Repository: pyscal/atomRDF (language: python)

Issue:
Add sample object



Discussion / hints:

Fix patch:
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 6154bd0..511d2d0 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.7
+current_version = 0.6.8
 commit = True
 tag = False
 
diff --git a/.gitignore b/.gitignore
index fb27c23..dbbd457 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,9 @@
 rdf_structure_store/
 *.json
 *.ttl
+*.db
+wf*
+*.data
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/CITATION.cff b/CITATION.cff
index ecf6b29..bde1143 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.6.7
+version: 0.6.8
diff --git a/atomrdf/graph.py b/atomrdf/graph.py
index 2a24aff..9ff9dde 100644
--- a/atomrdf/graph.py
+++ b/atomrdf/graph.py
@@ -33,6 +33,7 @@
 import tarfile
 import logging
 import warnings
+import re
 
 # from pyscal3.core import System
 from pyscal3.atoms import Atoms
@@ -45,6 +46,7 @@
 from atomrdf.stores import create_store
 import atomrdf.json_io as json_io
 from atomrdf.workflow.workflow import Workflow
+from atomrdf.sample import Sample
 
 from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO
 
@@ -81,6 +83,11 @@
     },
 }
 
+def _clean_string(input_string):
+    input_string = re.sub(r'\W', '_', input_string)
+    if input_string[0].isdigit():
+        input_string = "s" + input_string
+    return input_string
 
 def _replace_keys(refdict, indict):
     for key, val in indict.items():
@@ -528,7 +535,7 @@ def remove(self, triple):
         modified_triple = self._modify_triple(triple)
         return self.graph.remove(modified_triple)
 
-    def create_node(self, namestring, classtype):
+    def create_node(self, namestring, classtype, label=None):
         """
         Create a new node in the graph.
 
@@ -547,6 +554,8 @@ def create_node(self, namestring, classtype):
         """
         item = URIRef(namestring)
         self.add((item, RDF.type, classtype))
+        if label is not None:
+            self.add((item, RDFS.label, Literal(_clean_string(label))))
         return item
 
     def _initialize_graph(self):
@@ -1046,13 +1055,37 @@ def n_samples(self):
         return len([x for x in self.triples((None, RDF.type, CMSO.AtomicScaleSample))])
 
     @property
-    def samples(self):
+    def sample_ids(self):
         """
         Returns a list of all Samples in the graph
         """
 
         return [x[0] for x in self.triples((None, RDF.type, CMSO.AtomicScaleSample))]
 
