Merge pull request #125 from inab/full_circle

Release 1.0.0rc1

.github/workflows/pre-commit.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.7", "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13" ]
     name: Pre-commit python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
@@ -33,16 +33,15 @@ jobs:
         with:
           files: requirements.txt
 
-      - name: 'Install requirements (standard)'
-        if: ${{ matrix.python-version != '3.6' && steps.changed-requirements-txt.outputs.any_changed == 'true' }}
+      - name: 'Install requirements (standard or constraints ${{ matrix.python-version }})'
+        if: ${{ matrix.python-version != '3.6' }}
         run: |
           pip install --upgrade pip wheel
-          pip install -r requirements.txt
-      - name: 'Install requirements (constraints)'
-        if: ${{ matrix.python-version != '3.6' && steps.changed-requirements-txt.outputs.any_changed != 'true' }}
-        run: |
-          pip install --upgrade pip wheel
-          pip install -r requirements.txt -c constraints-${{ matrix.python-version }}.txt
+          if [ ${{ steps.changed-requirements-txt.outputs.any_changed }} != 'true' ] && [ -f constraints-${{ matrix.python-version }}.txt ] ; then
+            pip install -r requirements.txt -c constraints-${{ matrix.python-version }}.txt
+          else
+            pip install -r requirements.txt
+          fi
       #- name: 'Install requirements  (custom Python ${{ matrix.python-version }})'
       #  if: ${{ matrix.python-version == '3.6' }}
       #  run: |

CITATION.cff

@@ -25,7 +25,8 @@ keywords:
 license: Apache-2.0
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/inab/WfExS-backend"
+repository-artifact: "https://github.com/inab/WfExS-backend/pkgs/container/wfexs-backend"
 type: software
 title: "WfExS-backend"
-version: 1.0.0rc0
-date-released: "2024-08-07"
+version: 1.0.0rc1
+date-released: "2024-10-16"

README.md

@@ -40,6 +40,8 @@ Visit the [Zenodo record](https://doi.org/10.5281/zenodo.6567591) for the latest
 
 ### Presentations and outreach
 
+Additional present and future list of references is hosted at [WfExS-backend ReadTheDocs outreach](https://wfexs-backend.readthedocs.io/en/latest/outreach.html).
+
 Paula Iborra, José M. Fernández, Salvador Capella-Gutierrez (2024):  
 [**Onboarding Snakemake: Progress towards WfExS-backend integration**](https://doi.org/10.7490/f1000research.1119725.1).  
 _F1000Research_ **13**(ELIXIR):551 (poster)  

setup.py

@@ -82,7 +82,8 @@
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
-        "Development Status :: 3 - Alpha",
+        "Programming Language :: Python :: 3.13",
+        "Development Status :: 4 - Beta",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: OS Independent",
     ],

wfexs_backend/__init__.py

@@ -21,7 +21,7 @@
 __license__ = "Apache 2.0"
 
 # https://www.python.org/dev/peps/pep-0396/
-__version__ = "1.0.0rc0"
+__version__ = "1.0.0rc1"
 __url__ = "https://github.com/inab/WfExS-backend"
 __official_name__ = "WfExS-backend"
 

wfexs_backend/container_factories/abstract_docker_container.py

@@ -351,9 +351,7 @@ def _save(
                 stderr=d_err,
             ) as sp:
                 if sp.stdout is not None:
-                    shutil.copyfileobj(
-                        cast("IO[str]", sp.stdout), d_out, length=1024 * 1024
-                    )
+                    shutil.copyfileobj(sp.stdout, d_out, length=1024 * 1024)  # type: ignore[misc]
                 d_retval = sp.wait()
 
             self.logger.debug(

wfexs_backend/utils/marshalling_handling.py

@@ -18,7 +18,6 @@
 
 from __future__ import absolute_import
 
-from functools import partial
 import abc
 import collections.abc
 import copy
@@ -36,6 +35,7 @@
         Callable,
         Iterable,
         Mapping,
+        MutableMapping,
         Optional,
     )
 
@@ -51,30 +51,29 @@ def marshall_namedtuple(obj: "Any", workdir: "Optional[pathlib.Path]" = None) ->
     """
 
