Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/galaxy/tool_util/cwl/schema.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/galaxy/tool_util/cwl/schema.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,110 @@ +"""Abstraction around cwltool and related libraries for loading a CWL artifact.""" +import os +import tempfile +from collections import namedtuple + +from .cwltool_deps import ( + _has_relax_path_checks_flag, + default_loader, + ensure_cwltool_available, + load_tool, + LoadingContext, + resolve_and_validate_document, +) + +RawProcessReference = namedtuple("RawProcessReference", ["loading_context", "process_object", "uri"]) +ResolvedProcessDefinition = namedtuple("ResolvedProcessDefinition", ["loading_context", "uri", "raw_process_reference"]) +REWRITE_EXPRESSIONS = False + + +class SchemaLoader: + + def __init__(self, strict=True, validate=True): + self._strict = strict + self._validate = validate + + @property + def raw_document_loader(self): + ensure_cwltool_available() + return default_loader(None) + + def loading_context(self): + loading_context = LoadingContext() + loading_context.strict = self._strict + loading_context.do_validate = self._validate + loading_context.loader = self.raw_document_loader + loading_context.do_update = True + if _has_relax_path_checks_flag(): + loading_context.relax_path_checks = True + return loading_context + + def raw_process_reference(self, path, loading_context=None): + with tempfile.TemporaryDirectory() as output_dir: + suffix = '' + if '#' in path: + path, suffix = path.split('#') + print(f""" ------- + +{open(path).read()} + + ------- + """) + processed_path = os.path.join(output_dir, os.path.basename(path)) + path = os.path.abspath(path) + uri = "file://" + path + loading_context = loading_context or self.loading_context() + if REWRITE_EXPRESSIONS: + from cwl_utils import cwl_v1_0_expression_refactor + exit_code = cwl_v1_0_expression_refactor.main([output_dir, path, '--skip-some1', '--skip-some2']) + if exit_code == 0: + uri = f"file://{processed_path}" + print(f""" ------- + +{open(processed_path).read()} + + ------- + """) + if suffix: + uri = f"{uri}#{suffix}" + loading_context, process_object, uri = load_tool.fetch_document(uri, loadingContext=loading_context) + return RawProcessReference(loading_context, process_object, uri) + + def raw_process_reference_for_object(self, process_object, uri=None, loading_context=None): + if uri is None: + uri = "galaxy://" + loading_context = loading_context or self.loading_context() + process_object["id"] = uri + loading_context, process_object, uri = load_tool.fetch_document(process_object, loadingContext=loading_context) + return RawProcessReference(loading_context, process_object, uri) + + def process_definition(self, raw_process_reference): + assert raw_process_reference.loading_context is not None, "No loading context found for raw_process_reference" + loading_context, uri = resolve_and_validate_document( + raw_process_reference.loading_context, + raw_process_reference.process_object, + raw_process_reference.uri, + ) + process_def = ResolvedProcessDefinition( + loading_context, + uri, + raw_process_reference, + ) + return process_def + + def tool(self, **kwds): + process_definition = kwds.get("process_definition", None) + if process_definition is None: + raw_process_reference = kwds.get("raw_process_reference", None) + if raw_process_reference is None: + raw_process_reference = self.raw_process_reference(kwds["path"]) + process_definition = self.process_definition(raw_process_reference) + + tool = load_tool.make_tool( + process_definition.uri, + process_definition.loading_context, + ) + return tool + + +schema_loader = SchemaLoader() +non_strict_non_validating_schema_loader = SchemaLoader(strict=False, validate=False)