+    @property
+    def sample_names(self):
+        """
+        Returns a list of all Sample names in the graph
+        """
+        samples = [x[0] for x in self.triples((None, RDF.type, CMSO.AtomicScaleSample))]
+        samples_names = []
+        for sample in samples:
+            sample_name = self.value(sample, RDFS.label)
+            if sample_name is not None:
+                samples_names.append(sample_name.toPython())
+            else:
+                samples_names.append(sample.toPython())
+        return samples_names
+
+    @property
+    def samples(self):
+        sample_ids = self.sample_ids
+        sample_names = self.sample_names
+        sample_objects = []
+        for ids, name in zip(sample_ids, sample_names):
+            sample_objects.append(Sample(name, ids, self))
+        return sample_objects
+
     def iterate_graph(self, item, create_new_graph=False):
         """
         Iterate through the graph starting from the given item.
@@ -1102,7 +1135,17 @@ def get_sample(self, sample, no_atoms=False):
             na = self.sgraph.value(sample, CMSO.hasNumberOfAtoms).toPython()
             return self.sgraph, na
         return self.sgraph
-
+    
+    def get_sample_label(self, sample):
+        label = self.graph.value(sample, RDFS.label)
+        if label is not None:
+            return label.toPython()
+        return label
+    
+    def change_label(self, sample, label):
+        self.graph.remove((sample, RDFS.label, None))
+        self.graph.add((sample, RDFS.label, Literal(label, datatype=XSD.string)))
+    
     def get_system_from_sample(self, sample):
         """
         Get a pyscal :py:class:`atomrdf.structure.System` from the selected sample
diff --git a/atomrdf/sample.py b/atomrdf/sample.py
new file mode 100644
index 0000000..170a170
--- /dev/null
+++ b/atomrdf/sample.py
@@ -0,0 +1,144 @@
+"""
+Sample
+
+In this module a new Sample class is defined.
+"""
+from pyscal3.atoms import AttrSetter
+from atomrdf.namespace import CMSO, PLDO, PODO, ASMO, PROV
+from rdflib import RDFS
+import numpy as np
+
+class Sample:
+    def __init__(self, name, sample_id, graph):
+        self._name = name
+        self._sample_id = sample_id
+        self._graph = graph
+
+        #create attributes
+        self.properties = AttrSetter()
+        mapdict = {
+            'volume': self._volume,
+            'no_of_atoms': self._no_of_atoms,
+        }
+        self.properties._add_attribute(mapdict)
+
+        labels, props = self._input_properties
+        self.inputs = AttrSetter()
+        mapdict = {}
+        for key, value in zip(labels, props):
+            if key is not None:
+                mapdict[key] = value
+        self.inputs._add_attribute(mapdict)
+
+        labels, props = self._output_properties
+        self.outputs = AttrSetter()
+        mapdict = {}
+        for key, value in zip(labels, props):
+            if key is not None:
+                mapdict[key] = value
+        self.outputs._add_attribute(mapdict)
+
+    def __str__(self):
+        return f"{self._name}"
+    
+    def __repr__(self):
+        return f"{self._name}"
+    
+    @property
+    def _volume(self):
+        simcell = self._graph.value(self._sample_id, CMSO.hasSimulationCell)
+        volume = self._graph.value(simcell, CMSO.hasVolume)
+        return Property(volume.toPython(), graph=self._graph)
+    
+    @property
+    def _no_of_atoms(self):
+        no_atoms = self._graph.value(self._sample_id, CMSO.hasNumberOfAtoms)
+        return Property(no_atoms.toPython(), graph=self._graph)
+    
+    @property
+    def _input_properties(self):
+        activity = self._graph.value(self._sample_id, PROV.wasGeneratedBy)
+        if activity is not None:
+            inps = [k[2] for k in self._graph.triples((activity, ASMO.hasInputParameter, None))]
+            labels = [self._graph.value(inp, RDFS.label) for inp in inps]
+            labels = [label if label is None else label.toPython() for label in labels]
+            values = [self._graph.value(inp, ASMO.hasValue) for inp in inps]
+            units = [self._graph.value(inp, ASMO.hasUnit) for inp in inps]
+            units = [unit if unit is None else unit.toPython().split('/')[-1] for unit in units]
+
+            props = [Property(value.toPython(), unit=unit, graph=self._graph) for value, unit in zip(values, units)]
+            return labels, props
+        return [], []
+
+    @property
+    def _output_properties(self):
+        inps = [k[2] for k in self._graph.triples((self._sample_id, CMSO.hasCalculatedProperty, None))]
+        labels = [self._graph.value(inp, RDFS.label) for inp in inps]
+        labels = [label if label is None else label.toPython() for label in labels]
+        values = [self._graph.value(inp, ASMO.hasValue) for inp in inps]
+        units = [self._graph.value(inp, ASMO.hasUnit) for inp in inps]
+        units = [unit if unit is None else unit.toPython().split('/')[-1] for unit in units]
+
+        props = [Property(value.toPython(), unit=unit, graph=self._graph) for value, unit in zip(values, units)]
+        return labels, props   
+
+class Property:
+    def __init__(self, value, unit=None, graph=None):
+        self._value = value
+        self._unit = unit
+        self._graph = graph
+    
+    def __repr__(self):
+        if self._unit is not None:
+            return f"{self._value} {self._unit}"
+        return f"{self._value}"
+    
+    @property
+    def value(self):
+        return self._value
+    
+    def _declass(self, item):
+        if isinstance(item, Property):
+            return item.value
+        else:
+            return item
+        
+    #overloaded operations
+    def __add__(self, value):
+        return Property(self._value + self._declass(value), unit=self._unit, graph=self._graph)
+    
+    def __sub__(self, value):
+        return Property(self._value - self._declass(value), unit=self._unit, graph=self._graph)
+    
+    def __mul__(self, value):
+        return Property(self._value * self._declass(value), unit=self._unit, graph=self._graph)
+
+    def __truediv__(self, value):
+        return Property(self._value / self._declass(value), unit=self._unit, graph=self._graph)
+    
+    def __eq__(self, value):
+        return self._value == self._declass(value)
+
+    def __ne__(self, value):
+        return self._value != self._declass(value)
+    
+    def __lt__(self, value):
+        return self._value < self._declass(value)
+    
+    def __le__(self, value):
+        return self._value <= self._declass(value)
+    
+    def __gt__(self, value):
+        return self._value > self._declass(value)
+    
+    def __ge__(self, value):
+        return self._value >= self._declass(value)
+    
+    def __neg__(self):
+        return Property(-self._value, unit=self._unit, graph=self._graph)
+    
+    def __abs__(self):
+        return Property(abs(self._value), unit=self._unit, graph=self._graph)
+    
+    def __round__(self, n):
+        return Property(round(self._value, n), unit=self._unit, graph=self._graph)
\ No newline at end of file
diff --git a/atomrdf/structure.py b/atomrdf/structure.py
index edf54d2..603df60 100644
--- a/atomrdf/structure.py
+++ b/atomrdf/structure.py
@@ -17,6 +17,7 @@
 import tarfile
 import warnings
 
