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made Importer `zarr´ compatible #99

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merged 2 commits into from
Apr 1, 2024
Merged

made Importer `zarr´ compatible #99

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03cd2ae
made Importer `zarr´ compatible
jo-mueller Jan 30, 2024
db4f409
passing *args, **kwargs to `omero import`
erickmartins Mar 20, 2024
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88 changes: 42 additions & 46 deletions ezomero/_importer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,10 @@ def ezimport(conn: BlitzGateway, target: str,
project: Optional[Union[str, int]] = None,
dataset: Optional[Union[str, int]] = None,
screen: Optional[Union[str, int]] = None,
ln_s: Optional[bool] = False, ann: Optional[dict] = None,
ns: Optional[str] = None) -> Union[List[int], None]:
ann: Optional[dict] = None,
ns: Optional[str] = None, *args: str,
**kwargs: str
) -> Union[List[int], None]:
"""Entry point that creates Importer and runs import.

Parameters
Expand All @@ -35,12 +37,15 @@ def ezimport(conn: BlitzGateway, target: str,
The name or ID of the Dataset data will be imported into.
screen : str or int, optional
The name or ID of the Screen data will be imported into.
ln_s : boolean, optional
Whether to use ``ln_s`` softlinking during imports or not.
ann : dict, optional
Dictionary with key-value pairs to be added to imported images.
ns : str, optional
Namespace for the added key-value pairs.
*args, **kwargs : str, optional
You can also add any extra arguments you would like to pass to
``omero import`` to the end of the argument list in ``ezimport``.
For example, an in-place import can be done by adding
``transfer="ln_s"`` as an extra argument when calling `ezimport``.

Returns
-------
Expand All @@ -55,7 +60,7 @@ def ezimport(conn: BlitzGateway, target: str,
"""

imp_ctl = Importer(conn, target, project, dataset, screen,
ln_s, ann, ns)
ann, ns, *args, **kwargs)
imp_ctl.ezimport()
if imp_ctl.screen:
imp_ctl.get_plate_ids()
Expand Down Expand Up @@ -234,8 +239,6 @@ class Importer:
The name or ID of the Dataset data will be imported into.
screen : str or int, optional
The name or ID of the Screen data will be imported into.
ln_s : boolean, optional
Whether to use ``ln_s`` softlinking during imports or not.
ann : dict, optional
Dictionary with key-value pairs to be added to imported images.
ns : str, optional
Expand All @@ -244,6 +247,9 @@ class Importer:
Hostname of the OMERO server to which data will be imported.
port : int, optional
Port of the OMERO server to which data will be imported.
*args, **kwargs : str, optional
Receives the ``*args``, ``**kwargs`` from ``ezimport`` to pass it
onto ``omero import``.

Important notes:
1) Setting ``project`` also requires setting ``dataset``. Failing to do so
Expand All @@ -264,20 +270,22 @@ def __init__(self, conn: BlitzGateway, file_path: str,
project: Optional[Union[str, int]],
dataset: Optional[Union[str, int]],
screen: Optional[Union[str, int]],
ln_s: Optional[bool], ann: Optional[dict],
ns: Optional[str]):
ann: Optional[dict],
ns: Optional[str], *args, **kwargs):
self.conn = conn
self.file_path = abspath(file_path)
self.session_uuid = conn.getSession().getUuid().val
self.project = project
self.dataset = dataset
self.common_args = args
self.named_args = kwargs

if self.project and not self.dataset:
raise ValueError("Cannot define project but no dataset!")
self.screen = screen
self.imported = False
self.image_ids: Union[List[int], None] = None
self.plate_ids: Union[List[int], None] = None
self.ln_s = ln_s
self.ann = ann
self.ns = ns

Expand All @@ -301,6 +309,8 @@ def get_my_image_ids(self) -> Union[List[int], None]:
params = Parameters()
path_query = self.make_substitutions()
path_query = path_query.strip('/')
if path_query.endswith(".zarr"):
path_query = f"{path_query}/.zattrs"
params.map = {"cpath": rstring(path_query)}
results = q.projection(
"SELECT i.id FROM Image i"
Expand Down Expand Up @@ -453,50 +463,36 @@ def organize_plates(self) -> bool:
return True
return False

def ezimport_ln_s(self) -> bool:
"""Import file using the ``--transfer=ln_s`` option.
def ezimport(self) -> bool:
"""Import file.
Returns
-------
import_status : boolean
True if OMERO import returns a 0 exit status, else False.
"""

args = ""
if self.common_args:
args = args + " ".join(self.common_args)
if self.named_args:
for k, v in self.named_args.items():
args = args + " " + str(k) + "=" + str(v)
cli = CLI()
cli.register('import', ImportControl, '_')
cli.register('sessions', SessionsControl, '_')
cli.invoke(['import',
'-k', self.conn.getSession().getUuid().val,
'-s', self.conn.host,
'-p', str(self.conn.port),
'--transfer', 'ln_s',
str(self.file_path)])
if cli.rv == 0:
self.imported = True
print(f'Imported {self.file_path}')
return True
else:
logging.error(f'Import of {self.file_path} has failed!')
return False

def ezimport(self) -> bool:
"""Import file.
Returns
-------
import_status : boolean
True if OMERO import returns a 0 exit status, else False.
"""
if self.ln_s:
rs = self.ezimport_ln_s()
return rs
else:
cli = CLI()
cli.register('import', ImportControl, '_')
cli.register('sessions', SessionsControl, '_')
cli.invoke(['import',
'-k', self.conn.getSession().getUuid().val,
'-s', self.conn.host,
'-p', str(self.conn.port),
str(self.file_path)])
arguments = ['import',
'-k', self.conn.getSession().getUuid().val,
'-s', self.conn.host,
'-p', str(self.conn.port)]
if self.common_args:
str_args = ['--{}'.format(v) for v in self.common_args]
arguments.extend(str_args)
if self.named_args:
str_kwargs = ['--{}={}'.format(k, v) for k, v in
self.named_args.items()]
arguments.extend(str_kwargs)
arguments.append(str(self.file_path))
print(arguments)
cli.invoke(arguments)
if cli.rv == 0:
self.imported = True
print(f'Imported {self.file_path}')
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
url="https://github.com/TheJacksonLaboratory/ezomero",
packages=setuptools.find_packages(),
install_requires=[
'omero-py == 5.18.0',
'omero-py == 5.19.0',
'numpy >= 1.22, < 2.0'
],
extras_require={
Expand Down
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