setfacl

tools/setfacl/setfacl.xml

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+<tool id="setfact" name="setfacl: Grant permissions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <code file="tool_form_utils.py" />
+    <command detect_errors="exit_code"><![CDATA[
+        #for dir in $directories
+            echo '$dir' >> '$log' &&
+        #end for
+        true
+    ]]></command>
+    <inputs>
+        <param name="top_level" type="select" refresh_on_change="true">
+            <options from_data_table="setfacl_directories"/>
+        </param>
+        <param name="directories" type="drill_down" multiple="true" label="TODO" dynamic_options="get_trans(__trans__, top_level)"/>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+TODO: Fill in help in reStructuredText format (https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html)
+
+Usage
+.....
+
+**Input**
+
+**Output**
+
+    ]]></help>
+    <citations>
+        <!-- <citation type="doi"> </citation> -->
+    </citations>
+</tool>

tools/setfacl/test-data/setfacl_directories.loc

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+root_one	one level	/	1
+root_two	two levels	/	2

tools/setfacl/tool-data/setfacl_directories.loc.sample

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+# <unique_id>	<name>	<path>	<levels>

tools/setfacl/tool_data_table_conf.xml.sample

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+<?xml version="1.0"?>
+<tables>
+    <table name="setfacl_directories" comment_char="#">
+        <columns>value, name, path, levels</columns>
+        <file path="tool-data/setfacl_directories.sample.loc" />
+    </table>
+</tables>

tools/setfacl/tool_data_table_conf.xml.test

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+<?xml version="1.0"?>
+<tables>
+    <table name="setfacl_directories" comment_char="#">
+        <columns>value, name, path, levels</columns>
+        <file path="${__HERE__}/test-data/setfacl_directories.loc" />
+    </table>
+</tables>

tools/setfacl/tool_form_utils.py

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+import os
+
+def get_directory_list(dir):
+    return [(os.path.join(dir, d), os.path.join(dir, d), False) for d in os.listdir(dir) if os.path.isdir(os.path.join(dir, d)) and not d.startswith(".")]
+
+def get_trans(trans, top_level):
+    setfacl_data_table = trans.app.tool_data_tables.get('setfacl_directories')
+    data_field = setfacl_data_table.get_field(top_level)
+    path =  data_field['path']
+    try:
+        levels = int(data_field['levels'])
+    except ValueError:
+        levels = 0
+    return get_directory_hierarchy(path, levels)
+
+def get_directory_hierarchy(dir, levels=1):
+    options = []
+    if levels <= 0:
+        return options
+    subdirs = [os.path.join(dir, d) for d in os.listdir(dir) if os.path.isdir(os.path.join(dir, d)) and not d.startswith(".")]
+    for s in subdirs:
+        try:
+            sub = get_directory_hierarchy(s, levels-1)
+        except:
+            sub = []
+        options.append({"name": s, 'value': s, "selected": False, 'options': sub})
+    return options