New Tool: OMERO convert dataset to plate

.github/workflows/ci.yaml

@@ -191,6 +191,9 @@ jobs:
         omero tag create --name test_tag --desc 'description of my_tag'
         omero tag link Image:1 1
         echo "Created the dummy dataset into OMERO"
+        DID_HCS=$(omero obj new Dataset name='test_hcs_dts')
+        omero import -d $DID_HCS .github/dummy-hcs-omero
+        echo "Created the hcs dummy dataset into OMERO"
 
     # download or create large test data via script
     - name: Create test data

.github/workflows/pr.yaml

@@ -332,6 +332,9 @@ jobs:
         omero tag create --name test_tag --desc 'description of my_tag'
         omero tag link Image:1 1
         echo "Created the dummy dataset into OMERO"
+        DID_HCS=$(omero obj new Dataset name='test_hcs_dts')
+        omero import -d $DID_HCS .github/dummy-hcs-omero
+        echo "Created the hcs dummy dataset into OMERO"
 
     # download or create large test data via script
     - name: Create test data

tools/omero/omero_dataset_to_plate.py

@@ -0,0 +1,127 @@
+import argparse
+import csv
+import json
+import re
+import sys
+from collections import defaultdict
+
+
+import omero
+from omero.gateway import BlitzGateway
+from omero.rtypes import rint, rstring
+
+
+def convert_dataset_to_plate(host, user, pws, port, dataset_id, log_file, mapping_file, delete_dataset):
+    """
+    Connect to OMERO server, convert a dataset to a plate using the specified well mapping file
+    """
+    conn = BlitzGateway(user, pws, host=host, port=port, secure=True)
+    if not conn.connect():
+        sys.exit("ERROR: Failed to connect to OMERO server")
+
+    def log_message(message, status="INFO"):
+        with open(log_file, 'w') as f:
+            f.write(f"{message}")
+
+    dataset = conn.getObject("Dataset", dataset_id)
+    if dataset is None:
+        conn.close()
+        sys.exit("ERROR: Dataset not found")
+
+    update_service = conn.getUpdateService()
+
+    # Create a Plate
+    plate = omero.model.PlateI()
+    plate.name = rstring(dataset.getName())
+    plate = update_service.saveAndReturnObject(plate)
+
+    # Parse the mapping file
+    image_to_well_mapping = {}
+    if mapping_file:
+        with open(mapping_file, 'r') as f:
+            reader = csv.DictReader(f, delimiter='\t')
+            for row in reader:
+                filename = row['Filename']
+                well = row['Well']
+                match = re.match(r"([A-Z])(\d+)", well)
+                if match:
+                    row_char, col = match.groups()
+                    row = ord(row_char.upper()) - ord('A')
+                    col = int(col) - 1
+                    image_to_well_mapping[filename] = (row, col)
+                else:
+                    conn.close()
+                    sys.exit(f"Invalid well format '{well}' for file '{filename}'")
+
+    # List the dataset children
+    images = list(dataset.listChildren())
+    if not images:
+        conn.close()
+        sys.exit("ERROR: No images found in dataset")
+
+    # Compare images in the mapping file and in the dataset
+    grouped_images = defaultdict(list)
+    for image in images:
+        image_name = image.getName()
+        if image_to_well_mapping:
+            if image_name in image_to_well_mapping:
+                row, col = image_to_well_mapping[image_name]
+                grouped_images[(row, col)].append(image)
+            else:
+                conn.close()
+                sys.exit(f"Image '{image_name}' not found in mapping file.")
+
+    # Assign images to the well based on the mapping file
+    for (row, col), imgs_in_group in grouped_images.items():
+        well = omero.model.WellI()
+        well.plate = omero.model.PlateI(plate.id.val, False)
+        well.column = rint(col)
+        well.row = rint(row)
+
+        for image in imgs_in_group:
+            ws = omero.model.WellSampleI()
+            ws.image = omero.model.ImageI(image.id, False)
+            ws.well = well
+            well.addWellSample(ws)
+
+        try:
+            update_service.saveObject(well)
+        except ValueError as e:
+            conn.close()
+            sys.exit("ERROR: Failed to update plate for dataset '{}' due to: {}".format(dataset.getName(), str(e)))
+
+    # Close the connection and, in case, delete the dataset
+    if delete_dataset is True:
+        conn.deleteObjects("Dataset", [dataset_id], wait=True)
+    log_message(f"Images from Dataset {dataset_id} successfully added to Plate {plate.id.val}")
+    conn.close()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Convert an OMERO dataset to a plate.")
+    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='OMERO host')
+    parser.add_argument('--port', required=True, type=int, help='OMERO port')
+    parser.add_argument('--dataset_id', type=int, required=True, help="Dataset ID to convert plate")
+    parser.add_argument('--log_file', default='metadata_import_log.txt',
+                        help='Path to the log file')
+    parser.add_argument('--mapping_file',
+                        help='Tabular file mapping filenames to well positions (2 columns: filename, Well)')
+    parser.add_argument('--delete_dataset', action='store_true',
+                        help='Flag to delete the original dataset')
+    args = parser.parse_args()
+
+    with open(args.credential_file, 'r') as f:
+        crds = json.load(f)
+
+    convert_dataset_to_plate(
+        user=crds['username'],
+        pws=crds['password'],
+        host=args.host,
+        port=args.port,
+        dataset_id=args.dataset_id,
+        log_file=args.log_file,
+        mapping_file=args.mapping_file,
+        delete_dataset=args.delete_dataset
+    )

