# HG changeset patch
# User ufz
# Date 1749847611 0
# Node ID 7cd85e1c50f317ac6f90a6a663c65ee0fa55ce1f
# Parent  931eb5fed2c0ce235ca1f73edcc3eeb32da8fc94
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 3f4e79a4e8350481f3c8d70bc64f01b4cb0a4bf0

diff -r 931eb5fed2c0 -r 7cd85e1c50f3 omero_metadata_import.xml
--- a/omero_metadata_import.xml	Tue Apr 08 15:13:27 2025 +0000
+++ b/omero_metadata_import.xml	Fri Jun 13 20:46:51 2025 +0000
@@ -2,7 +2,7 @@
     <description> with ezomero </description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">4</token>
+        <token name="@VERSION_SUFFIX@">5</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">omero</xref>
@@ -47,6 +47,7 @@
         <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">
             <option value="table">Table</option>
             <option value="KV">Key-Value Pairs</option>
+            <option value="attachement">File Attachment</option>
         </param>
         <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
         <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
@@ -110,6 +111,25 @@
                 </assert_contents>
             </output>
         </test>
+            <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="obj_type" value="dataset"/>
+            <param name="ann_type" value="attachement"/>
+            <conditional name="object_id">
+                <param name="object_id_selection" value="existing_object"/>
+                <param name="did" value="1"/>
+            </conditional>
+            <param name="ann_file" value="metadata.tsv"/>
+            <param name="an_name" value="attachement_test"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_attachement_import.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 Description
diff -r 931eb5fed2c0 -r 7cd85e1c50f3 omero_metadata_upload.py
--- a/omero_metadata_upload.py	Tue Apr 08 15:13:27 2025 +0000
+++ b/omero_metadata_upload.py	Fri Jun 13 20:46:51 2025 +0000
@@ -19,6 +19,9 @@
                                           headers=True)
                 tb_dict = ez.get_table(conn, id_tb_ann)
                 return tb_dict
+            elif ann_type == "attachement":
+                id_file_attach = ez.post_file_annotation(conn, file_path=data_dict, ns=an_name, object_type=obj_type, object_id=int(did))
+                return id_file_attach
         except Exception as e:
             log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}")
             return None
@@ -41,6 +44,8 @@
         data_dict = df.to_dict(orient='records')
     elif ann_type == "KV":
         data_dict = {col: df[col].iloc[0] for col in df.columns}
+    elif ann_type == "attachement":
+        data_dict = ann_file
 
     try:
         with ez.connect(user, pws, "", host, port, secure=True) as conn:
@@ -86,7 +91,7 @@
                                                               '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')
+    parser.add_argument('--ann_type', required=True, choices=['table', 'KV', "attachement"], help='Annotation type')
     parser.add_argument('--ann_file', required=True, help='Path to the annotation file')
     parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation')
     parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file')
diff -r 931eb5fed2c0 -r 7cd85e1c50f3 test-data/output_attachement_import.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_attachement_import.txt	Fri Jun 13 20:46:51 2025 +0000
@@ -0,0 +1,1 @@
+SUCCESS: Successfully uploaded metadata for dataset with ID 1. Result: 12