Merge pull request #2 from simphony/v2.4.0-dev

v2.4.0 dev

.gitignore

@@ -2,6 +2,7 @@ __pycache__/
 build/
 dist/
 *~*
+*.egg-info
 .mypy_cache/
 coverage.xml
 .coverage

LICENSE

@@ -0,0 +1,13 @@
+BSD 3-Clause 
+Copyright 2020 SimPhoNy OSP-core developers
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,5 +1,5 @@
 # Wrapper Development
-*Version*: 2.3.0
+*Version*: 2.4.0
 
 The aim of this project is simplify as much as possible the development of a new Wrapper for __SimPhoNy v3__.
 For this, the general folder and file structure of a wrapper is simulated here, and notes on what to do are provided.
@@ -14,13 +14,16 @@ Material Informatics team, Fraunhofer IWM.
 
 ## Compatibility
 
-The following table describes the version compatibility between the [OSP core](https://gitlab.cc-asp.fraunhofer.de/simphony/osp-core) package and this project.
+The following table describes the version compatibility between the [OSP core](https://github.com/simphony/osp-core/) package and this project.
 
 | __Wrapper development__ | __OSP core__ |
 |:-----------------------:|:------------:|
+|          2.4.0          |  3.5.0-beta  |
 |          2.3.0          |  3.3.5-beta  |
 |          2.2.0          |  3.3.0-beta  |
 |          2.1.0          |  3.2.x-beta  |
 |          2.0.0          |  3.1.x-beta  |
 
-The releases of OSP core are available [here](https://github.com/simphony/osp-core/releases).
+The releases of OSP core are available [here](https://github.com/simphony/osp-core/releases).
+
+In `osp/wrappers/simple_simulation` you will find a minimalistic wrapper with the required elements implemented.

examples/simple_example.py

@@ -0,0 +1,28 @@
+# This code runs on the wrapper under ../osp/wrappers/simple_simulation
+
+from osp.core.namespaces import simple_ontology
+from osp.wrappers.simple_simulation import SimpleSimulationSession
+from osp.core.utils import pretty_print
+import numpy as np
+
+m = simple_ontology.Material()
+for i in range(3):
+    a = m.add(simple_ontology.Atom())
+    a.add(
+        simple_ontology.Position(value=[i, i, i], unit="m"),
+        simple_ontology.Velocity(value=np.random.random(3), unit="m/s")
+    )
+
+# Run a simulation
+with SimpleSimulationSession() as session:
+    w = simple_ontology.Wrapper(session=session)
+    m = w.add(m)
+    w.session.run()
+
+    pretty_print(m)
+
+    for atom in m.get(rel=simple_ontology.hasPart):
+        atom.get(oclass=simple_ontology.Velocity)[0].value = [0, 0, 0]
+    w.session.run()
+
+    pretty_print(m)

osp/wrappers/simple_simulation/__init__.py

@@ -0,0 +1,2 @@
+from osp.wrappers.simple_simulation.simulation_engine import SimulationEngine
+from osp.wrappers.simple_simulation.simple_simulation_session import SimpleSimulationSession

osp/wrappers/simple_simulation/simple_ontology.ontology.yml

@@ -0,0 +1,80 @@
+---
+version: 0.0.2
+author: Me
+namespace: simple_ontology
+
+ontology:
+
+  Atom:
+    subclass_of:
+    - cuba.Class
+    - simple_ontology.hasPart:
+        cardinality: some
+        exclusive: false
+        range: simple_ontology.Position
+    - simple_ontology.hasPart:
+        cardinality: some
+        exclusive: false
+        range: simple_ontology.Velocity
+
+  Material:
+    subclass_of:
+    - cuba.Class
+    - simple_ontology.hasPart:
+        cardinality: some
+        exclusive: true
+        range: simple_ontology.Atom
+
+  PhysicalQuantity:
+    attributes:
+      simple_ontology.unit: null
+      simple_ontology.value: null
+    subclass_of:
+    - cuba.Class
+
+  Position:
+    subclass_of:
+    - simple_ontology.PhysicalQuantity
+
+  Velocity:
+    subclass_of:
+    - simple_ontology.PhysicalQuantity
+
+  Wrapper:
+    subclass_of:
+    - cuba.Wrapper
+    - simple_ontology.hasPart:
+        cardinality: some
+        exclusive: true
+        range: simple_ontology.Material
+
+  encloses:
+    inverse: simple_ontology.isEnclosedBy
+    subclass_of:
+    - cuba.activeRelationship
+
+  hasPart:
+    default_rel: true
+    inverse: simple_ontology.isPartOf
+    subclass_of:
+    - simple_ontology.encloses
+
+  isEnclosedBy:
+    inverse: simple_ontology.encloses
+    subclass_of:
+    - cuba.passiveRelationship
+
+  isPartOf:
+    inverse: simple_ontology.hasPart
+    subclass_of:
+    - simple_ontology.isEnclosedBy
+
+  unit:
+    datatype: STRING
+    subclass_of:
+    - cuba.attribute
+
+  value:
+    datatype: VECTOR:3
+    subclass_of:
+    - cuba.attribute

