Merge branch 'main' into defense_finder

scripts/update-tool.py

@@ -1,72 +1,107 @@
-import yaml
-import os
-import glob
-import copy
 import argparse
+import copy
+import glob
 import logging
+import os
+import sys
 
+import yaml
 from bioblend import toolshed
 
-ts = toolshed.ToolShedInstance(url='https://toolshed.g2.bx.psu.edu')
+ts = toolshed.ToolShedInstance(url="https://toolshed.g2.bx.psu.edu")
 
 
 def update_file(fn, owner=None, name=None, without=False):
-    with open(fn + '.lock', 'r') as handle:
+    success = True
+    with open(fn + ".lock", "r") as handle:
         locked = yaml.safe_load(handle)
 
     # Update any locked tools.
-    for tool in 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:
+            if "revisions" in tool and not len(tool.get("revisions", [])) == 0:
                 continue
 
-        if not without and owner and tool['owner'] != owner:
+        if not without and owner and tool["owner"] != owner:
             continue
 
-        if not without and name and tool['name'] != name:
+        if not without and name and tool["name"] != name:
             continue
 
         logging.info("Fetching updates for {owner}/{name}".format(**tool))
 
         try:
-            revs = ts.repositories.get_ordered_installable_revisions(tool['name'], tool['owner'])
+            revs = ts.repositories.get_ordered_installable_revisions(
+                tool["name"], tool["owner"]
+            )
         except Exception as e:
-            print(e)
+            logging.error(
+                f"Could not get info for {tool['name']} ({tool['owner']}) from TS: {e}"
+            )
+            success = False
             continue
 
-        logging.debug('TS revisions: %s' % ','.join(revs))
+        if len(revs) == 0:
+            logging.error(
+                f"No installable revisions for {tool['name']} ({tool['owner']})"
+            )
+            success = False
+            continue
+        logging.debug("TS revisions: %s" % ",".join(revs))
         latest_rev = revs[-1]
-        if latest_rev in tool.get('revisions', []):
+        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))
+        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 "revisions" not in tool:
+            tool["revisions"] = []
 
-        if latest_rev not in 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))
+            tool["revisions"].append(str(latest_rev))
 
-        tool['revisions'] = sorted(list(set( tool['revisions'] )))
+        tool["revisions"] = sorted(list(set(tool["revisions"])))
 
-    with open(fn + '.lock', 'w') as handle:
+    with open(fn + ".lock", "w") as handle:
         yaml.dump(locked, handle, default_flow_style=False)
+    return success
 
 
-
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file")
-    parser.add_argument('--owner', help="Repository owner to filter on, anything matching this will be updated")
-    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')
+    parser.add_argument("fn", type=argparse.FileType("r"), help="Tool.yaml file")
+    parser.add_argument(
+        "--owner",
+        help="Repository owner to filter on, anything matching this will be updated",
+    )
+    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)
+    success = update_file(
+        args.fn.name, owner=args.owner, name=args.name, without=args.without
+    )
+    if not success:
+        sys.exit(1)

tool_list.yaml

@@ -3113,15 +3113,28 @@ tools:
 - name: data_manager_build_kraken2_database
   owner: iuc
   tool_panel_section_label: Data Managers
-- name: dose_response_analysis_tool
-  owner: ufz
-  tool_panel_section_label: Toxicology
+# Can't be deployed https://github.com/galaxyproject/galaxy/issues/18359 
+# - name: dose_response_analysis_tool
+#   owner: ufz
+#   tool_panel_section_label: Toxicology
 - name: baseline_toxicity_calculator
-  owner: ufz
+  owner: mbernt
   tool_panel_section_label: Toxicology
 - name: defense_finder
   owner: rplanel
   tool_panel_section_label: Genome annotation
 - name: data_manager_defense_finder
   owner: rplanel
   tool_panel_section_label: Data Managers
+- name: drep_compare
+  owner: iuc
+  tool_panel_section_label: Metagenomics
+- name: drep_dereplicate
+  owner: iuc
+  tool_panel_section_label: Metagenomics
+- name: genomad_end_to_end
+  owner: ufz
+  tool_panel_section_label: Metagenomics
+- name: genomad_build_database
+  owner: ufz
+  tool_panel_section_label: Data Managers