special treat

integrationtests/example_hdf5cfood.py

@@ -41,9 +41,13 @@ class ExampleH5CFood(H5CFood):
         return ExperimentCFood.get_re()[:-len(readme_pattern)] + r".*\.hdf5"
 
     def create_identifiables(self):
-        self.experiment, project = ExperimentCFood.create_identifiable_experiment(self.match)
-
         self.identifiable_root = db.Record()
         self.identifiable_root.add_property("hdf5File", self.crawled_file)
         self.identifiable_root.add_parent("ExampleH5")
         self.identifiables.append(self.identifiable_root)
+
+    def special_treatment(self, key, value, dtype):
+        if key == "attr_data_root":
+            return "single_attribute", value, dtype
+
+        return key, value, dtype

integrationtests/test_crawler_with_cfoods.py

@@ -486,3 +486,17 @@ class CrawlerTest(unittest.TestCase):
 
         # Should have a description
         self.assertIsNotNone(ana.description)
+
+    def test_exampleh5(self):
+        examp = db.execute_query("FIND Record ExampleH5", unique=True)
+
+        for ent in [p.value for p in examp.properties]:
+            if ent.parents[0].name == 'group_level1_a':
+                self.assertTrue(ent.get_property("group_level2_aa") is not None)
+                self.assertTrue(ent.get_property("group_level1_a") is None)
+            elif ent.parents[0].name == 'group_level1_b':
+                self.assertTrue(ent.get_property("level1_b_floats") is not None)
+            elif ent.parents[0].name == 'group_level1_c':
+                self.assertTrue(ent.get_property("level1_c_floats") is not None)
+            elif ent.parents[0].name == 'root_integers':
+                self.assertTrue(ent.get_property("single_attribute") is not None)

src/caosadvancedtools/cfoods/h5.py

@@ -130,7 +130,8 @@ class H5CFood(AbstractFileCFood):
 
     def collect_information(self):
         self.h5file = h5py.File(fileguide.access(self.crawled_path), 'r')
-        self.structure = self.create_structure(self.h5file)
+        self.structure = self.create_structure(self.h5file,
+                                               self.special_treatment)
 
     @staticmethod
     def get_re():
@@ -183,8 +184,20 @@ class H5CFood(AbstractFileCFood):
         # self.update_structure(self.structure)
         update_structure(self.em, self.to_be_updated, self.structure)
 
+    def special_treatment(self, key, value, dtype):
+        """define special treatment of attributes
+
+        to be overwritten by child classes.
+
+        key: attribute name
+        value: attribute value
+        """
+
+        return key, value, dtype
+
     @classmethod
-    def create_structure(cls, h5obj, create_recordTypes=False, collection=None):
+    def create_structure(cls, h5obj, create_recordTypes=False, collection=None,
+                         special_treatment=None):
         """Create Records and Record types from a given hdf5-object for all items in the tree.
            Attributes are added as properties, the values only if the dimension < 2.
 
@@ -198,6 +211,9 @@ class H5CFood(AbstractFileCFood):
         if collection is None:
             collection = []
 
+        if special_treatment is None:
+            def special_treatment(x, y, z): return x, y, z
+
         if h5obj.name == "/":
             name_without_path = cls.root_name
         else:
@@ -215,7 +231,8 @@ class H5CFood(AbstractFileCFood):
 
                 sub = H5CFood.create_structure(h5obj[subgroup],
                                                create_recordTypes=create_recordTypes,
-                                               collection=collection)
+                                               collection=collection,
+                                               special_treatment=special_treatment)
 
                 if create_recordTypes:
                     rec.add_property(subgroup_name)
@@ -239,7 +256,10 @@ class H5CFood(AbstractFileCFood):
                 collection.append(prop)
                 rec.add_property(name=key)
             else:
-                rec.add_property(name=key, value=val, datatype=dtype)
+                treated_k, treated_v, treated_dtype = special_treatment(
+                    key, val, dtype)
+                rec.add_property(name=treated_k, value=treated_v,
+                                 datatype=treated_dtype)
 
         return rec