tools/omero/omero_dataset_to_plate.xml

@@ -0,0 +1,67 @@
+<tool id="omero_dataset_to_plate" name="OMERO Dataset to Plate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+   <description> with omero-py </description>
+   <macros>
+       <import>macros.xml</import>
+       <token name="@VERSION_SUFFIX@">3</token>
+   </macros>
+   <xrefs>
+       <xref type="bio.tools">omero</xref>
+   </xrefs>
+   <expand macro="omeropy_requirements"/>
+   <command detect_errors="exit_code"><![CDATA[
+       python '$__tool_directory__/omero_dataset_to_plate.py'
+       --credential-file '$credentials'
+       @HOST_PORT@
+       --dataset_id '$dataset_id'
+       --log_file '$log'
+       --mapping_file '$mapping'
+       '$delete_dataset'
+   ]]></command>
+   <configfiles>
+       <expand macro="credentials"/>
+   </configfiles>
+   <inputs>
+       <expand macro="host_port"/>
+       <param name="dataset_id" type="integer" optional="false" min = "1" label="Dataset ID to convert to a plate"/>
+       <param name="mapping" type="data" format= "tabular" optional="false" label="Mapping file"/>
+       <param name="delete_dataset" type="boolean" truevalue="--delete_dataset" falsevalue="" checked="false" label="Delete Dataset" help="Delete dataset after import"/>
+   </inputs>
+   <outputs>
+       <data name="log" format="txt"/>
+   </outputs>
+   <tests>
+       <test>
+           <param name="omero_host" value="host.docker.internal"/>
+           <param name="omero_port" value="6064"/>
+           <param name="dataset_id" value="2"/>
+           <param name="test_username" value="root"/>
+           <param name="test_password" value="omero"/>
+           <param name="mapping" value="mapping.tsv"/>
+           <param name="delete_dataset" value="True"/>
+           <output name="log" value="dataset_conversion_log.txt" ftype="txt">
+               <assert_contents>
+                   <has_text text="Images from Dataset 2 successfully added to Plate 1"/>
+               </assert_contents>
+           </output>
+       </test>
+   </tests>
+   <help>
+Description
+-----------
+- Tool to convert an existing dataset to a plate in OMERO
+- The tool is taking as input a mapping tabular file with Filename and Well Position:
+  +------------+---------------+
+  | Filename   | Well          |
+  +============+===============+
+  | image1.tiff| A2            |
+  +------------+---------------+
+  | image2.tiff| B5            |
+  +------------+---------------+
+  | image3.tiff| H12           |
+  +------------+---------------+
+@SECURITY_DISCLAIMER@
+   </help>
+   <citations>
+       <citation type="doi">10.1038/nmeth.1896</citation>
+   </citations>
+</tool>

