Mod: few tests + test block

anisotropy/__init__.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from anisotropy.anisotropy import (
+from anisotropy.core import (
     Anisotropy,
     logger
 )
 
-from anisotropy.simple import simple
+from anisotropy.simple import Simple
-from anisotropy.bodyCentered import bodyCentered
+from anisotropy.bodyCentered import BodyCentered
-from anisotropy.faceCentered import faceCentered
+from anisotropy.faceCentered import FaceCentered
+
 

anisotropy/bodyCentered.py

@@ -1,6 +1,6 @@
 from math import pi, sqrt
 
-class simple(object):
+class BodyCentered(object):
     def __init__(self, **kwargs):
 
         self.direction = kwargs.get("direction", [1, 0, 0])
@@ -13,9 +13,9 @@ class simple(object):
 
 
     def build(self):
-        from salomepl import getGeom
+        import salomepl
 
-        geompy = getGeom()
+        geompy = salomepl.geometry.getGeom()
 
         ###
         #   Pore Cell

anisotropy/core.py

@@ -39,9 +39,10 @@ __version__ = "1.1"
 import os
 import toml
 from copy import deepcopy
-from anisotropy.models import db, Structure, Mesh
+from anisotropy.models import db, JOIN, Structure, Mesh, SubMesh, MeshResult
 from anisotropy.utils import struct, deepupdate
 import salomepl
+import openfoam
 
 ###
 #   Environment variables and config
@@ -59,20 +60,22 @@ _defaultConfig = os.path.join(env["ROOT"], "anisotropy/default.toml")
 if os.path.exists(_defaultConfig):
     env.update(toml.load(_defaultConfig))
 
-if os.path.exists(env["CONFIG"]):
+#if os.path.exists(env["CONFIG"]):
-    config = toml.load(env["CONFIG"])
+#    config = toml.load(env["CONFIG"])
 
-    for restricted in ["ROOT", "BUILD", "LOG", "CONFIG"]:
+#    for restricted in ["ROOT", "BUILD", "LOG", "CONFIG"]:
-        if config.get(restricted):
+#        if config.get(restricted):
-            config.pop(restricted)
+#            config.pop(restricted)
 
-    for m, structure in enumerate(config["structures"]):
+    # TODO: not working if custom config empty and etc
-        for n, estructure in enumerate(env["structures"]):
+#    for m, structure in enumerate(config["structures"]):
-            if estructure["name"] == structure["name"]:
+#        for n, estructure in enumerate(env["structures"]):
-                deepupdate(env["structures"][n], config["structures"][m])
+#            if estructure["name"] == structure["name"]:
+#                deepupdate(env["structures"][n], config["structures"][m])
+
+#    config.pop("structures")
+#    deepupdate(env, config)
 
-    config.pop("structures")
-    deepupdate(env, config)
 
 ###
 #   Logger
@@ -109,7 +112,7 @@ class Anisotropy(object):
         self.params = []
 
         #self.evalParameters(env)
-        self.setupDB()
+        #self.setupDB()
 
     @staticmethod
     def version():
@@ -121,8 +124,8 @@ class Anisotropy(object):
         }
 
         try:
-            salomeplVersion = salomepl.version()
+            versions["Salome"] = salomepl.utils.version()
-            openfoamVersion = openfoam.foamVersion()
+            versions["OpenFOAM"] = openfoam.version()
 
         except Exception:
             pass
@@ -131,6 +134,7 @@ class Anisotropy(object):
 
     def evalEnvParameters(self):
         """ 'Uncompress' and eval environment parameters """
+
         from math import sqrt
 
         structures = deepcopy(self.env["structures"])
@@ -211,7 +215,7 @@ class Anisotropy(object):
                     ))
 
