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Source code for cwltool.load_tool
"""Loads a CWL document."""
import copy
import hashlib
import logging
import os
import re
import urllib
import uuid
from functools import partial
from typing import (
Any,
Dict,
List,
MutableMapping,
MutableSequence,
Optional,
Tuple,
Union,
cast,
)
from cwl_utils.parser import cwl_v1_2, cwl_v1_2_utils
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.exceptions import ValidationException
from schema_salad.fetcher import Fetcher
from schema_salad.ref_resolver import Loader, file_uri
from schema_salad.schema import validate_doc
from schema_salad.sourceline import SourceLine, cmap
from schema_salad.utils import (
ContextType,
FetcherCallableType,
IdxResultType,
ResolveType,
json_dumps,
)
from . import CWL_CONTENT_TYPES, process, update
from .context import LoadingContext
from .errors import GraphTargetMissingException
from .loghandler import _logger
from .process import Process, get_schema, shortname
from .update import ALLUPDATES
from .utils import CWLObjectType, ResolverType, visit_class
docloaderctx: ContextType = {
"cwl": "https://w3id.org/cwl/cwl#",
"cwltool": "http://commonwl.org/cwltool#",
"path": {"@type": "@id"},
"location": {"@type": "@id"},
"id": "@id",
}
jobloader_id_name = "__id"
jobloaderctx: ContextType = {
"cwl": "https://w3id.org/cwl/cwl#",
"cwltool": "http://commonwl.org/cwltool#",
"path": {"@type": "@id"},
"location": {"@type": "@id"},
jobloader_id_name: "@id",
}
overrides_ctx: ContextType = {
"overrideTarget": {"@type": "@id"},
"cwltool": "http://commonwl.org/cwltool#",
"http://commonwl.org/cwltool#overrides": {
"@id": "cwltool:overrides",
"mapSubject": "overrideTarget",
},
"requirements": {
"@id": "https://w3id.org/cwl/cwl#requirements",
"mapSubject": "class",
},
}
[docs]def default_loader(
fetcher_constructor: Optional[FetcherCallableType] = None,
enable_dev: bool = False,
doc_cache: bool = True,
) -> Loader:
return Loader(
docloaderctx,
fetcher_constructor=fetcher_constructor,
allow_attachments=lambda r: enable_dev,
doc_cache=doc_cache,
)
def resolve_tool_uri(
argsworkflow: str,
resolver: Optional[ResolverType] = None,
fetcher_constructor: Optional[FetcherCallableType] = None,
document_loader: Optional[Loader] = None,
) -> Tuple[str, str]:
uri = None # type: Optional[str]
split = urllib.parse.urlsplit(argsworkflow)
# In case of Windows path, urlsplit misjudge Drive letters as scheme, here we are skipping that
if split.scheme and split.scheme in ["http", "https", "file"]:
uri = argsworkflow
elif os.path.exists(os.path.abspath(argsworkflow)):
uri = file_uri(str(os.path.abspath(argsworkflow)))
elif resolver is not None:
uri = resolver(document_loader or default_loader(fetcher_constructor), argsworkflow)
if uri is None:
raise ValidationException("Not found: '%s'" % argsworkflow)
if argsworkflow != uri:
_logger.info("Resolved '%s' to '%s'", argsworkflow, uri)
fileuri = urllib.parse.urldefrag(uri)[0]
return uri, fileuri
def fetch_document(
argsworkflow: Union[str, CWLObjectType],
loadingContext: Optional[LoadingContext] = None,
) -> Tuple[LoadingContext, CommentedMap, str]:
"""Retrieve a CWL document."""
if loadingContext is None:
loadingContext = LoadingContext()
loadingContext.loader = default_loader()
else:
loadingContext = loadingContext.copy()
if loadingContext.loader is None:
loadingContext.loader = default_loader(
loadingContext.fetcher_constructor,
enable_dev=loadingContext.enable_dev,
doc_cache=loadingContext.doc_cache,
)
if isinstance(argsworkflow, str):
uri, fileuri = resolve_tool_uri(
argsworkflow,
resolver=loadingContext.resolver,
document_loader=loadingContext.loader,
)
workflowobj = cast(
CommentedMap,
loadingContext.loader.fetch(fileuri, content_types=CWL_CONTENT_TYPES),
)
return loadingContext, workflowobj, uri
if isinstance(argsworkflow, MutableMapping):
uri = cast(str, argsworkflow["id"]) if argsworkflow.get("id") else "_:" + str(uuid.uuid4())
workflowobj = cast(CommentedMap, cmap(cast(Dict[str, Any], argsworkflow), fn=uri))
loadingContext.loader.idx[uri] = workflowobj
return loadingContext, workflowobj, uri
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
def _convert_stdstreams_to_files(
workflowobj: Union[CWLObjectType, MutableSequence[Union[CWLObjectType, str, int]], str]
) -> None:
if isinstance(workflowobj, MutableMapping):
if workflowobj.get("class") == "CommandLineTool":
with SourceLine(
workflowobj,
"outputs",
ValidationException,
_logger.isEnabledFor(logging.DEBUG),
):
outputs = workflowobj.get("outputs", [])
if not isinstance(outputs, CommentedSeq):
raise ValidationException('"outputs" section is not ' "valid.")
