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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 (

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.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 (

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

jobloaderctx = {
    "cwl": "https://w3id.org/cwl/cwl#",
    "cwltool": "http://commonwl.org/cwltool#",
    "path": {"@type": "@id"},
    "location": {"@type": "@id"},
    "id": "@id",
}  # type: ContextType

overrides_ctx = {
    "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",
}  # type: ContextType

[docs]def default_loader( fetcher_constructor: Optional[FetcherCallableType] = None, enable_dev: bool = False, doc_cache: bool = True, ) -> Loader: return Loader( jobloaderctx, 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}' 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, ) -> Tuple[Union[CommentedMap, CommentedSeq], CommentedMap]: lopt = cwl_v1_2.LoadingOptions(idx=loadingContext.codegen_idx, fileuri=fileuri) 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] 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), ) 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, skip_schemas: Optional[bool] = None, ) -> 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( "workflowjobj must be a dict, got '{}': {}".format( type(workflowobj), 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=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) 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) 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, skip_schemas: Optional[bool] = None, ) -> 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, skip_schemas=skip_schemas, ) tool = make_tool(uri, loadingContext) return loadingContext, uri, tool