diff --git a/tools/omero/omero_get.xml b/tools/omero/omero_get.xml
deleted file mode 100644
index b21a0cca..00000000
--- a/tools/omero/omero_get.xml
+++ /dev/null
@@ -1,118 +0,0 @@
-
- with ezomero
-
- 5.18.0
- 0
-
-
- omero
-
-
- ezomero
-
- openjdk
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- ^[a-zA-Z0-9._-]*$
- '..' not in value
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-Description
------------
-
-Tool to fetch project, dataset, images and ROIs IDs user defined OMERO.server.
-Additionally, this tool fetch attachments and tables linked to an Image
-
-Options:
-Project -> Project IDs present in the OMERO.server
-Dataset -> Dataset IDs present in a specific Project
-Image -> Image IDs present in a specific Dataset
-Annotation -> Annotation File (Key-Value Pairs) linked to an Image
-ROI -> ROI IDs linked to an Image
-Table -> Table linked to an Image
-
-
-
- 10.1038/nmeth.1896
-
-
\ No newline at end of file
diff --git a/tools/omero/omero_get_id.py b/tools/omero/omero_get_id.py
new file mode 100644
index 00000000..fc9cde96
--- /dev/null
+++ b/tools/omero/omero_get_id.py
@@ -0,0 +1,113 @@
+import argparse
+import csv
+import json
+
+import ezomero as ez
+
+
+def get_ids_ezo(user, pws, host, port, final_obj_type, parent_obj_type, parent_id=None, tsv_file="id_list.tsv"):
+ # Function to write tabular file from the ezomero output
+ def write_ids_to_tsv(data, header):
+ with open(tsv_file, 'a+', newline='') as f:
+ f.seek(0)
+ is_empty = f.tell() == 0 # Check if file is empty
+ writer = csv.writer(f, delimiter='\t')
+ if is_empty:
+ writer.writerow([header]) # Write the header
+ for item in data:
+ writer.writerow([item]) # Write each ID
+ try:
+ with ez.connect(user, pws, "", host, port, secure=True) as conn:
+ if final_obj_type == "Project":
+ proj_ids = ez.get_project_ids(conn)
+ write_ids_to_tsv(proj_ids, "Project IDs")
+ return proj_ids
+ elif final_obj_type == "Dataset":
+ args = {'project': None}
+ if parent_obj_type == "Project":
+ args['project'] = parent_id
+ ds_ids = ez.get_dataset_ids(conn, **args)
+ write_ids_to_tsv(ds_ids, "Dataset IDs")
+ return ds_ids
+ elif final_obj_type == "Image":
+ args = {
+ 'project': None,
+ 'dataset': None,
+ 'plate': None,
+ 'well': None
+ }
+ if parent_obj_type == "Project":
+ args['project'] = parent_id
+ elif parent_obj_type == "Dataset":
+ args['dataset'] = parent_id
+ elif parent_obj_type == "Plate":
+ args['plate'] = parent_id
+ elif parent_obj_type == "Well":
+ args['well'] = parent_id
+ elif parent_obj_type != "All":
+ raise ValueError("Object set as parent_obj_type is not compatible")
+ ds_ims = ez.get_image_ids(conn, **args)
+ write_ids_to_tsv(ds_ims, "Image IDs")
+ return ds_ims
+ elif final_obj_type == "Annotation":
+ map_annot_ids = ez.get_map_annotation_ids(conn, parent_obj_type, parent_id)
+ write_ids_to_tsv(map_annot_ids, "Annotation IDs")
+ return map_annot_ids
+ elif final_obj_type == "Tag":
+ tag_ids = ez.get_tag_ids(conn, parent_obj_type, parent_id)
+ write_ids_to_tsv(tag_ids, "Tag IDs")
+ return tag_ids
+ elif final_obj_type == "Roi":
+ roi_ids = ez.get_roi_ids(conn, parent_id)
+ write_ids_to_tsv(roi_ids, "ROI IDs")
+ return roi_ids
+ elif final_obj_type == "Table":
+ file_ann_ids = ez.get_file_annotation_ids(conn, parent_obj_type, parent_id)
+ write_ids_to_tsv(file_ann_ids, "Table IDs")
+ return file_ann_ids
+ else:
+ raise ValueError(f"Unsupported object type: {final_obj_type}")
+
+ except Exception as e:
+ print(f"Connection error: {str(e)}")
+ return None
+
+
+# Argument parsing
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Fetch OMERO object IDs as TSV from parent object.")
