Bring in usegalaxy-tools lockfile update script.

Author: jmchilton

setup.py

@@ -37,6 +37,7 @@ def get_var(var_name):
         setup-data-libraries=ephemeris.setup_data_libraries:main
         galaxy-wait=ephemeris.sleep:main
         install_tool_deps=ephemeris.install_tool_deps:main
+        shed-lockfile-update=ephemeris.shed_lockfile_update:main
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.

src/ephemeris/shed_lockfile_update.py

@@ -0,0 +1,95 @@
+# Script originally developed as part of the usegalaxy-tools project.
+# https://github.com/galaxyproject/usegalaxy-tools/blob/master/scripts/update-tool.py
+import argparse
+import logging
+import os
+import yaml
+from collections import defaultdict
+
+from bioblend import toolshed
+
+DEFAULT_TOOL_SHED_URL = 'https://toolshed.g2.bx.psu.edu'
+
+
+class ToolSheds(defaultdict):
+    default_factory = toolshed.ToolShedInstance
+
+    def __missing__(self, key):
+        logging.debug('Creating new ToolShedInstance for URL: %s', key)
+        return self.default_factory(url=key)
+
+
+tool_sheds = ToolSheds()
+
+
+def update_file(fn, owner=None, name=None, without=False):
+    locked_in_path = fn + ".lock"
+    if not os.path.exists(locked_in_path):
+        logging.info("Lockfile doesn't exist yet, starting with source as base.")
+        locked_in_path = fn
+
+    with open(locked_in_path, 'r') as handle:
+        locked = yaml.safe_load(handle)
+
+    # Update any locked tools.
+    for tool in locked['tools']:
+        # If without, then if it is lacking, we should exec.
+        logging.debug("Examining {owner}/{name}".format(**tool))
+
+        if without:
+            if 'revisions' in tool and not len(tool.get('revisions', [])) == 0:
+                continue
+
+        if not without and owner and tool['owner'] not in owner:
+            continue
+
+        if not without and name and tool['name'] != name:
+            continue
+
+        ts_url = tool.get('tool_shed_url', DEFAULT_TOOL_SHED_URL)
+        if ts_url != DEFAULT_TOOL_SHED_URL:
+            logging.warning('Non-default Tool Shed URL for %s/%s: %s', tool['owner'], tool['name'], ts_url)
+        ts = tool_sheds[ts_url]
+
+        logging.info("Fetching updates for {owner}/{name}".format(**tool))
+
+        try:
+            revs = ts.repositories.get_ordered_installable_revisions(tool['name'], tool['owner'])
+        except Exception as e:
+            print(e)
+            continue
+
+        logging.debug('TS revisions: %s' % ','.join(revs))
+        latest_rev = revs[-1]
+        if latest_rev in tool.get('revisions', []):
+            # The rev is already known, don't add again.
+            continue
+
+        logging.info("Found newer revision of {owner}/{name} ({rev})".format(rev=latest_rev, **tool))
+
+        # Get latest rev, if not already added, add it.
+        if 'revisions' not in tool:
+            tool['revisions'] = []
+
+        if latest_rev not in tool['revisions']:
+            # TS doesn't support utf8 and we don't want to either.
+            tool['revisions'].append(str(latest_rev))
+
+    with open(fn + '.lock', 'w') as handle:
+        yaml.dump(locked, handle, default_flow_style=False)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file")
+    parser.add_argument('--owner', action='append', help="Repository owner to filter on, anything matching this will be updated. Can be specified multiple times")
+    parser.add_argument('--name', help="Repository name to filter on, anything matching this will be updated")
+    parser.add_argument('--without', action='store_true', help="If supplied will ignore any owner/name and just automatically add the latest hash for anything lacking one.")
+    parser.add_argument('--log', choices=('critical', 'error', 'warning', 'info', 'debug'), default='info')
+    args = parser.parse_args()
+    logging.basicConfig(level=getattr(logging, args.log.upper()))
+    update_file(args.fn.name, owner=args.owner, name=args.name, without=args.without)
+
+
+if __name__ == '__main__':
+    main()