add new tools (omero get and omero filter) and updated the ci/pr pipe…

…line to add metadat to the dummy set)

.github/workflows/ci.yaml

@@ -188,6 +188,8 @@ jobs:
         DID=$(omero obj new Dataset name='test_dts')
         omero obj new ProjectDatasetLink parent=$PID child=$DID
         omero import -d $DID .github/dummy-dts-omero
+        omero tag create --name test_tag --desc 'description of my_tag'
+        omero tag link Image:1 1
         echo "Created the dummy dataset into OMERO"
 
     # download or create large test data via script

.github/workflows/pr.yaml

@@ -329,6 +329,8 @@ jobs:
         DID=$(omero obj new Dataset name='test_dts')
         omero obj new ProjectDatasetLink parent=$PID child=$DID
         omero import -d $DID .github/dummy-dts-omero
+        omero tag create --name test_tag --desc 'description of my_tag'
+        omero tag link Image:1 1
         echo "Created the dummy dataset into OMERO"
 
     # download or create large test data via script

tools/omero/.shed.yml

@@ -1,8 +1,8 @@
 categories:
 - Imaging
 name: omero_upload
-description: Import images, region of interest, metadata into an OMERO.server using omero-py
-long_description: Tool to import and link different objects into OMERO
+description: Interact with an OMERO.server using omero-py and ezomero.
+long_description:  This set of tool allows to import images and metadata into an OMERO.server.
 owner: ufz
 remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero
 homepage_url: https://github.com/ome/omero-py/
@@ -13,4 +13,4 @@ suite:
   name: "suite_omero_py"
   description: "A suite of tools that brings the omero-py and ezomero project into Galaxy."
   long_description: |
-    OMERO.py provides an interface to the OMERO.blitz server.
+    OMERO.py and ezomero provides an interface to the OMERO.blitz server.

tools/omero/omero_filter.py

@@ -0,0 +1,80 @@
+import argparse
+import csv
+import json
+
+import ezomero as ez
+
+
+def filter_ids_ezo(user, pws, host, port, filter, id, value1, value2=None, tsv_file="filter_list.tsv"):
+
+    # Transform the id input in a list of integer
+    id = id.split(',')
+    id = list(map(int, id))
+
+    # 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 filter == "filename":
+                fn_ids = ez.filter_by_filename(conn, id, value1)
+                write_ids_to_tsv(fn_ids, [f"Images with filename {value1}"])
+                return fn_ids
+            elif filter == "KP":
+                kp_ims = ez.filter_by_kv(conn, id, value1, value2)
+                write_ids_to_tsv(kp_ims, [f"Images with KV {value1} and {value2}"])
+                return kp_ims
+            elif filter == "tag":
+                tg_dict = ez.filter_by_tag_value(conn, id, value1)
+                write_ids_to_tsv(tg_dict, [f"Images with tag {value1}"])
+                return tg_dict
+
+            else:
+                raise ValueError(f"Unsupported object type")
+
+    except Exception as e:
+        print(f"Connection error: {str(e)}")
+        return None
+
+
+# Argument parsing
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.")
+    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('--filter', required=True,
+                        help="Filter type - Filename, Key-Value Pairs, Tag")
+    parser.add_argument('--id', required=True,
+                        help="List of images IDs")
+    parser.add_argument('--value1', required=True,
+                        help="First searching values - Filename, Key, Tag")
+    parser.add_argument('--value2', required=False,
+                        help="Second searching values - Value (necessary just for Key-Value Pairs filter")
+    parser.add_argument('--tsv_file', default='filter_list.tsv', required=True,
+                        help="Output TSV file path.")
+
+    args = parser.parse_args()
+
+    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
+    filter_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host,
+                   port=args.port,
+                   filter=args.filter,
+                   value1=args.value1,
+                   value2=args.value2,
+                   id=args.id,
+                   tsv_file=args.tsv_file)

tools/omero/omero_filter.xml

@@ -0,0 +1,102 @@
+<tool id="omero_filter_id" name="OMERO IDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="20.01" license="MIT">
+    <description> with ezomero </description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.18.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">omero</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="3.0.1">ezomero</requirement>
+        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
+        <requirement type="package" version="21.0.2">openjdk</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/omero_filter.py
+        --credential-file '$credentials'
+        --host $omero_host
+        --port $omero_port
+        --filter $filter
+        --value1 $value1
+        --id $did
+        --tsv_file $tsv
+        #if $filter == "KP"
+        --value2 $value2
+        #end if
+
+    ]]></command>
+    <configfiles>
+        <configfile name="credentials"><![CDATA[
+{
+    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
+    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
+}
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="omero_host" type="text" label="OMERO host URL">
+            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
+            <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
+        </param>
+        <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
+        <param argument="filter" type="select" optional="true" label="Select filter">
+            <option value="filename">Project</option>
+            <option value="KP">Screen</option>
+            <option value="tag">Dataset</option>
+        </param>
+        <param argument="value1" type="text" optional="false" label="First filter criteria (i.e. filename)"/>
+        <param argument="value2" type="text" optional="true" label="Second filter criteria (just valid for KP search)"/>
+        <param name="did" type="text" optional="false" label="List of images IDs"/>
+        <param name="test_username" type="hidden" value=""/>
+        <param name="test_password" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <data name="tsv" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="filter" value="filename"/>
+            <param name="value1" value="sample_image_2.jpg"/>
+            <param name="did" value="1,2"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="tsv" value="output_filter_filename.tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Images with filename sample_image_2.jpg"/>
+                    <has_text text="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="filter" value="tag"/>
+            <param name="value1" value="test_tag"/>
+            <param name="did" value="1,2"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="tsv" value="output_filter_tag.tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Images with tag test_tag"/>
+                    <has_text text="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+Description
+-----------
+
+Tool to filter images IDs by filename, Key-Value Pairs and Tag value.
+For Key-Value Pairs search, two values are required (Value1 = Key, Value2 = Pair).
+IDs are a list of image IDs which can be fetched using the omero_get tool.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>

tools/omero/omero_get.py

@@ -0,0 +1,90 @@
+import argparse
+import csv
+import json
+
+import ezomero as ez
+
+
+def get_object_ezo(user, pws, host, port, obj_type, 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
+
+    # Function to write tabular file from a dictionary ezomero output
+    def write_dict_to_tsv(data, headers):
+        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(headers)  # Write the headers
+            for key, value in data.items():
+                writer.writerow([key, value])  # Write each key-value pair
+
+    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))
+                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"])
+                return table
+            else:
+                raise ValueError(f"Unsupported object type: {obj_type}")
+
+    except Exception as e:
+        print(f"Connection error: {str(e)}")
+        return None
+
+
+# Argument parsing
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.")
+    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('--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.")
+    parser.add_argument('--tsv_file', default='id_list.tsv', required=True,
+                        help="Output TSV file path.")
+    args = parser.parse_args()
+
+    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_object_ezo(user=crds['username'], pws=crds['password'], host=args.host,
+                   port=args.port,
+                   obj_type=args.obj_type,
+                   id=args.id,
+                   tsv_file=args.tsv_file)