Remove taskid from baseresult table
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import datetime |
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3 | 8 |
from sqlalchemy import ( |
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JSON, |
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Boolean, |
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Column, |
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DateTime, |
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Enum, |
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ForeignKey, |
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Index, |
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Integer, |
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String, |
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UniqueConstraint, |
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func, |
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select, |
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)
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17 | 8 |
from sqlalchemy.dialects.postgresql import JSONB, aggregate_order_by |
18 | 8 |
from sqlalchemy.ext.hybrid import hybrid_property |
19 | 8 |
from sqlalchemy.ext.orderinglist import ordering_list |
20 | 8 |
from sqlalchemy.orm import column_property, relationship |
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22 | 8 |
from qcfractal.interface.models.records import DriverEnum, RecordStatusEnum |
23 | 8 |
from qcfractal.storage_sockets.models.sql_base import Base, MsgpackExt |
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from qcfractal.storage_sockets.models.sql_models import KeywordsORM, KVStoreORM, MoleculeORM |
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27 | 8 |
class BaseResultORM(Base): |
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"""
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Abstract Base class for ResultORMs and ProcedureORMs
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"""
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32 | 8 |
__tablename__ = "base_result" |
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# for SQL
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35 | 8 |
result_type = Column(String) # for inheritance |
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# Base identification
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38 | 8 |
id = Column(Integer, primary_key=True) |
39 |
# ondelete="SET NULL": when manger is deleted, set this field to None
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40 | 8 |
manager_name = Column(String, ForeignKey("queue_manager.name", ondelete="SET NULL"), nullable=True) |
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42 | 8 |
hash_index = Column(String) # TODO |
43 | 8 |
procedure = Column(String(100)) # TODO: may remove |
44 |
# program = Column(String(100)) # moved to subclasses
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45 | 8 |
version = Column(Integer) |
46 | 8 |
protocols = Column(JSONB) |
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# Extra fields
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49 | 8 |
extras = Column(MsgpackExt) |
50 | 8 |
stdout = Column(Integer, ForeignKey("kv_store.id")) |
51 | 8 |
stdout_obj = relationship( |
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KVStoreORM, lazy="noload", foreign_keys=stdout, cascade="all, delete-orphan", single_parent=True |
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)
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55 | 8 |
stderr = Column(Integer, ForeignKey("kv_store.id")) |
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stderr_obj = relationship( |
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KVStoreORM, lazy="noload", foreign_keys=stderr, cascade="all, delete-orphan", single_parent=True |
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)
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60 | 8 |
error = Column(Integer, ForeignKey("kv_store.id")) |
61 | 8 |
error_obj = relationship( |
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KVStoreORM, lazy="noload", foreign_keys=error, cascade="all, delete-orphan", single_parent=True |
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)
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# Compute status
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66 | 8 |
status = Column(Enum(RecordStatusEnum), nullable=False, default=RecordStatusEnum.incomplete) |
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68 | 8 |
created_on = Column(DateTime, default=datetime.datetime.utcnow) |
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modified_on = Column(DateTime, default=datetime.datetime.utcnow) |
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# Carry-ons
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72 | 8 |
provenance = Column(JSON) |
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74 | 8 |
__table_args__ = ( |
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Index("ix_base_result_status", "status"), |
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Index("ix_base_result_type", "result_type"), # todo: needed? |
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)
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__mapper_args__ = {"polymorphic_on": "result_type"} |
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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85 | 8 |
class WavefunctionStoreORM(Base): |
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87 | 8 |
__tablename__ = "wavefunction_store" |
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89 | 8 |
id = Column(Integer, primary_key=True) |
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# Sparsity is very cheap
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92 | 8 |
basis = Column(MsgpackExt, nullable=False) |
93 | 8 |
restricted = Column(Boolean, nullable=False) |
94 |
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# Core Hamiltonian
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96 | 8 |
h_core_a = Column(MsgpackExt, nullable=True) |
97 | 8 |
h_core_b = Column(MsgpackExt, nullable=True) |
98 | 8 |
h_effective_a = Column(MsgpackExt, nullable=True) |
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h_effective_b = Column(MsgpackExt, nullable=True) |
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# SCF Results
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102 | 8 |
scf_orbitals_a = Column(MsgpackExt, nullable=True) |
103 | 8 |
scf_orbitals_b = Column(MsgpackExt, nullable=True) |
104 | 8 |
scf_density_a = Column(MsgpackExt, nullable=True) |
105 | 8 |
scf_density_b = Column(MsgpackExt, nullable=True) |
106 | 8 |
scf_fock_a = Column(MsgpackExt, nullable=True) |
107 | 8 |
scf_fock_b = Column(MsgpackExt, nullable=True) |
108 | 8 |
scf_eigenvalues_a = Column(MsgpackExt, nullable=True) |
109 | 8 |
scf_eigenvalues_b = Column(MsgpackExt, nullable=True) |
110 | 8 |
scf_occupations_a = Column(MsgpackExt, nullable=True) |
111 | 8 |
scf_occupations_b = Column(MsgpackExt, nullable=True) |
112 |
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# Extras
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114 | 8 |
extras = Column(MsgpackExt, nullable=True) |
115 |
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117 | 8 |
class ResultORM(BaseResultORM): |
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"""
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Hold the result of an atomic single calculation
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"""
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122 | 8 |
__tablename__ = "result" |
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124 | 8 |
id = Column(Integer, ForeignKey("base_result.id", ondelete="CASCADE"), primary_key=True) |
125 |
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# uniquely identifying a result
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127 | 8 |
program = Column(String(100), nullable=False) # example "rdkit", is it the same as program in keywords? |
128 | 8 |
driver = Column(String(100), Enum(DriverEnum), nullable=False) |
129 | 8 |
method = Column(String(100), nullable=False) # example "uff" |
130 | 8 |
basis = Column(String(100)) |
131 | 8 |
molecule = Column(Integer, ForeignKey("molecule.id")) |
132 | 8 |
molecule_obj = relationship(MoleculeORM, lazy="select") |
133 |
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# This is a special case where KeywordsORM are denormalized intentionally as they are part of the
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# lookup for a single result and querying a result will not often request the keywords (LazyReference)
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136 | 8 |
keywords = Column(Integer, ForeignKey("keywords.id")) |
137 | 8 |
keywords_obj = relationship(KeywordsORM, lazy="select") |
138 |
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# Primary Result output
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140 | 8 |
return_result = Column(MsgpackExt) |
141 | 8 |
properties = Column(JSON) # TODO: may use JSONB in the future |
142 |
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# Wavefunction data
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144 | 8 |
wavefunction = Column(JSONB, nullable=True) |
145 | 8 |
wavefunction_data_id = Column(Integer, ForeignKey("wavefunction_store.id"), nullable=True) |
146 | 8 |
wavefunction_data_obj = relationship( |
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WavefunctionStoreORM, |
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lazy="noload", |
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foreign_keys=wavefunction_data_id, |
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cascade="all, delete-orphan", |
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single_parent=True, |
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)
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154 | 8 |
__table_args__ = ( |
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# TODO: optimize indexes
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# A multicolumn GIN index can be used with query conditions that involve any subset of
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# the index's columns. Unlike B-tree or GiST, index search effectiveness is the same
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# regardless of which index column(s) the query conditions use.
