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Source code for galaxy.tool_util.cwl.schema
"""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
[docs]class SchemaLoader:
[docs] 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)
[docs] 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
[docs] 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)
[docs] 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)
[docs] 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
[docs] 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)