osp/wrappers/simple_simulation/simple_simulation_session.py

@@ -0,0 +1,75 @@
+from osp.core.session import SimWrapperSession
+from osp.wrappers.simple_simulation import SimulationEngine
+from osp.core.namespaces import simple_ontology 
+
+
+class SimpleSimulationSession(SimWrapperSession):
+    """
+    Session class for some engine.
+    """
+
+    def __init__(self, engine=None, **kwargs):
+        super().__init__(engine or SimulationEngine(), **kwargs)
+        self.mapper = dict()  # maps uuid to index in the backend
+
+    def __str__(self):
+        return "Simple sample Wrapper Session"
+
+    # OVERRIDE
+    def _apply_added(self, root_obj, buffer):
+        """Adds the added cuds to the engine."""
+        for obj in buffer.values():
+            if obj.is_a(simple_ontology.Atom):
+                self.mapper[obj.uid] = len(self.mapper)
+                pos = obj.get(oclass=simple_ontology.Position)[0].value
+                vel = obj.get(oclass=simple_ontology.Velocity)[0].value
+                self._engine.add_atom(pos, vel)
+
+    # OVERRIDE
+    def _apply_updated(self, root_obj, buffer):
+        """Updates the updated cuds in the engine."""
+        for obj in buffer.values():
+
+            # case 1: we change the velocity
+            if obj.is_a(simple_ontology.Velocity):
+                atom = obj.get(rel=simple_ontology.isPartOf)[0]
+                idx = self.mapper[atom.uid]
+                self._engine.update_velocity(idx, obj.value)
+
+            # case 2: we change the position
+            elif obj.is_a(simple_ontology.Position):
+                atom = obj.get(rel=simple_ontology.isPartOf)[0]
+                idx = self.mapper[atom.uid]
+                self._engine.update_position(idx, obj.value)
+
+    # OVERRIDE
+    def _apply_deleted(self, root_obj, buffer):
+        """Deletes the deleted cuds from the engine."""
+
+    # OVERRIDE
+    def _load_from_backend(self, uids, expired=None):
+        """Loads the cuds object from the simulation engine"""
+        for uid in uids:
+            if uid in self._registry:
+                obj = self._registry.get(uid)
+
+                # check whether user wants to load a position
+                if obj.is_a(simple_ontology.Position):
+                    atom = obj.get(rel=simple_ontology.isPartOf)[0]
+                    idx = self.mapper[atom.uid]
+                    pos = self._engine.get_position(idx)
+                    obj.value = pos
+
+                # check whether user wants to load a velocity
+                elif obj.is_a(simple_ontology.Velocity):
+                    atom = obj.get(rel=simple_ontology.isPartOf)[0]
+                    idx = self.mapper[atom.uid]
+                    vel = self._engine.get_velocity(idx)
+                    obj.value = vel
+
+                yield obj
+
+    # OVERRIDE
+    def _run(self, root_cuds_object):
+        """Call the run command of the engine."""
+        self._engine.run()