+
 import pyscal3.structure_creator as pcs
 from pyscal3.grain_boundary import GrainBoundary
 from pyscal3.atoms import AttrSetter, Atoms
@@ -36,7 +37,6 @@
 with open(file_location, "r") as fin:
     element_indetifiers = yaml.safe_load(fin)
 
-
 def _make_crystal(
     structure,
     lattice_constant=1.00,
@@ -47,6 +47,7 @@ def _make_crystal(
     primitive=False,
     graph=None,
     names=False,
+    label=None,
 ):
     """
     Create a crystal structure using the specified parameters.
@@ -95,6 +96,7 @@ def _make_crystal(
     s.atoms._lattice = structure
     s.atoms._lattice_constant = lattice_constant
     s._structure_dict = sdict
+    s.label = label
     s.to_graph()
     return s
 
@@ -109,6 +111,7 @@ def _make_general_lattice(
     element=None,
     graph=None,
     names=False,
+    label=None,
 ):
     """
     Generate a general lattice structure.
@@ -157,6 +160,7 @@ def _make_general_lattice(
     s.atoms._lattice = "custom"
     s.atoms._lattice_constant = lattice_constant
     s._structure_dict = sdict
+    s.label = label
     s.to_graph()
 
     return s
@@ -177,6 +181,7 @@ def _make_dislocation(
     primitive=False,
     graph=None,
     names=False,
+    label=None,
 ):
     """
     Generate a dislocation structure. Wraps the atomman.defect.Dislocation class.
@@ -315,6 +320,7 @@ def _make_dislocation(
     output_structure.box = box
     output_structure.atoms = atom_obj
     output_structure = output_structure.modify.remap_to_box()
+    output_structure.label = label
     return output_structure
 
 
@@ -329,6 +335,7 @@ def _make_grain_boundary(
     overlap=0.0,
     graph=None,
     names=False,
+    label=None,
 ):
     """
     Create a grain boundary system.
@@ -383,6 +390,7 @@ def _make_grain_boundary(
     s.atoms._lattice = structure
     s.atoms._lattice_constant = lattice_constant
     s._structure_dict = sdict
+    s.label = label
     s.to_graph()
     gb_dict = {
         "GBPlane": " ".join(np.array(gb_plane).astype(str)),
@@ -405,6 +413,7 @@ def _read_structure(
     lattice_constant=None,
     basis_box=None,
     basis_positions=None,
+    label=None,
 ):
     """
     Read in structure from file or ase object
@@ -466,6 +475,7 @@ def _read_structure(
         warn_read_in=False,
     )
     s.lattice_properties = datadict
+    s.label = label
     s.to_graph()
     return s
 
@@ -535,6 +545,7 @@ def __init__(
 
         # this is the sample which will be stored
         self.sample = None
+        self.label = None
         # the graph object should also be attached
         # for post-processing of structures
         self.graph = graph
@@ -1075,7 +1086,7 @@ def _generate_name(self, name_index=None):
             self._name = f"sample:{str(uuid.uuid4())}"
 
     def _add_sample(self):
-        sample = self.graph.create_node(self._name, CMSO.AtomicScaleSample)
+        sample = self.graph.create_node(self._name, CMSO.AtomicScaleSample, label=self.label)
         self.sample = sample
 
     def _add_material(self):
diff --git a/atomrdf/workflow/pyiron.py b/atomrdf/workflow/pyiron.py
index 4bf990b..b925c86 100644
--- a/atomrdf/workflow/pyiron.py
+++ b/atomrdf/workflow/pyiron.py
@@ -72,6 +72,7 @@ def bulk(
             covera=None,
             cubic=True,
             graph=None,
+            label=None,
         ):
 
