diff env/lib/python3.7/site-packages/cwltool/resolver.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/cwltool/resolver.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,92 @@
+"""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