Merge branch 'f-reenable-rocrate-dep' into f-fix-rocrate

setup.cfg

@@ -51,4 +51,4 @@ h5-crawler =
 spss =
      pandas[spss]
 rocrate =
-     rocrate @ git+https://github.com/salexan2001/ro-crate-py.git@f-automatic-dummy-ids
+     rocrate

unittests/test_rocrate_converter.py

@@ -76,6 +76,12 @@ def eln_entities(basic_eln_converter):
     return entities
 
 
+@pytest.mark.xfail(
+    reason="The example files for PASTA have not yet been updated in:"
+    "https://github.com/TheELNConsortium/TheELNFileFormat/tree/master/examples/PASTA"
+    "However, there was the announcement that these files are going to follow the"
+    "flattened structure soon: https://github.com/TheELNConsortium/TheELNFileFormat/issues/98"
+)
 def test_load_pasta(basic_eln_converter):
     """
     Test for loading the .eln example export from PASTA.
@@ -99,7 +105,7 @@ def test_load_kadi4mat(basic_eln_converter):
     match = basic_eln_converter.match(f_k4mat)
     assert match is not None
     entities = basic_eln_converter.create_children(GeneralStore(), f_k4mat)
-    assert len(entities) == 10
+    assert len(entities) == 17
     assert isinstance(entities[0], ROCrateEntity)
     assert isinstance(entities[0].folder, str)
     assert isinstance(entities[0].entity, Entity)
@@ -131,7 +137,7 @@ match_properties:
 
     match = ds2.match(eln_entities[1])
     assert match is not None
-    assert match["dateCreated"] == "2024-08-21T12:07:45.115990+00:00"
+    assert match["dateCreated"] == "2024-11-19T13:44:35.476888+00:00"
 
     children = ds2.create_children(GeneralStore(), eln_entities[1])
     assert len(children) == 8
@@ -193,7 +199,20 @@ def test_scanner():
     assert len(rlist) == 1
     assert isinstance(rlist[0], db.Record)
     assert rlist[0].name == "records-example"
-    assert rlist[0].description == "This is a sample record."
+    # This assertion was moved to a different test, see below:
+    # assert rlist[0].description == "This is a sample record."
     assert rlist[0].parents[0].name == "Dataset"
     assert rlist[0].get_property("keywords").value == "sample"
     assert rlist[0].get_property("dateModified").value == "2024-08-21T11:43:17.626965+00:00"
+
+
+@pytest.mark.xfail(
+    reason="The description is no longer a simple string, but a reference to another record."
+    "The rocrate converter will be able to dereference this as soon as this feature is implemented:"
+    "https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/191"
+    "This test might need changes in the yaml definition."
+)
+def test_description_reference():
+    rlist = scanner.scan_directory(os.path.join(UNITTESTDIR, "eln_files/"),
+                                   os.path.join(UNITTESTDIR, "eln_cfood.yaml"))
+    assert rlist[0].description == "This is a sample record."

unittests/test_zipfile_converter.py

@@ -50,6 +50,12 @@ def converter_registry():
     return converter_registry
 
 
+@pytest.mark.xfail(
+    reason="The example files for PASTA have not yet been updated in:"
+    "https://github.com/TheELNConsortium/TheELNFileFormat/tree/master/examples/PASTA"
+    "However, there was the announcement that these files are going to follow the"
+    "flattened structure soon: https://github.com/TheELNConsortium/TheELNFileFormat/issues/98"
+)
 def test_zipfile_converter(converter_registry):
     zipfile = File("PASTA.eln", os.path.join(UNITTESTDIR, "eln_files", "PASTA.eln"))
     zip_conv = ZipFileConverter(yaml.safe_load("""
@@ -77,3 +83,29 @@ match: ^PASTA$
         assert isinstance(children[i], Directory)
     for i in range(2, 5):
         assert isinstance(children[i], File)
+
+
+def test_zipfile_minimal(converter_registry):
+    zipfile = File("empty.zip", os.path.join(UNITTESTDIR, "zip_minimal", "empty.zip"))
+    zip_conv = ZipFileConverter(yaml.safe_load("""
+type: ZipFile
+match: .*$
+"""), "TestZipFileConverter", converter_registry)
+
+    match = zip_conv.match(zipfile)
+    assert match is not None
+
+    children = zip_conv.create_children(GeneralStore(), zipfile)
+    assert len(children) == 2
+    assert children[1].name == "empty.txt"
+
+    dir_conv = DirectoryConverter(yaml.safe_load("""
+type: Directory
+match: ^folder$
+"""), "TestDirectory", converter_registry)
+    match = dir_conv.match(children[0])
+    assert match is not None
+    children = dir_conv.create_children(GeneralStore(), children[0])
+    assert len(children) == 3
+    for i in range(3):
+        assert isinstance(children[i], File)