def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
data_type = script_params["Data_Type"]
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = int(script_params["File_Annotation"])
link_file_ann(conn, data_type, object_id, file_ann_id)
original_file = get_original_file(conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
data_for_preprocessing = provider.get_original_file_data(original_file)
data = provider.get_original_file_data(original_file)
objecti = getattr(omero.model, data_type + 'I')
omero_object = objecti(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
try:
# Old
ctx.parse_from_handle(data)
ctx.write_to_omero()
except AttributeError:
# omero-metadata >= 0.3.0
ctx.preprocess_from_handle(data_for_preprocessing)
ctx.parse_from_handle_stream(data)
return "Table data populated for %s: %s" % (data_type, object_id)
def populate_metadata(client, conn, script_params):
object_id = long(script_params["IDs"])
file_id = long(script_params["File_ID"])
original_file = get_original_file(
conn, script_params["Data_Type"], object_id, file_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if script_params["Data_Type"] == "Plate":
omero_object = PlateI(long(object_id), False)
else:
omero_object = ScreenI(long(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
def populate_metadata(client, conn, script_params):
object_id = int(script_params["IDs"])
file_id = int(script_params["File_ID"])
original_file = get_original_file(conn, script_params["Data_Type"],
object_id, file_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if script_params["Data_Type"] == "Plate":
omero_object = PlateI(int(object_id), False)
else:
omero_object = ScreenI(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = long(script_params["File_Annotation"])
data_type = script_params["Data_Type"]
original_file = get_original_file(conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if data_type == "Plate":
omero_object = PlateI(long(object_id), False)
else:
omero_object = ScreenI(long(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
return "Table data populated for %s: %s" % (data_type, object_id)
def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
data_type = script_params["Data_Type"]
if data_type == "Image":
try:
from omero_metadata.populate import ImageWrapper # noqa: F401
except ImportError:
return "Please update omero-metadata to support Image type"
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = int(script_params["File_Annotation"])
link_file_ann(conn, data_type, object_id, file_ann_id)
original_file = get_original_file(
conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
data_for_preprocessing = provider.get_original_file_data(original_file)
temp_name = data_for_preprocessing.name
# 5.9.1 returns NamedTempFile where name is a string.
if isinstance(temp_name, int):
print("omero-py 5.9.1 DownloadingOriginalFileProvider returns "
"NamedTempFile. Please Upgrade to omero-py 5.9.1 or later")
return "Please upgrade omero-py to 5.9.1 or later"
objecti = getattr(omero.model, data_type + 'I')
omero_object = objecti(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
try:
if hasattr(ctx, "parse_from_handle"):
with open(temp_name, 'rt', encoding='utf-8-sig') as f1:
ctx.parse_from_handle(f1)
ctx.write_to_omero()
else:
# omero-metadata >= 0.3.0
with open(temp_name, 'rt', encoding='utf-8-sig') as f1:
ctx.preprocess_from_handle(f1)
with open(temp_name, 'rt', encoding='utf-8-sig') as f2:
ctx.parse_from_handle_stream(f2)
finally:
data_for_preprocessing.close()
return "Table data populated for %s: %s" % (data_type, object_id)
def populate_metadata(client, conn, script_params):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataType = script_params["Data_Type"]
ids = script_params["IDs"]
datasets = list(conn.getObjects(dataType, ids))
for ds in datasets:
ID = ds.getId()
# not sure what this is doing
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = long(script_params["File_Annotation"])
print("set ann id")
original_file = get_original_file(conn, dataType, ID, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
# create a dictionary for image_name:id
dict_name_id = {}
for img in ds.listChildren():
img_name = img.getName()
if (img_name in dict_name_id):
sys.stderr.write(
"File names not unique: {}".format(imageaname))
