No listing workflow

cwltool.code-workspace

@@ -0,0 +1,8 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}

cwltool/argparser.py

@@ -287,6 +287,24 @@ def arg_parser() -> argparse.ArgumentParser:
         type=str,
     )
 
+    # TO DO: Not yet implemented
+    provgroup.add_argument(
+        "--no-data",  # Maybe change to no-input and no-intermediate to ignore those kind of files?...
+        default=False,
+        action="store_true",
+        help="Disables the storage of input and output data files",
+        dest="no_data",
+    )
+
+    # TO DO: Not yet implemented
+    provgroup.add_argument(
+        "--no-input",  # Maybe change to no-input and no-intermediate to ignore those kind of files?...
+        default=False,
+        action="store_true",
+        help="Disables the storage of input data files",
+        dest="no_input",
+    )
+
     printgroup = parser.add_mutually_exclusive_group()
     printgroup.add_argument(
         "--print-rdf",

cwltool/builder.py

@@ -572,6 +572,10 @@ def addsf(
                 datum = cast(CWLObjectType, datum)
                 ll = schema.get("loadListing") or self.loadListing
                 if ll and ll != "no_listing":
+                    # Debug show
+                    for k in datum:
+                        _logger.debug("Datum:  %s: %s" % (k, datum[k]))
+                    _logger.debug("----------------------------------------")
                     get_listing(
                         self.fs_access,
                         datum,

cwltool/cwlprov/__init__.py

@@ -6,10 +6,14 @@
 import re
 import uuid
 from getpass import getuser
-from typing import IO, Any, Callable, Dict, List, Optional, Tuple, Union
+from typing import IO, Any, Dict, List, Optional, Tuple, Union
 
 from typing_extensions import TypedDict
 
+from cwltool.cwlprov.provenance_constants import Hasher
+
+from ..loghandler import _logger
+
 
 def _whoami() -> Tuple[str, str]:
     """Return the current operating system account as (username, fullname)."""
@@ -135,7 +139,7 @@
 def checksum_copy(
     src_file: IO[Any],
     dst_file: Optional[IO[Any]] = None,
-    hasher: Optional[Callable[[], "hashlib._Hash"]] = None,
+    hasher=Hasher,  # type: Callable[[], hashlib._Hash]
     buffersize: int = 1024 * 1024,
 ) -> str:
     """Compute checksums while copying a file."""
@@ -158,6 +162,35 @@
             pass
         if os.path.exists(temp_location):
             os.rename(temp_location, dst_file.name)  # type: ignore
+
+    return content_processor(contents, src_file, dst_file, checksum, buffersize)
+
+
+def checksum_only(
+    src_file: IO[Any],
+    dst_file: Optional[IO[Any]] = None,
+    hasher=Hasher,  # type: Callable[[], hashlib._Hash]
+    buffersize: int = 1024 * 1024,
+) -> str:
+    """Calculate the checksum only, does not copy the data files."""
+    if dst_file is not None:
+        _logger.error("Destination file should be None but it is %s", dst_file)
+    """Compute checksums while copying a file."""
+    # TODO: Use hashlib.new(Hasher_str) instead?
+    checksum = hasher()
+    contents = src_file.read(buffersize)
+    # TODO Could be a function for both checksum_only and checksum_copy?
+    return content_processor(contents, src_file, dst_file, checksum, buffersize)
+
+
+def content_processor(
+    contents: Any,
+    src_file: IO[Any],
+    dst_file: Optional[IO[Any]],
+    checksum: "hashlib._Hash",
+    buffersize: int,
+) -> str:
+    """Calculate the checksum based on the content."""
     while contents != b"":
         if dst_file is not None:
             dst_file.write(contents)

