Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/cwltool/update.py @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
children |
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from __future__ import absolute_import import copy import re from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence, Optional, Tuple, Union) from functools import partial from ruamel.yaml.comments import CommentedMap, CommentedSeq from schema_salad import validate from schema_salad.ref_resolver import Loader # pylint: disable=unused-import from six import string_types from six.moves import urllib from typing_extensions import Text from schema_salad.sourceline import SourceLine from .loghandler import _logger # move to a regular typing import when Python 3.3-3.6 is no longer supported from .utils import visit_class, visit_field, aslist def v1_0to1_1(doc, loader, baseuri): # pylint: disable=unused-argument # type: (Any, Loader, Text) -> Tuple[Any, Text] """Public updater for v1.0 to v1.1.""" doc = copy.deepcopy(doc) rewrite = { "http://commonwl.org/cwltool#WorkReuse": "WorkReuse", "http://arvados.org/cwl#ReuseRequirement": "WorkReuse", "http://commonwl.org/cwltool#TimeLimit": "ToolTimeLimit", "http://commonwl.org/cwltool#NetworkAccess": "NetworkAccess", "http://commonwl.org/cwltool#InplaceUpdateRequirement": "InplaceUpdateRequirement", "http://commonwl.org/cwltool#LoadListingRequirement": "LoadListingRequirement" } def rewrite_requirements(t): # type: (MutableMapping[Text, Union[Text, Dict[Text, Any]]]) -> None if "requirements" in t: for r in t["requirements"]: if isinstance(r, MutableMapping): if r["class"] in rewrite: r["class"] = rewrite[r["class"]] else: raise validate.ValidationException( "requirements entries must be dictionaries: {} {}.".format( type(r), r)) if "hints" in t: for r in t["hints"]: if isinstance(r, MutableMapping): if r["class"] in rewrite: r["class"] = rewrite[r["class"]] else: raise validate.ValidationException( "hints entries must be dictionaries: {} {}.".format( type(r), r)) if "steps" in t: for s in t["steps"]: if isinstance(s, MutableMapping): rewrite_requirements(s) else: raise validate.ValidationException( "steps entries must be dictionaries: {} {}.".format( type(s), s)) def update_secondaryFiles(t, top=False): # type: (Any, bool) -> Union[MutableSequence[MutableMapping[Text, Text]], MutableMapping[Text, Text]] if isinstance(t, CommentedSeq): new_seq = copy.deepcopy(t) for index, entry in enumerate(t): new_seq[index] = update_secondaryFiles(entry) return new_seq elif isinstance(t, MutableSequence): return CommentedSeq([update_secondaryFiles(p) for p in t]) elif isinstance(t, MutableMapping): return t elif top: return CommentedSeq([CommentedMap([("pattern", t)])]) else: return CommentedMap([("pattern", t)]) def fix_inputBinding(t): # type: (Dict[Text, Any]) -> None for i in t["inputs"]: if "inputBinding" in i: ib = i["inputBinding"] for k in list(ib.keys()): if k != "loadContents": _logger.warning(SourceLine(ib, k).makeError( "Will ignore field '{}' which is not valid in {} " "inputBinding".format(k, t["class"]))) del ib[k] visit_class(doc, ("CommandLineTool","Workflow"), rewrite_requirements) visit_class(doc, ("ExpressionTool","Workflow"), fix_inputBinding) visit_field(doc, "secondaryFiles", partial(update_secondaryFiles, top=True)) upd = doc if isinstance(upd, MutableMapping) and "$graph" in upd: upd = upd["$graph"] for proc in aslist(upd): proc.setdefault("hints", CommentedSeq()) proc["hints"].insert(0, CommentedMap([("class", "NetworkAccess"),( "networkAccess", True)])) proc["hints"].insert(0, CommentedMap([("class", "LoadListingRequirement"),("loadListing", "deep_listing")])) if "cwlVersion" in proc: del proc["cwlVersion"] return (doc, "v1.1") def v1_1_0dev1to1_1(doc, loader, baseuri): # pylint: disable=unused-argument # type: (Any, Loader, Text) -> Tuple[Any, Text] return (doc, "v1.1") UPDATES = { u"v1.0": v1_0to1_1, u"v1.1": None } # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]] DEVUPDATES = { u"v1.0": v1_0to1_1, u"v1.1.0-dev1": v1_1_0dev1to1_1, u"v1.1": None } # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]] ALLUPDATES = UPDATES.copy() ALLUPDATES.update(DEVUPDATES) INTERNAL_VERSION = u"v1.1" def identity(doc, loader, baseuri): # pylint: disable=unused-argument # type: (Any, Loader, Text) -> Tuple[Any, Union[Text, Text]] """Default, do-nothing, CWL document upgrade function.""" return (doc, doc["cwlVersion"]) def checkversion(doc, # type: Union[CommentedSeq, CommentedMap] metadata, # type: CommentedMap enable_dev # type: bool ): # type: (...) -> Tuple[CommentedMap, Text] """Check the validity of the version of the give CWL document. Returns the document and the validated version string. """ cdoc = None # type: Optional[CommentedMap] if isinstance(doc, CommentedSeq): if not isinstance(metadata, CommentedMap): raise Exception("Expected metadata to be CommentedMap") lc = metadata.lc metadata = copy.deepcopy(metadata) metadata.lc.data = copy.copy(lc.data) metadata.lc.filename = lc.filename metadata[u"$graph"] = doc cdoc = metadata elif isinstance(doc, CommentedMap): cdoc = doc else: raise Exception("Expected CommentedMap or CommentedSeq") version = metadata[u"cwlVersion"] cdoc["cwlVersion"] = version if version not in UPDATES: if version in DEVUPDATES: if enable_dev: pass else: keys = list(UPDATES.keys()) keys.sort() raise validate.ValidationException( u"Version '%s' is a development or deprecated version.\n " "Update your document to a stable version (%s) or use " "--enable-dev to enable support for development and " "deprecated versions." % (version, ", ".join(keys))) else: raise validate.ValidationException( u"Unrecognized version %s" % version) return (cdoc, version) def update(doc, loader, baseuri, enable_dev, metadata): # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> CommentedMap if isinstance(doc, CommentedMap): if metadata.get("http://commonwl.org/cwltool#original_cwlVersion") \ or doc.get("http://commonwl.org/cwltool#original_cwlVersion"): return doc (cdoc, version) = checkversion(doc, metadata, enable_dev) originalversion = copy.copy(version) nextupdate = identity # type: Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]] while nextupdate: (cdoc, version) = nextupdate(cdoc, loader, baseuri) nextupdate = ALLUPDATES[version] cdoc[u"cwlVersion"] = version metadata[u"cwlVersion"] = version metadata[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion cdoc[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion return cdoc