def update_table(self, columns):
"""Updates the OmeroTables instance backing our results."""
# Create a new OMERO table to store our measurement results
sr = self.service_factory.sharedResources()
name = self.get_name()
self.table = sr.newTable(1, "/%s.r5" % name)
if self.table is None:
raise MeasurementError("Unable to create table: %s" % name)
# Retrieve the original file corresponding to the table for the
# measurement, link it to the file annotation representing the
# umbrella measurement run, link the annotation to the plate from
# which it belongs and save the file annotation.
table_original_file = self.table.getOriginalFile()
table_original_file_id = table_original_file.id.val
log.info("Created new table: %d" % table_original_file_id)
unloaded_o_file = OriginalFileI(table_original_file_id, False)
self.file_annotation.file = unloaded_o_file
unloaded_plate = PlateI(self.analysis_ctx.plate_id, False)
plate_annotation_link = PlateAnnotationLinkI()
plate_annotation_link.parent = unloaded_plate
plate_annotation_link.child = self.file_annotation
plate_annotation_link = self.update_service.saveAndReturnObject(plate_annotation_link)
self.file_annotation = plate_annotation_link.child
t0 = int(time.time() * 1000)
self.table.initialize(columns)
log.debug("Table init took %sms" % (int(time.time() * 1000) - t0))
t0 = int(time.time() * 1000)
column_report = dict()
for column in columns:
column_report[column.name] = len(column.values)
log.debug("Column report: %r" % column_report)
self.table.addData(columns)
log.info("Table update took %sms" % (int(time.time() * 1000) - t0))
def create_table(client, plate_id):
'''Create a new OMERO table to store our measurement results.'''
session = client.getSession()
update_service = session.getUpdateService()
sr = session.sharedResources()
name = '/segmentation_simple.r5'
table = sr.newTable(1, name)
if table is None:
raise Exception(
'Unable to create table: %s' % name)
# Retrieve the original file corresponding to the table for the
# measurement, link it to the file annotation representing the
# umbrella measurement run, link the annotation to the plate from
# which it belongs and save the file annotation.
try:
table_original_file = table.getOriginalFile()
table_original_file_id = table_original_file.id.val
log.info('Created new table: %d' % table_original_file_id)
unloaded_o_file = OriginalFileI(table_original_file_id, False)
file_annotation = create_file_annotation()
file_annotation.file = unloaded_o_file
unloaded_plate = PlateI(plate_id, False)
plate_annotation_link = PlateAnnotationLinkI()
plate_annotation_link.parent = unloaded_plate
plate_annotation_link.child = file_annotation
plate_annotation_link = \
update_service.saveAndReturnObject(plate_annotation_link)
file_annotation = plate_annotation_link.child
table.initialize(get_columns())
except:
table.close()
raise
return (table, file_annotation)
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 create_annotation_link(self):
self.target_class = self.target_object.__class__
if ScreenI is self.target_class:
return ScreenAnnotationLinkI()
if PlateI is self.target_class:
return PlateAnnotationLinkI()
if DatasetI is self.target_class:
return DatasetAnnotationLinkI()
raise MetadataError('Unsupported target object class: %s' \
% target_class)
def plate_well_table(itest, well_grid_factory, update_service, conn):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A1 has one WellSample
plate.addWell(well_grid_factory({(0, 0): 1})[0])
plate = update_service.saveAndReturnObject(plate)
col1 = WellColumn('Well', '', [])
col2 = StringColumn('TestColumn', '', 64, [])
columns = [col1, col2]
tablename = "plate_well_table_test:%s" % str(random())
table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
wellIds = [w.id.val for w in plate.copyWells()]
print "WellIds", wellIds
data1 = WellColumn('Well', '', wellIds)
data2 = StringColumn('TestColumn', '', 64, ["foobar"])
data = [data1, data2]
table.addData(data)
table.close()
orig_file = table.getOriginalFile()
fileAnn = FileAnnotationI()
fileAnn.ns = rstring('openmicroscopy.org/omero/bulk_annotations')
fileAnn.setFile(OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = PlateAnnotationLinkI()
link.setParent(PlateI(plate.id.val, False))
link.setChild(FileAnnotationI(fileAnn.id.val, False))
update_service.saveAndReturnObject(link)
return plate, wellIds
def update_table(self, columns):
"""Updates the OmeroTables instance backing our results."""
# Create a new OMERO table to store our measurement results
sr = self.service_factory.sharedResources()
name = self.get_name()
self.table = sr.newTable(1, '/%s.r5' % name)
if self.table is None:
raise MeasurementError(
"Unable to create table: %s" % name)
# Retrieve the original file corresponding to the table for the
# measurement, link it to the file annotation representing the
# umbrella measurement run, link the annotation to the plate from
# which it belongs and save the file annotation.
table_original_file = self.table.getOriginalFile()
table_original_file_id = table_original_file.id.val
log.info("Created new table: %d" % table_original_file_id)
unloaded_o_file = OriginalFileI(table_original_file_id, False)
self.file_annotation.file = unloaded_o_file
unloaded_plate = PlateI(self.analysis_ctx.plate_id, False)
plate_annotation_link = PlateAnnotationLinkI()
plate_annotation_link.parent = unloaded_plate
plate_annotation_link.child = self.file_annotation
plate_annotation_link = \
self.update_service.saveAndReturnObject(plate_annotation_link)
self.file_annotation = plate_annotation_link.child
t0 = int(time.time() * 1000)
self.table.initialize(columns)
log.debug("Table init took %sms" % (int(time.time() * 1000) - t0))
t0 = int(time.time() * 1000)
column_report = dict()
for column in columns:
column_report[column.name] = len(column.values)
log.debug("Column report: %r" % column_report)
self.table.addData(columns)
self.table.close()
log.info("Table update took %sms" % (int(time.time() * 1000) - t0))
def plate_well_table(itest, well_grid_factory, update_service, conn):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{omeroweb.testlib.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A1 has one WellSample
plate.addWell(well_grid_factory({(0, 0): 1})[0])
plate = update_service.saveAndReturnObject(plate)
col1 = WellColumn('Well', '', [])
col2 = StringColumn('TestColumn', '', 64, [])
columns = [col1, col2]
tablename = "plate_well_table_test:%s" % str(random())
table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
wellIds = [w.id.val for w in plate.copyWells()]
print("WellIds", wellIds)
data1 = WellColumn('Well', '', wellIds)
data2 = StringColumn('TestColumn', '', 64, ["foobar"])
data = [data1, data2]
table.addData(data)
orig_file = table.getOriginalFile()
table.close()
fileAnn = FileAnnotationI()
fileAnn.ns = rstring('openmicroscopy.org/omero/bulk_annotations')
fileAnn.setFile(OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = PlateAnnotationLinkI()
link.setParent(PlateI(plate.id.val, False))
link.setChild(FileAnnotationI(fileAnn.id.val, False))
update_service.saveAndReturnObject(link)
return plate, wellIds
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
