Merge pull request #111 from pyscal/add_sample_operations

Add sample operations

atomrdf/graph.py

@@ -39,7 +39,7 @@
 # from pyscal3.core import System
 from pyscal3.atoms import Atoms
 
-from atomrdf.visualize import visualize_graph
+from atomrdf.visualize import visualize_graph, visualize_provenance
 from atomrdf.network.network import OntologyNetwork
 from atomrdf.network.ontology import read_ontology
 from atomrdf.structure import System
@@ -49,7 +49,7 @@
 from atomrdf.workflow.workflow import Workflow
 from atomrdf.sample import Sample
 
-from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO, PROV
+from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO, PROV, MATH, UNSAFECMSO, UNSAFEASMO
 
 # read element data file
 file_location = os.path.dirname(__file__).split("/")
@@ -103,7 +103,12 @@ def _replace_keys(refdict, indict):
 def _dummy_log(str):
     pass
 
-
+def _name(term):
+    try:
+        return str(term.toPython())
+    except:
+        return str(term)
+
 def _prepare_log(file):
     logger = logging.getLogger(__name__)
     handler = logging.FileHandler(file)
@@ -1173,10 +1178,13 @@ def get_sample(self, sample, no_atoms=False):
             return self.sgraph, na
         return self.sgraph
 
-    def get_sample_label(self, sample):
-        label = self.graph.value(sample, RDFS.label)
+    def get_label(self, item):
+        label = self.graph.value(item, RDFS.label)
         if label is not None:
             return label.toPython()
+
+    def get_sample_label(self, sample):
+        label = self.get_label(sample)
         return label
 
     def change_label(self, sample, label):
@@ -1229,6 +1237,7 @@ def get_system_from_sample(self, sample):
         sys.atoms = at
         sys.sample = sample
         sys.graph = self
+        sys._name = sample.toPython().split('sample:')[-1]
         return sys
 
     def to_file(self, sample, filename=None, format="poscar", add_sample_id=True,
@@ -1278,7 +1287,7 @@ def to_file(self, sample, filename=None, format="poscar", add_sample_id=True,
             filename = os.path.join(os.getcwd(), "out")
 
         sys = self.get_system_from_sample(sample)
-        sys.to_file(filename, format=format, add_sample_id=add_sample_id, input_data=input_data, 
+        sys.to_file(filename=filename, format=format, add_sample_id=add_sample_id, input_data=input_data, 
                 pseudopotentials=pseudopotentials, kspacing=kspacing, 
                 kpts=kpts, koffset=koffset, crystal_coordinates=crystal_coordinates)
 