 
-    def getParams(structure, direction, theta):
+    def getParams(structure: str, direction: list, theta: float):
         for entry in self.params:
             if entry["name"] == structure and \
                 entry["geometry"]["direction"] == direction and \
@@ -220,7 +224,8 @@ class Anisotropy(object):
 
 
     def setupDB(self):
-        self.db = db.init(self.env["db_path"])
+        self.db = db
+        self.db.init(self.env["db_path"])
 
         if not os.path.exists(self.env["db_path"]):
             self.db.create_tables([
@@ -236,6 +241,7 @@ class Anisotropy(object):
         for entry in self.params:
             query = (Structure
                 .select()
+                .join(Mesh, JOIN.INNER, on = (Mesh.structure_id == Structure.id))
                 .where(
                     Structure.name == entry["name"],
                     Structure.direction == str(entry["geometry"]["direction"]),
@@ -251,7 +257,7 @@ class Anisotropy(object):
 
             m = deepcopy(entry["mesh"])
 
-            sm = deepcopy(entry.get("submesh", {}))
+            sm = deepcopy(entry.get("submesh", []))
 
             mr = deepcopy(entry.get("meshResult", {}))
 
@@ -262,8 +268,8 @@ class Anisotropy(object):
                     m.update(structure_id = stab)
                     mtab = Mesh.create(**m)
 
-                    sm.update(mesh_id = mtab)
+                    for item in sm:
-                    smtab = SubMesh.create(**sm)
+                        smtab = SubMesh.create(**item, mesh_id = mtab)
 
                     mr.update(mesh_id = mtab)
                     mrtab = MeshResult.create(**mr)
@@ -284,13 +290,19 @@ class Anisotropy(object):
                         )
                         .execute())
 
-                    (SubMesh.update(**sm)
+                    for item in sm:
+                        (SubMesh.update(**item)
+                            .where(
+                                SubMesh.mesh_id == query.get().mesh_id,
+                                SubMesh.name == item["name"]
+                            )
+                            .execute())
+
+                    (MeshResult.update(**mr)
                         .where(
-                            Submesh.mesh_id == None # TODO: ???
+                            MeshResult.mesh_id == query.get().mesh_id)
-                        )
                         .execute())
 
-                    # TODO: for MeshResult
 
     @timer
     def updateFromDB(self):
@@ -316,7 +328,7 @@ class Anisotropy(object):
         scriptpath = os.path.join(self.env["ROOT"], "anisotropy/genmesh.py")
         port = 2900
 
-        out, err, returncode = salomepl.runSalome(port, scriptpath, env["ROOT"], name, direction, theta)
+        return salomepl.utils.runSalome(port, scriptpath, env["ROOT"], name, direction, theta)
 
     def computeFlow(self):
         pass
@@ -480,7 +492,6 @@ def computeMesh(case):
 
 
 
-import openfoam
 
 def computeFlow(case):
     ###

anisotropy/default.toml

@@ -56,7 +56,8 @@ faceCentered = true
     # auto # faces: list
     extrusionMethod = "SURF_OFFSET_SMOOTH"
 
-    [structures.submesh.strips]
+    [[structures.submesh]]
+    name = "strips"
     maxSize = 0.5
     minSize = 0.05
 
@@ -124,7 +125,8 @@ faceCentered = true
     # auto # faces: list
     extrusionMethod = "SURF_OFFSET_SMOOTH"
 
-    [structures.submesh.strips]
+    [[structures.submesh]]
+    name = "strips"
     maxSize = 0.5
     minSize = 0.05
 
@@ -192,7 +194,8 @@ faceCentered = true
     # auto # faces: list
     extrusionMethod = "SURF_OFFSET_SMOOTH"
 
-    [structures.submesh.strips]
+    [[structures.submesh]]
+    name = "strips"
     maxSize = 0.5
     minSize = 0.05
 

anisotropy/faceCentered.py

@@ -1,6 +1,6 @@
 from math import pi, sqrt
 
-class faceCentered(object):
+class FaceCentered(object):
     def __init__(self, **kwargs):
 
         self.direction = kwargs.get("direction", [1, 0, 0])
@@ -13,9 +13,9 @@ class faceCentered(object):
 
 
     def build(self):
-        from salomepl import getGeom
+        import salomepl
 
-        geompy = getGeom()
+        geompy = salomepl.geometry.getGeom()
 