tools/omero/omero_filter.xml

@@ -77,7 +77,7 @@
             <param name="test_password" value="omero"/>
             <output name="tsv" value="output_filter_filename.tsv" ftype="tabular">
                 <assert_contents>
-                    <has_text text="2"/>
+                    <has_text text="1"/>
                     <has_n_columns n="1"/>
                 </assert_contents>
             </output>
@@ -114,4 +114,4 @@ Description
     <citations>
         <citation type="doi">10.1038/nmeth.1896</citation>
     </citations>
-</tool>
+</tool>

tools/omero/omero_get_value.xml

@@ -41,7 +41,7 @@
                 </param>
             </when>
             <when value="file">
-                <param argument="--ids_path" type="data" format="txt,tabular" label="Dataset with ID(s) of the object(s) to fetch on OMERO (one per line)"/>
+                <param argument="--ids_path" type="data" format="txt,tabular" min="1" label="Dataset with ID(s) of the object(s) to fetch on OMERO (one per line)"/>
             </when>
         </conditional>
     </inputs>

tools/omero/omero_metadata_import.xml

@@ -30,16 +30,18 @@
             <option value="project">Project</option>
             <option value="screen">Screen</option>
             <option value="dataset">Dataset</option>
+            <option value="plate">Plate</option>
+            <option value="well">Well</option>
             <option value="image">Image</option>
         </param>
         <conditional name="object_id">
-        <param name="object_id_selection" type="select" label="Selection"  help="Create a new OMERO object or target an existing one">
+        <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one">
             <option value="new_object">Create new object</option>
             <option value="existing_object">Target an existing object</option>
         </param>
         <when value="new_object"/>
         <when value="existing_object">
-            <param name="did" type="integer" value="" optional="false" label="Object ID"/>
+            <param name="did" type="integer" min = "1" optional="false" label="Object ID"/>
         </when>
         </conditional>
         <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">

tools/omero/omero_metadata_upload.py

@@ -56,6 +56,10 @@ def log_success(message):
                 if did is None:
                     did = ez.post_dataset(conn, dataset_name=str(datetime.now()))
                 result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name)
+            elif obj_type == "plate":
+                result = upload_metadata(conn, "Plate", did, data_dict, df, ann_type, an_name)
+            elif obj_type == "well":
+                result = upload_metadata(conn, "Well", did, data_dict, df, ann_type, an_name)
             elif obj_type == "image":
                 result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name)
             else:
@@ -74,10 +78,12 @@ def log_success(message):
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Import metadata into OMERO.')
-    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("--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='OMERO host')
     parser.add_argument('--port', required=True, type=int, help='OMERO port')
-    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'image'],
+    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate',
+                                                              'well ', 'image'],
                         help='Type of OMERO object')
     parser.add_argument('--did', type=int, help='ID of the object (if it exists)')
     parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type')

tools/omero/omero_roi_import.xml

@@ -22,7 +22,7 @@
     <inputs>
         <expand macro="host_port"/>
         <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/>
-        <param argument="id" type="integer" value="" optional="false" label="Image ID where annotate the ROIs"/>
+        <param argument="id" type="integer" value="" optional="false" min = "1" label="Image ID where annotate the ROIs"/>
     </inputs>
     <outputs>
         <data name="log" format="txt"/>

tools/omero/test-data/dataset_conversion_log.txt

@@ -0,0 +1 @@
+Images from Dataset 2 successfully added to Plate 1

tools/omero/test-data/mapping.tsv

@@ -0,0 +1,3 @@
+Filename	Well
+sample_A03_image.jpg	A2
+sample_H11_image.jpg	H5

tools/omero/test-data/omero_output.txt

@@ -1,2 +1,2 @@
-Image:3
-Image:4
+Image:5
+Image:6

tools/omero/test-data/output_KV_import.txt

@@ -1 +1 @@
-SUCCESS: Successfully uploaded metadata for dataset with ID 3. Result: {'Key1': 'Value1', 'Key2': 'Value2'}
+SUCCESS: Successfully uploaded metadata for dataset with ID 4. Result: {'Key1': 'Value1', 'Key2': 'Value2'}