@@ -1293,3 +1302,153 @@ def add_workflow(self, job, workflow_environment=None, workflow_module=None, job
                             workflow_module=workflow_module, 
                             job_dicts=job_dicts,
                             add_intermediate_jobs=add_intermediate_jobs)
+
+    def find_property(self, label):
+        prop_list = list(self.graph.triples((None, RDFS.label, label)))
+        if len(prop_list) == 0:
+            raise RuntimeError(f'Property {label} not found in the graph')
+        prop = prop_list[0][0]
+        return prop        
+
+    def get_string_label(self, item):
+        label = self.get_label(item)
+
+        if label is None:
+            try:
+                label = str(item.toPython())
+            except:
+                label = str(item)
+
+        if "activity" in label:
+            method = self.value(item, ASMO.hasComputationalMethod)
+            if method is not None:
+                method_name = self.value(method, RDF.type)
+                if method_name is not None:
+                    label = method_name.toPython().split("/")[-1]
+        return label
+
+    def _add_to_dict(self, prop, indict):
+        name = _name(prop)
+        if name not in indict.keys():
+            indict[name] = {}
+            indict[name]['found'] = False
+            indict[name]['label'] = self.get_string_label(prop)
+
+    def _get_ancestor(self, prop, prov):
+        #note that only one operation and parent are present!
+        if isinstance(prop, str):
+            prop = URIRef(prop)
+        propname = _name(prop)
+
+        operation = [x[1] for x in self.triples((prop, ASMO.wasCalculatedBy, None))]
+        if len(operation) > 0:
+            parent = [x[2] for x in self.triples((prop, ASMO.wasCalculatedBy, None))]
+            operation = operation[0]
+            parent = parent[0]        
+            prov[propname]['operation'] = 'output_parameter'
+            prov[propname]['inputs'] = {}
+            prov[propname]['inputs']['0'] = _name(parent)
+            self._add_to_dict(parent, prov)
+            prov[_name(parent)]['inputs'] = {}
+            associated_samples = [x[0] for x in self.triples((None, PROV.wasGeneratedBy, parent))]
+            for count, sample in enumerate(associated_samples):
+                prov[_name(parent)]['inputs'][str(count)] = _name(sample)
+                self._add_to_dict(sample, prov)
+            prov[_name(parent)]['found'] = True
+            prov[_name(parent)]['operation'] = 'sample_for_activity'
+
+        else:
+            operation = [x[1] for x in self.triples((None, None, prop))]
+            parent = [list(self.triples((None, op, prop)))[0][0] for op in operation]
+            if len(operation) == 0:
+                prov[propname]['found'] = True
+                return prov
+            operation = operation[0]
+            parent = parent[0]
+
+            if operation.toPython() == "http://purls.helmholtz-metadaten.de/asmo/hasInputParameter":
+                #print(f'we ran 1 for {operation.toPython()}')
+                prov[propname]['operation'] = 'input_parameter'
+                prov[propname]['inputs'] = {}
+                prov[propname]['inputs']['0'] = _name(parent)
+                self._add_to_dict(parent, prov)
+                prov[_name(parent)]['inputs'] = {}
+                associated_samples = [x[0] for x in self.triples((None, PROV.wasGeneratedBy, parent))]
+                for count, sample in enumerate(associated_samples):
+                    prov[_name(parent)]['inputs'][str(count)] = _name(sample)
+                    self._add_to_dict(sample, prov)
+                prov[_name(parent)]['found'] = True
+                prov[_name(parent)]['operation'] = 'sample_for_activity'
+
+            elif operation.toPython() == "http://purls.helmholtz-metadaten.de/cmso/hasCalculatedProperty":
+                #print(f'we ran 2 for {operation.toPython()}')
+                prov[propname]['operation'] = 'output_parameter'
+                prov[propname]['inputs'] = {}
+                prov[propname]['inputs']['0'] = _name(parent)
+                self._add_to_dict(parent, prov)            
+                prov[_name(parent)]['found'] = True
+                prov[_name(parent)]['operation'] = 'sample_output'
+
+            elif operation == MATH.hasSum:
+                addends = list(x[2] for x in self.triples((parent, MATH.hasAddend, None)))
+                prov[propname]['operation'] = 'addition'
+                prov[propname]['inputs'] = {}
+                for count, term in enumerate(addends):
+                    prov[propname]['inputs'][f'{count}'] = _name(term)
+                    self._add_to_dict(term, prov)
+
+            elif operation == MATH.hasDifference:
+                minuend = self.value(parent, MATH.hasMinuend)
+                subtrahend = self.value(parent, MATH.hasSubtrahend)
+                prov[propname]['operation'] = 'subtraction'
+                prov[propname]['inputs'] = {}
+                prov[propname]['inputs']['0'] = _name(minuend)
+                prov[propname]['inputs']['1'] = _name(subtrahend)
+                self._add_to_dict(minuend, prov)
+                self._add_to_dict(subtrahend, prov)
+
+            elif operation == MATH.hasProduct:
+                factors = list(x[2] for x in self.triples((parent, MATH.hasFactor, None)))
+                prov[propname]['operation'] = 'multiplication'
+                prov[propname]['inputs'] = {}
+                for count, term in enumerate(factors):
+                    prov[propname]['inputs'][f'{count}'] = _name(term)
+                    self._add_to_dict(term, prov)
+
+            elif operation == MATH.hasQuotient:
+                divisor = self.value(parent, MATH.hasDivisor)
+                dividend = self.value(parent, MATH.hasDividend)
+                prov[propname]['operation'] = 'division'
+                prov[propname]['inputs'] = {}
+                prov[propname]['inputs']['0'] = _name(divisor)
+                prov[propname]['inputs']['1'] = _name(dividend)
+                self._add_to_dict(divisor, prov)
+                self._add_to_dict(dividend, prov)
+
+        prov[propname]['found'] = True
+        return prov
+
+    def generate_provenance(self, prop=None, label=None, visualize=False):
+        if (prop is None) and (label is None):
+            raise ValueError('Either prop or label must be provided')
+
+        if prop is None:
+            prop = self.find_property(label)
+
+        name = _name(prop)
+        prov = {}
+        self._add_to_dict(prop, prov)
+
+        done = False
+        while not done:
+            done = True
+            keys = list(prov.keys()) 
+            for prop in keys:
+                if not prov[prop]['found']:
+                    prov = self._get_ancestor(prop, prov)
+                    done = False
+
+        if visualize:
+            return visualize_provenance(prov)
+
+        return prov

atomrdf/namespace.py

@@ -72,3 +72,7 @@ def __init__(self, infile, delimiter="/"):
 ASMO = Namespace(os.path.join(file_location, "data/asmo.owl"))
 PROV = RDFLibNamespace("http://www.w3.org/ns/prov#")
 MDO = RDFLibNamespace("https://w3id.org/mdo/calculation/")
+
+MATH = RDFLibNamespace("http://purls.helmholtz-metadaten.de/asmo/")
+UNSAFECMSO = RDFLibNamespace(os.path.join(file_location, "data/cmso.owl"))
+UNSAFEASMO = RDFLibNamespace(os.path.join(file_location, "data/asmo.owl"))