     # recurse_orig = lambda x: map(marshall_namedtuple, x)
-    obj_is = partial(isinstance, obj)
     if hasattr(obj, "_marshall"):
         return marshall_namedtuple(obj._marshall(), workdir=workdir)
-    elif obj_is(enum.Enum):  # Enum
+    elif isinstance(obj, enum.Enum):  # Enum
         return {
             "_enum": obj.__class__.__name__,
             "value": obj.value,
         }
-    elif obj_is(pathlib.Path):
+    elif isinstance(obj, pathlib.Path):
         # Store the relative path, not the instance
         # Path.is_relative_to was introduced in Python 3.9
-        is_relative_path = False
         if workdir is not None:
             # Path.is_relative_to was introduced in Python 3.9
             # is_relative_path = obj.is_relative_to(workdir)
             is_relative_path = obj == workdir or workdir in obj.parents
-        return (
-            obj.relative_to(workdir).as_posix() if is_relative_path else obj.as_posix()
-        )
-    elif obj_is(tuple) and hasattr(obj, "_fields"):  # namedtuple
+
+            if is_relative_path:
+                return obj.relative_to(workdir).as_posix()
+        return obj.as_posix()
+    elif isinstance(obj, tuple) and hasattr(obj, "_fields"):  # namedtuple
         fields = zip(obj._fields, _recurse_m(obj, workdir))
         class_name = obj.__class__.__name__
         return dict(fields, **{"_type": class_name})
-    elif obj_is(object) and hasattr(obj, "__dataclass_fields__"):  # dataclass
+    elif isinstance(obj, object) and hasattr(obj, "__dataclass_fields__"):  # dataclass
         fields_m = map(
             lambda field: (
                 field,
@@ -84,13 +83,13 @@ def marshall_namedtuple(obj: "Any", workdir: "Optional[pathlib.Path]" = None) ->
         )
         class_name = obj.__class__.__name__
         return dict(fields_m, **{"_type": class_name})
-    elif obj_is((collections.abc.Mapping, dict)):
-        return type(obj)(zip(obj.keys(), _recurse_m(obj.values(), workdir)))
-    elif obj_is(collections.abc.Iterable) and not obj_is(str):
-        return type(obj)(_recurse_m(obj, workdir))
-    elif obj_is(abc.ABC):
+    elif isinstance(obj, (collections.abc.Mapping, dict)):
+        return type(obj)(zip(obj.keys(), _recurse_m(obj.values(), workdir)))  # type: ignore[call-arg]
+    elif isinstance(obj, collections.abc.Iterable) and not isinstance(obj, str):
+        return type(obj)(_recurse_m(obj, workdir))  # type: ignore[call-arg]
+    elif isinstance(obj, abc.ABC):
         return {"_instance_of": obj.__class__.__name__}
-    elif obj_is(abc.ABCMeta):
+    elif isinstance(obj, abc.ABCMeta):
         return {"_class": obj.__name__}
     else:
         return obj
@@ -120,8 +119,7 @@ def unmarshall_namedtuple(
 
     # recurse_orig = lambda x, myglobals: map(lambda l: unmarshall_namedtuple(l, myglobals, workdir), x)
     objres = obj
-    obj_is = partial(isinstance, obj)
-    if obj_is((collections.abc.Mapping, dict)):
+    if isinstance(obj, (collections.abc.Mapping, dict)):
         if "_enum" in obj:  # originally an enum
             try:
                 clazz = myglobals[obj["_enum"]]
@@ -151,7 +149,7 @@ def unmarshall_namedtuple(
             return clazz
 
         if "_type" in obj:  # originally namedtuple
-            objn = obj.copy()
+            objn = cast("MutableMapping[str, Any]", copy.copy(obj))
             theTypeName = objn.pop("_type")
             try:
                 clazz = myglobals[theTypeName]
@@ -161,7 +159,7 @@ def unmarshall_namedtuple(
                 )
                 raise
         else:
-            objn = obj
+            objn = obj  # type: ignore[assignment]
             clazz = type(obj)
             # theTypeName = clazz.__name__
 
@@ -188,19 +186,19 @@ def unmarshall_namedtuple(
         m_fixes_m = getattr(clazz, "_mapping_fixes", None)
         if callable(m_fixes_m):
             c_objn = cast(
-                "Callable[[Mapping[str, Any], Optional[pathlib.Path]], Mapping[str, Any]]",
+                "Callable[[MutableMapping[str, Any], Optional[pathlib.Path]], MutableMapping[str, Any]]",
                 m_fixes_m,
             )(c_objn, workdir)
 
