def write_to_omero(self):
sf = self.client.getSession()
group = str(self.value_resolver.target_object.details.group.id.val)
sr = sf.sharedResources()
update_service = sf.getUpdateService()
name = 'bulk_annotations'
table = sr.newTable(1, name, {'omero.group': group})
if table is None:
raise MetadataError(
"Unable to create table: %s" % name)
original_file = table.getOriginalFile()
log.info('Created new table OriginalFile:%d' % original_file.id.val)
table.initialize(self.columns)
log.info('Table initialized with %d columns.' % (len(self.columns)))
table.addData(self.columns)
log.info('Added data column data.')
table.close()
file_annotation = FileAnnotationI()
file_annotation.ns = \
rstring('openmicroscopy.org/omero/bulk_annotations')
file_annotation.description = rstring(name)
file_annotation.file = OriginalFileI(original_file.id.val, False)
link = self.create_annotation_link()
link.parent = self.target_object
link.child = file_annotation
update_service.saveObject(link, {'omero.group': group})
def testPopulateRoisPlate(self):
"""
Create a small csv file, use populate_roi.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = self.createCsv(colNames="Well,Field,X,Y,Type",
rowData=("A1,0,15,15,Test", ))
rowCount = 1
colCount = 1
plate = self.createPlate(rowCount, colCount)
# As opposed to the ParsingContext, here we are expected
# to link the file ourselves
ofile = self.client.upload(csvName).proxy()
ann = FileAnnotationI()
ann.file = ofile
link = PlateAnnotationLinkI()
link.parent = plate.proxy()
link.child = ann
link = self.client.sf.getUpdateService()\
.saveAndReturnObject(link)
# End linking
factory = PlateAnalysisCtxFactory(self.client.sf)
factory.implementations = (MockPlateAnalysisCtx, )
ctx = factory.get_analysis_ctx(plate.id.val)
assert 1 == ctx.get_measurement_count()
meas = ctx.get_measurement_ctx(0)
meas.parse_and_populate()
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child as ann
left outer join fetch ann.file as file
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
# the other is the original CSV
assert len(anns) == 2
files = dict([(a.ns.val, a.file.id.val) for a in anns if a.ns])
fileid = files[NSMEASUREMENT]
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == 1
data = t.read(range(len(cols)), 0, 1)
imag = data.columns[0].values[0]
rois = self.client.sf.getRoiService()
anns = rois.getRoiMeasurements(imag, RoiOptions())
assert anns
def test_file_annotation(self):
"""Tests AnnotationWrapper methods return strings"""
file_name = u'₩€_file_$$'
f = OriginalFileI()
f.name = rstring(file_name)
obj = FileAnnotationI()
obj.file = f
file_ann = MockConnection(obj).getObject("Annotation", 1)
assert file_ann.getFileName() == file_name.encode('utf8')
def testPopulateRoisPlate(self):
"""
Create a small csv file, use populate_roi.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = self.createCsv(
colNames="Well,Field,X,Y,Type",
rowData=("A1,0,15,15,Test",))
rowCount = 1
colCount = 1
plate = self.createPlate(rowCount, colCount)
# As opposed to the ParsingContext, here we are expected
# to link the file ourselves
ofile = self.client.upload(csvName).proxy()
ann = FileAnnotationI()
ann.file = ofile
link = PlateAnnotationLinkI()
link.parent = plate.proxy()
link.child = ann
link = self.client.sf.getUpdateService()\
.saveAndReturnObject(link)
# End linking
factory = PlateAnalysisCtxFactory(self.client.sf)
factory.implementations = (MockPlateAnalysisCtx,)
ctx = factory.get_analysis_ctx(plate.id.val)
assert 1 == ctx.get_measurement_count()
meas = ctx.get_measurement_ctx(0)
meas.parse_and_populate()
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child as ann
left outer join fetch ann.file as file
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
# the other is the original CSV
assert len(anns) == 2
files = dict(
[(a.ns.val, a.file.id.val) for a in anns if a.ns])
fileid = files[NSMEASUREMENT]
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == 1
data = t.read(range(len(cols)), 0, 1)
imag = data.columns[0].values[0]
rois = self.client.sf.getRoiService()
anns = rois.getRoiMeasurements(imag, RoiOptions())
assert anns
