# HG changeset patch
# User ufz
# Date 1726158636 0
# Node ID 4f4dc352d660ccaf172ef1e3b7e5e76573431e06
# Parent  e957793051a84707194d1f1e5fee5fc5d41d97b2
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 266752b0162fbdb32f132a6702cb661ae36f48f0

diff -r e957793051a8 -r 4f4dc352d660 omero_metadata_upload.py
--- a/omero_metadata_upload.py	Fri Sep 06 08:26:12 2024 +0000
+++ b/omero_metadata_upload.py	Thu Sep 12 16:30:36 2024 +0000
@@ -1,4 +1,5 @@
 import argparse
+import json
 from datetime import datetime
 
 import ezomero as ez
@@ -73,8 +74,7 @@
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Import metadata into OMERO.')
-    parser.add_argument('--user', required=True, help='OMERO username')
-    parser.add_argument('--pws', required=True, help='OMERO password')
+    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'],
@@ -87,6 +87,9 @@
 
     args = parser.parse_args()
 
-    metadata_import_ezo(user=args.user, pws=args.pws, host=args.host, port=args.port,
+    with open(args.credential_file, 'r') as f:
+        crds = json.load(f)
+
+    metadata_import_ezo(user=crds['username'], pws=crds['password'], host=args.host, port=args.port,
                         obj_type=args.obj_type, did=args.did, ann_type=args.ann_type,
                         ann_file=args.ann_file, an_name=args.an_name, log_file=args.log_file)
diff -r e957793051a8 -r 4f4dc352d660 omero_roi_import.xml
--- a/omero_roi_import.xml	Fri Sep 06 08:26:12 2024 +0000
+++ b/omero_roi_import.xml	Thu Sep 12 16:30:36 2024 +0000
@@ -3,7 +3,7 @@
     <description> with ezomero </description>
     <macros>
         <token name="@TOOL_VERSION@">5.18.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">omero</xref>
@@ -15,15 +15,22 @@
         <requirement type="package" version="21.0.2">openjdk</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/omero_roi_upload.py'  
-        --input_file '$input'  
-        --image_id $id  
-        --user '$__user__.extra_preferences.get("omero_account|username", $test_username)'  
-        --psw '$__user__.extra_preferences.get("omero_account|password", $test_password)'  
-        --host '$omero_host'  
-        --port $omero_port  
-        --log_file '$log'  
+        python '$__tool_directory__/omero_roi_upload.py'
+        --input_file '$input'
+        --image_id $id
+        --credential-file '$credentials'
+        --host '$omero_host'
+        --port $omero_port
+        --log_file '$log'
     ]]></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 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"/>
@@ -52,6 +59,19 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="id" value="1"/>
+            <param name="input" value="input_roi_minimal.tsv"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_table_roi_minimal.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="ROI ID: 8 for row 1"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 
@@ -62,7 +82,7 @@
 in a tabular format (TSV file). The tool reads the shape information from the TSV file, creates the
 corresponding ROIs in OMERO, and links them to a specified image.
 
-**Column Headers**:
+**Column Headers** (not all columns are required for all shapes):
 
         - shape, x, y, x_rad, y_rad, width, height, label, fontSize, x1, y1, x2, y2, points, fill_color, stroke_color, stroke_width, z, c, t, roi_name, roi_description
 
@@ -74,6 +94,10 @@
 
     The columns **x**, **y**, **x_rad**, **y_rad**, **width**, and **height** specify the position and dimensions of the shapes, where applicable. For example, Ellipse uses x, y, x_rad, and y_rad, while Rectangle uses x, y, width, and height.
 
+- *Label*:
+
+    Any ROI can be labelled using the column **label**, this label will appear on the OMERO web interface.
+
 - *Text Labels*:
 
     The **label** and **fontSize** columns are used for the Label shape, specifying the text content and font size.
@@ -84,11 +108,11 @@
 
 - *Point Coordinates*:
 
-    The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs.
+    The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs, like '(300,300),(350,350),(300,400)'
 
 - *Colors*:
 
-    The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format.
+    The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format, like '(0,255,255,128)'.
 
