New: cli command 'query'

Remove: unknown trash
Mod: database micro migration

anisotropy/config/default.toml

@@ -78,7 +78,7 @@ faceCentered = true
     fuseEdges = true
     checkChartBoundary = false
 
-    [structures.flowapprox]
+    [structures.flowapproximation]
     transportProperties.nu = 1e-6
 
     pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
@@ -167,7 +167,7 @@ faceCentered = true
     fuseEdges = true
     checkChartBoundary = false
 
-    [structures.flowapprox]
+    [structures.flowapproximation]
     transportProperties.nu = 1e-6
 
     pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
@@ -256,7 +256,7 @@ faceCentered = true
     fuseEdges = true
     checkChartBoundary = false
 
-    [structures.flowapprox]
+    [structures.flowapproximation]
     transportProperties.nu = 1e-6
 
     pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }

anisotropy/core/cli.py

@@ -4,7 +4,7 @@
 
 import click
 import ast
-import os, shutil
+import os, sys, shutil
 import logging
 
 class LiteralOption(click.Option):
@@ -192,7 +192,7 @@ def compute(stage, nprocs, force, update, params, path):
         logger.info(f"Stage: { stage }")
 
         if stage == "all" or stage == "mesh":
-            if not case.params.get("meshresult", {}).get("status") == "Done" or force:
+            if not case.params.get("meshresult", {}).get("meshStatus") == "Done" or force:
                 (out, err, returncode), elapsed = timer(case.computeMesh)(path)
 
                 if out: logger.info(out)
@@ -201,7 +201,7 @@ def compute(stage, nprocs, force, update, params, path):
                 case.load(type, direction, theta)
 
                 if case.params.get("meshresult"):
-                    case.params["meshresult"]["calculationTime"] = elapsed
+                    case.params["meshresult"]["meshCalculationTime"] = elapsed
                     case.update()
 
                 if returncode:
@@ -212,7 +212,7 @@ def compute(stage, nprocs, force, update, params, path):
                 logger.info("Mesh exists. Skipping ...")
 
         if stage == "all" or stage == "flow":
-            if not case.params.get("flowresult", {}).get("status") == "Done" or force:
+            if not case.params.get("flowresult", {}).get("flowStatus") == "Done" or force:
                 (out, err, returncode), elapsed = timer(case.computeFlow)(path)
 
                 if out: logger.info(out)
@@ -221,7 +221,7 @@ def compute(stage, nprocs, force, update, params, path):
                 case.load(type, direction, theta)
 
                 if case.params.get("flowresult"):
-                    case.params["flowresult"]["calculationTime"] = elapsed
+                    case.params["flowresult"]["flowCalculationTime"] = elapsed
                     case.update()
             
                 if returncode:
@@ -281,7 +281,7 @@ def kill(path, pidfile):
     SalomeManager().killall()
 
 @anisotropy.command(
-    help = "! Not a user command"
+    help = "! Internal command"
 )
 @click.argument("root")
 @click.argument("type")
@@ -392,9 +392,118 @@ def postprocessing(path, plot):
             plt.show()
 
 
+@anisotropy.command()
+@click.option(
+    "-p", "--param", "params", 
+    metavar = "key=value", 
+    multiple = True, 
+    cls = KeyValueOption,
+    help = "Select by control parameter (type, direction, theta)"
+)
+@click.option(
+    "-P", "--path", "path",
+    default = os.getcwd(),
+    help = "Specify directory to use (instead of cwd)"
+)
+@click.option(
+    "--list", "printlist",
+    is_flag = True,
+    help = "Print a list of avaliable fields."
+)
+@click.option(
+    "--export",
+    metavar = "PATH",
+    help = "Export query result to CSV."
+)
+@click.argument(
+    "fields",
+    required = False
+)
+def query(params, path, printlist, export, fields):
+    from anisotropy import env
+    from anisotropy.core.database import Database, Structure
+    from pandas import DataFrame
+
+    env.update(
+        LOG = os.path.join(path, "logs"),
+        BUILD = os.path.join(path, "build"),
+        CONFIG = os.path.join(path, "anisotropy.toml"),
+        db_path = path
+    )
+
+    args = dict()
+
+    for param in params:
+        args.update(param)
+
+    fields = [ field.strip() for field in fields.split(",") ] if fields else []
+
+    ###
+    db = Database(env["db_name"], env["db_path"]) 
+    db.setup()
+
+    searchargs = []
+
+    if args.get("type"):
+        searchargs.append(Structure.type == args["type"])
+
+    if args.get("direction"):
+        searchargs.append(Structure.direction == str(args["direction"]))
+
+    if args.get("theta"):
+        searchargs.append(Structure.theta == args["theta"])
+
+    result = db.search(searchargs)
+    result.sort(key = lambda src: f"{ src['type'] }{ src['direction'] }{ src['theta'] }")
+
+    df = DataFrame(result)
+    df_keys = [ key for key in df.keys() ]
+    
+    if printlist:
+        click.echo("Avaliable fields for query:")
+        click.echo("\t{}".format("\n\t".join(df_keys)))
+
+        return
+
+    if not result:
+        click.echo("Empty result.")
+
+        return
+
+    
+    if fields:
+        for field in fields:
+            if field not in df_keys:
+                click.echo(f"Unknown field '{ field }'. Try to use '--list' flag to see all avaliable fields.")
+
+                return
+        
+        df = df[fields]
+
+    if export:
+        df.to_csv(export, sep = ";")
+
+    else:
+        click.echo(df.to_string())
+
     
