add get_name option

lldelisle · Jun 14, 2024 · 1781e31 · 1781e31
1 parent b97db80
commit 1781e31
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Showing 2 changed files with 37 additions and 6 deletions.
diff --git a/tools/omero_get_children_ids/omero_get_children_ids.py b/tools/omero_get_children_ids/omero_get_children_ids.py
@@ -20,22 +20,29 @@ def get_omero_credentials(config_file):
     return (omero_username, omero_password)
 
 
-def recursive_get_children_id(parent_object, final_object_type):
+def recursive_get_children_id(parent_object, final_object_type, get_name):
     output = []
     if parent_object.OMERO_CLASS == 'WellSample':
-        return [parent_object.getImage().id]
+        if get_name:
+            return [f"{parent_object.getImage().id}\t{parent_object.getImage().getName()}"]
+        else:
+            return [parent_object.getImage().id]
     for children in parent_object.listChildren():
         if children.OMERO_CLASS == final_object_type.title():
-            output.append(children.id)
+            if get_name:
+                output.append(f"{children.id}\t{children.getName()}")
+            else:
+                output.append(children.id)
         else:
             # We need to go one step further
-            output += recursive_get_children_id(children, final_object_type)
+            output += recursive_get_children_id(children, final_object_type, get_name)
     return output
 
 
 def get_children_ids(parent_object_type,
                      omero_id,
                      final_object_type,
+                     get_name,
                      omero_username,
                      omero_password,
                      omero_host="idr.openmicroscopy.org",
@@ -46,7 +53,7 @@ def get_children_ids(parent_object_type,
     ) as conn:
         # Retrieve omero object
         parent_object = conn.getObject(parent_object_type.title(), omero_id)
-        return recursive_get_children_id(parent_object, final_object_type)
+        return recursive_get_children_id(parent_object, final_object_type, get_name)
 
 
 if __name__ == "__main__":
@@ -62,12 +69,15 @@ def get_children_ids(parent_object_type,
                    type=int, default=None, required=True)
     p.add_argument("--final-object-type", dest="final_object_type",
                    type=str, default=None, required=True)
+    p.add_argument("--get-name", dest="get_name",
+                   action="store_true", default=False)
     p.add_argument("--output", type=str, default=None, required=True)
     args = p.parse_args()
     children_ids = get_children_ids(
         args.parent_object_type,
         args.omero_id,
         args.final_object_type,
+        args.get_name,
         *get_omero_credentials(args.config_file),
         omero_host=args.omero_host,
         omero_secured=args.omero_secured,

diff --git a/tools/omero_get_children_ids/omero_get_children_ids.xml b/tools/omero_get_children_ids/omero_get_children_ids.xml
@@ -1,7 +1,7 @@
 <tool id="omero_get_children_ids" name="Omero" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
     <description>Get children ids</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.1.0</token>
+        <token name="@TOOL_VERSION@">0.2.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -29,6 +29,7 @@
         --omero-id '$omero_object.omero_id'
         --final-object-type '$omero_object.final_object_type'
         --output '$output'
+        $get_name
     ]]></command>
     <configfiles>
         <configfile name="credentials"><![CDATA[
@@ -105,6 +106,7 @@
                 </param>
             </when>
         </conditional>
+        <param name="get_name" type="boolean" truevalue="--get-name" falsevalue="" checked="false" label="Retrieve names into a second column" />
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="All ${omero_object.final_object_type} from ${omero_object.parent_object_type} ID ${omero_object.omero_id}" />
@@ -126,6 +128,23 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="omero_instance_type">
+                <param name="omero_instance" value="idr"/>
+            </conditional>
+            <conditional name="omero_object">
+                <param name="parent_object_type" value="well"/>
+                <param name="omero_id" value="2184933"/>
+                <param name="final_object_type" value="image"/>
+            </conditional>
+            <param name="get_name" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="003012001.flex [Well A-1; Field #1]"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
         <test expect_num_outputs="1">
             <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr"/>
@@ -263,5 +282,7 @@
 
 This tool will create a file with the list of all children ids of a given omero object.
 
+If the option is set, it can also retrive the names.
+
     ]]></help>
 </tool>