add get_value

tools/omero/omero_get_value.py

@@ -0,0 +1,107 @@
+import argparse
+import csv
+import json
+
+import ezomero as ez
+
+
+def get_object_ezo(user, pws, host, port, obj_type, ids, tsv_file):
+    # Function to write tabular file from the ezomero output
+    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
+            writer = csv.writer(f, delimiter='\t')
+            if is_empty:
+                writer.writerow([header])  # Write the header
+            for item in data:
+                writer.writerow([item])  # Write each value
+
+    # 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
+
+    # 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 == "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 == "Tag":
+                tags = []
+                for tag_id in ids:
+                    tags.append(ez.get_tag(conn, tag_id))
+                # Sort the tags for consistency:
+                tags.sort
+                write_ids_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}")
+
+    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: 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)
+
+    # 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,
+                   ids=args.ids,
+                   tsv_file=args.tsv_file)

tools/omero/omero_get_value.xml

@@ -0,0 +1,83 @@
+<tool id="omero_get_value" name="OMERO get Object" 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 $__tool_directory__/omero_get_value.py
+        --credential-file '$credentials'
+        --host $omero_host
+        --port $omero_port
+        --obj_type $obj_type
+        #if $ids_input.ids_format == "values":
+            --ids str($ids_input.ids).replace(',', ' ')
+        #else:
+            --ids_path $ids_input.ids_path
+        #end if
+        --tsv_file $tsv
+    ]]></command>
+    <configfiles>
+        <configfile name="credentials"><![CDATA[
+{
+    "username": "$__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="obj_type" type="select" optional="false" label="Type of object to fetch:">
+            <option value="Annotation">Annotation</option>
+            <option value="Tag">Tag</option>
+            <option value="Table">Table</option>
+        </param>
+        <conditional name="ids_input">
+            <param name="ids_format" type="select" label="How do you provide the ID(s) of the OMERO object?">
+                <option value="values">Comma separated values</option>
+                <option value="file">From a dataset (one per line)</option>
+            </param>
+            <when value="values">
+                <param argument="--ids" type="text" value="" label="ID(s) of the object(s) to fetch on OMERO separated by comma">
+                    <validator type="regex">[0-9]+(,[0-9]+)*</validator>
+                </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)"/>
+            </when>
+        </conditional>
+        <param name="test_username" type="hidden" value=""/>
+        <param name="test_password" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <data name="tsv" format="tabular"/>
+    </outputs>
+    <tests>
+        <!-- TODO -->
+    </tests>
+    <help>
+Description
+-----------
+
+Tool to fetch Annotation, Tag and Tables from IDs.
+
+The IDs can be obtained with the tool OMERO get IDs with ezomero
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>