Merge pull request #105 from inab/full_circle

Full circle 1.0.0a1

CITATION.cff

@@ -28,4 +28,4 @@ message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/inab/WfExS-backend"
 type: software
 title: "WfExS-backend"
-version: 1.0.0a0
+version: 1.0.0a1

tests/containers/util.py

@@ -22,13 +22,17 @@
 )
 
 if TYPE_CHECKING:
+    from typing import (
+        Sequence,
+    )
+
     from wfexs_backend.common import (
         RelPath,
         URIType,
     )
 
 
-def simpleTestContainerFileName(imageUrl: "URIType") -> "RelPath":
+def simpleTestContainerFileName(imageUrl: "URIType") -> "Sequence[RelPath]":
     """
     This method was borrowed from
     https://github.com/nextflow-io/nextflow/blob/539a22b68c114c94eaf4a88ea8d26b7bfe2d0c39/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy#L80
@@ -46,4 +50,4 @@ def simpleTestContainerFileName(imageUrl: "URIType") -> "RelPath":
 
     name = name.replace(":", "-").replace("/", "-")
 
-    return cast("RelPath", name + extension)
+    return [cast("RelPath", name + extension)]

wfexs_backend/__init__.py

@@ -21,7 +21,7 @@
 __license__ = "Apache 2.0"
 
 # https://www.python.org/dev/peps/pep-0396/
-__version__ = "1.0.0a0"
+__version__ = "1.0.0a1"
 __url__ = "https://github.com/inab/WfExS-backend"
 __official_name__ = "WfExS-backend"
 

wfexs_backend/__main__.py

@@ -256,6 +256,20 @@ def genParserSub(
                 help="Workflow Run RO-Crate describing a previous workflow execution. It can be either a local path or an URI resolvable from WfExS with no authentication",
             )
 
+            ap_.add_argument(
+                "--ignore-retrospective-provenance",
+                dest="retrospective_first",
+                action="store_false",
+                default=True,
+                help="Retrospective provenance is ignored",
+            )
+            ap_.add_argument(
+                "--prefer-retrospective-provenance",
+                dest="retrospective_first",
+                action="store_true",
+                help="Retrospective provenance is first inspected",
+            )
+
         not_restage = command not in (WfExS_Commands.Import, WfExS_Commands.ReStage)
         ap_.add_argument(
             "-W",
@@ -1483,6 +1497,7 @@ def main() -> None:
             secure=args.secure,
             reproducibility_level=ReproducibilityLevel(args.reproducibility_level),
             strict_reproducibility_level=args.strict_reproducibility_level,
+            retrospective_first=args.retrospective_first,
         )
     else:
         print(

wfexs_backend/common.py

@@ -401,6 +401,32 @@ def _key_fixes(cls) -> "Mapping[str, str]":
     ]
 
 
+if TYPE_CHECKING:
+
+    class ContentWithURIsSetup(TypedDict):
+        """
+        headerRows: Number of header rows
+        rowSep: Line separator
+        columnSep: Expression used to break a line into its column values
+        uriColumns: The 0-based numbers of the columns containing URIs to be fetched
+        """
+
+        headerRows: "int"
+        rowSep: "str"
+        columnSep: "str"
+        uriColumns: "Sequence[int]"
+
+
+class ContentWithURIsDesc(NamedTuple):
+    """
+    encodingFormat: the kind of content with URIs (currently implemented is text/csv => tabular)
+    setup: The dictionary describing the setup
+    """
+
+    encodingFormat: "str"
+    setup: "ContentWithURIsSetup"
+
+
 class MaterializedInput(NamedTuple):
     """
     name: Name of the input
@@ -413,6 +439,7 @@ class MaterializedInput(NamedTuple):
     secondaryInputs: "Optional[Sequence[MaterializedContent]]" = None
     autoFilled: "bool" = False
     implicit: "bool" = False
+    contentWithURIs: "Optional[ContentWithURIsDesc]" = None
 
 
 if TYPE_CHECKING: