def testFileAnnotation(author_testimg_generated, gatewaywrapper):
""" Creates a file annotation from a local file """
tempFileName = "tempFile"
f = open(tempFileName, "w")
fileText = "Test text for writing to file for upload"
f.write(fileText)
f.close()
fileSize = os.path.getsize(tempFileName)
ns = TESTANN_NS
image = author_testimg_generated
# use the same file to create various file annotations with different namespaces
fileAnn = gatewaywrapper.gateway.createFileAnnfromLocalFile(tempFileName, mimetype="text/plain", ns=ns)
image.linkAnnotation(fileAnn)
compAnn = gatewaywrapper.gateway.createFileAnnfromLocalFile(
tempFileName, mimetype="text/plain", ns=omero.constants.namespaces.NSCOMPANIONFILE
)
image.linkAnnotation(compAnn)
os.remove(tempFileName)
# get user-id of another user to use below.
gatewaywrapper.loginAsAdmin()
adminId = gatewaywrapper.gateway.getUser().getId()
gatewaywrapper.loginAsAuthor()
# test listing of File Annotations. Should exclude companion files by default and all files should be loaded
gateway = gatewaywrapper.gateway
eid = gateway.getUser().getId()
fas = list(gateway.listFileAnnotations(eid=eid, toInclude=[ns]))
faIds = [fa.id for fa in fas]
assert fileAnn.getId() in faIds
assert compAnn.getId() not in faIds
for fa in fas:
assert fa.getNs() == ns, "All files should be filtered by this namespace"
assert fa._obj.file.loaded, "All file annotations should have files loaded"
# filtering by namespace
fas = list(gateway.listFileAnnotations(toInclude=["nothing.with.this.namespace"], eid=eid))
assert len(fas) == 0, "No file annotations should exist with bogus namespace"
# filtering files by a different user should not return the annotations above.
fas = list(gateway.listFileAnnotations(eid=adminId))
faIds = [fa.id for fa in fas]
assert fileAnn.getId() not in faIds
assert compAnn.getId() not in faIds
image._conn = gatewaywrapper.gateway # needs a fresh connection, original was closed already
ann = image.getAnnotation(ns)
annId = ann.getId()
assert ann.OMERO_TYPE == omero.model.FileAnnotationI
for t in ann.getFileInChunks():
assert str(t) == fileText # we get whole text in one chunk
# delete what we created
assert gateway.getObject("Annotation", annId) is not None
link = ann.link
gateway.deleteObjectDirect(link._obj) # delete link
gateway.deleteObjectDirect(ann._obj) # then the annotation
gateway.deleteObjectDirect(ann._obj.file) # then the file
assert gateway.getObject("Annotation", annId) is None
def test9655(self):
# Create an image without statsinfo objects and attempt
# to retrieve it from the Rendering service.
# Get the pixels
image_id = self.testCreateImage()
gateway = omero.gateway.BlitzGateway(client_obj=self.client)
image = gateway.getObject("Image", image_id)
pixels_id = image.getPrimaryPixels().id
# Save the pixels
rps = self.client.sf.createRawPixelsStore()
rps.setPixelsId(pixels_id, False)
rps.setPlane([0], 0, 0, 0)
rps.save()
rps.close()
# Now use the RE to load
re = self.client.sf.createRenderingEngine()
re.lookupPixels(pixels_id)
re.resetDefaults()
re.lookupPixels(pixels_id)
re.lookupRenderingDef(pixels_id)
re.getPixels()
def test9655(self):
# Create an image without statsinfo objects and attempt
# to retrieve it from the Rendering service.
# Get the pixels
image_id = self.testCreateImage()
gateway = omero.gateway.BlitzGateway(client_obj=self.client)
image = gateway.getObject("Image", image_id)
pixels_id = image.getPrimaryPixels().id
# Save the pixels
rps = self.client.sf.createRawPixelsStore()
rps.setPixelsId(pixels_id, False)
rps.setPlane([0], 0, 0, 0)
rps.save()
rps.close()
# Now use the RE to load
re = self.client.sf.createRenderingEngine()
re.lookupPixels(pixels_id)
re.resetDefaults()
re.lookupPixels(pixels_id)
re.lookupRenderingDef(pixels_id)
re.getPixels()
def testFileAnnotation(author_testimg_generated, gatewaywrapper):
""" Creates a file annotation from a local file """
tempFileName = "tempFile"
f = open(tempFileName, 'w')
fileText = "Test text for writing to file for upload"
f.write(fileText)
f.close()
ns = TESTANN_NS
image = author_testimg_generated
# use the same file to create various file annotations with different
# namespaces
fileAnn = gatewaywrapper.gateway.createFileAnnfromLocalFile(
tempFileName, mimetype='text/plain', ns=ns)
image.linkAnnotation(fileAnn)
compAnn = gatewaywrapper.gateway.createFileAnnfromLocalFile(
tempFileName,
mimetype='text/plain',
ns=omero.constants.namespaces.NSCOMPANIONFILE)
image.linkAnnotation(compAnn)
os.remove(tempFileName)
# get user-id of another user to use below.
gatewaywrapper.loginAsAdmin()
adminId = gatewaywrapper.gateway.getUser().getId()
gatewaywrapper.loginAsAuthor()
# test listing of File Annotations. Should exclude companion files by
# default and all files should be loaded
gateway = gatewaywrapper.gateway
eid = gateway.getUser().getId()
fas = list(gateway.listFileAnnotations(eid=eid, toInclude=[ns]))
faIds = [fa.id for fa in fas]
assert fileAnn.getId() in faIds
assert compAnn.getId() not in faIds
for fa in fas:
assert fa.getNs() == ns, \
"All files should be filtered by this namespace"
assert fa._obj.file.loaded, \
"All file annotations should have files loaded"
# filtering by namespace
fas = list(
gateway.listFileAnnotations(toInclude=["nothing.with.this.namespace"],
eid=eid))
assert len(fas) == 0, \
"No file annotations should exist with bogus namespace"
# filtering files by a different user should not return the annotations
# above.
fas = list(gateway.listFileAnnotations(eid=adminId))
faIds = [fa.id for fa in fas]
assert fileAnn.getId() not in faIds
assert compAnn.getId() not in faIds
# needs a fresh connection, original was closed already
image._conn = gatewaywrapper.gateway
ann = image.getAnnotation(ns)
annId = ann.getId()
assert ann.OMERO_TYPE == omero.model.FileAnnotationI
for t in ann.getFileInChunks():
assert str(t) == fileText # we get whole text in one chunk
# delete what we created
assert gateway.getObject("Annotation", annId) is not None
link = ann.link
gateway.deleteObjectDirect(link._obj) # delete link
gateway.deleteObjectDirect(ann._obj) # then the annotation
gateway.deleteObjectDirect(ann._obj.file) # then the file
assert gateway.getObject("Annotation", annId) is None
