Re: Parsing embl format with biojava4

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Ok thank you, I'll consider Biojava 1.9 if embl files are not supported in
later versions.

By the way, I tried to compile biojava-legacy-1.9.2 and I got some tests
failing:

----------------------
cd biojava-legacy-biojava-legacy-1.9.2
mvn package
....
....

Results :


Failed tests:

  GenbankRichSequenceDBTest.testeFetch:24 Unexpected Bioexception:
org.biojava.bio.BioException: Failed to read Genbank sequence

  GenpeptRichSequenceDBTest.testeFetch:24 Unexpected BioException:
org.biojava.bio.BioException: Failed to read Genbank sequence


Tests run: 883, Failures: 2, Errors: 0, Skipped: 0


[INFO]
------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO]

[INFO] biojava-legacy ..................................... SUCCESS [
0.725 s]

[INFO] bytecode ........................................... SUCCESS [
1.505 s]

[INFO] core ............................................... FAILURE [
10.232 s]

[INFO] alignment .......................................... SKIPPED

[INFO] biosql ............................................. SKIPPED

[INFO] blast .............................................. SKIPPED

[INFO] sequencing ......................................... SKIPPED

[INFO] gui ................................................ SKIPPED

[INFO] phylo .............................................. SKIPPED

[INFO]
------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO]
------------------------------------------------------------------------

[INFO] Total time: 12.692 s

[INFO] Finished at: 2016-12-28T16:38:18+00:00

[INFO] Final Memory: 11M/220M

[INFO]
------------------------------------------------------------------------

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) on
project core: There are test failures.

[ERROR]

[ERROR] Please refer to
/Users/berald01/Downloads/biojava-legacy-biojava-legacy-1.9.2/core/target/surefire-reports
for the individual test results.

[ERROR] -> [Help 1]

[ERROR]

[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.

[ERROR] Re-run Maven using the -X switch to enable full debug logging.

[ERROR]

[ERROR] For more information about the errors and possible solutions,
please read the following articles:

[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[ERROR]

[ERROR] After correcting the problems, you can resume the build with the
command

[ERROR]   mvn <goals> -rf :core

On 28 December 2016 at 15:45, Michael Heuer <[email protected]> wrote:

> On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <[email protected]>
> wrote:
>
>> Hello,
>>
>> First, thanks for the great Biojava project!
>>
>> Is it possible to parse embl files using (Bio)Java?
>>
>> By Googling "biojava  embl format" I get some hits for the legacy Biojava
>> 1.9 but I'm wondering weather I could (should?) use the more recent Biojava
>> 4?
>>
>
> If biojava-legacy works fine for you, feel confident using it.  It is
> actively maintained; there just won't be any new features.
>
>
>
>> A more general question... Which is the primary source of documentation
>> for Biojava 4? Is it the tutorial at https://github.com/biojava/bio
>> java-tutorial together with the Javadocs (http://biojava.org/docs/api4.
>> 2.1/)?
>>
>> I find the home page Biojava.org a little confusing... The tutorial page
>> http://biojava.org/wiki/BioJava:CookBook4.0/ gives me a 404 error. The
>> wiki pages http://biojava.org/wiki.html seem a mixture of various topics.
>>
>
> The biojava.org website didn't survive a wiki migration to github without
> running into some problems.  If you find any, please file them as issues at
>
> https://github.com/biojava/biojava.github.io
>
>    michael
>

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<div dir=3D"ltr">Ok thank you, I&#39;ll consider Biojava 1.9 if embl files =
are not supported in later versions.=C2=A0<div><br></div><div>By the way, I=
 tried to compile biojava-legacy-1.9.2 and I got some tests failing:</div><=
div><br></div><div>----------------------</div><div>cd biojava-legacy-bioja=
va-legacy-1.9.2</div><div>mvn package</div><div>....</div><div>....</div><d=
iv>







