Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/cwltool/resolver.py @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
---|---|
date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
children |
line wrap: on
line source
"""Resolves references to CWL documents from local or remote places.""" from __future__ import absolute_import import os import sys from typing import Any, Optional, Text from six.moves import urllib from schema_salad.ref_resolver import Loader from .loghandler import _logger from schema_salad.ref_resolver import Loader from pathlib2 import Path if not getattr(__builtins__, "WindowsError", None): class WindowsError(OSError): pass def resolve_local(document_loader, uri): # type: (Loader, Text) -> Optional[Text] pathpart, frag = urllib.parse.urldefrag(uri) try: pathobj = Path(pathpart).resolve() except (WindowsError, OSError): _logger.debug("local resolver could not resolve %s", uri) return None if pathobj.is_file(): if frag: return "{}#{}".format(pathobj.as_uri(), frag) return pathobj.as_uri() sharepaths = [os.environ.get("XDG_DATA_HOME", os.path.join( os.path.expanduser('~'), ".local", "share"))] sharepaths.extend(os.environ.get( "XDG_DATA_DIRS", "/usr/local/share/:/usr/share/").split(":")) shares = [os.path.join(s, "commonwl", uri) for s in sharepaths] _logger.debug("Search path is %s", shares) for path in shares: if os.path.exists(path): return Path(uri).as_uri() if os.path.exists("{}.cwl".format(path)): return Path("{}.cwl".format(path)).as_uri() return None def tool_resolver(document_loader, uri): # type: (Loader, Text) -> Optional[Text] for r in [resolve_local, resolve_ga4gh_tool]: ret = r(document_loader, uri) if ret is not None: return ret return None ga4gh_tool_registries = ["https://dockstore.org/api"] # in the TRS registry, a primary descriptor can be reached at {0}/api/ga4gh/v2/tools/{1}/versions/{2}/plain-CWL/descriptor # The primary descriptor is a CommandLineTool in the case that the files endpoint only describes one file # When the primary descriptor is a Workflow, files need to be imported without stripping off "descriptor", looking at the files endpoint is a workaround # tested with TRS version 2.0.0-beta.2 # TODO not stripping off "descriptor" when looking for local imports would also work https://github.com/ga4gh/tool-registry-service-schemas/blob/2.0.0-beta.2/src/main/resources/swagger/ga4gh-tool-discovery.yaml#L273 GA4GH_TRS_FILES = "{0}/api/ga4gh/v2/tools/{1}/versions/{2}/CWL/files" GA4GH_TRS_PRIMARY_DESCRIPTOR = "{0}/api/ga4gh/v2/tools/{1}/versions/{2}/plain-CWL/descriptor/{3}" def resolve_ga4gh_tool(document_loader, uri): # type: (Loader, Text) -> Optional[Text] path, version = uri.partition(":")[::2] if not version: version = "latest" for reg in ga4gh_tool_registries: ds = GA4GH_TRS_FILES.format(reg, urllib.parse.quote(path, ""), urllib.parse.quote(version, "")) try: _logger.debug("Head path is %s", ds) resp = document_loader.session.head(ds) resp.raise_for_status() _logger.debug("Passed head path of %s", ds) resp = document_loader.session.get(ds) for file_listing in resp.json(): if file_listing.get('file_type') == 'PRIMARY_DESCRIPTOR': primary_path = file_listing.get('path') ds2 = GA4GH_TRS_PRIMARY_DESCRIPTOR.format(reg, urllib.parse.quote(path, ""), urllib.parse.quote(version, ""), urllib.parse.quote(primary_path, "")) _logger.debug("Resolved %s", ds2) return ds2 except Exception: # nosec pass return None