+ parser.add_argument("--credential-file", dest="credential_file", type=str,
+ required=True, help="Credential file (JSON file with username and password for OMERO)")
+ parser.add_argument('--host', required=True,
+ help="Host server address.")
+ parser.add_argument('--port', required=True, type=int,
+ help='OMERO port')
+ parser.add_argument('--final_obj_type', required=True,
+ help="Type of object to fetch ID: Project, Dataset, Image, Annotation, Tag, Roi, or Table.")
+ parser.add_argument('--parent_obj_type', required=True,
+ help="Type of object from which you fetch IDs: Project, Dataset, Plate, Well, Image (or 'All' if you want to get all objects).")
+ parser.add_argument('--parent_id', required=False, type=int,
+ help="ID of the OMERO object in `--parent_obj_type`, not required if you used `--parent_obj_type All`.")
+ parser.add_argument('--tsv_file', default='id_list.tsv', required=True,
+ help="Output TSV file path.")
+ args = parser.parse_args()
+
+ if args.parent_id is None and args.parent_obj_type != "All":
+ raise ValueError("ID is only optional is you use `--parent_obj_type All`")
+
+ if args.final_obj_type == "Roi" and args.parent_obj_type != "Image":
+ raise ValueError("Roi IDs can only be retrived from images, use `--parent_obj_type Image`")
+
+ if args.parent_obj_type == "All" and args.final_obj_type not in ["Image", "Dataset", "Project"]:
+ raise ValueError("Only Images, Datasets and Projects is compatible with `--parent_obj_type All`")
+
+ with open(args.credential_file, 'r') as f:
+ crds = json.load(f)
+
+ # Call the main function to get the object and save it as a TSV
+ get_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host,
+ port=args.port,
+ final_obj_type=args.final_obj_type,
+ parent_obj_type=args.parent_obj_type,
+ parent_id=args.parent_id,
+ tsv_file=args.tsv_file)
diff --git a/tools/omero/omero_get_id.xml b/tools/omero/omero_get_id.xml
new file mode 100644
index 00000000..823f07fe
--- /dev/null
+++ b/tools/omero/omero_get_id.xml
@@ -0,0 +1,199 @@
+
+ with ezomero
+
+ 5.18.0
+ 0
+
+
+ omero
+
+
+ ezomero
+
+ openjdk
+
+
+
+
+
+
+
+ ^[a-zA-Z0-9._-]*$
+ '..' not in value
+
+
+
+
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+
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+
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+
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+
+
+Description
+-----------
+
+Tool to fetch project, dataset, images, annotations, tags, table and ROIs IDs user defined OMERO.server.
+
+Options:
+Project -> Project IDs present in the OMERO.server
+Dataset -> Dataset IDs present in a specific Project or in the server
+Image -> Image IDs present in a specific Dataset or Project or Well or Plate or in the server
+Annotation (Key-Value Pairs) -> Annotation IDs linked to an Image or Dataset or Project or Well or Plate
+Tag -> Tag IDs linked to an Image or Dataset or Project or Well or Plate
+ROI -> ROI IDs linked to an Image
+Table -> Table linked to an Image or Dataset or Project or Well or Plate
+
+
+
+ 10.1038/nmeth.1896
+
+
\ No newline at end of file
diff --git a/tools/omero/omero_get.py b/tools/omero/omero_get_value.py
similarity index 55%
rename from tools/omero/omero_get.py
rename to tools/omero/omero_get_value.py
index c8cc484d..597c830a 100644
--- a/tools/omero/omero_get.py
+++ b/tools/omero/omero_get_value.py
@@ -5,9 +5,9 @@
import ezomero as ez
-def get_object_ezo(user, pws, host, port, obj_type, id=None, tsv_file="id_list.tsv"):
+def get_object_ezo(user, pws, host, port, obj_type, ids, tsv_file):
# Function to write tabular file from the ezomero output
- def write_ids_to_tsv(data, header):
+ def write_values_to_tsv(data, header):
with open(tsv_file, 'a+', newline='') as f:
f.seek(0)
is_empty = f.tell() == 0 # Check if file is empty
@@ -15,7 +15,7 @@ def write_ids_to_tsv(data, header):
if is_empty:
writer.writerow([header]) # Write the header
for item in data:
- writer.writerow([item]) # Write each ID