cwltool/cwlprov/provenance_profile.py

@@ -29,7 +29,7 @@
 from ..loghandler import _logger
 from ..process import Process, shortname
 from ..stdfsaccess import StdFsAccess
-from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring
+from ..utils import CWLObjectType, JobsType, posix_path, versionstring
 from ..workflow_job import WorkflowJob
 from .provenance_constants import (
     ACCOUNT_UUID,
@@ -243,6 +243,7 @@ def evaluate(
             # record provenance of workflow executions
             self.prospective_prov(job)
             customised_job = copy_job_order(job, job_order_object)
+            # Note to self: Listing goes ok here
             self.used_artefacts(customised_job, self.workflow_run_uri)
 
     def record_process_start(
@@ -287,6 +288,7 @@ def record_process_end(
         process_run_id: str,
         outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None],
         when: datetime.datetime,
+        # load_listing: None,
     ) -> None:
         self.generate_output_prov(outputs, process_run_id, process_name)
         self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when)
@@ -408,8 +410,8 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity:
         # a later call to this method will sort that
         is_empty = True
 
-        if "listing" not in value:
-            get_listing(self.fsaccess, value)
+        # if "listing" not in value:
+        #     get_listing(self.fsaccess, value)
         for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])):
             is_empty = False
             # Declare child-artifacts
@@ -604,6 +606,7 @@ def used_artefacts(
         job_order: Union[CWLObjectType, List[CWLObjectType]],
         process_run_id: str,
         name: Optional[str] = None,
+        load_listing=None,
     ) -> None:
         """Add used() for each data artefact."""
         if isinstance(job_order, list):

cwltool/cwlprov/ro.py

@@ -34,7 +34,15 @@
     posix_path,
     versionstring,
 )
-from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy
+from . import (
+    Aggregate,
+    Annotation,
+    AuthoredBy,
+    _valid_orcid,
+    _whoami,
+    checksum_copy,
+    checksum_only,
+)
 from .provenance_constants import (
     ACCOUNT_UUID,
     CWLPROV_VERSION,
@@ -66,6 +74,8 @@
         temp_prefix_ro: str = "tmp",
         orcid: str = "",
         full_name: str = "",
+        no_data: bool = False,
+        no_input: bool = False,
     ) -> None:
         """Initialize the ResearchObject."""
         self.temp_prefix = temp_prefix_ro
@@ -88,6 +98,8 @@
         self.cwltool_version = f"cwltool {versionstring().split()[-1]}"
         self.has_manifest = False
         self.relativised_input_object: CWLObjectType = {}
+        self.no_data = no_data
+        self.no_input = no_input
 
         self._initialize()
         _logger.debug("[provenance] Temporary research object: %s", self.folder)
@@ -180,13 +192,22 @@
             # Below probably OK for now as metadata files
             # are not too large..?
 
-            checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1)
+            if self.no_input:
+                _logger.debug("NO INPUT DATA TO BE CAPTURED!!!")
+
+                checksums[SHA1] = checksum_only(tag_file, hasher=hashlib.sha1)
+                tag_file.seek(0)
+                checksums[SHA256] = checksum_only(tag_file, hasher=hashlib.sha256)
+                tag_file.seek(0)
+                checksums[SHA512] = checksum_only(tag_file, hasher=hashlib.sha512)
+            else:
+                checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1)
 
-            tag_file.seek(0)
-            checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256)
+                tag_file.seek(0)
+                checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256)
 
-            tag_file.seek(0)
-            checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512)
+                tag_file.seek(0)
+                checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512)
 
         rel_path = posix_path(os.path.relpath(path, self.folder))
         self.tagfiles.add(rel_path)
@@ -469,10 +490,14 @@
         content_type: Optional[str] = None,
     ) -> str:
         """Copy inputs to data/ folder."""
+        # TODO Skip if no-input or no-data is used...?
         self.self_check()
         tmp_dir, tmp_prefix = os.path.split(self.temp_prefix)
         with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp:
-            checksum = checksum_copy(from_fp, tmp)
+            if self.no_data:
+                checksum = checksum_only(from_fp)
+            else:
+                checksum = checksum_copy(from_fp, tmp)
 
