changeset 4:d0c0f3c95368 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,47 @@
+<macros>
+    <!-- for historic reasons the omero-py version is used as the version for all tools -->
+    <token name="@TOOL_VERSION@">5.18.0</token>
+    <token name="@EZOMERO_VERSION@">3.0.1</token>
+    <token name="@PROFILE@">23.0</token>
+
+    <xml name="ezomero_requirements">
+        <requirements>
+            <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement>
+            <requirement type="package" version="2.2.2">pandas</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="omeropy_requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
+            <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
+            <requirement type="package" version="21.0.2">openjdk</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    
+
+    <xml name="host_port">
+        <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._-]*$</validator>
+            <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
+        </param>
+        <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
+        <param name="test_username" type="hidden" value=""/>
+        <param name="test_password" type="hidden" value=""/>
+    </xml>
+    <token name="@HOST_PORT@">
+        --host '$omero_host'
+        --port $omero_port
+    </token>
+
+    <xml name="credentials">
+        <configfile name="credentials"><![CDATA[
+{
+    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
+    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
+}
+        ]]></configfile>
+    </xml>
+</macros>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_filter.py	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,77 @@
+import argparse
+import csv
+import json
+import sys
+
+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):
+        with open(tsv_file, 'w', newline='') as f:
+            writer = csv.writer(f, delimiter='\t')
+            for item in data:
+                writer.writerow([item])  # Write each ID
+
+    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)
+            return fn_ids
+
+        elif filter == "KP":
+            kp_ims = ez.filter_by_kv(conn, id, value1, value2)
+            write_ids_to_tsv(kp_ims)
+            return kp_ims
+
+        elif filter == "tag":
+            tg_dict = ez.filter_by_tag_value(conn, id, value1)
+            write_ids_to_tsv(tg_dict)
+            return tg_dict
+
+        else:
+            sys.exit(f"Unsupported object type: {filter}")
+
+
+# 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',
+                        help="Output TSV file path.")
+    args = parser.parse_args()
+
+    if args.filter == "KP" and args.value2 is None:
+        raise ValueError("'--value 2' is necessary to retrieve KP")
+
+    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)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_id.py	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,116 @@
+import argparse
+import csv
+import json
+import sys
+
+import ezomero as ez
+
+
+def get_ids_ezo(user, pws, host, port, final_obj_type, parent_obj_type, parent_id=None, tsv_file="id_list.tsv"):
+
+    # Function to write tabular file from the ezomero output
+    def write_ids_to_tsv(data):
+        with open(tsv_file, 'w', newline='') as f:
+            writer = csv.writer(f, delimiter='\t')
+            for item in data:
+                writer.writerow([item])  # Write each ID
+
+    with ez.connect(user, pws, "", host, port, secure=True) as conn:
+
+        if final_obj_type == "Project":
+            proj_ids = ez.get_project_ids(conn)
+            write_ids_to_tsv(proj_ids)
+            return proj_ids
+
+        elif final_obj_type == "Dataset":
+            args = {'project': None}
+            if parent_obj_type == "Project":
+                args['project'] = parent_id
+            ds_ids = ez.get_dataset_ids(conn, **args)
+            write_ids_to_tsv(ds_ids)
+            return ds_ids
+
+        elif final_obj_type == "Image":
+            args = {
+                'project': None,
+                'dataset': None,
+                'plate': None,
+                'well': None
+            }
+            if parent_obj_type == "Project":
+                args['project'] = parent_id
+            elif parent_obj_type == "Dataset":
+                args['dataset'] = parent_id
+            elif parent_obj_type == "Plate":
+                args['plate'] = parent_id
+            elif parent_obj_type == "Well":
+                args['well'] = parent_id
+            elif parent_obj_type != "All":
+                raise ValueError("Object set as parent_obj_type is not compatible")
+
+            ds_ims = ez.get_image_ids(conn, **args)
+            write_ids_to_tsv(ds_ims)
+            return ds_ims
+
+        elif final_obj_type == "Annotation":
+            map_annot_ids = ez.get_map_annotation_ids(conn, parent_obj_type, parent_id)
+            write_ids_to_tsv(map_annot_ids)
+            return map_annot_ids
+
+        elif final_obj_type == "Tag":
+            tag_ids = ez.get_tag_ids(conn, parent_obj_type, parent_id)
+            write_ids_to_tsv(tag_ids)
+            return tag_ids
+
+        elif final_obj_type == "Roi":
+            roi_ids = ez.get_roi_ids(conn, parent_id)
+            write_ids_to_tsv(roi_ids)
+            return roi_ids
+
+        elif final_obj_type == "Table":
+            file_ann_ids = ez.get_file_annotation_ids(conn, parent_obj_type, parent_id)
+            write_ids_to_tsv(file_ann_ids)
+            return file_ann_ids
+
+        else:
+            sys.exit(f"Unsupported object type: {filter}")
+
+
+# Argument parsing
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Fetch OMERO object IDs as TSV from parent object.")
+    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('--final_obj_type', required=True,
+                        help="Type of object to fetch ID: Project, Dataset, Image, Annotation, Tag, Roi, or Table.")
+    parser.add_argument('--parent_obj_type', required=True,
+                        help="Type of object from which you fetch IDs: Project, Dataset, Plate, Well, Image (or 'All' if you want to get all objects).")
+    parser.add_argument('--parent_id', required=False, type=int,
+                        help="ID of the OMERO object in `--parent_obj_type`, not required if you used `--parent_obj_type All`.")
+    parser.add_argument('--tsv_file', default='id_list.tsv',
+                        help="Output TSV file path.")
+    args = parser.parse_args()
+
+    if args.parent_id is None and args.parent_obj_type != "All":
+        raise ValueError("ID is only optional is you use `--parent_obj_type All`")
+
+    if args.final_obj_type == "Roi" and args.parent_obj_type != "Image":
+        raise ValueError("Roi IDs can only be retrived from images, use `--parent_obj_type Image`")
+
+    if args.parent_obj_type == "All" and args.final_obj_type not in ["Image", "Dataset", "Project"]:
+        raise ValueError("Only Images, Datasets and Projects is compatible with `--parent_obj_type All`")
+
+    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_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host,
+                port=args.port,
+                final_obj_type=args.final_obj_type,
+                parent_obj_type=args.parent_obj_type,
+                parent_id=args.parent_id,
+                tsv_file=args.tsv_file)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_value.py	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,98 @@
+import argparse
+import csv
+import json
+import sys
+
+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, 'w', newline='') as f:
+            writer = csv.writer(f, delimiter='\t')
+            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, 'w', newline='') as f:
+            writer = csv.writer(f, delimiter='\t')
+            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')
+
+    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_values_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:
+            sys.exit(f"Unsupported object type: {filter}")
+
+
+# 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)