         ###
         #   Pore Cell

anisotropy/genmesh.py

@@ -15,6 +15,10 @@ import click
 @click.argument("direction")
 @click.argument("theta", type = click.FLOAT)
 def genmesh(root, name, direction, theta):
+    print(root)
+    print(name)
+    print(direction)
+    print(theta)
     ###
     #   Args
     ##
@@ -37,13 +41,7 @@ def genmesh(root, name, direction, theta):
         faceCentered
     )
 
-    from salomepl.geometry import getGeom
+    import salomepl
-    from salomepl.mesh import (
-        Mesh, 
-        Fineness, 
-        ExtrusionMethod, 
-        defaultParameters
-    )
 
     ###
     #   Model
@@ -71,7 +69,7 @@ def genmesh(root, name, direction, theta):
     ###
     #   Shape
     ##
-    geompy = getGeom()
+    geompy = salomepl.geometry.getGeom()
     structure = locals().get(p["name"])
     shape, groups = structure(**p["geometry"])
 
@@ -104,7 +102,7 @@ def genmesh(root, name, direction, theta):
             faces.append(group)
 
 
-    mesh = Mesh(shape)
+    mesh = salomepl.mesh.Mesh(shape)
     mesh.Tetrahedron(**mp)
 
     if mp["viscousLayers"]:
@@ -112,16 +110,16 @@ def genmesh(root, name, direction, theta):
 
     smp = p["submesh"]
 
-    for name in smp.keys():
+    for submesh in smp:
         for group in groups:
-            if group.GetName() == name:
+            if submesh["name"] == group.GetName():
                 subshape = group
 
-        smp["maxSize"] = meanSize * 1e-1
+                submesh["maxSize"] = meanSize * 1e-1
-        smp["minSize"] = meanSize * 1e-3
+                submesh["minSize"] = meanSize * 1e-3
-        smp["chordalError"] = smp["minSize"] * 1e+1
+                submesh["chordalError"] = submesh["minSize"] * 1e+1
 
-        mesh.Triangle(subshape, **smp)
+                mesh.Triangle(subshape, **submesh)
 
 
     model.updateDB()
@@ -154,3 +152,4 @@ def genmesh(root, name, direction, theta):
 
     salome.salome_close()
 
+genmesh()

anisotropy/models.py

@@ -77,8 +77,27 @@ class Mesh(BaseModel):
     extrusionMethod = TextField(null = True)
 
 
-class SubMesh(Mesh):
+class SubMesh(BaseModel):
     mesh_id = ForeignKeyField(Mesh, backref = "submeshes")
+    name = TextField()
+
+    maxSize = FloatField(null = True) 
+    minSize = FloatField(null = True) 
+
+    fineness = IntegerField(null = True) 
+    growthRate = FloatField(null = True)
+    nbSegPerEdge = FloatField(null = True)
+    nbSegPerRadius = FloatField(null = True)
+    
+    chordalErrorEnabled = BooleanField(null = True)
+    chordalError = FloatField(null = True)
+    
+    secondOrder = BooleanField(null = True)
+    optimize = BooleanField(null = True)
+    quadAllowed = BooleanField(null = True)
+    useSurfaceCurvature = BooleanField(null = True)
+    fuseEdges = BooleanField(null = True)
+    checkChartBoundary = BooleanField(null = True)
 
 
 class MeshResult(BaseModel):

anisotropy/simple.py

@@ -1,6 +1,6 @@
 from math import pi, sqrt
 
-class simple(object):
+class Simple(object):
     def __init__(self, **kwargs):
 
         self.direction = kwargs.get("direction", [1, 0, 0])
@@ -13,9 +13,9 @@ class simple(object):
 
 
     def build(self):
-        from salomepl import getGeom
+        import salomepl
 
-        geompy = getGeom()
+        geompy = salomepl.geometry.getGeom()
 