             if crystalstructure is None:
@@ -87,6 +88,7 @@ def bulk(
                 element=element,
                 primitive=not cubic,
                 graph=self._graph,
+                label=label,
             )
 
             ase_structure = struct.write.ase()
@@ -105,6 +107,7 @@ def grain_boundary(
             a=1,
             overlap=0.0,
             graph=None,
+            label=None,
         ):
 
             struct = self._graph._annotated_make_grain_boundary(
@@ -117,6 +120,7 @@ def grain_boundary(
                 repetitions=repetitions,
                 overlap=overlap,
                 graph=self._graph,
+                label=label,
             )
 
             ase_structure = struct.write.ase()
diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py
index 3814947..7d3a915 100644
--- a/atomrdf/workflow/workflow.py
+++ b/atomrdf/workflow/workflow.py
@@ -137,6 +137,14 @@ def _add_structural_relation(
         if parent_sample is not None:
             self.kg.add((parent_sample, RDF.type, PROV.Entity))
             self.kg.add((sample, PROV.wasDerivedFrom, parent_sample))
+            #update label
+            label = self.kg.get_sample_label(sample)
+            parent_label = self.kg.get_sample_label(parent_sample)
+            if label is None:
+                new_label = f"{parent_label}_derivative"
+            else:
+                new_label = f"{label}_from_{parent_label}"
+            self.kg.change_label(sample, new_label)
             self._get_lattice_properties(parent_sample, sample, structure,)
             self._add_inherited_properties(parent_sample, sample,)
 
diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb
index 5396661..fd64e79 100644
--- a/examples/01_getting_started.ipynb
+++ b/examples/01_getting_started.ipynb
@@ -115,813 +115,813 @@
        "<!-- Generated by graphviz version 9.0.0 (20231125.0833)\n",
        " -->\n",
        "<!-- Pages: 1 -->\n",
-       "<svg width=\"2132pt\" height=\"1953pt\"\n",
-       " viewBox=\"0.00 0.00 2132.00 1953.07\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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-       "<!-- sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_LatticeAngle -->\n",
+       "<svg width=\"1795pt\" height=\"1766pt\"\n",
+       " viewBox=\"0.00 0.00 1794.98 1766.06\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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        "<g id=\"node1\" class=\"node\">\n",
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        "</g>\n",
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+       "<title>sample_80aed8c7&#45;832e&#45;4900&#45;8ca5&#45;c9200363248b_SpaceGroup&#45;&gt;df627daa&#45;5584&#45;4e36&#45;9f31&#45;00133ee4ed6c</title>\n",
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+       "<title>sample_80aed8c7&#45;832e&#45;4900&#45;8ca5&#45;c9200363248b_LatticeParameter&#45;&gt;68a13293&#45;46a3&#45;4c01&#45;8851&#45;b60996e0bd13</title>\n",
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+       "</g>\n",
+       "<!-- cmso.SimulationCellLength -->\n",
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+       "<title>cmso.SimulationCellLength</title>\n",
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+       "<title>cmso.Length</title>\n",
+       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"1474.01,-1647.53 1406.26,-1647.53 1406.26,-1611.53 1474.01,-1611.53 1474.01,-1647.53\"/>\n",
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-       "<g id=\"node34\" class=\"node\">\n",
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+       "<title>cmso.SimulationCellLength&#45;&gt;cmso.Length</title>\n",
+       "<path fill=\"none\" stroke=\"#263238\" d=\"M1391.32,-1613.49C1392.56,-1613.9 1393.8,-1614.31 1395.04,-1614.71\"/>\n",
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-       "<g id=\"node40\" class=\"node\">\n",
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+       "<!-- unit.ANGSTROM -->\n",
+       "<g id=\"node54\" class=\"node\">\n",
+       "<title>unit.ANGSTROM</title>\n",
+       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"1569.69,-1584.87 1489.94,-1584.87 1489.94,-1548.87 1569.69,-1548.87 1569.69,-1584.87\"/>\n",
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-       "<title>sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_LatticeParameter&#45;&gt;8e25ce19&#45;0e1a&#45;42aa&#45;b2ce&#45;4ee203b32620</title>\n",
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-       "<text text-anchor=\"middle\" x=\"565.72\" y=\"-144.82\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasLength_x</text>\n",
+       "<!-- cmso.Length&#45;&gt;unit.ANGSTROM -->\n",
+       "<g id=\"edge54\" class=\"edge\">\n",
+       "<title>cmso.Length&#45;&gt;unit.ANGSTROM</title>\n",
+       "<path fill=\"none\" stroke=\"#263238\" d=\"M1466.56,-1611.07C1475.22,-1605.01 1485,-1598.18 1494.23,-1591.73\"/>\n",
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-       "<!-- sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_SimulationCell -->\n",
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-       "<!-- cmso.SimulationCellAngle -->\n",
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+       "<title>cmso.SimulationCellLength&#45;&gt;cmso.Length</title>\n",
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+       "<g id=\"edge67\" class=\"edge\">\n",
+       "<title>cmso.Length&#45;&gt;unit.ANGSTROM</title>\n",
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+       "<g id=\"edge95\" class=\"edge\">\n",
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+       "<g id=\"edge27\" class=\"edge\">\n",
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+       "<text text-anchor=\"middle\" x=\"1754.84\" y=\"-630.1\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">Position</text>\n",
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-       "<text text-anchor=\"middle\" x=\"469.62\" y=\"-1326.41\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">Pm&#45;3M</text>\n",
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-       "<g id=\"edge129\" class=\"edge\">\n",
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-       "<text text-anchor=\"middle\" x=\"597.83\" y=\"-1291.36\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasSpaceGroupSymbol</text>\n",
+       "<!-- 2f4765de&#45;1384&#45;4ad6&#45;abad&#45;80d672240674 -->\n",
+       "<g id=\"node153\" class=\"node\">\n",
+       "<title>2f4765de&#45;1384&#45;4ad6&#45;abad&#45;80d672240674</title>\n",
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-       "<text text-anchor=\"middle\" x=\"1902.92\" y=\"-1840.05\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasAngle</text>\n",
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+       "<g id=\"edge143\" class=\"edge\">\n",