 ###
 #   CLI entry
 ##
 if __name__ == "__main__":
-    anisotropy()
+    try:
+        anisotropy()
+
+    except KeyboardInterrupt:
+        click.echo("Interrupted!")
+
+    finally:
+        from anisotropy.salomepl.utils import SalomeManager
+        click.echo("Exiting ...")
+
+        if os.path.exists("anisotropy.pid"):
+            os.remove("anisotropy.pid")
+
+        SalomeManager().killall()
+
+        sys.exit(0)

anisotropy/core/database.py

@@ -29,8 +29,8 @@ def tryUntilDone(func):
                 ret = func(*args, **kwargs)
                 done = True
 
-            except OperationalError:
+            except OperationalError as e:
-                pass
+                logger.error(e)
 
         return ret
 
@@ -110,10 +110,10 @@ class Database(object):
                 if flowQuery.exists():
                     params["flow"] = flowQuery.dicts().get()
 
-                    flowapproxQuery = flowQuery.get().flowapprox
+                    flowapproximationQuery = flowQuery.get().flowapproximations
 
-                    if flowapproxQuery.exists():
+                    if flowapproximationQuery.exists():
-                        params["flowapprox"] = flowapproxQuery.dicts().get()
+                        params["flowapproximation"] = flowapproximationQuery.dicts().get()
 
                     flowresultsQuery = flowQuery.get().flowresults
 
@@ -173,22 +173,73 @@ class Database(object):
             )
         )
         
-        structureID = tryUntilDone(self._updateStructure)(params["structure"], query)
+        structureID = tryUntilDone(self._updateStructure)(params.get("structure", {}), query)
         
-        meshID = tryUntilDone(self._updateMesh)(params["mesh"], query, structureID)
+        meshID = tryUntilDone(self._updateMesh)(params.get("mesh", {}), query, structureID)
 
         for submeshParams in params.get("submesh", []):
             tryUntilDone(self._updateSubMesh)(submeshParams, query, meshID)
 
         tryUntilDone(self._updateMeshResult)(params.get("meshresult", {}), query, meshID)
 
-        flowID = tryUntilDone(self._updateFlow)(params["flow"], query, structureID)
+        flowID = tryUntilDone(self._updateFlow)(params.get("flow", {}), query, structureID)
 
-        tryUntilDone(self._updateFlowApproximation)(params.get("flowapprox", {}), query, flowID)
+        tryUntilDone(self._updateFlowApproximation)(params.get("flowapproximation", {}), query, flowID)
 
         tryUntilDone(self._updateFlowResult)(params.get("flowresult", {}), query, flowID)
 
 
+    def search(self, args: list):
+        result = {}
+        query = (
+            Structure
+            .select(Structure, Mesh, SubMesh, MeshResult, Flow, FlowApproximation, FlowResult)
+            .join(
+                Mesh,
+                JOIN.INNER,
+                on = (Mesh.structure_id == Structure.structure_id)
+            )
+            .join(
+                SubMesh,
+                JOIN.INNER,
+                on = (SubMesh.mesh_id == Mesh.mesh_id)
+            )
+            .join(
+                MeshResult,
+                JOIN.INNER,
+                on = (MeshResult.mesh_id == Mesh.mesh_id)
+            )
+            .join(
+                Flow,
+                JOIN.INNER,
+                on = (Flow.structure_id == Structure.structure_id)
+            )
+            .join(
+                FlowApproximation,
+                JOIN.INNER,
+                on = (FlowApproximation.flow_id == Flow.flow_id)
+            )
+            .join(
+                FlowResult,
+                JOIN.INNER,
+                on = (FlowResult.flow_id == Flow.flow_id)
+            )
+        )
+
+        for arg in args:
+            query = query.where(arg)
+
+
+        with self.__db.atomic():
+            if not self.isempty():
+                result = [ entry for entry in query.dicts() ] 
+
+            else:
+                logger.error("Missed Structure table")
+
+        return result
+
+
     def _updateStructure(self, src: dict, queryMain) -> int:
         raw = deepcopy(src)
 