<p class=3D"gmail-p1"><span class=3D"gmail-s1">Results :</span></p>
<p class=3D"gmail-p2"><span class=3D"gmail-s1"></span><br></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">Failed tests:=C2=A0</span></=
p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">=C2=A0 GenbankRichSequenceDB=
Test.testeFetch:24 Unexpected Bioexception: org.biojava.bio.BioException: F=
ailed to read Genbank sequence</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">=C2=A0 GenpeptRichSequenceDB=
Test.testeFetch:24 Unexpected BioException: org.biojava.bio.BioException: F=
ailed to read Genbank sequence</span></p>
<p class=3D"gmail-p2"><span class=3D"gmail-s1"></span><br></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">Tests run: 883, Failures: 2,=
 Errors: 0, Skipped: 0</span></p>
<p class=3D"gmail-p2"><span class=3D"gmail-s1"></span><br></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] ---------------------=
---------------------------------------------------</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] Reactor Summary:</spa=
n></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO]=C2=A0</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] biojava-legacy ......=
............................... SUCCESS [=C2=A0 0.725 s]</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] bytecode ............=
............................... SUCCESS [=C2=A0 1.505 s]</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] core ................=
............................... FAILURE [ 10.232 s]</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] alignment ...........=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] biosql ..............=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] blast ...............=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] sequencing ..........=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] gui .................=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] phylo ...............=
............................... SKIPPED</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] ---------------------=
---------------------------------------------------</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] BUILD FAILURE</span><=
/p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] ---------------------=
---------------------------------------------------</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] Total time: 12.692 s<=
/span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] Finished at: 2016-12-=
28T16:38:18+00:00</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] Final Memory: 11M/220=
M</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[INFO] ---------------------=
---------------------------------------------------</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] Failed to execute go=
al org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) =
on project core: There are test failures.</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] Please refer to /Use=
rs/berald01/Downloads/biojava-legacy-biojava-legacy-1.9.2/core/target/suref=
ire-reports for the individual test results.</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] -&gt; [Help 1]</span=
></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] To see the full stac=
k trace of the errors, re-run Maven with the -e switch.</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] Re-run Maven using t=
he -X switch to enable full debug logging.</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] For more information=
 about the errors and possible solutions, please read the following article=
s:</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] [Help 1] <a href=3D"=
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException">http=
://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException</a></span=
></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] After correcting the=
 problems, you can resume the build with the command</span></p>
<p class=3D"gmail-p1"><span class=3D"gmail-s1">[ERROR] =C2=A0 mvn &lt;goals=
&gt; -rf :core</span></p></div></div><div class=3D"gmail_extra"><br><div cl=
ass=3D"gmail_quote">On 28 December 2016 at 15:45, Michael Heuer <span dir=
=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">heuermh=
@gmail.com</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=
=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=
=3D"ltr">On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <span dir=3D"ltr">&=
lt;<a href=3D"mailto:[email protected]" target=3D"_blank">dario.beral=
[email protected]</a>&gt;</span> wrote:<br><div class=3D"gmail_extra"><div class=
=3D"gmail_quote"><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px =
0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=
=3D"ltr">Hello,<div><br></div><div>First, thanks for the great Biojava proj=
ect!</div><div><br></div><div>Is it possible to parse embl files using (Bio=
)Java?=C2=A0</div><div><br></div><div>By Googling &quot;biojava =C2=A0embl =
format&quot; I get some hits for the legacy Biojava 1.9 but I&#39;m wonderi=
ng weather I could (should?) use the more recent Biojava 4?</div></div></bl=
ockquote><div><br></div><div>If biojava-legacy works fine for you, feel con=
fident using it.=C2=A0 It is actively maintained; there just won&#39;t be a=
ny new features.<br><br></div><div>=C2=A0</div><blockquote class=3D"gmail_q=
uote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,2=
04);padding-left:1ex"><div dir=3D"ltr"><div>A more general question... Whic=
h is the primary source of documentation for Biojava 4? Is it the tutorial =
at <a href=3D"https://github.com/biojava/biojava-tutorial" target=3D"_blank=
">https://github.com/biojava/bio<wbr>java-tutorial</a> together with the Ja=
vadocs (<a href=3D"http://biojava.org/docs/api4.2.1/" target=3D"_blank">htt=
p://biojava.org/docs/api4.<wbr>2.1/</a>)?=C2=A0</div><div><br></div><div>I =
find the home page Biojava.org a little confusing... The tutorial page=C2=
=A0<a href=3D"http://biojava.org/wiki/BioJava:CookBook4.0/" target=3D"_blan=
k">http://biojava.org/wiki/B<wbr>ioJava:CookBook4.0/</a> gives me a 404 err=
or. The wiki pages=C2=A0<a href=3D"http://biojava.org/wiki.html" target=3D"=
_blank">http://biojava.org/wiki.<wbr>html</a> seem a mixture of various top=
ics.</div></div></blockquote><div><br></div><div>The <a href=3D"http://bioj=
ava.org" target=3D"_blank">biojava.org</a> website didn&#39;t survive a wik=
i migration to github without running into some problems.=C2=A0 If you find=
 any, please file them as issues at<br><br><a href=3D"https://github.com/bi=
ojava/biojava.github.io" target=3D"_blank">https://github.com/biojava/<wbr>=
biojava.github.io<span class=3D"HOEnZb"><font color=3D"#888888"><br></font>=
</span></a><span class=3D"HOEnZb"><font color=3D"#888888"><br></font></span=
></div><span class=3D"HOEnZb"><font color=3D"#888888">=C2=A0=C2=A0 michael<=
br></font></span></div></div></div>
</blockquote></div><br></div>

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