for out in cast(MutableSequence[CWLObjectType], workflowobj.get("outputs", [])):
if not isinstance(out, CommentedMap):
raise ValidationException(f"Output {out!r} is not a valid OutputParameter.")
for streamtype in ["stdout", "stderr"]:
if out.get("type") == streamtype:
if "outputBinding" in out:
raise ValidationException(
"Not allowed to specify outputBinding when"
" using %s shortcut." % streamtype
)
if streamtype in workflowobj:
filename = workflowobj[streamtype]
else:
filename = str(
hashlib.sha1( # nosec
json_dumps(workflowobj, sort_keys=True).encode("utf-8")
).hexdigest()
)
workflowobj[streamtype] = filename
out["type"] = "File"
out["outputBinding"] = cmap({"glob": filename})
for inp in cast(MutableSequence[CWLObjectType], workflowobj.get("inputs", [])):
if inp.get("type") == "stdin":
if "inputBinding" in inp:
raise ValidationException(
"Not allowed to specify inputBinding when" " using stdin shortcut."
)
if "stdin" in workflowobj:
raise ValidationException(
"Not allowed to specify stdin path when" " using stdin type shortcut."
)
else:
workflowobj["stdin"] = (
"$(inputs.%s.path)"
% cast(str, inp["id"]).rpartition("#")[2].split("/")[-1]
)
inp["type"] = "File"
else:
for entry in workflowobj.values():
_convert_stdstreams_to_files(
cast(
Union[
CWLObjectType,
MutableSequence[Union[CWLObjectType, str, int]],
str,
],
entry,
)
)
if isinstance(workflowobj, MutableSequence):
for entry in workflowobj:
_convert_stdstreams_to_files(
cast(
Union[
CWLObjectType,
MutableSequence[Union[CWLObjectType, str, int]],
str,
],
entry,
)
)
def _add_blank_ids(
workflowobj: Union[CWLObjectType, MutableSequence[Union[CWLObjectType, str]]]
) -> None:
if isinstance(workflowobj, MutableMapping):
if (
"run" in workflowobj
and isinstance(workflowobj["run"], MutableMapping)
and "id" not in workflowobj["run"]
and "$import" not in workflowobj["run"]
):
workflowobj["run"]["id"] = str(uuid.uuid4())
for entry in workflowobj.values():
_add_blank_ids(
cast(
Union[CWLObjectType, MutableSequence[Union[CWLObjectType, str]]],
entry,
)
)
if isinstance(workflowobj, MutableSequence):
for entry in workflowobj:
_add_blank_ids(
cast(
Union[CWLObjectType, MutableSequence[Union[CWLObjectType, str]]],
entry,
)
)
def _fast_parser_convert_stdstreams_to_files(
processobj: Union[cwl_v1_2.Process, MutableSequence[cwl_v1_2.Process]]
) -> None:
if isinstance(processobj, cwl_v1_2.CommandLineTool):
cwl_v1_2_utils.convert_stdstreams_to_files(processobj)
elif isinstance(processobj, cwl_v1_2.Workflow):
for st in processobj.steps:
_fast_parser_convert_stdstreams_to_files(st.run)
elif isinstance(processobj, MutableSequence):
for p in processobj:
_fast_parser_convert_stdstreams_to_files(p)
def _fast_parser_expand_hint_class(
hints: Optional[Any], loadingOptions: cwl_v1_2.LoadingOptions
) -> None:
if isinstance(hints, MutableSequence):
for h in hints:
if isinstance(h, MutableMapping) and "class" in h:
for k, v in loadingOptions.namespaces.items():
if h["class"].startswith(k + ":"):
h["class"] = v + h["class"][len(k) + 1 :]
def _fast_parser_handle_hints(
processobj: Union[cwl_v1_2.Process, MutableSequence[cwl_v1_2.Process]],