 - *Stroke Width*:
 
@@ -100,7 +124,7 @@
 
 - *ROI Identification*:
 
-    The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO.
+    The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO however they do not appear on the OMERO web interface.
 
     </help>
     <citations>
diff -r e957793051a8 -r 4f4dc352d660 omero_roi_upload.py
--- a/omero_roi_upload.py	Fri Sep 06 08:26:12 2024 +0000
+++ b/omero_roi_upload.py	Thu Sep 12 16:30:36 2024 +0000
@@ -1,6 +1,8 @@
 import argparse
+import json
 import re
 
+import numpy as np
 import pandas as pd
 from ezomero import connect, post_roi
 from ezomero.rois import Ellipse, Label, Line, Point, Polygon, Polyline, Rectangle
@@ -35,6 +37,7 @@
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
+            label=row.get('label'),
             fill_color=parse_color(row.get('fill_color')),
             stroke_color=parse_color(row.get('stroke_color')),
             stroke_width=row.get('stroke_width')
@@ -60,7 +63,7 @@
             y2=row['y2'],
             markerStart=row.get('markerStart', None),
             markerEnd=row.get('markerEnd', None),
-            label=row.get('label', None),
+            label=row.get('label'),
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
@@ -75,6 +78,7 @@
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
+            label=row.get('label'),
             fill_color=parse_color(row.get('fill_color')),
             stroke_color=parse_color(row.get('stroke_color')),
             stroke_width=row.get('stroke_width')
@@ -85,6 +89,7 @@
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
+            label=row.get('label'),
             fill_color=parse_color(row.get('fill_color')),
             stroke_color=parse_color(row.get('stroke_color')),
             stroke_width=row.get('stroke_width')
@@ -95,6 +100,7 @@
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
+            label=row.get('label'),
             fill_color=parse_color(row.get('fill_color')),
             stroke_color=parse_color(row.get('stroke_color')),
             stroke_width=row.get('stroke_width')
@@ -108,6 +114,7 @@
             z=row.get('z'),
             c=row.get('c'),
             t=row.get('t'),
+            label=row.get('label'),
             fill_color=parse_color(row.get('fill_color')),
             stroke_color=parse_color(row.get('stroke_color')),
             stroke_width=row.get('stroke_width')
@@ -119,6 +126,8 @@
     # Open log file
     with open(log_file, 'w') as log:
         df = pd.read_csv(input_file, sep='\t')
+        # Replace nan to none
+        df = df.replace({np.nan: None})
         for index, row in df.iterrows():
             msg = f"Processing row {index + 1}/{len(df)}: {row.to_dict()}"
             print(msg)
@@ -143,17 +152,19 @@
     parser.add_argument("--input_file", help="Path to the input tabular file.")
     parser.add_argument("--image_id", type=int, required=True, help="ID of the image to which the ROI will be linked")
     parser.add_argument("--host", type=str, required=True, help="OMERO server host")
-    parser.add_argument("--user", type=str, required=True, help="OMERO username")
-    parser.add_argument("--psw", type=str, required=True, help="OMERO password")
+    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("--port", type=int, default=4064, help="OMERO server port")
     parser.add_argument("--log_file", type=str, default="process.txt", help="Log file path")
 
     args = parser.parse_args()
 