+       "<title>sample_04b6e198&#45;f1de&#45;4ebd&#45;a045&#45;eb16fe4ddc7e_Position&#45;&gt;2f4765de&#45;1384&#45;4ad6&#45;abad&#45;80d672240674</title>\n",
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+       "<text text-anchor=\"middle\" x=\"1478.49\" y=\"-546.93\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasPath</text>\n",
        "</g>\n",
-       "<!-- sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_UnitCell&#45;&gt;sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_LatticeParameter -->\n",
-       "<g id=\"edge165\" class=\"edge\">\n",
-       "<title>sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_UnitCell&#45;&gt;sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_LatticeParameter</title>\n",
-       "<path fill=\"none\" stroke=\"#263238\" d=\"M1909.39,-1977.59C1877.44,-1990.51 1834.57,-2007.85 1800.59,-2021.6\"/>\n",
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-       "<text text-anchor=\"middle\" x=\"1800.99\" y=\"-2001.74\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasLatticeParameter</text>\n",
+       "<!-- cmso.LatticeVector -->\n",
+       "<g id=\"node121\" class=\"node\">\n",
+       "<title>cmso.LatticeVector</title>\n",
+       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"752.5,-1267.4 660,-1267.4 660,-1231.4 752.5,-1231.4 752.5,-1267.4\"/>\n",
+       "<text text-anchor=\"middle\" x=\"706.25\" y=\"-1246.68\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.LatticeVector</text>\n",
        "</g>\n",
-       "<!-- wiki.Q851536 -->\n",
-       "<g id=\"node138\" class=\"node\">\n",
-       "<title>wiki.Q851536</title>\n",
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-       "<text text-anchor=\"middle\" x=\"1853.05\" y=\"-1871.36\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">wiki.Q851536</text>\n",
+       "<!-- cmso.LatticeVector&#45;&gt;cmso.Vector -->\n",
+       "<g id=\"edge93\" class=\"edge\">\n",
+       "<title>cmso.LatticeVector&#45;&gt;cmso.Vector</title>\n",
+       "<path fill=\"none\" stroke=\"#263238\" d=\"M726.63,-1231.04C730.86,-1227.22 735.39,-1223.14 739.86,-1219.11\"/>\n",
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+       "<text text-anchor=\"middle\" x=\"710.37\" y=\"-1217.48\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">subClassOf</text>\n",
        "</g>\n",
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-       "<title>sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_UnitCell&#45;&gt;wiki.Q851536</title>\n",
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-       "<text text-anchor=\"middle\" x=\"1860.21\" y=\"-1922.27\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasBravaisLattice</text>\n",
+       "<!-- cmso.SimulationCellAngle -->\n",
+       "<g id=\"node134\" class=\"node\">\n",
+       "<title>cmso.SimulationCellAngle</title>\n",
+       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"673.53,-36 552.53,-36 552.53,0 673.53,0 673.53,-36\"/>\n",
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        "</g>\n",
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-       "<title>sample_07576914&#45;65df&#45;4fde&#45;8a5e&#45;77f81c8e6670_ChemicalSpecies&#45;&gt;CHEBI.18248</title>\n",
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-       "<text text-anchor=\"middle\" x=\"2990.86\" y=\"-1884.61\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.hasElement</text>\n",
+       "<!-- cmso.SimulationCellAngle&#45;&gt;cmso.Angle -->\n",
+       "<g id=\"edge114\" class=\"edge\">\n",
+       "<title>cmso.SimulationCellAngle&#45;&gt;cmso.Angle</title>\n",
+       "<path fill=\"none\" stroke=\"#263238\" d=\"M620.07,-36.45C621.94,-41.33 623.99,-46.72 626.01,-52.01\"/>\n",
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        "</g>\n",
        "<!-- cmso.LatticeAngle -->\n",
-       "<g id=\"node148\" class=\"node\">\n",
+       "<g id=\"node142\" class=\"node\">\n",
        "<title>cmso.LatticeAngle</title>\n",
-       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"1918.12,-304 1827.87,-304 1827.87,-268 1918.12,-268 1918.12,-304\"/>\n",
-       "<text text-anchor=\"middle\" x=\"1873\" y=\"-283.27\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.LatticeAngle</text>\n",
+       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"640.25,-151 550,-151 550,-115 640.25,-115 640.25,-151\"/>\n",
+       "<text text-anchor=\"middle\" x=\"595.13\" y=\"-130.27\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">cmso.LatticeAngle</text>\n",
        "</g>\n",
        "<!-- cmso.LatticeAngle&#45;&gt;cmso.Angle -->\n",
-       "<g id=\"edge133\" class=\"edge\">\n",
+       "<g id=\"edge125\" class=\"edge\">\n",
        "<title>cmso.LatticeAngle&#45;&gt;cmso.Angle</title>\n",
-       "<path fill=\"none\" stroke=\"#263238\" d=\"M1859.3,-304.23C1851.63,-314.42 1841.92,-327.34 1833.34,-338.75\"/>\n",
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-       "</g>\n",
-       "<!-- cmso.SimulationCellLength -->\n",
-       "<g id=\"node164\" class=\"node\">\n",
-       "<title>cmso.SimulationCellLength</title>\n",
-       "<polygon fill=\"#c9daf8\" stroke=\"#c9daf8\" points=\"1599.41,-706 1473.16,-706 1473.16,-670 1599.41,-670 1599.41,-706\"/>\n",
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-       "</g>\n",
-       "<!-- cmso.SimulationCellLength&#45;&gt;cmso.Length -->\n",
