def omero_table_file(self, user1, table_data):
"""Create a new OMERO Table and returns the original file ID."""
client = user1[0]
col_types, col_names, rows = table_data
columns = []
for col_type, name in zip(col_types, col_names):
if col_type == StringColumn:
columns.append(StringColumn(name, '', 64, []))
else:
columns.append(col_type(name, '', []))
tablename = "omero_table_test:%s" % str(random())
table = client.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
table.setMetadata("test", rstring("value"))
table.setMetadata("my_number", rint(100))
data = []
for col_type, name, idx in zip(col_types, col_names,
range(len(col_names))):
col_data = [row[idx] for row in rows]
if col_type == StringColumn:
data.append(StringColumn(name, '', 64, col_data))
else:
data.append(col_type(name, '', col_data))
table.addData(data)
orig_file = table.getOriginalFile()
table.close()
return orig_file.id.val
def create_columns_plate(self):
columns = list()
for i, header_as_lower in enumerate(self.headers_as_lower):
name = self.headers[i]
try:
column = self.plate_keys[header_as_lower](name, '', list())
except KeyError:
column = StringColumn(name, '', self.DEFAULT_COLUMN_SIZE,
list())
columns.append(column)
for column in columns:
if column.__class__ is PlateColumn:
columns.append(StringColumn(PLATE_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
if column.__class__ is WellColumn:
columns.append(StringColumn(WELL_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
return columns
def create_columns_plate(self):
columns = list()
for i, header_as_lower in enumerate(self.headers_as_lower):
name = self.headers[i]
try:
column = self.plate_keys[header_as_lower](name, '', list())
except KeyError:
column = StringColumn(name, '', self.DEFAULT_COLUMN_SIZE,
list())
columns.append(column)
return columns
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 create_columns_plate(self):
columns = list()
for i, header_as_lower in enumerate(self.headers_as_lower):
name = self.headers[i]
description = ""
if "%%" in name:
name, description = name.split("%%", 1)
name = name.strip()
# description is key=value. Convert to json
if "=" in description:
k, v = description.split("=", 1)
k = k.strip()
description = json.dumps({k: v.strip()})
# HDF5 does not allow / in column names
name = name.replace('/', '\\')
try:
column = self.plate_keys[header_as_lower](name, description,
list())
except KeyError:
column = StringColumn(name, description,
self.DEFAULT_COLUMN_SIZE, list())
columns.append(column)
for column in columns:
if column.__class__ is PlateColumn:
columns.append(
StringColumn(PLATE_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
if column.__class__ is WellColumn:
columns.append(
StringColumn(WELL_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
if column.__class__ is ImageColumn:
columns.append(
StringColumn(IMAGE_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
self.columns_sanity_check(columns)
return columns
def testTableRead(self, gatewaywrapper):
gatewaywrapper.loginAsAuthor()
# we are Author
pr = gatewaywrapper.getTestProject()
assert pr is not None
sr = gatewaywrapper.gateway.getSharedResources()
name = 'bulk_annotations'
table = sr.newTable(1, name)
data = [StringColumn('col1', '', 2, ['A1', 'B1', 'C1'])]
original_file = table.getOriginalFile()
assert table is not None
table.initialize(data)
table.addData(data)
file_annotation = omero.gateway.FileAnnotationWrapper(
gatewaywrapper.gateway)
file_annotation.setNs('openmicroscopy.org/omero/bulk_annotations')
file_annotation.setDescription(name)
file_annotation.setFile(original_file)
pr.linkAnnotation(file_annotation)
# table created, can we read it back?
pr = gatewaywrapper.getTestProject()
assert pr is not None
file_annotation = pr.getAnnotation(
ns='openmicroscopy.org/omero/bulk_annotations')
assert file_annotation is not None
table = sr.openTable(file_annotation._obj.file)
assert table is not None
# now as Admin
gatewaywrapper.loginAsAdmin()
sr = gatewaywrapper.gateway.getSharedResources()
gatewaywrapper.gateway.SERVICE_OPTS.setOmeroGroup('-1')
pr = gatewaywrapper.getTestProject()
assert pr is not None
file_annotation = pr.getAnnotation(
ns='openmicroscopy.org/omero/bulk_annotations')
assert file_annotation is not None
table = sr.openTable(
file_annotation._obj.file, gatewaywrapper.gateway.SERVICE_OPTS)
assert table is not None
def testTableRead(self):
# we are Author
pr = self.getTestProject()
self.assertNotEqual(pr, None)
sr = self.gateway.getSharedResources()
name = 'bulk_annotations'
table = sr.newTable(1, name)
data = [StringColumn('col1', '', 1, ['A1', 'B1', 'C1'])]
original_file = table.getOriginalFile()
self.assertNotEqual(table, None)
table.initialize(data)
table.addData(data)
file_annotation = omero.gateway.FileAnnotationWrapper(self.gateway)
file_annotation.setNs('openmicroscopy.org/omero/bulk_annotations')
file_annotation.setDescription(name)
file_annotation.setFile(original_file)
pr.linkAnnotation(file_annotation)
# table created, can we read it back?
pr = self.getTestProject()
self.assertNotEqual(pr, None)
file_annotation = pr.getAnnotation(
ns='openmicroscopy.org/omero/bulk_annotations')
self.assertNotEqual(file_annotation, None)
table = sr.openTable(file_annotation._obj.file)
self.assertNotEqual(table, None)
# now as Admin
self.loginAsAdmin()
sr = self.gateway.getSharedResources()
self.gateway.SERVICE_OPTS.setOmeroGroup('-1')
pr = self.getTestProject()
self.assertNotEqual(pr, None)
file_annotation = pr.getAnnotation(
ns='openmicroscopy.org/omero/bulk_annotations')
self.assertNotEqual(file_annotation, None)
table = sr.openTable(file_annotation._obj.file,
self.gateway.SERVICE_OPTS)
self.assertNotEqual(table, None)
def parse(self):
provider = self.original_file_provider
data = provider.get_original_file_data(self.original_file)
try:
rows = list(csv.reader(data, delimiter=","))
finally:
data.close()
columns = [
ImageColumn("Image", "", list()),
RoiColumn("ROI", "", list()),
StringColumn("Type", "", 12, list()),
]
for row in rows[1:]:
wellnumber = self.well_name_to_number(row[0])
image = self.analysis_ctx.\
image_from_wellnumber(wellnumber)
# TODO: what to do with the field?!
# field = int(row[1])
# image = images[field]
roi = RoiI()
shape = PointI()
shape.cx = rdouble(float(row[2]))
shape.cy = rdouble(float(row[3]))
shape.textValue = rstring(row[4])
roi.addShape(shape)
roi.image = image.proxy()
rid = self.update_service\
.saveAndReturnIds([roi])[0]
columns[0].values.append(image.id.val)
columns[1].values.append(rid)
columns[2].values.append(row[4])
return MeasurementParsingResult([columns])