Re: Parsing embl format with biojava4

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Ah yes, the eFetch endpoints have changed.  Looks like biojava-legacy needs
some maintaining.  :)

Please file an issue at https://github.com/biojava/biojava-legacy or I'll
get to it later today.

Thanks!

   michael


On Wed, Dec 28, 2016 at 10:46 AM, Dario Beraldi <[email protected]>
wrote:

> 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"><div><div>Ah yes, the eFetch endpoints have changed.=C2=A0=
 Looks like biojava-legacy needs some maintaining.=C2=A0 :)<br><br></div>Pl=
ease file an issue at <a href=3D"https://github.com/biojava/biojava-legacy"=
>https://github.com/biojava/biojava-legacy</a> or I&#39;ll get to it later =
today.<br><br></div><div>Thanks!<br><br></div><div>=C2=A0=C2=A0 michael<br>=
<br></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">O=
n Wed, Dec 28, 2016 at 10:46 AM, Dario Beraldi <span dir=3D"ltr">&lt;<a hre=
f=3D"mailto:[email protected]" target=3D"_blank">dario.beraldi@gmail.=
com</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"mar=
gin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr=
">Ok thank you, I&#39;ll consider Biojava 1.9 if embl files are not support=
ed in later versions.=C2=A0<div><br></div><div>By the way, I tried to compi=
le biojava-legacy-1.9.2 and I got some tests failing:</div><div><br></div><=
div>----------------------</div><div>cd biojava-legacy-biojava-legacy-<wbr>=
1.9.2</div><div>mvn package</div><div>....</div><div>....</div><div>







<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">Results :</span></p>
<p class=3D"m_5561533009265014368gmail-p2"><span class=3D"m_556153300926501=
4368gmail-s1"></span><br></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">Failed tests:=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">=C2=A0 GenbankRichSequenceDBTest.<wbr>testeFetch:24 Unexpecte=
d Bioexception: org.biojava.bio.BioException: Failed to read Genbank sequen=
ce</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">=C2=A0 GenpeptRichSequenceDBTest.<wbr>testeFetch:24 Unexpecte=
d BioException: org.biojava.bio.BioException: Failed to read Genbank sequen=
ce</span></p>
<p class=3D"m_5561533009265014368gmail-p2"><span class=3D"m_556153300926501=
4368gmail-s1"></span><br></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">Tests run: 883, Failures: 2, Errors: 0, Skipped: 0</span></p>
<p class=3D"m_5561533009265014368gmail-p2"><span class=3D"m_556153300926501=
4368gmail-s1"></span><br></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] ------------------------------<wbr>-------------------=
-----------<wbr>------------</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] Reactor Summary:</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO]=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] biojava-legacy ..............................<wbr>....=
... SUCCESS [=C2=A0 0.725 s]</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] bytecode ..............................<wbr>..........=
... SUCCESS [=C2=A0 1.505 s]</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] core ..............................<wbr>..............=
... FAILURE [ 10.232 s]</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] alignment ..............................<wbr>.........=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] biosql ..............................<wbr>............=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] blast ..............................<wbr>.............=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] sequencing ..............................<wbr>........=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] gui ..............................<wbr>...............=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] phylo ..............................<wbr>.............=
... SKIPPED</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] ------------------------------<wbr>-------------------=
-----------<wbr>------------</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] BUILD FAILURE</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] ------------------------------<wbr>-------------------=
-----------<wbr>------------</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] Total time: 12.692 s</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] Finished at: 2016-12-28T16:38:18+00:00</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] Final Memory: 11M/220M</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[INFO] ------------------------------<wbr>-------------------=
-----------<wbr>------------</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] Failed to execute goal org.apache.maven.plugins:<wbr>=
maven-surefire-plugin:2.17:<wbr>test (default-test) on project core: There =
are test failures.</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] Please refer to /Users/berald01/Downloads/<wbr>biojav=
a-legacy-biojava-legacy-<wbr>1.9.2/core/target/surefire-<wbr>reports for th=
e individual test results.</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] -&gt; [Help 1]</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] To see the full stack trace of the errors, re-run Mav=
en with the -e switch.</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] Re-run Maven using the -X switch to enable full debug=
 logging.</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] For more information about the errors and possible so=
lutions, please read the following articles:</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] [Help 1] <a href=3D"http://cwiki.apache.org/confluenc=
e/display/MAVEN/MojoFailureException" target=3D"_blank">http://cwiki.apache=
.org/<wbr>confluence/display/MAVEN/<wbr>MojoFailureException</a></span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR]=C2=A0</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] After correcting the problems, you can resume the bui=
ld with the command</span></p>
<p class=3D"m_5561533009265014368gmail-p1"><span class=3D"m_556153300926501=
4368gmail-s1">[ERROR] =C2=A0 mvn &lt;goals&gt; -rf :core</span></p></div></=
div><div class=3D"HOEnZb"><div class=3D"h5"><div class=3D"gmail_extra"><br>=
<div class=3D"gmail_quote">On 28 December 2016 at 15:45, Michael Heuer <spa=
n dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">he=
[email protected]</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"><di=
v dir=3D"ltr">On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <span dir=3D"l=
tr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">dario.=
[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"><di=
v dir=3D"ltr">Hello,<div><br></div><div>First, thanks for the great Biojava=
 project!</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=A0=
embl format&quot; I get some hits for the legacy Biojava 1.9 but I&#39;m wo=
ndering weather I could (should?) use the more recent Biojava 4?</div></div=
></blockquote><div><br></div><div>If biojava-legacy works fine for you, fee=
l confident using it.=C2=A0 It is actively maintained; there just won&#39;t=
 be any new features.<br><br></div><div>=C2=A0</div><blockquote class=3D"gm=
ail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,=
204,204);padding-left:1ex"><div dir=3D"ltr"><div>A more general question...=
 Which is the primary source of documentation for Biojava 4? Is it the tuto=
rial at <a href=3D"https://github.com/biojava/biojava-tutorial" target=3D"_=
blank">https://github.com/biojava/bio<wbr>java-tutorial</a> together with t=
he Javadocs (<a href=3D"http://biojava.org/docs/api4.2.1/" target=3D"_blank=
">http://biojava.org/docs/api4.<wbr>2.1/</a>)?=C2=A0</div><div><br></div><d=
iv>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"_b=
lank">http://biojava.org/wiki/B<wbr>ioJava:CookBook4.0/</a> gives me a 404 =
error. 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=
 topics.</div></div></blockquote><div><br></div><div>The <a href=3D"http://=
biojava.org" target=3D"_blank">biojava.org</a> website didn&#39;t survive a=
 wiki 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.co=
m/biojava/biojava.github.io" target=3D"_blank">https://github.com/biojava/b=
io<wbr>java.github.io<span class=3D"m_5561533009265014368HOEnZb"><font colo=
r=3D"#888888"><br></font></span></a><span class=3D"m_5561533009265014368HOE=
nZb"><font color=3D"#888888"><br></font></span></div><span class=3D"m_55615=
33009265014368HOEnZb"><font color=3D"#888888">=C2=A0=C2=A0 michael<br></fon=
t></span></div></div></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>

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