sys.exit(1)
dict_name_id[img_name] = int(img.getId())
# step through the csv file
data = list(csv.reader(file_handle, delimiter=','))
# keys are in the header row
header = data[0]
kv_data = header[1:] # first header is the fimename columns
rows = data[1:]
nimg_updated = 0
for row in rows: # first row is the header
print(row)
img_name = row[0]
if (img_name not in dict_name_id):
print("Can't find filename : {}".format(img_name))
else:
img_ID = dict_name_id[img_name] # look up the ID
img = conn.getObject('Image', img_ID) # get the img
existing_kv = get_existing_MapAnnotions(img)
updated_kv = copy.deepcopy(existing_kv)
print("Existing kv ")
for k, v in existing_kv.iteritems():
print(k, v)
for i in range(1, len(row)): # first entry is the filename
key = header[i].strip()
vals = row[i].strip().split(';')
if (len(vals) > 0):
for val in vals:
if (len(val) > 0): updated_kv[key] = val
if (existing_kv != updated_kv):
nimg_updated = nimg_updated + 1
print("The key-values pairs are different")
remove_MapAnnotations(conn, 'Image', img.getId())
map_ann = omero.gateway.MapAnnotationWrapper(conn)
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
namesoace = omero.constants.metadata.NSBULKANNOTATIONS
map_ann.setNs(namespace)
# convert the ordered dict to a list of lists
map_ann.setValue([[k, v]
for k, v in updated_kv.iteritems()])
map_ann.save()
img.linkAnnotation(map_ann)
else:
print("No change change in kv's")
return "Added {} kv pairs to {}/{} files ".format(
len(header) - 1, nimg_updated, len(dict_name_id))
def keyval_from_csv(conn, script_params):
data_type = script_params["Data_Type"]
ids = script_params["IDs"]
for target_object in conn.getObjects(data_type, ids):
# file_ann_id is Optional. If not supplied, use first .csv attached
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = int(script_params["File_Annotation"])
link_file_ann(conn, data_type, target_object.id, file_ann_id)
print("set ann id", file_ann_id)
original_file = get_original_file(target_object, file_ann_id)
print("Original File", original_file.id.val, original_file.name.val)
provider = DownloadingOriginalFileProvider(conn)
# read the csv
file_handle = provider.get_original_file_data(original_file)
try:
delimiter = csv.Sniffer().sniff(file_handle.read(1024)).delimiter
print("Using delimiter: ", delimiter)
except Exception:
print("Failed to sniff delimiter, using ','")
delimiter = ","
# reset to start and read whole file...
file_handle.seek(0)
data = list(csv.reader(file_handle, delimiter=delimiter))
file_handle.close()
# keys are in the header row
header = data[0]
print("header", header)
# create dictionaries for well/image name:object
images_by_name, wells_by_name = get_children_by_name(target_object)
image_index = header.index("image")
well_index = header.index("well")
plate_index = header.index("plate")
if image_index == -1:
# first header is the img-name column, if 'image' not found
image_index = 0
print("image_index:", image_index, "well_index:", well_index,
"plate_index:", plate_index)
rows = data[1:]
nimg_updated = 0
missing_names = 0
# loop over csv rows...
for row in rows:
# try to find 'image', then 'well', then 'plate'
image_name = row[image_index]
well_name = None
plate_name = None
obj = None
if len(image_name) > 0:
if image_name in images_by_name:
obj = images_by_name[image_name]
print("Annotating Image:", obj.id, image_name)
else:
missing_names += 1
print("Image not found:", image_name)
if obj is None and well_index > -1 and len(row[well_index]) > 0:
well_name = row[well_index]
if well_name in wells_by_name:
obj = wells_by_name[well_name]
print("Annotating Well:", obj.id, well_name)
else:
missing_names += 1
print("Well not found:", well_name)
if obj is None and plate_index > -1:
plate_name = row[plate_index]
if plate_name == target_object.name:
obj = target_object
print("Annotating Plate:", obj.id, plate_name)
if obj is None:
msg = f"Can't find object by image, well or plate name"
print(msg)
continue
cols_to_ignore = [image_index, well_index, plate_index]
updated = annotate_object(conn, obj, header, row, cols_to_ignore)
if updated:
nimg_updated += 1
message = "Added {} kv pairs to {}/{} files".format(
len(header) - 1, nimg_updated, len(images_by_name))
if missing_names > 0:
message += f". {missing_names} image names not found."
return message