loadingOptions: cwl_v1_2.LoadingOptions,
) -> None:
if isinstance(processobj, (cwl_v1_2.CommandLineTool, cwl_v1_2.Workflow)):
_fast_parser_expand_hint_class(processobj.hints, loadingOptions)
if isinstance(processobj, cwl_v1_2.Workflow):
for st in processobj.steps:
_fast_parser_expand_hint_class(st.hints, loadingOptions)
_fast_parser_handle_hints(st.run, loadingOptions)
elif isinstance(processobj, MutableSequence):
for p in processobj:
_fast_parser_handle_hints(p, loadingOptions)
def update_index(document_loader: Loader, pr: CommentedMap) -> None:
if "id" in pr:
document_loader.idx[pr["id"]] = pr
def fast_parser(
workflowobj: Union[CommentedMap, CommentedSeq, None],
fileuri: Optional[str],
uri: str,
loadingContext: LoadingContext,
fetcher: Fetcher,
) -> Tuple[Union[CommentedMap, CommentedSeq], CommentedMap]:
lopt = cwl_v1_2.LoadingOptions(idx=loadingContext.codegen_idx, fileuri=fileuri, fetcher=fetcher)
if uri not in loadingContext.codegen_idx:
cwl_v1_2.load_document_with_metadata(
workflowobj,
fileuri,
loadingOptions=lopt,
addl_metadata_fields=["id", "cwlVersion"],
)
objects, loadopt = loadingContext.codegen_idx[uri]
_fast_parser_convert_stdstreams_to_files(objects)
_fast_parser_handle_hints(objects, loadopt)
processobj: Union[MutableMapping[str, Any], MutableSequence[Any], float, str, None]
processobj = cwl_v1_2.save(objects, relative_uris=False)
metadata: Dict[str, Any] = {}
metadata["id"] = loadopt.fileuri
if loadopt.namespaces:
metadata["$namespaces"] = loadopt.namespaces
if loadopt.schemas:
metadata["$schemas"] = loadopt.schemas
if loadopt.baseuri:
metadata["$base"] = loadopt.baseuri
for k, v in loadopt.addl_metadata.items():
if isinstance(processobj, MutableMapping) and k in processobj:
metadata[k] = processobj[k]
else:
metadata[k] = v
if loadingContext.loader:
loadingContext.loader.graph += loadopt.graph
# Need to match the document loader's index with the fast parser index
# Get the base URI (no fragments) for documents that use $graph
nofrag = urllib.parse.urldefrag(uri)[0]
flag = "fastparser-idx-from:" + nofrag
if not loadingContext.loader.idx.get(flag):
objects, loadopt = loadingContext.codegen_idx[nofrag]
fileobj = cmap(
cast(
Union[int, float, str, Dict[str, Any], List[Any], None],
cwl_v1_2.save(objects, relative_uris=False),
)
)
visit_class(
fileobj,
("CommandLineTool", "Workflow", "ExpressionTool"),
partial(update_index, loadingContext.loader),
)
loadingContext.loader.idx[flag] = flag
for u in lopt.imports:
loadingContext.loader.idx["import:" + u] = "import:" + u
for u in lopt.includes:
loadingContext.loader.idx["include:" + u] = "include:" + u
return cast(
Union[CommentedMap, CommentedSeq],
cmap(cast(Union[Dict[str, Any], List[Any]], processobj)),
), cast(CommentedMap, cmap(metadata))
[docs]def resolve_and_validate_document(
loadingContext: LoadingContext,
workflowobj: Union[CommentedMap, CommentedSeq],
uri: str,
preprocess_only: bool = False,
) -> Tuple[LoadingContext, str]:
"""Validate a CWL document."""
if not loadingContext.loader:
raise ValueError("loadingContext must have a loader.")
