diff env/lib/python3.9/site-packages/planemo/tools.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/planemo/tools.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,96 @@
+"""Planemo-specific wrappers around galaxy-tool-util tool functionality."""
+from __future__ import absolute_import
+
+import os
+import sys
+import traceback
+
+from galaxy.tool_util import loader_directory
+from galaxy.tool_util.fetcher import ToolLocationFetcher
+
+from planemo.io import error, info
+
+is_tool_load_error = loader_directory.is_tool_load_error
+SKIP_XML_MESSAGE = "Skipping XML file - does not appear to be a tool %s."
+SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"]
+LOAD_ERROR_MESSAGE = "Error loading tool with path %s"
+
+
+def uri_to_path(ctx, uri):
+    """Fetch URI to a local path."""
+    fetcher = ToolLocationFetcher()
+    return fetcher.to_tool_path(uri)
+
+
+def uris_to_paths(ctx, uris):
+    """Fetch multiple URIs to a local path."""
+    fetcher = ToolLocationFetcher()
+    paths = []
+    for uri in uris:
+        path = fetcher.to_tool_path(uri)
+        paths.append(path)
+    return paths
+
+
+def yield_tool_sources_on_paths(ctx, paths, recursive=False, yield_load_errors=True, exclude_deprecated=False):
+    """Walk paths and yield ToolSource objects discovered."""
+    for path in paths:
+        for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive, yield_load_errors):
+            if exclude_deprecated and 'deprecated' in tool_path:
+                continue
+            yield (tool_path, tool_source)
+
+
+def yield_tool_sources(ctx, path, recursive=False, yield_load_errors=True):
+    """Walk single path and yield ToolSource objects discovered."""
+    tools = load_tool_sources_from_path(
+        path,
+        recursive,
+        register_load_errors=True,
+    )
+    for (tool_path, tool_source) in tools:
+        if is_tool_load_error(tool_source):
+            if yield_load_errors:
+                yield (tool_path, tool_source)
+            else:
+                error(LOAD_ERROR_MESSAGE % tool_path)
+            continue
+
+        if not _is_tool_source(ctx, tool_path, tool_source):
+            continue
+        yield (tool_path, tool_source)
+
+
+def load_tool_sources_from_path(path, recursive, register_load_errors=False):
+    """Generate a list for tool sources found down specified path."""
+    return loader_directory.load_tool_sources_from_path(
+        path,
+        _load_exception_handler,
+        recursive=recursive,
+        register_load_errors=register_load_errors,
+    )
+
+
+def _load_exception_handler(path, exc_info):
+    error(LOAD_ERROR_MESSAGE % path)
+    traceback.print_exception(*exc_info, limit=1, file=sys.stderr)
+
+
+def _is_tool_source(ctx, tool_path, tool_source):
+    if os.path.basename(tool_path) in SHED_FILES:
+        return False
+    root = getattr(tool_source, "root", None)
+    if root is not None:
+        if root.tag != "tool":
+            if ctx.verbose:
+                info(SKIP_XML_MESSAGE % tool_path)
+            return False
+    return True
+
+
+__all__ = (
+    "is_tool_load_error",
+    "load_tool_sources_from_path",
+    "yield_tool_sources",
+    "yield_tool_sources_on_paths",
+)