CDB project

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CDB project

Nicolas Berveglieri
Hello,

we're a group of 4 students learning pharo since a few weeks. We picked up the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by march. If you have any specific request about the project let us now.

Oudjail Veis
Gamelin Kevin
Maroine Maxime
Berveglieri Nicolas
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Re: CDB project

Pierce Ng-3
On Fri, Feb 05, 2016 at 01:53:08PM +0100, Nicolas Berveglieri wrote:
> we're a group of 4 students learning pharo since a few weeks. We picked up
> the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by
> march. If you have any specific request about the project let us now.

Cool! I suppose you are going to implement CDB in Pharo that interoperates with
djb's C version and not just write an FFI wrapper, yes?

Pierce

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Re: CDB project

Ben Coman
In reply to this post by Nicolas Berveglieri
On Fri, Feb 5, 2016 at 8:53 PM, Nicolas Berveglieri
<[hidden email]> wrote:

> Hello,
>
> we're a group of 4 students learning pharo since a few weeks. We picked up
> the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by
> march. If you have any specific request about the project let us now.
>
> Oudjail Veis
> Gamelin Kevin
> Maroine Maxime
> Berveglieri Nicolas

Cool. Thanks for sharing.  I had not heard of CDB before.
cheers -ben

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Re: CDB project

Nicolas Berveglieri
We're going to do it in pure pharo first. If we can make it fast enough, we'll then wrappe the C version so we can compare them.

2016-02-05 15:04 GMT+01:00 Ben Coman <[hidden email]>:
On Fri, Feb 5, 2016 at 8:53 PM, Nicolas Berveglieri
<[hidden email]> wrote:
> Hello,
>
> we're a group of 4 students learning pharo since a few weeks. We picked up
> the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by
> march. If you have any specific request about the project let us now.
>
> Oudjail Veis
> Gamelin Kevin
> Maroine Maxime
> Berveglieri Nicolas

Cool. Thanks for sharing.  I had not heard of CDB before.
cheers -ben


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Re: CDB project

hernanmd
In reply to this post by Nicolas Berveglieri
Hello Nicolas,

Do you plan to bypass the 4GB index file limit?
Cheers,

Hernán


2016-02-05 9:53 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hello,

we're a group of 4 students learning pharo since a few weeks. We picked up the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by march. If you have any specific request about the project let us now.

Oudjail Veis
Gamelin Kevin
Maroine Maxime
Berveglieri Nicolas

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Re: CDB project

Nicolas Berveglieri
Hi, 

Thanks for the question, Tbh we didnt even think about bypassing it. Still we gave it a though because of your mail and we feel like doing so would create some problems. Mainly because its already coded like that in other languages, and a >4GB files wouldn't be able to be used with other languages so it would be restricted to pharo.

Nicolas

2016-02-08 16:13 GMT+01:00 Hernán Morales Durand <[hidden email]>:
Hello Nicolas,

Do you plan to bypass the 4GB index file limit?
Cheers,

Hernán


2016-02-05 9:53 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hello,

we're a group of 4 students learning pharo since a few weeks. We picked up the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by march. If you have any specific request about the project let us now.

Oudjail Veis
Gamelin Kevin
Maroine Maxime
Berveglieri Nicolas


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Re: CDB project

hernanmd
Hi Nicolas,

Thank you for checking. The reason why I ask is because such limit is important for bioinformatics. Next-Generation Sequencing (NGS) machines are generating bigger files (these are typically FASTQ files) everyday, have a look at this cdbfasta forum http://seqanswers.com/forums/showthread.php?t=15331 for an example of what's happening. Maybe the CDB designers didn't anticipated genomes would be available today. However, it's a nice project and is an important library.
Cheers,

Hernán



2016-02-12 9:33 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hi, 

Thanks for the question, Tbh we didnt even think about bypassing it. Still we gave it a though because of your mail and we feel like doing so would create some problems. Mainly because its already coded like that in other languages, and a >4GB files wouldn't be able to be used with other languages so it would be restricted to pharo.

Nicolas

2016-02-08 16:13 GMT+01:00 Hernán Morales Durand <[hidden email]>:
Hello Nicolas,

Do you plan to bypass the 4GB index file limit?
Cheers,

Hernán


2016-02-05 9:53 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hello,

we're a group of 4 students learning pharo since a few weeks. We picked up the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by march. If you have any specific request about the project let us now.

Oudjail Veis
Gamelin Kevin
Maroine Maxime
Berveglieri Nicolas



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Re: CDB project

Nicolas Berveglieri
hi sorry for responding so late we had a few days off. We checked your link and talked about it with Mr Ducasse, aswell as some bioinfo searchers from inria. They indeed told us that it would be interesting not to have the files size limitation. Since we split the team earlier in 2 different implementation of the same project. We decided that some of us will keep the limitation, and the other will remove it.

Also we're looking for some help about file reading with pharo. We couldn't find sufficient info about it on the web, if anyone has a link to share we would be gratefull. 

Nicolas

2016-02-12 22:05 GMT+01:00 Hernán Morales Durand <[hidden email]>:
Hi Nicolas,

Thank you for checking. The reason why I ask is because such limit is important for bioinformatics. Next-Generation Sequencing (NGS) machines are generating bigger files (these are typically FASTQ files) everyday, have a look at this cdbfasta forum http://seqanswers.com/forums/showthread.php?t=15331 for an example of what's happening. Maybe the CDB designers didn't anticipated genomes would be available today. However, it's a nice project and is an important library.
Cheers,

Hernán



2016-02-12 9:33 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hi, 

Thanks for the question, Tbh we didnt even think about bypassing it. Still we gave it a though because of your mail and we feel like doing so would create some problems. Mainly because its already coded like that in other languages, and a >4GB files wouldn't be able to be used with other languages so it would be restricted to pharo.

