Task #8905 (closed)
Opened 12 years ago
Closed 12 years ago
Bug: Schema re.getPixels()
Reported by: | wmoore | Owned by: | cxallan |
---|---|---|---|
Priority: | critical | Milestone: | OMERO-4.4 |
Component: | Services | Version: | n.a. |
Keywords: | n.a. | Cc: | cxallan, jburel |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | 0.0d |
Sprint: | 2012-06-05 (16) |
Description
When trying to render an Image in the Blitz Gateway, we call imageWrapper.getChannels() which uses re.getPixels().iterateChannels()
Environment: Request Method: GET Request URL: http://localhost:8000/webgateway/render_image/1/0/0/?c=1,2,3,4 Traceback: File "/Users/will/Desktop/OMERO/dist/lib/python/django/core/handlers/base.py" in get_response 111. response = callback(request, *callback_args, **callback_kwargs) File "/Users/will/Desktop/OMERO/components/tools/OmeroWeb/omeroweb/webgateway/views.py" in handler 539. return func(request, *args, **kwargs) File "/Users/will/Desktop/OMERO/components/tools/OmeroWeb/omeroweb/webgateway/views.py" in render_image 1078. pi = _get_prepared_image(request, iid, server_id=server_id, _conn=_conn) File "/Users/will/Desktop/OMERO/components/tools/OmeroWeb/omeroweb/webgateway/views.py" in handler 539. return func(request, *args, **kwargs) File "/Users/will/Desktop/OMERO/components/tools/OmeroWeb/omeroweb/webgateway/views.py" in _get_prepared_image 961. if not img.setActiveChannels(channels, windows, colors): File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py" in setActiveChannels 5989. for c in range(len(self.getChannels())): File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py" in wrapped 5363. return f(self, *args, **kwargs) File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py" in getChannels 5968. return [ChannelWrapper(self._conn, c, idx=n, re=self._re, img=self) for n,c in enumerate(self._re.getPixels(self._conn.CONFIG['SERVICE_OPTS']).iterateChannels())] File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py" in __call__ 3197. return self.handle_exception(e, *args, **kwargs) File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py" in __call__ 3194. return self.f(*args, **kwargs) File "/Users/will/Desktop/OMERO/dist/lib/python/omero_api_RenderingEngine_ice.py" in getPixels 491. return _M_omero.api.RenderingEngine._op_getPixels.invoke(self, ((), _ctx)) Exception Type: InternalException at /webgateway/render_image/1/0/0/ Exception Value:
This is also used in Gateway tests, E.g.
python gatewaytest/rdefs.py
Although these tests fail with different (related?) error:
====================================================================== ERROR: testEmissionWave (__main__.RDefsTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "gatewaytest/rdefs.py", line 27, in setUp super(RDefsTest, self).setUp() File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/testdb_create.py", line 54, in setUp self.prepTestDB() File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/testdb_create.py", line 126, in prepTestDB dbhelpers.bootstrap() File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/dbhelpers.py", line 412, in bootstrap i = i.create() File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/dbhelpers.py", line 311, in create self._createWithoutPixels(client, dataset) File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/dbhelpers.py", line 378, in _createWithoutPixels dataset.save() File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py", line 344, in save self._obj = self._conn.getUpdateService().saveAndReturnObject(self._obj, sopts) File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py", line 3197, in __call__ return self.handle_exception(e, *args, **kwargs) File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/__init__.py", line 3194, in __call__ return self.f(*args, **kwargs) File "/Users/will/Desktop/OMERO/dist/lib/python/omero_api_IUpdate_ice.py", line 127, in saveAndReturnObject return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.core.Image.pixels; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.Image.pixels at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648) at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
I am currently on a recent merge of my schema branch and the main schema branch:
* 835c133 (HEAD, schema-2012-06) Merge remote-tracking branch 'ome/schema-2012-06' into schema-2012-06 |\ | * 7b709e0 (ome/schema-2012-06) Merge pull request #176 from ximenesuk/schema-2012-python-tests | |\ | * | f12673a Fix test-compile compilation errors related to Timestamp addition. | * | c4e9c89 Fix cardinality in Instrument.Objectives query. (See #8884) | * | 405ec57 String --> Timestamp throughout. (See #8862) | * | 6c838d7 Optional names and Timestamp primitive.
I'll push this to my gh.
Change History (4)
comment:1 Changed 12 years ago by cxallan
- Owner changed from jmoore to cxallan
- Remaining Time set to 0.25
comment:2 Changed 12 years ago by cxallan
- Status changed from new to accepted
comment:3 Changed 12 years ago by jburel
- Sprint changed from 2012-05-22 (15) to 2012-06-05 (16)
comment:4 Changed 12 years ago by cxallan
- Remaining Time changed from 0.25 to 0
- Status changed from accepted to closed
Moved from sprint 2012-05-22 (15)