Parse tools for usegalaxy.org.au

subdomains/scripts/parse_tools_to_produce_yml_files.py

@@ -5,6 +5,8 @@
 import re 
 import argparse
 
+import tools_au
+
 parser = argparse.ArgumentParser(description='Create installation yaml files from a Yaml file containing the panel_view/Toolkit data')
 parser.add_argument('--tk', action="store", dest='toolkit', help='Path of the toolkit.yaml file') # Toolkit.yaml file
 parser.add_argument('--yml-folder', action="store", dest='dest', help='Folder containing the yml files with tool installed in the target instance') # Folder containing the .yml and yml.lock containing the tools installed in the target instance
@@ -33,3 +35,5 @@
                 f.write("- name: "+tool+"\n")
                 f.write("  owner: "+owner+"\n")
     f.close()
+
+tools_au.parse()

subdomains/scripts/tools_au.py

@@ -0,0 +1,49 @@
+"""Convert YAML files for install on AU.
+
+Assumes that wdir contains tool yaml files.
+"""
+
+import yaml
+from pathlib import Path
+
+WDIR = Path(__file__).parent
+EXCLUDE_KEYS = [
+    'install_repository_dependencies',
+    'tool_panel_section_label',
+]
+OUTPUT_FILE = WDIR / 'usegalaxy.org.au.yml'
+
+
+def parse():
+    data = {'tools': []}
+    for f in WDIR.glob('*.yml.lock'):
+        if not f.name.endswith('.yml.lock'):
+            continue
+        print(f"Extracting data from {f}...")
+        with open(f, 'r') as handle:
+            section_data = yaml.safe_load(handle)
+        section_data['tools'] = [
+            _transcribe_to_au(x) for x in section_data['tools']
+        ]
+        for key in EXCLUDE_KEYS:
+            section_data.pop(key)
+        data['tools'] += section_data['tools']
+    for key in ('install_resolver_dependencies', 'install_tool_dependencies'):
+        data[key] = section_data[key]
+    write_data(data)
+    print(f'Data transcribed and written to {OUTPUT_FILE}')
+
+
+def _transcribe_to_au(tool):
+    tool['tool_panel_section_label'] = 'Single-Cell'
+    tool.pop('tool_panel_section_id')
+    return tool
+
+
+def write_data(data):
+    with open(OUTPUT_FILE, 'w') as handle:
+        yaml.dump(data, handle, default_flow_style=False)
+
+
+if __name__ == '__main__':
+    parse()