anisotropy/core/main.py

@@ -101,7 +101,6 @@ class Anisotropy(object):
         buf = toml.load(config).get("structures")
         paramsAll = []
 
-        # TODO: custom config and merge
 
         for entry in buf:
             #   Shortcuts
@@ -133,12 +132,12 @@ class Anisotropy(object):
                         "mesh": mesh,
                         "submesh": deepcopy(entry["submesh"]),
                         "flow": deepcopy(entry["flow"]),
-                        "flowapprox": deepcopy(entry["flowapprox"])
+                        "flowapproximation": deepcopy(entry["flowapproximation"])
                     }
 
                     # For `type = fixedValue` only
-                    _velocity = entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"]
+                    _velocity = entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"]
-                    entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"] = [ 
+                    entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"] = [ 
                         val * _velocity for val in entryNew["structure"]["direction"] 
                     ]
 
@@ -380,7 +379,7 @@ class Anisotropy(object):
         foamCase = [ "0", "constant", "system" ]
 
         flow = self.params["flow"]
-        flowapprox = self.params["flowapprox"]
+        flowapproximation = self.params["flowapproximation"]
 
         # ISSUE: ideasUnvToFoam cannot import mesh with '-case' flag so 'os.chdir' for that
         casePath = self.getCasePath()
@@ -447,8 +446,8 @@ class Anisotropy(object):
 
         openfoam.renumberMesh()
 
-        pressureBF = flowapprox["pressure"]["boundaryField"]
+        pressureBF = flowapproximation["pressure"]["boundaryField"]
-        velocityBF = flowapprox["velocity"]["boundaryField"]
+        velocityBF = flowapproximation["velocity"]["boundaryField"]
 
         openfoam.foamDictionary(
             "0/p", 

anisotropy/core/models.py

@@ -138,8 +138,9 @@ class MeshResult(BaseModel):
     prisms = IntegerField(null = True)
     pyramids = IntegerField(null = True)
 
-    status = TextField(null = True, default = "Idle")
+    meshStatus = TextField(null = True, default = "Idle")
-    calculationTime = TimeField(null = True)
+    meshCalculationTime = TimeField(null = True)
+
 
 class Flow(BaseModel):
     flow_id = AutoField()
@@ -153,17 +154,20 @@ class Flow(BaseModel):
    
 class FlowApproximation(BaseModel):
     flow_approximation_id = AutoField()
-    flow_id = ForeignKeyField(Flow, backref = "flowapprox")
+    flow_id = ForeignKeyField(Flow, backref = "flowapproximations")
 
     pressure = JSONField(null = True)
     velocity = JSONField(null = True)
     transportProperties = JSONField(null = True)
 
+
 class FlowResult(BaseModel):
     flowresult_id = AutoField()
     flow_id = ForeignKeyField(Flow, backref = "flowresults")
 
     flowRate = FloatField(null = True)
+    porosity = FloatField(null = True)
+    permeability = FloatField(null = True)
 
-    status = TextField(null = True, default = "Idle")
+    flowStatus = TextField(null = True, default = "Idle")
-    calculationTime = TimeField(null = True)
+    flowCalculationTime = TimeField(null = True)

docs/source/notes/database.rst

@@ -5,3 +5,21 @@ Current anisotropy database hierarchy:
 
 .. figure:: ../static/er-diagram.png
     :align: center
+
+peewee migration
+----------------
+
+Example of Sqlite database migration and etc:
+
+.. code-block:: python
+
+    from playhouse.migrate import SqliteMigrator, migrate
+    from peewee import SqliteDatabase, FloatField
+
+    db = SqliteDatabase("anisotropy.db")
+    migrator = SqliteDatabase(db)
+
+    migrate(
+        migrator.rename_column("MeshResult", "status", "meshStatus"),
+        migrator.add_column("FlowResult", "porosity", FloatField(null = True))
+    )