[Biojava-l] Parsing embl format with biojava4

[Michael Heuer]

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 <dario.beraldi at gmail.com>
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 <heuermh at gmail.com> wrote:
>
>> On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <dario.beraldi at gmail.com>
>> 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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