-       "<g id=\"edge158\" class=\"edge\">\n",
-       "<title>cmso.SimulationCellLength&#45;&gt;cmso.Length</title>\n",
-       "<path fill=\"none\" stroke=\"#263238\" d=\"M1536.96,-706.08C1537.56,-722.24 1538.46,-746.2 1539.16,-765.12\"/>\n",
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-       "<text text-anchor=\"middle\" x=\"1515.19\" y=\"-737.75\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">subClassOf</text>\n",
+       "<path fill=\"none\" stroke=\"#263238\" d=\"M609.75,-114.68C611.52,-112.46 613.36,-110.15 615.2,-107.84\"/>\n",
+       "<polygon fill=\"#263238\" stroke=\"#263238\" points=\"617.8,-110.2 621.3,-100.2 612.33,-105.83 617.8,-110.2\"/>\n",
+       "<text text-anchor=\"middle\" x=\"589.6\" y=\"-103.66\" font-family=\"Helvetica,sans-Serif\" font-size=\"8.00\">subClassOf</text>\n",
        "</g>\n",
        "</g>\n",
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x7f3422e3b390>"
+       "<graphviz.graphs.Digraph at 0x7fcb9857e090>"
       ]
      },
      "execution_count": 7,
@@ -3253,7 +3253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "id": "8ffe7592-4349-4c46-bf40-7edea50c652c",
    "metadata": {
     "tags": []
@@ -3275,7 +3275,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "4a8eba1e-3ffb-4129-8818-5caf8ce0de4b",
    "metadata": {
     "tags": []
@@ -3295,7 +3295,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "id": "f4b6f799-ff85-45c7-a318-f2598a32a48c",
    "metadata": {
     "tags": []
@@ -3339,7 +3339,7 @@
        "0  Pm-3m"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3358,7 +3358,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "id": "7613387a",
    "metadata": {},
    "outputs": [
@@ -3391,7 +3391,7 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>sample:d0ce94f4-178b-4ae4-aea6-ec833de5911e</td>\n",
+       "      <td>sample:04b6e198-f1de-4ebd-a045-eb16fe4ddc7e</td>\n",
        "      <td>Pm-3m</td>\n",
        "      <td>4</td>\n",
        "    </tr>\n",
@@ -3401,14 +3401,15 @@
       ],
       "text/plain": [
        "                             AtomicScaleSample hasSpaceGroupSymbolvalue  \\\n",
-       "0  sample:d0ce94f4-178b-4ae4-aea6-ec833de5911e                    Pm-3m   \n",
+       "0  sample:04b6e198-f1de-4ebd-a045-eb16fe4ddc7e                    Pm-3m   \n",
        "\n",
        "  hasNumberOfAtomsvalue  \n",
        "0                     4  "
       ]
      },
+     "execution_count": 14,
      "metadata": {},
-     "output_type": "display_data"
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -3425,7 +3426,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 15,
    "id": "08f1d892-64a8-40ce-af52-657ef4f59baf",
    "metadata": {},
    "outputs": [
@@ -3457,7 +3458,7 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>sample:e70dc37a-a159-49b1-8653-da4faf44dd3e</td>\n",
+       "      <td>sample:80aed8c7-832e-4900-8ca5-c9200363248b</td>\n",
        "      <td>bcc</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
@@ -3466,10 +3467,10 @@
       ],
       "text/plain": [
        "                             AtomicScaleSample hasAltNamevalue\n",
-       "0  sample:e70dc37a-a159-49b1-8653-da4faf44dd3e             bcc"
+       "0  sample:80aed8c7-832e-4900-8ca5-c9200363248b             bcc"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3490,7 +3491,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "efde861c-b9dd-4b97-861b-a330bbd95de0",
    "metadata": {},
    "outputs": [],
@@ -3508,7 +3509,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "id": "0cb6b043-abb3-41ca-bee7-fb3bf1e7e615",
    "metadata": {
     "tags": []
@@ -3520,7 +3521,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "id": "ae884716-a31b-4170-b4d4-9cf8309a6d74",
    "metadata": {
     "tags": []
@@ -3562,7 +3563,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "id": "7ba5d551-f85b-4c33-be37-b997feffd7d7",
    "metadata": {
     "tags": []
@@ -3574,7 +3575,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 20,
    "id": "f4a90cbe-cf6a-4285-a0d2-b7525726c6dc",
    "metadata": {
     "tags": []
@@ -3586,7 +3587,7 @@
        "Atoms(symbols='Fe2', pbc=True, cell=[2.87, 2.87, 2.87])"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
diff --git a/setup.py b/setup.py
index 4504774..8c9f682 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.6.7',
+    version='0.6.8',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='sarath.menon@pyscal.org',
     description='Ontology based structural manipulation and quering',


Test patch:
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 7bf9f2a..91e8d68 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -38,7 +38,7 @@ def test_add_structure():
 	s = KnowledgeGraph()
 	sys = System.create.element.Fe()
 	s.add_structure(sys)
-	assert sys.sample in s.samples
+	assert sys.sample in s.sample_ids
 
 def test_add_cross_triple():
 	
@@ -111,7 +111,7 @@ def test_extract_sample():
 	struct_Fe = System.create.element.Fe(graph=kg)
 	sample_graph, no_atoms = kg.get_sample(struct_Fe.sample, no_atoms=True)
 	assert no_atoms == 2
-	assert sample_graph.samples[0] == struct_Fe.sample
+	assert sample_graph.sample_ids[0] == struct_Fe.sample
 
 	struct = kg.get_system_from_sample(struct_Fe.sample)
 	assert len(struct.atoms.positions) == 2