+    with open(args.credential_file, 'r') as f:
+        crds = json.load(f)
+
     conn = connect(
         host=args.host,
-        user=args.user,
-        password=args.psw,
+        user=crds['username'],
+        password=crds['password'],
         port=args.port,
         group="",
         secure=True
diff -r e957793051a8 -r 4f4dc352d660 test-data/input_roi_minimal.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_roi_minimal.tsv	Thu Sep 12 16:30:36 2024 +0000
@@ -0,0 +1,2 @@
+shape	points	label
+Polygon	(300,300),(350,350),(300,400)	Example ROI
diff -r e957793051a8 -r 4f4dc352d660 test-data/output_table_roi.txt
--- a/test-data/output_table_roi.txt	Fri Sep 06 08:26:12 2024 +0000
+++ b/test-data/output_table_roi.txt	Thu Sep 12 16:30:36 2024 +0000
@@ -1,14 +1,14 @@
-Processing row 1/7: {'shape': 'Ellipse', 'x': 50.0, 'y': 50.0, 'x_rad': 20.0, 'y_rad': 10.0, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, 'fill_color': '(255,0,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 1/7: {'shape': 'Ellipse', 'x': 50.0, 'y': 50.0, 'x_rad': 20.0, 'y_rad': 10.0, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(255,0,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 1 for row 1
-Processing row 2/7: {'shape': 'Label', 'x': 100.0, 'y': 100.0, 'x_rad': nan, 'y_rad': nan, 'label': 'Test Label', 'fontSize': 12.0, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, 'fill_color': '(255,255,255,0)', 'stroke_color': '(0,0,255,255)', 'stroke_width': 1, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 2/7: {'shape': 'Label', 'x': 100.0, 'y': 100.0, 'x_rad': None, 'y_rad': None, 'label': 'Test Label', 'fontSize': 12.0, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(255,255,255,0)', 'stroke_color': '(0,0,255,255)', 'stroke_width': 1, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 2 for row 2
-Processing row 3/7: {'shape': 'Line', 'x': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': 200.0, 'y1': 200.0, 'x2': 250.0, 'y2': 250.0, 'points': nan, 'width': nan, 'height': nan, 'fill_color': '(0,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 1, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 3/7: {'shape': 'Line', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': 200.0, 'y1': 200.0, 'x2': 250.0, 'y2': 250.0, 'points': None, 'width': None, 'height': None, 'fill_color': '(0,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 1, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 3 for row 3
-Processing row 4/7: {'shape': 'Point', 'x': 150.0, 'y': 150.0, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, 'fill_color': '(0,0,255,128)', 'stroke_color': '(255,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 2, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 4/7: {'shape': 'Point', 'x': 150.0, 'y': 150.0, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(0,0,255,128)', 'stroke_color': '(255,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 2, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 4 for row 4
-Processing row 5/7: {'shape': 'Polygon', 'x': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': '(300,300),(350,350),(300,400)', 'width': nan, 'height': nan, 'fill_color': '(255,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 1, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 5/7: {'shape': 'Polygon', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': '(300,300),(350,350),(300,400)', 'width': None, 'height': None, 'fill_color': '(255,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 1, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 5 for row 5
-Processing row 6/7: {'shape': 'Polyline', 'x': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': '(400,400),(450,450),(400,500)', 'width': nan, 'height': nan, 'fill_color': '(0,255,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 6/7: {'shape': 'Polyline', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': '(400,400),(450,450),(400,500)', 'width': None, 'height': None, 'fill_color': '(0,255,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 6 for row 6
-Processing row 7/7: {'shape': 'Rectangle', 'x': 500.0, 'y': 500.0, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': 100.0, 'height': 50.0, 'fill_color': '(255,0,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
+Processing row 7/7: {'shape': 'Rectangle', 'x': 500.0, 'y': 500.0, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': 100.0, 'height': 50.0, 'fill_color': '(255,0,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'}
 ROI ID: 7 for row 7
diff -r e957793051a8 -r 4f4dc352d660 test-data/output_table_roi_minimal.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_table_roi_minimal.txt	Thu Sep 12 16:30:36 2024 +0000
@@ -0,0 +1,2 @@
+Processing row 1/1: {'shape': 'Polygon', 'points': '(300,300),(350,350),(300,400)', 'label': 'Example ROI'}
+ROI ID: 8 for row 1