Hi Lubos,

I opened a Pull Request on https://github.com/galaxyproject/galaxy/pull/1930,
which should hopefully fix the problem.
If you want to give it a try, you can do
`git fetch origin pull/1930/head:more_bytestring_for_pysam`
and
`git checkout more_bytestring_for_pysam`.
When the problem has been solved, you can switch back to release_16.01 by
doing `git checkout release_16.01`.

Thanks for reporting the error,
Marius


On 15 March 2016 at 19:25, Marius van den Beek <m.vandenb...@gmail.com>
wrote:

> Yes, `git checkout release_16.01` should do it, but wait a second, there
> might actually be a problem,
> since ` File 
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 892, in get_iterator`,
> while the PR addresses 354-356!
>
>
> On 15 March 2016 at 19:23, Lubos Klucar <klu...@embnet.sk> wrote:
>
>>
>>
>> On 15. 3. 2016 19:15, Marius van den Beek wrote:
>>
>>> Hi Lubos,
>>>
>>> hmm, I'm surprised about this.
>>> Just to make sure, you are on the release_16.01 branch?
>>> (`git branch` should highlight release_16.01)
>>> This PR hasn't been merged into dev yet.
>>>
>>>
>> Hi Marius,
>>
>> it seems I need more help with git, not the Galaxy!. ;-) My git branch
>> gives me:
>>
>>   dev
>> * master
>>
>> How should I 'switch' to 16.01??..
>>
>> regards
>>
>> Lubos
>>
>> Cheers,
>>> Marius
>>>
>>> On 15 March 2016 at 19:08, Lubos Klucar <klu...@embnet.sk
>>> <mailto:klu...@embnet.sk>> wrote:
>>>
>>>     Dear Marius,
>>>
>>>     thanks for help, but it looks our galaxy is up to date:
>>>
>>>     remote: Counting objects: 111, done.
>>>     remote: Compressing objects: 100% (23/23), done.
>>>     remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13
>>>     Receiving objects: 100% (111/111), 39.85 KiB, done.
>>>     Resolving deltas: 100% (82/82), completed with 29 local objects.
>>>      >From https://github.com/galaxyproject/galaxy
>>>         8423fe7..23c3300  dev        -> origin/dev
>>>         5a50a46..65a5b08  release_16.01 -> origin/release_16.01
>>>     Already up-to-date.
>>>
>>>     After Galaxy restart the problem still persist...
>>>
>>>     all the best
>>>
>>>     Lubos
>>>
>>>     On 15. 3. 2016 18:59, Marius van den Beek wrote:
>>>
>>>         Hello Lubos,
>>>
>>>         this should be fixed with
>>>         https://github.com/galaxyproject/galaxy/pull/1897.
>>>         If you pull in the latest changes (git pull) on the
>>>         release_16.01 branch
>>>         things should work again.
>>>
>>>         Cheers,
>>>         Marius
>>>
>>>         On 15 March 2016 at 18:54, Lubos Klucar <klu...@embnet.sk
>>>         <mailto:klu...@embnet.sk>
>>>         <mailto:klu...@embnet.sk <mailto:klu...@embnet.sk>>> wrote:
>>>
>>>              Hi,
>>>
>>>              after upgrading from 15.10 to 16.01, the trackster
>>>         visualisation
>>>              tool is partly defective. It can successfully show e.g. GFF
>>>         tracks,
>>>              but after adding e.g. BAM track nothing is shown. The only
>>>              suspicious debug output I could get when loading
>>>         non-working-track is:
>>>
>>>              galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15
>>>         11:44:38,853
>>>              Error in dataset API at listing contents: Expected bytes,
>>> got
>>>              unicode: Expected bytes, got unicode
>>>              Traceback (most recent call last):
>>>                 File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>>              line 66, in show
>>>                   rval = self._data( trans, dataset, **kwd )
>>>                 File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>>              line 235, in _data
>>>                   ref_seq=region, mean_depth=mean_depth, **kwargs )
>>>                 File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>>              line 192, in get_data
>>>                   iterator = self.get_iterator( data_file, chrom, start,
>>>         end,
>>>              **kwargs )
>>>                 File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>>              line 892, in get_iterator
>>>                   data = data_file.fetch( start=start, end=end,
>>>         reference=chrom )
>>>                 File "pysam/calignmentfile.pyx", line 868, in
>>>              pysam.calignmentfile.AlignmentFile.fetch
>>>         (pysam/calignmentfile.c:10170)
>>>                 File "pysam/calignmentfile.pyx", line 787, in
>>>              pysam.calignmentfile.AlignmentFile.parse_region
>>>              (pysam/calignmentfile.c:9605)
>>>                 File "pysam/calignmentfile.pyx", line 1576, in
>>>              pysam.calignmentfile.AlignmentFile.gettid
>>>         (pysam/calignmentfile.c:16665)
>>>                 File "pysam/calignmentfile.pyx", line 640, in
>>>              pysam.calignmentfile.AlignmentFile.get_tid
>>>         (pysam/calignmentfile.c:8208)
>>>                 File "pysam/cutils.pyx", line 106, in
>>>         pysam.cutils.force_bytes
>>>              (pysam/cutils.c:2170)
>>>              TypeError: Expected bytes, got unicode
>>>
>>>              Any help to solve this problem would be highly appreciated!
>>>
>>>              many thanks
>>>              --
>>>
>>>                               Lubos Klucar
>>>              ___________________________________________________________
>>>              Please keep all replies on the list by using "reply all"
>>>              in your mail client.  To manage your subscriptions to this
>>>              and other Galaxy lists, please use the interface at:
>>>         https://lists.galaxyproject.org/
>>>
>>>              To search Galaxy mailing lists use the unified search at:
>>>         http://galaxyproject.org/search/mailinglists/
>>>
>>>
>>>
>>>     --
>>>
>>>                      Lubos Klucar
>>>
>>>                      Institute of Molecular Biology
>>>                      Slovak Academy of Science
>>>                      Dubravska cesta 21
>>>                      845 51  Bratislava 45
>>>                      Slovakia
>>>
>>>                      Tel.: +421 2 5930 7413
>>> <tel:%2B421%202%205930%207413>
>>>                      Fax.: +421 2 5930 7416
>>> <tel:%2B421%202%205930%207416>
>>>
>>>
>>>
>> --
>>
>>                 Lubos Klucar
>>
>>                 Institute of Molecular Biology
>>                 Slovak Academy of Science
>>                 Dubravska cesta 21
>>                 845 51  Bratislava 45
>>                 Slovakia
>>
>>                 Tel.: +421 2 5930 7413
>>                 Fax.: +421 2 5930 7416
>>
>
>
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