Merge pull request #145 from pyscal/add_purge

Add purge

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.6
+current_version = 0.9.7
 commit = True
 tag = False
 

CITATION.cff

@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.6
+version: 0.9.7

atomrdf/graph.py

@@ -44,7 +44,7 @@
 from atomrdf.network.ontology import read_ontology
 from atomrdf.structure import System
 import atomrdf.properties as prp
-from atomrdf.stores import create_store
+from atomrdf.stores import create_store, purge
 import atomrdf.json_io as json_io
 from atomrdf.workflow.workflow import Workflow
 from atomrdf.sample import Sample
@@ -195,7 +195,6 @@ def __init__(
         enable_log : bool, optional
             Whether to enable logging. Default is False.
         """
-
         create_store(
             self,
             store,
@@ -204,6 +203,10 @@ def __init__(
             structure_store=structure_store,
         )
 
+        self._store = store
+        self._identifier = identifier
+        self._store_file = store_file
+
         # enable logging
         if enable_log:
             logger = _prepare_log(os.path.join(os.getcwd(), "atomrdf.log"))
@@ -229,6 +232,37 @@ def __init__(
         self._initialize_graph()
         self.workflow = Workflow(self)
 
+    def purge(self, force=False):
+        """
+        Remove all information from the KnowledgeGraph.
+
+        Parameters
+        ----------
+        force : bool, optional
+            Whether to proceed with purging the graph. Default is False.
+        
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        This method removes all information from the KnowledgeGraph. If the `force` parameter is set to False, a warning is issued before proceeding with the purging.
+        """
+        if not force:
+            warnings.warn('This will remove all information from the KnowledgeGraph. Call with force=True to proceed.')
+            return
+        else:
+            #clean up files
+            sample_files = self.sample_files
+            for file in sample_files:
+                if os.path.exists(file):
+                    os.remove(file)
+
+            graph = purge(self._store, self._identifier, self._store_file)
+            self.graph = graph
+            self._n_triples = 0
+
     def add_structure(self, structure):
         """
         Add a structure to the knowledge graph.
@@ -1085,6 +1119,16 @@ def sample_ids(self):
 
         return [x[0] for x in self.triples((None, RDF.type, CMSO.AtomicScaleSample))]
 
+    @property
+    def sample_files(self):
+        files = []
+        for sample_id in self.sample_ids:
+            filepath = self.value(
+                URIRef(f"{sample_id}_Position"), CMSO.hasPath
+            ).toPython()
+            files.append(filepath)
+        return files
+
     @property
     def sample_names(self):
         """

atomrdf/stores.py

@@ -4,7 +4,7 @@
 from atomrdf.namespace import Literal
 
 import os
-
+import shutil
 
 def create_store(kg, store, identifier, store_file=None, structure_store=None):
     """
@@ -130,3 +130,25 @@ def _setup_structure_store(structure_store=None):
     if not os.path.exists(structure_store):
         os.mkdir(structure_store)
     return structure_store
+
+def purge(store, identifier, store_file):
+    if store in ["Memory", "memory"]:
+        return _purge_memory(identifier, store_file)
+
+    elif store in ["SQLAlchemy", "db", "database", "sqlalchemy"]:
+        return _purge_alchemy(identifier, store_file)
+
+    else:
+        raise ValueError("Unknown store found!")    
+
+
+def _purge_memory(identifier, store_file):
+    graph = Graph(store="Memory", identifier=identifier)
+    return graph
+
+def _purge_alchemy(identifier, store_file):
+    os.remove(store_file)
+    graph = Graph(store="SQLAlchemy", identifier=identifier)
+    uri = Literal(f"sqlite:///{store_file}")
+    graph.open(uri, create=True)
+    return graph

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.9.6',
+    version='0.9.7',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='[email protected]',
     description='Ontology based structural manipulation and quering',

tests/test_graph.py

@@ -131,5 +131,13 @@ def test_extract_sample():
 #	status, _ = s._check_domain_if_ontoterm((CMSO.Material, CMSO.hasDefect, PLDO.AntiphaseBoundary))
 #	assert status == True
 
+def test_purge():
+	s = KnowledgeGraph()
+	sys = System.create.element.Fe(graph=s)
+	s.purge(force=True)
+	assert s.n_samples == 0
 
-
+	s = KnowledgeGraph(store='db', store_file=f'testr.db')
+	sys = System.create.element.Fe(graph=s)
+	s.purge(force=True)
+	assert s.n_samples == 0

tests/test_structuregraph.py

@@ -31,3 +31,5 @@ def test_structuregraph():
 	assert(sys.sample != None)
 
 
+
+