else:
loader = loadingContext.loader
loadingContext = loadingContext.copy()
if not isinstance(workflowobj, MutableMapping):
raise ValueError(f"workflowjobj must be a dict, got {type(workflowobj)!r}: {workflowobj}")
jobobj = None
if "cwl:tool" in workflowobj:
jobobj, _ = loader.resolve_all(workflowobj, uri)
uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
del cast(Dict[str, Any], jobobj)["https://w3id.org/cwl/cwl#tool"]
workflowobj = fetch_document(uri, loadingContext)[1]
fileuri = urllib.parse.urldefrag(uri)[0]
metadata: CWLObjectType
cwlVersion = loadingContext.metadata.get("cwlVersion")
if not cwlVersion:
cwlVersion = workflowobj.get("cwlVersion")
if not cwlVersion and fileuri != uri:
# The tool we're loading is a fragment of a bigger file. Get
# the document root element and look for cwlVersion there.
metadata = cast(CWLObjectType, fetch_document(fileuri, loadingContext)[1])
cwlVersion = cast(str, metadata.get("cwlVersion"))
if not cwlVersion:
raise ValidationException(
"No cwlVersion found. "
"Use the following syntax in your CWL document to declare "
"the version: cwlVersion: <version>.\n"
"Note: if this is a CWL draft-3 (pre v1.0) document then it "
"will need to be upgraded first using https://pypi.org/project/cwl-upgrader/ . "
"'sbg:draft-2' documents can be upgraded using "
"https://pypi.org/project/sevenbridges-cwl-draft2-upgrader/ ."
)
if not isinstance(cwlVersion, str):
with SourceLine(workflowobj, "cwlVersion", ValidationException, loadingContext.debug):
raise ValidationException(f"'cwlVersion' must be a string, got {type(cwlVersion)}")
# strip out version
cwlVersion = re.sub(r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "", cwlVersion)
if cwlVersion not in list(ALLUPDATES):
# print out all the Supported Versions of cwlVersion
versions = []
for version in list(ALLUPDATES):
if "dev" in version:
version += " (with --enable-dev flag only)"
versions.append(version)
versions.sort()
raise ValidationException(
"The CWL reference runner no longer supports pre CWL v1.0 "
"documents. Supported versions are: "
"\n{}".format("\n".join(versions))
)
if isinstance(jobobj, CommentedMap) and "http://commonwl.org/cwltool#overrides" in jobobj:
loadingContext.overrides_list.extend(resolve_overrides(jobobj, uri, uri))
del jobobj["http://commonwl.org/cwltool#overrides"]
if isinstance(jobobj, CommentedMap) and "https://w3id.org/cwl/cwl#requirements" in jobobj:
if cwlVersion not in ("v1.1.0-dev1", "v1.1"):
raise ValidationException(
"`cwl:requirements` in the input object is not part of CWL "
"v1.0. You can adjust to use `cwltool:overrides` instead; or you "
"can set the cwlVersion to v1.1 or greater."
)
loadingContext.overrides_list.append(
{
"overrideTarget": uri,
"requirements": jobobj["https://w3id.org/cwl/cwl#requirements"],
}
)
del jobobj["https://w3id.org/cwl/cwl#requirements"]
(sch_document_loader, avsc_names) = process.get_schema(cwlVersion)[:2]
if isinstance(avsc_names, Exception):
raise avsc_names
processobj: ResolveType
document_loader = Loader(
sch_document_loader.ctx,
schemagraph=sch_document_loader.graph,
idx=loader.idx,
cache=sch_document_loader.cache,
fetcher_constructor=loadingContext.fetcher_constructor,
skip_schemas=loadingContext.skip_schemas,
doc_cache=loadingContext.doc_cache,
)
loadingContext.loader = document_loader
if cwlVersion == "v1.0":
_add_blank_ids(workflowobj)
if cwlVersion != "v1.2":
loadingContext.fast_parser = False
if loadingContext.skip_resolve_all:
# Some integrations (e.g. Arvados) loads documents, makes
# in-memory changes to them (which are applied to the objects
# in the document_loader index), and then sends them back
# through the loading machinery.
#
# In this case, the functions of resolve_all() have already
# happened. Because resolve_all() is expensive, we don't want
# to do it again if it's going to be a no-op, so the
# skip_resolve_all flag tells us just to use the document
# as-is from the loader index.
#
# Note that at the moment, fast_parser code path is considered
# functionally the same as resolve_all() for this case.
#
processobj, metadata = document_loader.resolve_ref(uri)
elif loadingContext.fast_parser:
processobj, metadata = fast_parser(
workflowobj, fileuri, uri, loadingContext, document_loader.fetcher
)
else:
document_loader.resolve_all(workflowobj, fileuri)
processobj, metadata = document_loader.resolve_ref(uri)
if not isinstance(processobj, (CommentedMap, CommentedSeq)):
raise ValidationException("Workflow must be a CommentedMap or CommentedSeq.")