         # Calculate hash-based file path
         folder = os.path.join(self.folder, DATA, checksum[0:2])
@@ -493,7 +518,12 @@
             _logger.warning("[provenance] Unknown hash method %s for bagit manifest", Hasher)
             # Inefficient, bagit support need to checksum again
             self._add_to_bagit(rel_path)
-        _logger.debug("[provenance] Added data file %s", path)
+        if "dir" in self.relativised_input_object:
+            _logger.debug(
+                "[provenance] Directory :%s", self.relativised_input_object["dir"]["basename"]
+            )
+        else:
+            _logger.debug("[provenance] Added data file %s", path)
         if timestamp is not None:
             createdOn, createdBy = self._self_made(timestamp)
             self._file_provenance[rel_path] = cast(
@@ -557,7 +587,10 @@
             checksums = dict(checksums)
             with open(lpath, "rb") as file_path:
                 # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile?
-                checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1)
+                if self.data_option:
+                    checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1)
+                else:
+                    checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1)
 
         self.add_to_manifest(rel_path, checksums)
 

cwltool/executors.py

@@ -172,7 +172,9 @@
             ):
                 process_run_id: Optional[str] = None
                 name = "primary"
-                process.parent_wf.generate_output_prov(self.final_output[0], process_run_id, name)
+                process.parent_wf.generate_output_prov(
+                    self.final_output[0], process_run_id, name
+                )  # Note to self... # , "generate_output_prov")
                 process.parent_wf.document.wasEndedBy(
                     process.parent_wf.workflow_run_uri,
                     None,

cwltool/job.py

@@ -285,7 +285,10 @@ def _execute(
                 and isinstance(job_order, (list, dict))
             ):
                 runtimeContext.prov_obj.used_artefacts(
-                    job_order, runtimeContext.process_run_id, str(self.name)
+                    job_order,
+                    runtimeContext.process_run_id,
+                    str(self.name),
+                    load_listing=self.builder.loadListing,
                 )
             else:
                 _logger.warning(
@@ -411,6 +414,7 @@ def stderr_stdout_log_path(
                 runtimeContext.process_run_id,
                 outputs,
                 datetime.datetime.now(),
+                # builder.loadListing  # TODO FIX THIS
             )
         if processStatus != "success":
             _logger.warning("[job %s] completed %s", self.name, processStatus)

cwltool/main.py

@@ -11,6 +11,7 @@
 import signal
 import subprocess  # nosec
 import sys
+import tempfile
 import time
 import urllib
 import warnings
@@ -693,6 +694,8 @@
         temp_prefix_ro=args.tmpdir_prefix,
         orcid=args.orcid,
         full_name=args.cwl_full_name,
+        no_data=args.no_data,
+        no_input=args.no_input,
     )
     runtimeContext.research_obj = ro
     log_file_io = open_log_file_for_activity(ro, ro.engine_uuid)
@@ -1138,12 +1141,28 @@
                 print(f"{args.workflow} is valid CWL.", file=stdout)
                 return 0
 
-            if args.print_rdf:
+            if args.print_rdf or args.provenance:
+                output = stdout
+                if args.provenance:
+                    # Write workflow to temp directory
+                    temp_workflow_dir = tempfile.TemporaryDirectory()
+                    os.makedirs(temp_workflow_dir.name, exist_ok=True)
+                    workflow_provenance = temp_workflow_dir.name + "/workflow.ttl"
+                    # Sets up a turtle file for the workflow information
+                    # (not yet in the provenance folder as it does
+                    # not exist and creating it will give issues).
+                    output = open(workflow_provenance, "w")
+                    _logger.info("Writing workflow rdf to %s", workflow_provenance)
                 print(
                     printrdf(tool, loadingContext.loader.ctx, args.rdf_serializer),
-                    file=stdout,
+                    file=output,
                 )
-                return 0
+                # close the output
+                if args.provenance:
+                    output.close()
+                # Only print_rdf exits this way
+                if args.print_rdf:
+                    return 0
 
             if args.print_dot:
                 printdot(tool, loadingContext.loader.ctx, stdout)