Nicolas

2016-02-08 16:13 GMT+01:00 Hernán Morales Durand <[hidden email]>:
Hello Nicolas,

Do you plan to bypass the 4GB index file limit?
Cheers,

Hernán


2016-02-05 9:53 GMT-03:00 Nicolas Berveglieri <[hidden email]>:
Hello,

we're a group of 4 students learning pharo since a few weeks. We picked up the CDB project (http://cr.yp.to/cdb.html), to hopefully get it done by march. If you have any specific request about the project let us now.

Oudjail Veis
Gamelin Kevin
Maroine Maxime
Berveglieri Nicolas




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Re: CDB project

Damien Cassou-2
Nicolas Berveglieri <[hidden email]> writes:

> Also we're looking for some help about file reading with pharo. We couldn't
> find sufficient info about it on the web, if anyone has a link to share we
> would be gratefull.

the Pharo Mooc contains a few slides about that:

    https://ci.inria.fr/pharo-contribution/job/PharoMooc/lastSuccessfulBuild/artifact/book-result/Slides/Week5/C019-W5S07-Files.pdf

--
Damien Cassou
http://damiencassou.seasidehosting.st

"Success is the ability to go from one failure to another without
losing enthusiasm." --Winston Churchill

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Re: CDB project

Nicolas Berveglieri
Hello, we're looking for a function similar to the function read, having this prototype:

public int read(byte[] b,
       int off,
       int len)
         throws IOException
(found there: https://docs.oracle.com/javase/7/docs/api/java/io/InputStream.html)

cheers,
Nicolas. B

2016-02-26 16:24 GMT+01:00 Damien Cassou <[hidden email]>:
Nicolas Berveglieri <[hidden email]> writes:

> Also we're looking for some help about file reading with pharo. We couldn't
> find sufficient info about it on the web, if anyone has a link to share we
> would be gratefull.

the Pharo Mooc contains a few slides about that:

    https://ci.inria.fr/pharo-contribution/job/PharoMooc/lastSuccessfulBuild/artifact/book-result/Slides/Week5/C019-W5S07-Files.pdf

--
Damien Cassou
http://damiencassou.seasidehosting.st

"Success is the ability to go from one failure to another without
losing enthusiasm." --Winston Churchill

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Re: CDB project

Sven Van Caekenberghe-2
I am not sure I understand the question correctly, but the closest equivalent in Pharo is

readInto: collection startingAt: offset count: requestedCount
  "Read requestedCount elements into collection starting at offset,
   returning the number of elements read, there could be less elements available."

There are others, but this is a fundamental one.

> On 04 Mar 2016, at 15:43, Nicolas Berveglieri <[hidden email]> wrote:
>
> Hello, we're looking for a function similar to the function read, having this prototype:
>
> public int read(byte[] b,
>        int off,
>        int len)
>          throws
> IOException
> (found there: https://docs.oracle.com/javase/7/docs/api/java/io/InputStream.html)
>
> cheers,
> Nicolas. B
>
> 2016-02-26 16:24 GMT+01:00 Damien Cassou <[hidden email]>:
> Nicolas Berveglieri <[hidden email]> writes:
>
> > Also we're looking for some help about file reading with pharo. We couldn't
> > find sufficient info about it on the web, if anyone has a link to share we
> > would be gratefull.
>
> the Pharo Mooc contains a few slides about that:
>
>     https://ci.inria.fr/pharo-contribution/job/PharoMooc/lastSuccessfulBuild/artifact/book-result/Slides/Week5/C019-W5S07-Files.pdf
>
> --
> Damien Cassou
> http://damiencassou.seasidehosting.st
>
> "Success is the ability to go from one failure to another without
> losing enthusiasm." --Winston Churchill
>


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Re: CDB project

Nicolas Berveglieri
Thx a lot thats exactly what we wanted !

Nicolas. B

2016-03-04 15:49 GMT+01:00 Sven Van Caekenberghe <[hidden email]>:
I am not sure I understand the question correctly, but the closest equivalent in Pharo is

readInto: collection startingAt: offset count: requestedCount
  "Read requestedCount elements into collection starting at offset,
   returning the number of elements read, there could be less elements available."

There are others, but this is a fundamental one.

> On 04 Mar 2016, at 15:43, Nicolas Berveglieri <[hidden email]> wrote:
>
> Hello, we're looking for a function similar to the function read, having this prototype:
>
> public int read(byte[] b,
>        int off,
>        int len)
>          throws
> IOException
> (found there: https://docs.oracle.com/javase/7/docs/api/java/io/InputStream.html)
>
> cheers,
> Nicolas. B
>
> 2016-02-26 16:24 GMT+01:00 Damien Cassou <[hidden email]>:
> Nicolas Berveglieri <[hidden email]> writes:
>
> > Also we're looking for some help about file reading with pharo. We couldn't
> > find sufficient info about it on the web, if anyone has a link to share we
> > would be gratefull.
>
> the Pharo Mooc contains a few slides about that:
>
>     https://ci.inria.fr/pharo-contribution/job/PharoMooc/lastSuccessfulBuild/artifact/book-result/Slides/Week5/C019-W5S07-Files.pdf
>
> --
> Damien Cassou
> http://damiencassou.seasidehosting.st
>
> "Success is the ability to go from one failure to another without
> losing enthusiasm." --Winston Churchill
>