osp/wrappers/simple_simulation/simulation_engine.py

@@ -0,0 +1,82 @@
+# This file contains simple code to emulate communication with an engine.
+# It acts like a dummy syntactic layer.
+
+class Atom():
+
+    def __init__(self, position, velocity):
+        self.position = position
+        self.velocity = velocity
+
+
+class SimulationEngine:
+    """
+    Simple engine sample code.
+    """
+
+    def __init__(self):
+        self.atoms = list()
+        print("Engine instantiated!")
+
+    def __str__(self):
+        return "Some Engine Connection"
+
+    def run(self, timesteps=1):
+        """Call the run command of the engine."""
+        print("Now the engine is running")
+        for atom in self.atoms:
+            atom.position += atom.velocity * timesteps
+
+    def add_atom(self, position, velocity):
+        """Add an atom to the engine.
+
+        Args:
+            position (array): A 3D array for the position of the atom.
+            velocity (array): A 3D array for the velocity of the atom.
+        """
+        print("Add atom %s with position %s and velocity %s"
+              % (len(self.atoms), position, velocity))
+        self.atoms.append(Atom(position, velocity))
+
+    def update_position(self, idx, position):
+        """Update the position of the atom
+
+        Args:
+            idx (int): The index of the atom to update
+            position (array): The new position.
+        """
+        print("Update atom %s. Setting position to %s"
+              % (idx, position))
+        self.atoms[idx].position = position
+
+    def update_velocity(self, idx, velocity):
+        """Update the velocity of an atom.
+
+        Args:
+            idx (int): The index of the atom
+            velocity (array): The new velocity.
+        """
+        print("Update atom %s. Setting velocity to %s"
+              % (idx, velocity))
+        self.atoms[idx].velocity = velocity
+
+    def get_velocity(self, idx):
+        """Get the velocity of an atom.
+
+        Args:
+            idx (int): The index of the atom.
+
+        Returns:
+            array: The velocity of the atom.
+        """
+        return self.atoms[idx].velocity
+
+    def get_position(self, idx):
+        """Get the position of the atom.
+
+        Args:
+            idx (int): The index of the atom.
+
+        Returns:
+            array: The position of the atom.
+        """
+        return self.atoms[idx].position

osp/wrappers/some_database_session.py

@@ -1,12 +1,4 @@
-# Copyright (c) 2014-2019, Adham Hashibon, Materials Informatics Team,
-# Fraunhofer IWM.
-# All rights reserved.
-# Redistribution and use are limited to the scope agreed with the end user.
-# No parts of this software may be used outside of this context.
-# No redistribution is allowed without explicit written permission.
-
 # TODO: Import the python connection to the DB
-
 from osp.core.session import DbWrapperSession
 
 
@@ -81,11 +73,7 @@ def _load_first_level(self):
         # that are direct neighbors of the wrapper
         pass
 
+    # OVERRIDE
     def _load_from_backend(self, uids, expired=None):
         # TODO load cuds objects from the backend
-        print("WARNING: please override _load_from_backend method of your session")
-        for uid in uids:
-            if uid in self._registry:
-                yield self._registry[uid]
-            else:
-                yield None
+        pass

osp/wrappers/some_simulation_session.py

@@ -1,5 +1,3 @@
-# Maybe some copyright stuff goes here
-
 # TODO: Import the python connection to the engine
 
 from osp.core.session import SimWrapperSession
@@ -26,7 +24,6 @@ def _run(self, root_cuds_object):
     # OVERRIDE
     def _load_from_backend(self, uids, expired=None):
         """Loads the cuds object from the simulation engine"""
-        print("WARNING: please override _load_from_backend method of your session")
         for uid in uids:
             if uid in self._registry:
                 yield self._registry[uid]

osp/wrappers/some_sql_database_session.py

@@ -1,10 +1,3 @@
-# Copyright (c) 2014-2019, Adham Hashibon, Materials Informatics Team,
-# Fraunhofer IWM.
-# All rights reserved.
-# Redistribution and use are limited to the scope agreed with the end user.
-# No parts of this software may be used outside of this context.
-# No redistribution is allowed without explicit written permission.
-
 # TODO: Import the python connection to the DB
 
 from osp.core.session import SqlWrapperSession

packageinfo.py

@@ -1,5 +1,5 @@
 NAME = "simphony_wrapper_for_something"
 VERSION = "0.0.1"
 # These are used for the compatibility in the Docker and CI images
-OSP_CORE_MIN = "3.3.5"
-OSP_CORE_MAX = "3.4.0"
+OSP_CORE_MIN = "3.5.0"
+OSP_CORE_MAX = "3.6.0"