F h5 cfood

https://gitlab.com/caosdb/caosdb-advanced-user-tools/-/merge_requests/78

src/caosadvancedtools/cfoods/h5.py

@@ -41,6 +41,7 @@ from caosadvancedtools.cfood import fileguide
 from caosdb.common.datatype import is_reference as basic_is_reference
 from caosdb.common.utils import uuid
 
+from ..structure_mapping import EntityMapping, collect_existing_structure
 from ..cfood import (AbstractFileCFood, assure_has_description,
                      assure_has_parent, assure_has_property,
                      assure_property_is)
@@ -124,25 +125,6 @@ def h5_attr_to_property(val):
         return val, dtype
 
 
-class EntityMapping(object):
-    """
-    map local entities to in the server existing entities
-
-    the dict to_existing maps _cuid property to entity objects
-    the dict to_target maps id property to entity objects
-    """
-
-    def __init__(self):
-        self.to_existing = {}
-        self.to_target = {}
-
-    def add(self, target, existing):
-        if target._cuid is None:
-            target._cuid = str(uuid())
-        self.to_existing[str(target._cuid)] = existing
-        self.to_target[existing.id] = target
-
-
 def get_entity(eid):
     return db.execute_query("FIND ENTITY WITH ID={}".format(eid),
                             unique=True)
@@ -182,46 +164,6 @@ def resolve_property(entity, property_name):
             prop.value = get_entity(prop.value)
 
 
-def collect_existing_structure(target_structure, existing_root, em):
-    """ recursively collects existing entities
-
-    The collected entities are those that correspond to the ones in
-    target_structure.
-
-
-    em: EntityMapping
-    """
-
-    for prop in target_structure.properties:
-        if prop.value is None:
-            continue
-
-        if is_reference(prop):
-            # TODO case where multiple properties of same name exist is not
-            # treated
-
-            if (existing_root.get_property(prop.name) is not None and
-                    existing_root.get_property(prop.name).value is not None):
-                resolve_property(existing_root, prop.name)
-
-                # TODO Lists of reference are not yet treated properly
-                referenced = existing_root.get_property(prop.name).value
-
-                if not isinstance(referenced, list):
-                    referenced = [referenced]
-                target_value = prop.value
-
-                if not isinstance(target_value, list):
-                    target_value = [target_value]
-
-                if len(target_value) != len(referenced):
-                    raise ValueError()
-
-                for tent, eent in zip(target_value, referenced):
-                    em.add(tent, eent)
-                    collect_existing_structure(tent, eent, em)
-
-
 class H5CFood(AbstractFileCFood):
     """H5CFood which consumes HDF5 files.