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create MongoDB with DMS (data management system) and dot-notation #11

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eudoxos opened this issue Jul 27, 2022 · 2 comments
Open

create MongoDB with DMS (data management system) and dot-notation #11

eudoxos opened this issue Jul 27, 2022 · 2 comments

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@eudoxos
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eudoxos commented Jul 27, 2022 •
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Table Beam {
  id int [unique]
  cs CrossSection
  length double
  height double
  density double
  bc_0 boolean[3]
  bc_l boolean[3]
}

Table CrossSection {
  id int [unique]
  beamId int
  rve ConcreteRVE
  rvePositions double[npoints]
  
}

Table ConcreteRVE {
  id int [unique]
  ct CTScan
  origin position
  size double
  //cs CrossSection // cs to which rve belongs to
  //z double // position in a stack
  vectorizedMicrostructure list_of_particle_gometries
  discretizedMicrostructure mesh
  particleStatistics TBD
  nmat int
  materials int[nmat]
}

Table CTScan {
  id int [unique]
  image varbinary
}

// Creating references
// You can also define relaionship separately
// > many-to-one; < one-to-many; - one-to-one
Ref: ConcreteRVE.ct  > CTScan.id
Ref: CrossSection.beamId - Beam.id
Ref: CrossSection.rve < ConcreteRVE.id

Table BeamState {
  id int [unique]
  beam Beam
  npointz int // number of rve per height
  csState CrossSectionState[npointsz]
  w double(nsteps, npos)
}

Ref: BeamState.beam < Beam.id
Ref: BeamState.csState - CrossSectionState.id

Table CrossSectionState {
  id int [unique]
  cs id
  rveStates ConcreteRVEState[npoints]
  BendingMoment double[t]
  kappa double[t]
  eps_axial double[t]
}
 
Ref: CrossSectionState.cs < CrossSection.id

Table ConcreteRVEState {
  id int [unique] 
  rve ConcreteRVE
  sigmaHom double[t]
  epsHom double[t]
  Stiffness double[3t]
  eps0Hom [t]
}

Ref: ConcreteRVEState.rve < ConcreteRVE.id
Ref: CrossSectionState.rveStates < ConcreteRVEState.id

Table MaterialRecord {
  id int [unique]
  name varcharacter
  type mattype
  props dict
}

Ref: ConcreteRVE.materials < MaterialRecord.id
@eudoxos eudoxos mentioned this issue Aug 2, 2022
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@eudoxos
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eudoxos commented Aug 2, 2022 •
edited
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For the record, attaching MongoDB dump with these collections
DMS00-dump.zip
. Follows an example on traversing the structure via AST.

# connect to Mongo and open the top-level database
from pymongo import MongoClient
client = MongoClient('mongodb://localhost:27017/')['DMS00']
from rich.pretty import pprint
import pymongo
# maps Collection.attribute to another Collection in the same DB (lookup by "id")
structs={
    'Beam.cs':'CrossSection',
    'CrossSection.rve':'ConcreteRVE',
    'ConcreteRVE.ct':'CTScan',
    'ConcreteRVE.materials':'MaterialRecord',
    'BeamState.beam':'Beam',
    'BeamState.csState':'CrossSectionState',
    'CrossSectionState.rveStates':'ConcreteRVEState',
    'CrossSectionState.cs':'CrossSection',
    'ConcreteRVEState.rve':'ConcreteRVE'
}
import typing
import dataclasses
@dataclasses.dataclass
class DotNode:
    what: str
    param: str
    value: typing.Any

import ast
class MupifObjectTraversal(ast.NodeVisitor):
    def __init__(self,db,expr):
        self.tree=ast.parse(expr,filename='<mupif-expr>')
        self.seq=[]
        self.val=None
        self.db=self.curr=db
    def __call__(self): 
        self.generic_visit(self.tree)
        return self.seq
    def visit(self,node):
        if isinstance(node,ast.Load): return # ignored
        allowed=[ast.Expr,ast.Attribute,ast.Name,ast.Subscript,ast.Load,ast.Constant]
        if node.__class__ not in allowed: raise SyntaxError(f'Node {node.__class__.__name__} not allowed (only {",".join([c.__name__ for c in allowed])} are)')
        return super().visit(node)
    def visit_Subscript(self,node):
        'bracketed subscript'
        self.generic_visit(node)
        assert isinstance(self.curr,pymongo.collection.Collection)
        self.val=self.curr.find_one({'id':node.slice.value})
        if self.val is None: raise IndexError(f'Invalid id {node.slice.value} (not found in {self.curr})')
        self.seq.append(DotNode(node.__class__.__name__.upper(),node.slice.value,self.val))
    def visit_Attribute(self,node):
        'dotted attribute'
        self.generic_visit(node)
        # is a pointer to another database
        if (k:=f'{self.curr.name}.{node.attr}') in structs: self.curr=self.db[structs[k]]
        # is a terminal value
        else: self.curr=self.val[node.attr]
        self.seq.append(DotNode(node.__class__.__name__.upper(),node.attr,self.curr))
    def visit_Name(self,node):
        'top named object'
        self.generic_visit(node)
        self.curr=self.curr[node.id]
        self.seq.append(DotNode(node.__class__.__name__.upper(),node.id,self.curr))

