diff env/lib/python3.9/site-packages/galaxy/tool_util/parser/factory.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/galaxy/tool_util/parser/factory.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,74 @@
+"""Constructors for concrete tool and input source objects."""
+
+import logging
+
+from galaxy.tool_util.loader import load_tool_with_refereces
+from galaxy.util.yaml_util import ordered_load
+from .cwl import CwlToolSource
+from .interface import InputSource
+from .xml import XmlInputSource, XmlToolSource
+from .yaml import YamlInputSource, YamlToolSource
+from ..fetcher import ToolLocationFetcher
+
+log = logging.getLogger(__name__)
+
+
+def get_tool_source(config_file=None, xml_tree=None, enable_beta_formats=True, tool_location_fetcher=None, macro_paths=None):
+    """Return a ToolSource object corresponding to supplied source.
+
+    The supplied source may be specified as a file path (using the config_file
+    parameter) or as an XML object loaded with load_tool_with_refereces.
+    """
+    if xml_tree is not None:
+        return XmlToolSource(xml_tree, source_path=config_file, macro_paths=macro_paths)
+    elif config_file is None:
+        raise ValueError("get_tool_source called with invalid config_file None.")
+
+    if tool_location_fetcher is None:
+        tool_location_fetcher = ToolLocationFetcher()
+
+    config_file = tool_location_fetcher.to_tool_path(config_file)
+    if not enable_beta_formats:
+        tree, macro_paths = load_tool_with_refereces(config_file)
+        return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths)
+
+    if config_file.endswith(".yml"):
+        log.info("Loading tool from YAML - this is experimental - tool will not function in future.")
+        with open(config_file) as f:
+            as_dict = ordered_load(f)
+            return YamlToolSource(as_dict, source_path=config_file)
+    elif config_file.endswith(".json") or config_file.endswith(".cwl"):
+        log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.")
+        return CwlToolSource(config_file)
+    else:
+        tree, macro_paths = load_tool_with_refereces(config_file)
+        return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths)
+
+
+def get_tool_source_from_representation(tool_format, tool_representation):
+    # TODO: make sure whatever is consuming this method uses ordered load.
+    log.info("Loading dynamic tool - this is experimental - tool may not function in future.")
+    if tool_format == "GalaxyTool":
+        if "version" not in tool_representation:
+            tool_representation["version"] = "1.0.0"  # Don't require version for embedded tools.
+        return YamlToolSource(tool_representation)
+    else:
+        raise Exception("Unknown tool representation format [%s]." % tool_format)
+
+
+def get_input_source(content):
+    """Wrap dicts or XML elements as InputSource if needed.
+
+    If the supplied content is already an InputSource object,
+    it is simply returned. This allow Galaxy to uniformly
+    consume using the tool input source interface.
+    """
+    if not isinstance(content, InputSource):
+        if isinstance(content, dict):
+            content = YamlInputSource(content)
+        else:
+            content = XmlInputSource(content)
+    return content
+
+
+__all__ = ("get_tool_source", "get_input_source")