diff env/lib/python3.9/site-packages/ephemeris/install_tool_deps.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/ephemeris/install_tool_deps.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+'''Tool to install tool dependencies on a Galaxy instance.'''
+import argparse
+import logging as log
+import os
+import xml.etree.ElementTree as ET
+
+import yaml
+from bioblend import ConnectionError as ConnErr
+from bioblend.galaxy.tools import ToolClient
+
+from ephemeris import get_galaxy_connection
+from ephemeris.common_parser import get_common_args
+
+timeout_codes = (408, 502, 504)
+
+
+def _parser():
+    parent = get_common_args()
+    parser = argparse.ArgumentParser(parents=[parent])
+    parser.add_argument("-t", "--tool", help='Path to a tool file, tool_conf file, or yaml file containing a sequence of tool ids', nargs='*')
+    parser.add_argument("-i", "--id", help='Space-separated list of tool ids', nargs='*')
+
+    return parser
+
+
+def _install(tool_client, tool_id):
+    try:
+        tool_client.install_dependencies(tool_id)
+    except ConnErr as e:
+        if e.status_code in timeout_codes:
+            log.warning(e.body)
+        else:
+            raise
+
+
+def main():
+    """
+    This script uses bioblend to trigger dependencies installations for the provided tools
+    """
+    args = _parser().parse_args()
+    gi = get_galaxy_connection(args)
+    tool_client = ToolClient(gi)
+
+    if args.verbose:
+        log.basicConfig(level=log.DEBUG)
+
+    if args.tool:
+        for tool_conf_path in args.tool:  # type: str
+            _, ext = os.path.splitext(tool_conf_path)
+            if ext == '.xml':
+                log.info("tool_conf xml found, parsing..")
+                # install all
+                root = ET.ElementTree(file=tool_conf_path).getroot()
+                if root.tag == "toolbox":
+                    # Install all from tool_conf
+                    tool_path = root.get('tool_path', '')
+                    tool_path = tool_path.replace('${tool_conf_dir}', os.path.abspath(os.path.dirname(tool_conf_path)))
+                    if tool_path:
+                        log.info("Searching for tools relative to " + tool_path)
+                    tools = root.findall(".//tool[@file]")
+                    if len(tools) == 0:
+                        log.warning("No tools found in tool_conf")
+                        continue
+
+                    for tool in tools:
+                        tool_id = ET.ElementTree(file=os.path.join(tool_path, tool.get('file'))).getroot().get('id')
+                        if tool_id:
+                            log.info("Installing tool dependencies for " + tool_id + " from: " + tool.get('file'))
+                            _install(tool_client, tool_id)
+                elif root.tag == "tool" and root.get('id'):
+                    # Install from single tool file
+                    log.info("Tool xml found. Installing " + root.get('id') + " dependencies..")
+                    _install(tool_client, root.get('id'))
+            else:
+                log.info("YAML tool list found, parsing..")
+                with open(tool_conf_path) as fh:
+                    tool_ids = yaml.safe_load(fh)
+                for tool_id in tool_ids:
+                    # Install from yaml file
+                    log.info("Installing " + tool_id + " dependencies..")
+                    _install(tool_client, tool_id)
+
+    if args.id:
+        for tool_id in args.id:  # type: str
+            log.info("Installing " + tool_id + " dependencies..")
+            _install(tool_client, tool_id.strip())
+
+
+if __name__ == '__main__':
+    main()