if not hasattr(processobj.lc, "filename"):
processobj.lc.filename = fileuri
if loadingContext.metadata:
metadata = loadingContext.metadata
# Make a shallow copy. If we do a version update later, metadata
# will be updated, we don't want to write through and change the
# original object.
metadata = copy.copy(metadata)
if not isinstance(metadata, CommentedMap):
raise ValidationException("metadata must be a CommentedMap, was %s" % type(metadata))
if isinstance(processobj, CommentedMap):
uri = processobj["id"]
if not loadingContext.fast_parser:
_convert_stdstreams_to_files(workflowobj)
if isinstance(jobobj, CommentedMap):
loadingContext.jobdefaults = jobobj
loadingContext.avsc_names = avsc_names
loadingContext.metadata = metadata
if preprocess_only:
return loadingContext, uri
if loadingContext.do_validate:
validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)
# None means default behavior (do update)
if loadingContext.do_update in (True, None):
if "cwlVersion" not in metadata:
metadata["cwlVersion"] = cwlVersion
processobj = update.update(
processobj, document_loader, fileuri, loadingContext.enable_dev, metadata
)
document_loader.idx[processobj["id"]] = processobj
visit_class(
processobj,
("CommandLineTool", "Workflow", "ExpressionTool"),
partial(update_index, document_loader),
)
return loadingContext, uri
def make_tool(
uri: Union[str, CommentedMap, CommentedSeq], loadingContext: LoadingContext
) -> Process:
"""Make a Python CWL object."""
if loadingContext.loader is None:
raise ValueError("loadingContext must have a loader")
resolveduri: Union[float, str, CommentedMap, CommentedSeq, None]
metadata: CWLObjectType
if loadingContext.fast_parser and isinstance(uri, str) and not loadingContext.skip_resolve_all:
resolveduri, metadata = fast_parser(
None, None, uri, loadingContext, loadingContext.loader.fetcher
)
else:
resolveduri, metadata = loadingContext.loader.resolve_ref(uri)
processobj = None
if isinstance(resolveduri, MutableSequence):
for obj in resolveduri:
if obj["id"].endswith("#main"):
processobj = obj
break
if not processobj:
raise GraphTargetMissingException(
"Tool file contains graph of multiple objects, must specify "
"one of #%s"
% ", #".join(urllib.parse.urldefrag(i["id"])[1] for i in resolveduri if "id" in i)
)
elif isinstance(resolveduri, MutableMapping):
processobj = resolveduri
else:
raise Exception("Must resolve to list or dict")
tool = loadingContext.construct_tool_object(processobj, loadingContext)
if loadingContext.jobdefaults:
jobobj = loadingContext.jobdefaults
for inp in tool.tool["inputs"]:
if shortname(inp["id"]) in jobobj:
inp["default"] = jobobj[shortname(inp["id"])]
return tool
def load_tool(
argsworkflow: Union[str, CWLObjectType],
loadingContext: Optional[LoadingContext] = None,
) -> Process:
loadingContext, workflowobj, uri = fetch_document(argsworkflow, loadingContext)
loadingContext, uri = resolve_and_validate_document(
loadingContext,
workflowobj,
uri,
)
return make_tool(uri, loadingContext)
def resolve_overrides(
ov: IdxResultType,
ov_uri: str,
baseurl: str,
) -> List[CWLObjectType]:
ovloader = Loader(overrides_ctx)
ret, _ = ovloader.resolve_all(ov, baseurl)
if not isinstance(ret, CommentedMap):
raise Exception("Expected CommentedMap, got %s" % type(ret))
cwl_docloader = get_schema("v1.0")[0]
cwl_docloader.resolve_all(ret, ov_uri)
return cast(List[CWLObjectType], ret["http://commonwl.org/cwltool#overrides"])
def load_overrides(ov: str, base_url: str) -> List[CWLObjectType]:
ovloader = Loader(overrides_ctx)
return resolve_overrides(ovloader.fetch(ov), ov, base_url)
def recursive_resolve_and_validate_document(
loadingContext: LoadingContext,
workflowobj: Union[CommentedMap, CommentedSeq],
uri: str,
preprocess_only: bool = False,
) -> Tuple[LoadingContext, str, Process]:
"""Validate a CWL document, checking that a tool object can be built."""
loadingContext, uri = resolve_and_validate_document(
loadingContext,
workflowobj,
uri,
preprocess_only=preprocess_only,
)
tool = make_tool(uri, loadingContext)
return loadingContext, uri, tool