         ###
         #   Pore Cell

openfoam/__init__.py

@@ -4,7 +4,7 @@ from .meshManipulation import createPatch, transformPoints, checkMesh, renumberM
 from .miscellaneous import foamDictionary
 from .parallelProcessing import decomposePar
 from .solvers import potentialFoam, simpleFoam
-from .utils import foamVersion, foamClean, uniform
+from .utils import version, foamClean, uniform
 
 __all__ = [
     # meshConversion
@@ -27,7 +27,7 @@ __all__ = [
     "simpleFoam",
 
     # utils
-    "foamVersion",
+    "version",
     "foamClean",
     "uniform"
 ]

openfoam/utils.py

@@ -1,8 +1,8 @@
 import os
 import shutil
 
-def foamVersion() -> str:
+def version() -> str:
-    return "OpenFOAM-{}".format(os.environ["WM_PROJECT_VERSION"])
+    return os.environ["WM_PROJECT_VERSION"]
 
 
 def foamClean(case: str = None):

salomepl/__init__.py

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from salomepl import (
+    geometry,
+    mesh,
+    utils
+)

salomepl/geometry.py

@@ -1,7 +1,15 @@
-import GEOM
+try:
-from salome.geom import geomBuilder
+    import GEOM
+    from salome.geom import geomBuilder
 
-geompy = geomBuilder.New()
+except ImportError:
+    print("[Warning] Trying to get SALOME geometry modules outside SALOME environment. Modules won't be imported.")
+
+if globals().get("geomBuilder"):
+    geompy = geomBuilder.New()
+
+else:
+    geompy = None
 
 def getGeom():
     return geompy

salomepl/mesh.py

@@ -1,6 +1,15 @@
-import SMESH
+try:
-from salome.smesh import smeshBuilder
+    import SMESH
-smesh = smeshBuilder.New()
+    from salome.smesh import smeshBuilder
+
+except ImportError:
+    print("[Warning] Trying to get SALOME mesh modules outside SALOME environment. Modules won't be imported.")
+
+if globals().get("smeshBuilder"):
+    smesh = smeshBuilder.New()
+
+else:
+    smesh = None
 
 import enum
 
@@ -13,9 +22,10 @@ class Fineness(enum.Enum):
     Custom = 5
 
 class ExtrusionMethod(object):
-    SURF_OFFSET_SMOOTH = smeshBuilder.SURF_OFFSET_SMOOTH
+    pass
-    FACE_OFFSET = smeshBuilder.FACE_OFFSET
+    #SURF_OFFSET_SMOOTH = smeshBuilder.SURF_OFFSET_SMOOTH
-    NODE_OFFSET = smeshBuilder.NODE_OFFSET
+    #FACE_OFFSET = smeshBuilder.FACE_OFFSET
+    #NODE_OFFSET = smeshBuilder.NODE_OFFSET
 
 def getSmesh():
     return smesh
@@ -108,7 +118,7 @@ class Mesh(object):
             stretchFactor = 0,
             faces = [], 
             isFacesToIgnore = True, 
-            extrMethod = ExtrusionMethod.SURF_OFFSET_SMOOTH, 
+            extrMethod = None,#ExtrusionMethod.SURF_OFFSET_SMOOTH, 
             **kwargs
         ):
 

salomepl/utils.py

@@ -32,7 +32,7 @@ def version() -> str:
 def runSalome(port: int, scriptpath: str, root: str, logpath: str = None, *args) -> int:
 
     if os.environ.get("SALOME_PATH"):
-        cmd = os.path.join(os.environ["SALOME_PATH"], salome)
+        cmd = [ os.path.join(os.environ["SALOME_PATH"], "salome") ]
 
     else:
         raise(SalomeNotFound("Can't find salome executable."))
@@ -51,8 +51,10 @@ def runSalome(port: int, scriptpath: str, root: str, logpath: str = None, *args)
         fmtargs
     ]
 
