[Biojava-dev] newLine is not consistent across platforms

[Andreas Prlic]

I am just taking a look at the XML spec and what they recommend about
this issue. I am sure we are not the first to encounter this...

http://www.w3.org/TR/REC-xml/#sec-line-ends

I haven't looked at your commit yet. I'll comment on this after I have
thought about this a bit more.

Andreas



On Fri, Sep 16, 2011 at 6:05 AM, Amr AL-Hossary
<amr_alhossary at hotmail.com> wrote:
> Well,
> looking at the org.biojava.bio.structure.TestSECalignment..
> Using AFPChainXMLParser.fromXML then AFPChainXMLConverter.toXML doesn't
> generate the same XML in accordance to the end line delimiter: The first
> implementation validated XML equality using assertEquals(String,String),
> which doesn't -by all means- tolerate any difference in any single
> character.
>
> I agree with Dr. Andreas that we should end the lines using
> printStream.println(), leaving the matter of selecting which line delimiter
> to choose to the system.
> The drawback of this approach is we can't guarantee where (on which OS) was
> the XML produced & where will it be consumed in order to be sure that the
> delimiter of choice is \n or \r\n.
> So, we need a utility function that asserts equality of XML (if there is not
> one already present in the assertXXX() suit).
>
> So, as a 1ry solution, I made a utility method that compares Strings line by
> line, ignoring the end line delimiter. I used the standard java class
> java.util.Scanner because it tolerate all & every type of line delimiter.
> Here is a line of Scanner source code:
> private static final String LINE_SEPARATOR_PATTERN =
> "\r\n|[\n\r\u2028\u2029\u0085]";
>
>
> Please inspect SVN revision 9232 to have my full picture. I welcome all
> comments
>
>
> Amr
> I hope this mail is delivered to the group this time :(
>
> ------------------
>
> --------------------------------------------------
> From: "Andreas Prlic" <andreas at sdsc.edu>
> Sent: Thursday, September 15, 2011 8:57 PM
> To: "Scooter Willis" <HWillis at scripps.edu>
> Cc: "Amr AL-Hossary" <amr_alhossary at hotmail.com>;
> <biojava-dev at lists.open-bio.org>
> Subject: Re: [Biojava-dev] newLine is not consistent across platforms
>
>> ok, that sounds like a bug with the genome browser who shall not be
>> named. I still think the correct default behaviour for an API is to
>> use the system property. The GFF3 export method could allow to work
>> around this by getting a flag "use unix style newline". If people
>> think this is a problem at more places, we can provide a central
>> utility method which could allow to switch the newline across the
>> API..
>>
>> A
>>
>> On Thu, Sep 15, 2011 at 10:59 AM, Scooter Willis <HWillis at scripps.edu>
>> wrote:
>>>
>>> Andreas
>>>
>>> You can't win that way either. As an example I think GFF3 file format
>>> when
>>> used with a unmentioned open source genome browser will only work if \n
>>> is
>>> the line terminator.
>>>
>>> Scooter
>>>
>>> On 9/15/11 1:20 PM, "Andreas Prlic" <andreas at sdsc.edu> wrote:
>>>
>>>> Hi Amr,
>>>>
>>>> yea, the newline should never be written as \n or \r\n but requested
>>>> from System.getProperty("line.separator"); Did we have many instances
>>>> of this? I thought we were pretty consistent in avoiding this.. I am
>>>> not sure if we need a central place for this. Perhaps all we need is
>>>> to remind all developers to avoid hard coding this and using the
>>>> System property instead.
>>>>
>>>> Andreas
>>>>
>>>>
>>>> 2011/9/15 Amr AL-Hossary <amr_alhossary at hotmail.com>:
>>>>>
>>>>> Here is another assertion exception:
>>>>> The end line delimiter is different across platforms.
>>>>> So, I created a new helper class for common String assertion
>>>>> manipulation
>>>>> tasks.
>>>>>
>>>>> Please feel free to use it in all common String manipulation tasks.
>>>>>
>>>>> Well, my question is: where could it be put (a common place) to be used
>>>>> by
>>>>> all test classes?
>>>>>
>>>>> Amr
>>>>> ------------
>>>>> This mail is sent for the 5th time
>>>>>
>>>>>
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>>
>>
>>
>>