Experimental fast validator code path, using cwl-utils (#1720)

On a very large workflow I was testing with, the validation time went
120 seconds to 20 seconds.

* conformance testing: use CWLTOOL_OPTIONS
* CWLTOOL_OPTIONS: ignore an empty string
* Add loadingContext.skip_resolve_all with note
* conformance tests: report CWLTOOL_OPTIONS
* CI: include extra options in coverge classname
* conformance coverage: normalize paths
* Bump cwl-utils version requirement

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: tetron

Diff for: .github/workflows/ci-tests.yml

@@ -121,6 +121,11 @@ jobs:
       matrix:
         cwl-version: [v1.0, v1.1, v1.2]
         container: [docker, singularity, podman]
+        extras: [""]
+        include:
+          - cwl-version: v1.2
+            container: docker
+            extras: "--fast-parser"
 
     steps:
       - uses: actions/checkout@v3
@@ -141,6 +146,7 @@ jobs:
           version: ${{ matrix.cwl-version }}
           container: ${{ matrix.container }}
           spec_branch: main
+          CWLTOOL_OPTIONS: ${{ matrix.extras }}
         run: ./conformance-test.sh
 
   release_test:

Diff for: README.rst

@@ -667,6 +667,19 @@ given in the following table; all are optional.
 +----------------+------------------+----------+------------------------------+
 
 
+Enabling Fast Parser (experimental)
+-----------------------------------
+
+For very large workflows, `cwltool` can spend a lot of time in
+initialization, before the first step runs.  There is an experimental
+flag ``--fast-parser`` which can dramatically reduce the
+initialization overhead, however as of this writing it has several limitations:
+
+- Error reporting in general is worse than the standard parser, you will want to use it with workflows that you know are already correct.
+
+- It does not check for dangling links (these will become runtime errors instead of loading errors)
+
+- Several other cases fail, as documented in https://github.com/common-workflow-language/cwltool/pull/1720
 
 ===========
 Development

Diff for: conformance-test.sh

@@ -56,6 +56,7 @@ pip3 install -U setuptools wheel pip
 pip3 uninstall -y cwltool
 pip3 install -e .
 pip3 install codecov cwltest>=2.1
+root_folder=${PWD}
 pushd "${repo}-${spec_branch}" || exit 1
 
 # shellcheck disable=SC2043
@@ -71,6 +72,7 @@ cat > "${COVERAGE_RC}" <<EOF
 [run]
 branch = True
 source_pkgs = cwltool
+source = ${root_folder}
 
 [report]
 exclude_lines =
@@ -92,15 +94,15 @@ chmod a+x "${CWLTOOL_WITH_COV}"
 unset exclusions
 declare -a exclusions
 
-EXTRA="--parallel"
+CWLTOOL_OPTIONS+=" --parallel"
 # shellcheck disable=SC2154
 if [[ "$version" = *dev* ]]
 then
-    EXTRA+=" --enable-dev"
+    CWLTOOL_OPTIONS+=" --enable-dev"
 fi
 
 if [[ "$container" = "singularity" ]]; then
-    EXTRA+=" --singularity"
+    CWLTOOL_OPTIONS+=" --singularity"
     # This test fails because Singularity and Docker have
     # different views on how to deal with this.
     exclusions+=(docker_entrypoint)
@@ -113,13 +115,9 @@ if [[ "$container" = "singularity" ]]; then
         exclusions+=(stdin_shorcut)
     fi
 elif [[ "$container" = "podman" ]]; then
-    EXTRA+=" --podman"
+    CWLTOOL_OPTIONS+=" --podman"
 fi
 
-if [ -n "$EXTRA" ]
-then
-    EXTRA="EXTRA=${EXTRA}"
-fi
 if [ "$GIT_BRANCH" = "origin/main" ] && [[ "$version" = "v1.0" ]] && [[ "$container" = "docker" ]]
 then
     rm -Rf conformance
@@ -133,6 +131,7 @@ Conformance test of cwltool ${tool_ver} for CWL ${version}
 Commit: ${GIT_COMMIT}
 Python version: 3
 Container: ${container}
+Extra options: ${CWLTOOL_OPTIONS}
 EOM
 )
 
@@ -148,11 +147,13 @@ if (( "${#exclusions[*]}" > 0 )); then
 else
     EXCLUDE=""
 fi
+export CWLTOOL_OPTIONS
+echo CWLTOOL_OPTIONS="${CWLTOOL_OPTIONS}"
 # shellcheck disable=SC2086
 LC_ALL=C.UTF-8 ./run_test.sh --junit-xml=result3.xml ${EXCLUDE} \
       RUNNER=${CWLTOOL_WITH_COV} "-j$(nproc)" ${BADGE} \
-      ${DRAFT} "${EXTRA}" \
-      "--classname=py3_${container}"
+      ${DRAFT} \
+      "--classname=py3_${container}_$(echo ${CWLTOOL_OPTIONS} | tr "[:blank:]-" _)"
 # LC_ALL=C is to work around junit-xml ASCII only bug
 
 # capture return code of ./run_test.sh

Diff for: cwltool/argparser.py

@@ -576,6 +576,13 @@ def arg_parser() -> argparse.ArgumentParser:
         default=True,
         help=argparse.SUPPRESS,
     )
+    parser.add_argument(
+        "--fast-parser",
+        dest="fast_parser",
+        action="store_true",
+        default=False,
+        help=argparse.SUPPRESS,
+    )
 
     reggroup = parser.add_mutually_exclusive_group()
     reggroup.add_argument(

Diff for: cwltool/context.py

@@ -4,7 +4,18 @@
 import shutil
 import tempfile
 import threading
-from typing import IO, Any, Callable, Dict, Iterable, List, Optional, TextIO, Union
+from typing import (
+    IO,
+    Any,
+    Callable,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    TextIO,
+    Tuple,
+    Union,
+)
 
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 from ruamel.yaml.comments import CommentedMap
@@ -23,6 +34,8 @@
 from .utils import DEFAULT_TMP_PREFIX, CWLObjectType, HasReqsHints, ResolverType
 
 if TYPE_CHECKING:
+    from cwl_utils.parser.cwl_v1_2 import LoadingOptions
+
     from .process import Process
     from .provenance import ResearchObject  # pylint: disable=unused-import
     from .provenance_profile import ProvenanceProfile
@@ -102,7 +115,10 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.relax_path_checks = False  # type: bool
         self.singularity = False  # type: bool
         self.podman = False  # type: bool
-        self.eval_timeout = 60  # type: float
+        self.eval_timeout: float = 60
+        self.codegen_idx: Dict[str, Tuple[Any, "LoadingOptions"]] = {}
+        self.fast_parser = False
+        self.skip_resolve_all = False
 
         super().__init__(kwargs)