Merge pull request #183 from simleo/crate_from_dict

Add ro-crate instantiation from a dictionary

.github/workflows/python-package.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     runs-on: ${{ matrix.os }}
 

rocrate/metadata.py

@@ -30,8 +30,11 @@ def read_metadata(metadata_path):
     Return a tuple of two elements: the context; a dictionary that maps entity
     ids to the entities themselves.
     """
-    with open(metadata_path) as f:
-        metadata = json.load(f)
+    if isinstance(metadata_path, dict):
+        metadata = metadata_path
+    else:
+        with open(metadata_path) as f:
+            metadata = json.load(f)
     try:
         context = metadata['@context']
         graph = metadata['@graph']

rocrate/rocrate.py

@@ -113,26 +113,31 @@ def __init_from_tree(self, top_dir, gen_preview=False):
                     self.add(Preview(self, source))
 
     def __read(self, source, gen_preview=False):
-        source = Path(source)
-        if not source.exists():
-            raise FileNotFoundError(errno.ENOENT, f"'{source}' not found")
-        if zipfile.is_zipfile(source):
-            zip_path = tempfile.mkdtemp(prefix="rocrate_")
-            atexit.register(shutil.rmtree, zip_path)
-            with zipfile.ZipFile(source, "r") as zf:
-                zf.extractall(zip_path)
-            source = Path(zip_path)
-        metadata_path = source / Metadata.BASENAME
-        if not metadata_path.is_file():
-            metadata_path = source / LegacyMetadata.BASENAME
-        if not metadata_path.is_file():
-            raise ValueError(f"Not a valid RO-Crate: missing {Metadata.BASENAME}")
+        if isinstance(source, dict):
+            metadata_path = source
+        else:
+            source = Path(source)
+            if not source.exists():
+                raise FileNotFoundError(errno.ENOENT, f"'{source}' not found")
+            if zipfile.is_zipfile(source):
+                zip_path = tempfile.mkdtemp(prefix="rocrate_")
+                atexit.register(shutil.rmtree, zip_path)
+                with zipfile.ZipFile(source, "r") as zf:
+                    zf.extractall(zip_path)
+                source = Path(zip_path)
+            metadata_path = source / Metadata.BASENAME
+            if not metadata_path.is_file():
+                metadata_path = source / LegacyMetadata.BASENAME
+            if not metadata_path.is_file():
+                raise ValueError(f"Not a valid RO-Crate: missing {Metadata.BASENAME}")
         _, entities = read_metadata(metadata_path)
         self.__read_data_entities(entities, source, gen_preview)
         self.__read_contextual_entities(entities)
         return source
 
     def __read_data_entities(self, entities, source, gen_preview):
+        if isinstance(source, dict):
+            source = Path("")
         metadata_id, root_id = find_root_entity_id(entities)
         root_entity = entities.pop(root_id)
         assert root_id == root_entity.pop('@id')
@@ -447,7 +452,7 @@ def _copy_unlisted(self, top, base_path):
     def write(self, base_path):
         base_path = Path(base_path)
         base_path.mkdir(parents=True, exist_ok=True)
-        if self.source:
+        if self.source and not isinstance(self.source, dict):
             self._copy_unlisted(self.source, base_path)
         for writable_entity in self.data_entities + self.default_entities:
             writable_entity.write(base_path)

test/test_read.py

@@ -535,3 +535,61 @@ def test_indirect_data_entity(tmpdir):
     d2_e = crate.dereference("d1/d2")
     assert d2_e
     assert d2_e in crate.data_entities
+
+
+@pytest.mark.filterwarnings("ignore")
+def test_from_dict(tmpdir):
+    metadata = {
+        "@context": "https://w3id.org/ro/crate/1.1/context",
+        "@graph": [
+            {
+                "@id": "ro-crate-metadata.json",
+                "@type": "CreativeWork",
+                "about": {"@id": "./"},
+                "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}
+            },
+            {
+                "@id": "./",
+                "@type": "Dataset",
+                "creator": {"@id": "#josiah"},
+                "hasPart": {"@id": "d1"}
+            },
+            {
+                "@id": "d1",
+                "@type": "Dataset",
+                "hasPart": {"@id": "d1/d2"}
+            },
+            {
+                "@id": "d1/d2",
+                "@type": "Dataset",
+                "hasPart": {"@id": "d1/d2/f1"}
+            },
+            {
+                "@id": "d1/d2/f1",
+                "@type": "File"
+            },
+            {
+                "@id": "#josiah",
+                "@type": "Person",
+                'name': 'Josiah Carberry'
+            },
+        ]
+    }
+    crate = ROCrate(metadata)
+    d1 = crate.dereference("d1")
+    assert d1
+    d2 = crate.dereference("d1/d2")
+    assert d2
+    f1 = crate.dereference("d1/d2/f1")
+    assert f1
+    p = crate.dereference("#josiah")
+    assert p
+    assert set(crate.data_entities) == {d1, d2, f1}
+    assert set(crate.contextual_entities) == {p}
+    out_path = tmpdir / 'out_crate'
+    with pytest.raises(OSError):
+        crate.write(out_path)
+    # make it writable
+    for entity in d1, d2, f1:
+        entity.source = None
+    crate.write(out_path)