+ writer.writerow([item]) # Write each value
# Function to write tabular file from a dictionary ezomero output
def write_dict_to_tsv(data, headers):
@@ -28,31 +28,34 @@ def write_dict_to_tsv(data, headers):
for key, value in data.items():
writer.writerow([key, value]) # Write each key-value pair
+ # Function to write tabular file from list of list ezomero output
+ def write_table_to_tsv(data):
+ with open(tsv_file, 'w') as f:
+ for row in data:
+ f.write('\t'.join([str(val) for val in row]) + '\n')
+
try:
with ez.connect(user, pws, "", host, port, secure=True) as conn:
- if obj_type == "dataset":
- ds_ids = ez.get_dataset_ids(conn, project=int(id))
- write_ids_to_tsv(ds_ids, "Dataset IDs")
- return ds_ids
- elif obj_type == "image":
- ds_ims = ez.get_image_ids(conn, dataset=int(id))
- write_ids_to_tsv(ds_ims, "Image IDs")
- return ds_ims
- elif obj_type == "annotation":
- ma_dict = ez.get_map_annotation(conn, int(id))
+ if obj_type == "Annotation":
+ ma_dict = {}
+ for maid in ids:
+ current_ma_dict = ez.get_map_annotation(conn, maid)
+ ma_dict = {**ma_dict, **current_ma_dict}
write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"])
return ma_dict
- elif obj_type == "project":
- proj_ids = ez.get_project_ids(conn)
- write_ids_to_tsv(proj_ids, "Project IDs")
- return proj_ids
- elif obj_type == "roi":
- roi_ids = ez.get_roi_ids(conn, int(id))
- write_ids_to_tsv(roi_ids, "ROI IDs")
- return roi_ids
- elif obj_type == "table":
- table = ez.get_table(conn, int(id))
- write_dict_to_tsv(table, ["Table ID", "Table Value"])
+ elif obj_type == "Tag":
+ tags = []
+ for tag_id in ids:
+ tags.append(ez.get_tag(conn, tag_id))
+ # Sort the tags for consistency:
+ tags.sort
+ write_values_to_tsv(tags, "Tags")
+ return tags
+ elif obj_type == "Table":
+ if len(ids) > 1:
+ raise ValueError("Only one table can be exported at a time")
+ table = ez.get_table(conn, ids[0])
+ write_table_to_tsv(table)
return table
else:
raise ValueError(f"Unsupported object type: {obj_type}")
@@ -72,13 +75,27 @@ def write_dict_to_tsv(data, headers):
parser.add_argument('--port', required=True, type=int,
help='OMERO port')
parser.add_argument('--obj_type', required=True,
- help="Type of object to fetch: dataset, image, annotation, project, roi, or table.")
- parser.add_argument('--id', required=False,
- help="ID of the specific OMERO object.")
+ help="Type of object to fetch: Annotation, Table or Tag.")
+ group = parser.add_mutually_exclusive_group()
+ group.add_argument('--ids', nargs='+', type=int,
+ help="IDs of the OMERO objects.")
+ group.add_argument('--ids_path',
+ help="File with IDs of the OMERO objects (one per line).")
parser.add_argument('--tsv_file', default='id_list.tsv', required=True,
help="Output TSV file path.")
args = parser.parse_args()
+ if args.ids_path:
+ args.ids = []
+ with open(args.ids_path, 'r') as f:
+ for line in f:
+ try:
+ args.ids.append(int(line))
+ except ValueError:
+ print(f"{line.strip()} is not a valid ID.")
+ if len(args.ids) == 0:
+ raise ValueError("Cound not find a single ID in the file.")
+
with open(args.credential_file, 'r') as f:
crds = json.load(f)
@@ -86,5 +103,5 @@ def write_dict_to_tsv(data, headers):
get_object_ezo(user=crds['username'], pws=crds['password'], host=args.host,
port=args.port,
obj_type=args.obj_type,
- id=args.id,
+ ids=args.ids,
tsv_file=args.tsv_file)
diff --git a/tools/omero/omero_get_value.xml b/tools/omero/omero_get_value.xml
new file mode 100644
index 00000000..991ff95c
--- /dev/null
+++ b/tools/omero/omero_get_value.xml
@@ -0,0 +1,99 @@
+
+ with ezomero
+
+ 5.18.0
+ 0
+
+
+ omero
+
+
+ ezomero
+
+ openjdk
+
+
+
+
+
+
+
+ ^[a-zA-Z0-9._-]*$
+ '..' not in value
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ [0-9]+(,[0-9]+)*
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Description
+-----------
+
+Tool to fetch Annotation, Tag and Tables from IDs.
+
+The IDs can be obtained with the tool OMERO get IDs with ezomero
+
+
+
+ 10.1038/nmeth.1896
+
+
\ No newline at end of file