Merge pull request #100 from pyscal/further_restructure_workflows

Further restructure workflows

.gitignore

@@ -1,6 +1,7 @@
 #custom
 rdf_structure_store/
 *.json
+*.ttl
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

atomrdf/graph.py

@@ -44,6 +44,7 @@
 import atomrdf.properties as prp
 from atomrdf.stores import create_store
 import atomrdf.json_io as json_io
+from atomrdf.workflow.workflow import Workflow
 
 from atomrdf.namespace import Namespace, CMSO, PLDO, PODO, ASMO
 
@@ -212,6 +213,7 @@ def __init__(
         self.store = store
         self._n_triples = 0
         self._initialize_graph()
+        self.workflow = Workflow(self)
 
     def add_structure(self, structure):
         """
@@ -697,6 +699,7 @@ def visualise(
         rankdir="BT",
         hide_types=False,
         workflow_view=False,
+        sample_view=False,
         size=None,
         layout="neato",
     ):
@@ -713,6 +716,8 @@ def visualise(
             Whether to hide the types in the visualization. Default is False.
         workflow_view : bool, optional
             Whether to enable the workflow view. Default is False.
+        sample_view : bool, optional
+            Whether to enable the sample view. Default is False.
         size : tuple, optional
             The size of the visualization. Default is None.
         layout : str, optional
@@ -765,6 +770,7 @@ def visualise(
             rankdir=rankdir,
             hide_types=hide_types,
             workflow_view=workflow_view,
+            sample_view=sample_view,
             size=size,
             layout=layout,
         )
@@ -1178,3 +1184,13 @@ def to_file(self, sample, filename=None, format="poscar"):
         else:
             asesys = sys.write.ase()
             write(filename, asesys, format=format)
+
+    def enable_workflow(self, workflow_object, workflow_environment=None, workflow_module=None):
+        self.workflow.inform_graph(workflow_object, 
+                        workflow_environment=workflow_environment, 
+                        workflow_module=workflow_module)
+
+    def add_workflow(self, job, workflow_environment=None, workflow_module=None, job_dict=None):
+        self.workflow.to_graph(job, workflow_environment=workflow_environment, 
+                            workflow_module=workflow_module, 
+                            job_dict=job_dict)

atomrdf/stores.py

@@ -4,9 +4,6 @@
 
 import os
 
-# special methods; for supporting workflow envs
-from atomrdf.workflow import inform_graph
-
 
 def create_store(kg, store, identifier, store_file=None, structure_store=None):
     """
@@ -32,30 +29,22 @@ def create_store(kg, store, identifier, store_file=None, structure_store=None):
 
     """
     kg.store_file = store_file
-    if store == "Memory":
+    if store in ["Memory", "memory"]:
         store_memory(
             kg,
             store,
             identifier,
             store_file=store_file,
             structure_store=structure_store,
         )
-    elif store == "SQLAlchemy":
+    elif store in ["SQLAlchemy", "db", "database", "sqlalchemy"]:
         store_alchemy(
             kg,
             store,
             identifier,
             store_file=store_file,
             structure_store=structure_store,
         )
-    elif type(store).__name__ == "Project":
-        store_pyiron(
-            kg,
-            store,
-            identifier,
-            store_file=store_file,
-            structure_store=structure_store,
-        )
     else:
         raise ValueError("Unknown store found!")
 
@@ -121,37 +110,6 @@ def store_alchemy(kg, store, identifier, store_file=None, structure_store=None):
     kg.graph.open(uri, create=True)
     kg.structure_store = _setup_structure_store(structure_store=structure_store)
 
-
-def store_pyiron(kg, store, identifier, store_file=None, structure_store=None):
-    """
-    Store the pyiron knowledge graph in a database.
-
-    Parameters
-    ----------
-    kg : pyiron.atomistics.structure.pyiron_atomistics.structure.AtomisticStructure
-        The pyiron knowledge graph to be stored.
-    store : pyiron.atomistics.structure.pyiron_atomistics.structure.AtomisticStructure
-        The store object where the knowledge graph will be stored.
-    identifier : str
-        The identifier for the knowledge graph.
-    store_file : str, optional
-        The path to the store file. If not provided, a default path will be used.
-    structure_store : str, optional
-        The path to the structure store. If not provided, a default path will be used.
-
-    Returns
-    -------
-    None
-
-    """
-    structure_store = os.path.join(store.path, "rdf_structure_store")
-    kg.structure_store = _setup_structure_store(structure_store=structure_store)
-    store_file = os.path.join(store.path, f"{store.name}.db")
-    store_alchemy(kg, store, identifier, store_file, structure_store=structure_store)
-    # finally update project object
-    inform_graph(store, kg)
-
-
 def _check_if_sqlalchemy_is_available():
     try:
         import sqlalchemy as sa

atomrdf/visualize.py

@@ -102,6 +102,7 @@ def visualize_graph(
     rankdir="TB",
     hide_types=False,
     workflow_view=False,
+    sample_view=False,
     size=None,
     layout="dot",
 ):
@@ -120,6 +121,8 @@ def visualize_graph(
         Whether to hide nodes with the "type" attribute. Default is False.
     workflow_view : bool, optional
         Whether to enable the workflow view. Default is False.
+    sample_view : bool, optional
+        Whether to enable the sample view. Default is False.
     size : str, optional
         The size of the graph. Default is None.
     layout : str, optional
@@ -173,6 +176,12 @@ def visualize_graph(
                         fontname=styledict[istype1]["fontname"],
                     )
                     plot = False
+
+        elif sample_view:
+            green_list = ['wasDerivedFrom', 'wasGeneratedBy']
+            if string3 not in green_list:
+                plot = False
+
 
         if hide_types and (string3 == "type"):
             plot = False

atomrdf/workflow/__init__.py

@@ -1 +1 @@
-from atomrdf.workflow.pyiron import inform_graph
+