+    cmd.extend(cmdargs)
+
     with subprocess.Popen(
-        [ cmd, cmdargs ],
+        cmd,
         stdout = subprocess.PIPE,
         stderr = subprocess.PIPE
     ) as proc, open(logpath, "wb") as logfile:
@@ -61,7 +63,7 @@ def runSalome(port: int, scriptpath: str, root: str, logpath: str = None, *args)
         for line in proc.stdout:
             logfile.write(line)
 
-        out, err = p.communicate()
+        out, err = proc.communicate()
 
         if err:
             logfile.write(err)

simple

@@ -0,0 +1,34 @@
+runSalome running on localhost
+Check if port can be used: 2900 - KO: port is busy
+Searching for a free port for naming service: 2810 - OK
+Searching Naming Service  + found in 0.1 seconds 
+Searching /Registry in Naming Service  + found in 0.5 seconds 
+Searching /Kernel/ModulCatalog in Naming Service  + found in 0.5 seconds 
+RunStudy
+Searching /Study in Naming Service  + found in 0.5 seconds 
+Searching /Containers/elnafo/FactoryServer in Naming Service  ++[1,
+0,
+0]
+0.01
+ found in 1.0 seconds 
+Start SALOME, elapsed time :   2.7 seconds
+th. 139821375270848 - Trace /volatile/salome/jenkins/workspace/Salome_master_CO7_MPI/SALOME-9.7.0-MPI-CO7/SOURCES/KERNEL/src/ModuleCatalog/SALOME_ModuleCatalog_Server.cxx [98] : Module Catalog Server: Naming Service was found
+Warning, no type found for resource "localhost", using default value "single_machine"
+Traceback (most recent call last):
+  File "/home/nafaryus/.vault/projects/anisotropy/anisotropy/genmesh.py", line 155, in <module>
+    genmesh()
+  File "/home/nafaryus/.vault/programs/SALOME/SALOME-9.7.0-MPI/BINARIES-CO7/Python/lib/python3.6/site-packages/click/core.py", line 722, in __call__
+    return self.main(*args, **kwargs)
+  File "/home/nafaryus/.vault/programs/SALOME/SALOME-9.7.0-MPI/BINARIES-CO7/Python/lib/python3.6/site-packages/click/core.py", line 697, in main
+    rv = self.invoke(ctx)
+  File "/home/nafaryus/.vault/programs/SALOME/SALOME-9.7.0-MPI/BINARIES-CO7/Python/lib/python3.6/site-packages/click/core.py", line 895, in invoke
+    return ctx.invoke(self.callback, **ctx.params)
+  File "/home/nafaryus/.vault/programs/SALOME/SALOME-9.7.0-MPI/BINARIES-CO7/Python/lib/python3.6/site-packages/click/core.py", line 535, in invoke
+    return callback(*args, **kwargs)
+  File "/home/nafaryus/.vault/projects/anisotropy/anisotropy/genmesh.py", line 25, in genmesh
+    direction = list(map(lambda num: float(num), direction[1:-1].split(",")))
+  File "/home/nafaryus/.vault/projects/anisotropy/anisotropy/genmesh.py", line 25, in <lambda>
+    direction = list(map(lambda num: float(num), direction[1:-1].split(",")))
+ValueError: could not convert string to float: 
+ERROR:salomeContext:SystemExit 1 in method _runAppli.
+th. 140195594066816 - Trace /volatile/salome/jenkins/workspace/Salome_master_CO7_MPI/SALOME-9.7.0-MPI-CO7/SOURCES/KERNEL/src/NamingService/SALOME_NamingService.cxx [1192] : Destroy_Name(): CORBA::SystemException: unable to contact the naming service

tests/test_anisotropy.py

@@ -0,0 +1,17 @@
+import os
+
+class TestAnisotropy:
+    def test_import(self):
+        import anisotropy
+
+    def test_db(self):
+        import anisotropy
+
+        a = anisotropy.Anisotropy()
+        a.setupDB()
+        a.evalEnvParameters()
+        a.updateDB()
+
+        if os.path.exists("build/anisotropy.db"):
+            os.remove("build/anisotropy.db")
+