[ome-devel] ometiff download toubles

[Wood, Christopher]

Hi Will,

I looked at that. The code for exportOMETIFF in the version I am using (4.2.2) only returns the ome tiff as one large chunk, but I want to save it to a temp file in chunks. The code Josh linked to does that, so I assumed it was from a yet to be released version.

The code in exportOMETIFF looks very much like what I originally tried to do (maybe it was my inspiration?) by addImage() and generateTIFF(), so I tried something different.

Do you have any ideas as to why the method I first described would cause the server to stop responding?

Another question:
If the image large (100 MB), the web server or django will timeout while the tiff is generating. Does anyone know what setting(s) to adjust to account for this?

Thanks
Chris

On 2/24/11 5:39 PM, "Will Moore" <will at lifesci.dundee.ac.uk> wrote:

Sorry, should have replied to the lists too.....

On 24 Feb 2011, at 23:38, Will Moore wrote:

> Hi Chris,
>
>  Are you developing within the OmeroWeb framework, as described
> http://trac.openmicroscopy.org.uk/ome/wiki/OmeroWeb
>
> Based on the simplified example on that page, you would do
> something like
>
>
> from omeroweb.webgateway.views import getBlitzConnection
>
> def dataset(request, imageId):
>     conn = getBlitzConnection (request)     # get a connection to
> OMERO using values in the http request
>     img = conn.getImage(imageId)         # get image by ID
>     data = img.exportOmeTiff()
>
> Docs for that method are here:
> http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/epydoc/
> omero.gateway._ImageWrapper-class.html#exportOmeTiff
>
> I don't have a complete example to hand just now (not on my work
> laptop) but can find more details for you tomorrow.
>
>
>   Will.
>
>
>
> On 24 Feb 2011, at 18:59, Wood, Christopher wrote:
>
>> Josh,
>>
>> I used
>> client = omero.client(host)
>> session = client.createSession(user, pw)
>> gateway = session.createGateway()
>>
>> image = gateway.getImage(id)
>> exporter = session.createExporter()
>>
>> and it is working like I expect.
>>
>> I  am getting the username and password from the request object,
>> e.g.,
>>
>> username = request.session.get('username', r.get('username', None))
>>
>> Is it necessary to do this, or is the user, password, host, and
>> port already set by the request?
>>
>> Thanks
>> Chris
>>
>> On 2/24/11 9:33 AM, "Josh Moore" <josh at glencoesoftware.com> wrote:
>>
>> Hi Chris,
>>
>> the message "Cannot configure during output" comes from
>> ExporterI.java:
>>
>>   http://git.openmicroscopy.org/?p=ome.git;a=blob;f=components/
>> blitz/src/ome/services/blitz/impl/ExporterI.java;#l230
>>
>> and implies that addImage() was called after generateTiff(), but
>> that certainly doesn't look possible from your code snippet. This
>> may be caused by the service wrapper from omero.gateway, but I'll
>> let others speak to that. You might want to try either using the
>> raw service (acquired from the session as opposed to the
>> BlitzGateway), or use the facilities of the gateway, like the
>> exportOmeTiff method:
>>
>>   http://git.openmicroscopy.org/?p=ome.git;a=blob;f=components/
>> tools/OmeroPy/src/omero/gateway/__init__.py#l5641
>>
>> Cheers,
>> ~Josh.
>>
>>
>> On Feb 24, 2011, at 4:14 PM, Wood, Christopher wrote:
>>
>>> Hi,
>>>
>>> I am trying to write a python script to be able to download an
>>> OME-TIFF from omeroweb.  The code below will work, but it only
>>> works once. On the second attempt I get the error below the code.
>>> On the third attempt, it stops working at omero needs to be
>>> restarted.
>>>
>>> I do this same sort of thing for original raw files and I don't
>>> have a problem.
>>>
>>> OMERO Beta4.2.2-r8718-Beta4.2-b56
>>> python 2.4
>>>
>>> Here is the process:
