your support.

Regards,
Pedro



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Re: error on Loading large text csv file to weka

Peter Reutemann
> First of all thanks for your support, unfortunately I followed your steps to
> load the globalterrorismdb_0718dist.csv and Spreadsheet file viewer gave me
> the following error:
>
> <http://weka.8497.n7.nabble.com/file/t6717/SPREADSHEET.jpg>
>
> Please could you help me with this problem.
> Thanks in advance for your support.

Hmm, never seen an empty error dialog before...

Just downloaded the snapshot, started it via "bin/start_gui.sh" (I'm
on Linux 64bit, Oracle JDK 10.0.2) and loaded the CSV file without any
problems (see attachment).

Any errors in the terminal or the "Console window" (main menu: Program
-> Console window)?

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/

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Re: error on Loading large text csv file to weka

Peter Reutemann
> Just downloaded the snapshot, started it via "bin/start_gui.sh" (I'm
> on Linux 64bit, Oracle JDK 10.0.2) and loaded the CSV file without any
> problems (see attachment).

Also worked fine on a virtualized Windows 10 64bit with Oracle JDK
1.8.0_171 64bit.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/
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