pprint(MupifObjectTraversal(db=client,expr='BeamState[0].beam.cs.rve.ct.id')())

pprint(MupifObjectTraversal(db=client,expr='BeamState[0].csState[0].rveStates[1].rve.ct.id')())

pprint(MupifObjectTraversal(db=client,expr='BeamState[0].csState[0].rveStates[1].rve.materials[0].name')())
[
│   DotNode(
│   │   what='NAME',
│   │   param='BeamState',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'BeamState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e9145b9bb766a61709416b'),
│   │   │   'id': 0,
│   │   │   'npointz': 1,
│   │   │   'csState': [0, '1'],
│   │   │   'w': []
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='beam',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'Beam')
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='cs',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'CrossSection')
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='rve',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'ConcreteRVE')
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='ct',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'CTScan')
│   ),
│   DotNode(what='ATTRIBUTE', param='id', value=0)
]

[
│   DotNode(
│   │   what='NAME',
│   │   param='BeamState',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'BeamState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e9145b9bb766a61709416b'),
│   │   │   'id': 0,
│   │   │   'npointz': 1,
│   │   │   'csState': [0, '1'],
│   │   │   'w': []
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='csState',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'CrossSectionState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e969d69bb766a6170941bd'),
│   │   │   'id': 0,
│   │   │   'cs': 0,
│   │   │   'rveStates': [0, 1],
│   │   │   'BendingMoment': [0, 0],
│   │   │   'kappa': [1, 1],
│   │   │   'eps_axial': [2, 2, 2]
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='rveStates',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'ConcreteRVEState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=1,
│   │   value={
│   │   │   '_id': ObjectId('62e969c39bb766a6170941b2'),
│   │   │   'id': 1,
│   │   │   'rve': 1,
│   │   │   'sigmaHom': [1, 1, 1],
│   │   │   'epsHom': [1, 1, 1],
│   │   │   'Stiffness': [11, 12, 13, 14, 15, 16, 17, 18, 19],
│   │   │   'eps0Hom': [1, 1, 1]
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='rve',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'ConcreteRVE')
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='ct',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'CTScan')
│   ),
│   DotNode(what='ATTRIBUTE', param='id', value=1)
]

[
│   DotNode(
│   │   what='NAME',
│   │   param='BeamState',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'BeamState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e9145b9bb766a61709416b'),
│   │   │   'id': 0,
│   │   │   'npointz': 1,
│   │   │   'csState': [0, '1'],
│   │   │   'w': []
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='csState',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'CrossSectionState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e969d69bb766a6170941bd'),
│   │   │   'id': 0,
│   │   │   'cs': 0,
│   │   │   'rveStates': [0, 1],
│   │   │   'BendingMoment': [0, 0],
│   │   │   'kappa': [1, 1],
│   │   │   'eps_axial': [2, 2, 2]
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='rveStates',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'ConcreteRVEState')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=1,
│   │   value={
│   │   │   '_id': ObjectId('62e969c39bb766a6170941b2'),
│   │   │   'id': 1,
│   │   │   'rve': 1,
│   │   │   'sigmaHom': [1, 1, 1],
│   │   │   'epsHom': [1, 1, 1],
│   │   │   'Stiffness': [11, 12, 13, 14, 15, 16, 17, 18, 19],
│   │   │   'eps0Hom': [1, 1, 1]
│   │   }
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='rve',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'ConcreteRVE')
│   ),
│   DotNode(
│   │   what='ATTRIBUTE',
│   │   param='materials',
│   │   value=Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True), 'DMS00'), 'MaterialRecord')
│   ),
│   DotNode(
│   │   what='SUBSCRIPT',
│   │   param=0,
│   │   value={
│   │   │   '_id': ObjectId('62e914fb9bb766a617094171'),
│   │   │   'id': 0,
│   │   │   'name': 'material0',
│   │   │   'type': None,
│   │   │   'props': {'manufacturer': 'Unemployed Philosophers Guild'}
│   │   }
│   ),
│   DotNode(what='ATTRIBUTE', param='name', value='material0')
]

@eudoxos
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eudoxos commented Aug 2, 2022

The beanie module might be useful for defining the data structure: as pydantic classes, beanie interfacing with MongoDB.

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