add fix_outdated script from Matthias Bernt

Author: martenson

requirements.txt

@@ -2,3 +2,7 @@ bioblend
 ephemeris
 pykwalify
 PyYAML
+
+# for fix_uninstallable.py
+mercurial
+galaxy-tool-util

scripts/fix_outdated.py

@@ -0,0 +1,114 @@
+# Check all revisions in the lockfile if they are installable.
+# Remove if not and add the next installable revision.
+#
+# Only updates the lock file and does not install
+# or uninstall any tools from a Galaxy instance.
+#
+# Backgroud: for each tool version there can be only one revision installed
+# (multiple revisions with the same version happen e.g. if the version
+# is not bumped but some files are updated)
+#
+# Revisions that became not-installable are treated as a safe update
+# because the author claims the tool did not change its behavior from
+# the reproducibility perspective.
+#
+# The script queries the TS to get_ordered_installable_revisions
+# and clones (to /tmp/) the mercurial repos to get all revisions
+# (the later is only done for tools with revisions that are not
+# installable).
+
+import argparse
+import subprocess
+import os.path
+import yaml
+
+from bioblend import toolshed
+from galaxy.tool_util.loader_directory import load_tool_sources_from_path
+
+
+def clone(toolshed_url, name, owner, repo_path):
+    if not os.path.exists(repo_path):
+        print(f"Cloning {toolshed_url} {owner} {name} {repo_path}")
+        cmd = [
+            "hg",
+            "clone",
+            f"{toolshed_url}/repos/{owner}/{name}",
+            repo_path,
+        ]
+        subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+
+def get_all_revisions(toolshed_url, name, owner):
+    repo_path = f"/tmp/toolshed-{owner}-{name}"
+    clone(toolshed_url, name, owner, repo_path)
+    cmd = ["hg", "log", "--template", "{node|short}\n"]
+    result = subprocess.run(cmd, cwd=repo_path, capture_output=True, text=True)
+    return list(reversed(result.stdout.splitlines()))
+
+
+def fix_uninstallable(lockfile_name, toolshed_url):
+    ts = toolshed.ToolShedInstance(url=toolshed_url)
+
+    with open(lockfile_name) as f:
+        lockfile = yaml.safe_load(f)
+        tools = lockfile["tools"]
+
+    for i, tool in enumerate(tools):
+        name = tool["name"]
+        owner = tool["owner"]
+        print(f"Checking {toolshed_url} {owner} {name} ")
+        # get ordered_installable_revisions from oldest to newest
+        ordered_installable_revisions = (
+            ts.repositories.get_ordered_installable_revisions(name, owner)
+        )
+
+        if len(set(tool["revisions"]) - set(ordered_installable_revisions)):
+            all_revisions = get_all_revisions(toolshed_url, name, owner)
+
+        to_remove = []
+        to_append = []
+        for cur in tool["revisions"]:
+            if cur in ordered_installable_revisions:
+                continue
+            if cur not in all_revisions:
+                print(f"Removing {cur} -- it is not a valid revision of {name} {owner}")
+                to_remove.append(cur)
+                continue
+            start = all_revisions.index(cur)
+            nxt = None
+            for i in range(start, len(all_revisions)):
+                if all_revisions[i] in ordered_installable_revisions:
+                    nxt = all_revisions[i]
+                    break
+            if nxt:
+                print(f"Removing {cur} in favor of {nxt} {name} {owner}")
+                to_remove.append(cur)
+                if nxt not in tool["revisions"]:
+                    print(f"Adding {nxt} which was absent so far {name} {owner}")
+                    to_append.append(nxt)
+            else:
+                print(f"Could not determine the next revision for {cur} {name} {owner}")
+
+        for r in to_remove:
+            tool["revisions"].remove(r)
+        tool["revisions"].extend(to_append)
+
+        # maintaing unified sorting standard
+        tool["revisions"] = sorted(list(set(map(str, tool['revisions']))))
+
+    with open(lockfile_name, "w") as handle:
+        yaml.dump(lockfile, handle, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "lockfile", type=argparse.FileType("r"), help="Tool.yaml.lock file"
+    )
+    parser.add_argument(
+        "--toolshed",
+        default="https://toolshed.g2.bx.psu.edu",
+        help="Toolshed to test against",
+    )
+    args = parser.parse_args()
+    fix_uninstallable(args.lockfile.name, args.toolshed)