--- a/omero_import.xml	Thu Sep 12 16:30:43 2024 +0000
+++ b/omero_import.xml	Tue Oct 22 11:53:53 2024 +0000
@@ -1,17 +1,13 @@
-<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description> with omero-py </description>
     <macros>
-        <token name="@TOOL_VERSION@">5.18.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">omero</xref>
     </xrefs>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
-        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
-        <requirement type="package" version="21.0.2">openjdk</requirement>
-    </requirements>
+    <expand macro="omeropy_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #import re
 
@@ -24,10 +20,9 @@
 
         source '$credentials' &&
         omero import folder -T Dataset:name:$dataset_name
-            -s $omero_host
+            -s '$omero_host'
             -p $omero_port
             -u "\$OMERO_USER"
-            -w "\$OMERO_PASSWORD"
         > $log &&
 
         omero logout
@@ -39,15 +34,9 @@
         ]]></configfile>
     </configfiles>
     <inputs>
+        <expand macro="host_port"/>
         <param name="folder" type="data" format="avi,bmp,btf,cif,csv,eps,fits,fli,gif,hdr,html,jp2,jpg,mov,mrc,ndpi,nhdr,nrrd,ome.tiff,par,pbm,pcx,pgm,png,ppm,psd,scn,sif,svs,tf2,tf8,tif,tif,tiff,top,txt,vms,wav,xml,zip" multiple="true" optional="false" label="Images to import into OMERO"/>
         <param name="dataset_name" type="text" optional="false" label="Target Dataset Name"/>
-        <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 name="omero_port" type="integer" value="4064" optional="false" label="OMERO port"/>
-        <param name="test_username" type="hidden" value=""/>
-        <param name="test_password" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="log" format="txt"/>

--- a/test-data/output_KV_import.txt	Thu Sep 12 16:30:43 2024 +0000
+++ b/test-data/output_KV_import.txt	Tue Oct 22 11:53:53 2024 +0000
@@ -1,1 +1,1 @@
-SUCCESS: Successfully uploaded metadata for dataset with ID 2. Result: {'Key1': 'Value1', 'Key2': 'Value2'}
+SUCCESS: Successfully uploaded metadata for dataset with ID 3. Result: {'Key1': 'Value1', 'Key2': 'Value2'}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_filter_filename.tsv	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,1 @@
+2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_filter_tag.tsv	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,1 @@
+1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_ids_dataset.tsv	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,1 @@
+1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_ids_image.tsv	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,2 @@
+1
+2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_ids_project.tsv	Tue Oct 22 11:53:53 2024 +0000
@@ -0,0 +1,1 @@
+1