         # Fixes where some key was renamed along the development
         fixes_m = getattr(clazz, "_key_fixes", None)
         if callable(fixes_m):
             fixes = cast("Callable[[], Mapping[str, str]]", fixes_m)()
-            c_objn_keys = map(
-                lambda c_objn_key: fixes.get(c_objn_key, c_objn_key), c_objn.keys()
+            c_objn_keys = list(
+                map(lambda c_objn_key: fixes.get(c_objn_key, c_objn_key), c_objn.keys())
             )
         else:
-            c_objn_keys = c_objn.keys()
+            c_objn_keys = list(c_objn.keys())
 
         fields_list = list(
             zip(c_objn_keys, _recurse_u(c_objn.values(), myglobals, workdir))
@@ -224,9 +222,9 @@ def unmarshall_namedtuple(
             except:
                 logger.exception(f"Unmarshalling Error instantiating {clazz.__name__}")
                 raise
-    elif obj_is(collections.abc.Iterable) and not obj_is(str):
+    elif isinstance(obj, collections.abc.Iterable) and not isinstance(obj, str):
         # print(type(obj))
-        return type(obj)(_recurse_u(obj, myglobals, workdir))
+        return type(obj)(_recurse_u(obj, myglobals, workdir))  # type: ignore[call-arg]
 
     if isinstance(objres, object):
         if hasattr(objres, "_value_defaults_fixes") and callable(

wfexs_backend/utils/rocrate.py

@@ -398,10 +398,23 @@ def __init__(self, wfexs: "WfExSBackend"):
         STRSTARTS(str(?rocrateprofile), str(rocrate:))
     ) .
     OPTIONAL {
-        ?rocratejson dcterms:conformsTo ?wfcrateprofile .
-        FILTER (
-            ?wfcrateprofile = wfhprofile: || STRSTARTS(str(?wfcrateprofile), str(wfcrate:))
-        ) .
+        {
+            FILTER NOT EXISTS {
+                ?rocratejson dcterms:conformsTo ?somewfcrateprofile .
+                FILTER (
+                    ?somewfcrateprofile = wfhprofile: || STRSTARTS(str(?somewfcrateprofile), str(wfcrate:))
+                ) .
+            }
+            ?rootdataset dcterms:conformsTo ?wfcrateprofile .
+            FILTER (
+                ?wfcrateprofile = wfhprofile: || STRSTARTS(str(?wfcrateprofile), str(wfcrate:))
+            ) .
+        } UNION {
+            ?rocratejson dcterms:conformsTo ?wfcrateprofile .
+            FILTER (
+                ?wfcrateprofile = wfhprofile: || STRSTARTS(str(?wfcrateprofile), str(wfcrate:))
+            ) .
+        }
         OPTIONAL  {
             ?rootdataset
                 s:mainEntity ?mainentity .

wfexs_backend/utils/zipfile_path.py

@@ -372,11 +372,13 @@ def _is_child(self, path: "ZipfilePath") -> "bool":
     def _next(self, at: "str") -> "ZipfilePath":
         return self.__class__(self._root, at)
 
-    def is_dir(self) -> "bool":
+    def is_dir(self, *, follow_symlinks: bool = False) -> "bool":
         return not self._at or self._at.endswith("/")
 
-    def is_file(self) -> "bool":
-        return self.exists() and not self.is_dir()
+    def is_file(self, *, follow_symlinks: bool = False) -> "bool":
+        return self.exists(follow_symlinks=follow_symlinks) and not self.is_dir(
+            follow_symlinks=follow_symlinks
+        )
 
     def exists(self, *, follow_symlinks: bool = False) -> "bool":
         return self._at in self._root._name_set()

wfexs_backend/wfexs_backend.py

@@ -2080,7 +2080,7 @@ def cacheWorkflow(
                         f"Ill-formed TRS CURIE {putative_repo_url}. It should be in the format of {TRS_SCHEME_PREFIX}://id/version or {TRS_SCHEME_PREFIX}://prefix-with-slashes/id/version"
                     )
                 trs_steps = cast("MutableSequence[str]", path_steps[0:-2])
-                trs_steps.extend(["ga4gh", "trs", "v2", "tools"])
+                trs_steps.extend(["ga4gh", "trs", "v2", ""])
                 trs_endpoint = urllib.parse.urlunparse(
                     urllib.parse.ParseResult(
                         scheme="https",
@@ -2227,6 +2227,9 @@ def getWorkflowRepoFromTRS(
         else:
             workflow_id_str = workflow_id
 
+        # The base URL must end with a slash
+        if trs_endpoint[-1] != "/":
+            trs_endpoint += "/"
         # Now, time to check whether it is a TRSv2
         trs_endpoint_v2_meta_url = cast("URIType", trs_endpoint + "service-info")
         trs_endpoint_v2_beta2_meta_url = cast("URIType", trs_endpoint + "metadata")