>>> 1) restart omero and omeroweb
>>> 2) goto http://chi/websimr/getOMETIFF/3914/
>>> 3) file downloads as expected
>>> 4) try the same or different file again, I get the error below
>>> 5) try again and omero need to be restarted. (Insight stop
>>> responding,  webclient stop responding, ....)
>>>
>>> Let me know if you need anything from the log files.
>>>
>>> Thanks,
>>> Chris
>>> ====================================================
>>> def getOMETIFF(request, iid):
>>>
>>>    if conn is None or not conn.isConnected():
>>>        return HttpResponseRedirect(reverse('websimr_login'))
>>>
>>>    iid = int(iid)
>>>    image = conn.getImage(iid)
>>>    name = image.getName()
>>>    name = name.replace('\\', '/')
>>>    name = os.path.basename(name)
>>>    name = os.path.splitext(name)[0] + '.ome.tif'
>>>
>>>    exporter = conn.createExporter()
>>>    exporter.addImage(iid)            <------------ this line
>>> causes problems **********************
>>>    exporter.generateTiff()
>>>
>>>
>>>    tempdir = settings.FILE_UPLOAD_TEMP_DIR
>>>    v1 = iid
>>>    v2 = conn._sessionUuid
>>>    tempname = os.path.join(tempdir,('%i-%s.download' % (v1, v2)))
>>>    temp = tempname.replace('\\','/')
>>>
>>>    handle = open(temp, 'wb')
>>>    offset = 0
>>>
>>>    while 1==1:
>>>        rv = exporter.read(offset, 512*512)
>>>        if not rv:
>>>            break
>>>        offset += len(rv)
>>>        handle.write(rv)
>>>
>>>
>>>    handle.close()
>>>
>>>    ometiff = FileWrapper(file(temp))
>>>    response = HttpResponse(ometiff)
>>>
>>>    response['Content-Length'] = str(offset)
>>>    response['Content-Type'] = 'application/force-download'
>>>
>>>    response['Content-Disposition']='attachment;filename=' + name
>>>    return response
>>>
>>> ====================================================
>>> this is the debuggingout put from the web page
>>> ---
>>> Environment:
>>>
>>> Request Method: GET
>>> Request URL: http://chi/websimr/getOMETIFF/3914/
>>> Django Version: 1.1.1
>>> Python Version: 2.4.3
>>> Installed Applications:
>>> ['django.contrib.admin',
>>> 'django.contrib.markup',
>>> 'django.contrib.auth',
>>> 'django.contrib.contenttypes',
>>> 'django.contrib.sessions',
>>> 'django.contrib.sites',
>>> 'omeroweb.feedback',
>>> 'omeroweb.webadmin',
>>> 'omeroweb.webclient',
>>> 'omeroweb.webgateway',
>>> 'omeroweb.webtest',
>>> 'omeroweb.websimr',
>>> 'omeroweb.limsweb',
>>> 'omeroweb.webmobile']
>>> Installed Middleware:
>>> ('django.middleware.common.CommonMiddleware',
>>> 'django.contrib.sessions.middleware.SessionMiddleware',
>>> 'django.middleware.doc.XViewMiddleware')
>>>
>>>
>>> Traceback:
>>> File "/OMERO/omero_dist/lib/python/django/core/handlers/base.py"
>>> in get_response
>>>  92.                 response = callback(request, *callback_args,
>>> **callback_kwargs)
>>> File "/OMERO/omero_dist/lib/python/omeroweb/websimr/views.py" in
>>> getOMETIFF
>>>  114.     exporter.addImage(iid)
>>> File "/OMERO/omero_dist/lib/python/omero/gateway/__init__.py" in
>>> wrapped
>>>  2306.             return inner(*args, **kwargs)
>>> File "/OMERO/omero_dist/lib/python/omero/gateway/__init__.py" in
>>> inner
>>>  2267.             return f(*args, **kwargs)
>>> File "/OMERO/omero_dist/lib/python/omero_api_Exporter_ice.py" in
>>> addImage
>>>  81.             return _M_omero.api.Exporter._op_addImage.invoke
>>> (self, ((id, ), _ctx))
>>>
>>> Exception Type: ApiUsageException at /websimr/getOMETIFF/3914/
>>> Exception Value: exception ::omero::ApiUsageException
>>> {
>>>    serverStackTrace =
>>>    serverExceptionClass =
>>>    message = Cannot configure during output
>>> }
>>>
>>
>>
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>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>

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