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# Index('ix_result_combined', "program", "driver", "method", "basis",
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# "keywords", postgresql_using='gin'), # gin index
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# Index('ix_results_molecule', 'molecule'), # b-tree index
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UniqueConstraint("program", "driver", "method", "basis", "keywords", "molecule", name="uix_results_keys"), |
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)
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165 | 8 |
__mapper_args__ = { |
166 |
"polymorphic_identity": "result", |
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# to have separate select when querying BaseResultsORM
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"polymorphic_load": "selectin", |
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}
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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175 | 8 |
class ProcedureMixin: |
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"""
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A procedure mixin to be used by specific procedure types
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"""
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179 |
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180 | 8 |
program = Column(String(100), nullable=False) |
181 | 8 |
keywords = Column(JSON) |
182 | 8 |
qc_spec = Column(JSON) |
183 |
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184 |
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185 |
# ================== Types of ProcedureORMs ================== #
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186 |
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188 | 8 |
class Trajectory(Base): |
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"""Association table for many to many"""
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190 |
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191 | 8 |
__tablename__ = "opt_result_association" |
192 |
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193 | 8 |
opt_id = Column(Integer, ForeignKey("optimization_procedure.id", ondelete="cascade"), primary_key=True) |
194 | 8 |
result_id = Column(Integer, ForeignKey("result.id", ondelete="cascade"), primary_key=True) |
195 | 8 |
position = Column(Integer, primary_key=True) |
196 |
# Index('opt_id', 'result_id', unique=True)
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# trajectory_obj = relationship(ResultORM, lazy="noload")
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200 |
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201 | 8 |
class OptimizationProcedureORM(ProcedureMixin, BaseResultORM): |
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"""
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An Optimization procedure
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"""
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205 |
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206 | 8 |
__tablename__ = "optimization_procedure" |
207 |
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208 | 8 |
id = Column(Integer, ForeignKey("base_result.id", ondelete="cascade"), primary_key=True) |
209 |
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210 | 8 |
def __init__(self, **kwargs): |
211 | 8 |
kwargs.setdefault("version", 1) |
212 | 8 |
self.procedure = "optimization" |
213 | 8 |
super().__init__(**kwargs) |
214 |
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215 | 8 |
schema_version = Column(Integer, default=1) |
216 | 8 |
initial_molecule = Column(Integer, ForeignKey("molecule.id")) |
217 | 8 |
initial_molecule_obj = relationship(MoleculeORM, lazy="select", foreign_keys=initial_molecule) |
218 |
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# # Results
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220 | 8 |
energies = Column(JSON) # Column(ARRAY(Float)) |
221 | 8 |
final_molecule = Column(Integer, ForeignKey("molecule.id")) |
222 | 8 |
final_molecule_obj = relationship(MoleculeORM, lazy="select", foreign_keys=final_molecule) |
223 |
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# ids, calculated not stored in this table
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# NOTE: this won't work in SQLite since it returns ARRAYS, aggregate_order_by
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226 | 8 |
trajectory = column_property( |
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select([func.array_agg(aggregate_order_by(Trajectory.result_id, Trajectory.position))]).where( |
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Trajectory.opt_id == id |
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)
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)
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# array of objects (results) - Lazy - raise error of accessed
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233 | 8 |
trajectory_obj = relationship( |
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Trajectory, |
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cascade="all, delete-orphan", |
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# backref="optimization_procedure",
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order_by=Trajectory.position, |
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collection_class=ordering_list("position"), |
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)
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240 |
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241 | 8 |
__mapper_args__ = { |
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"polymorphic_identity": "optimization_procedure", |
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# to have separate select when querying BaseResultsORM
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244 |
"polymorphic_load": "selectin", |
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}
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246 |
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247 | 8 |
__table_args__ = (Index("ix_optimization_program", "program"),) # todo: needed for procedures? |
248 |
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249 | 8 |
def update_relations(self, trajectory=None, **kwarg): |
250 |
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# update optimization_results relations
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# self._update_many_to_many(opt_result_association, 'opt_id', 'result_id',
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# self.id, trajectory, self.trajectory)
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254 |
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255 | 8 |
self.trajectory_obj = [] |
256 | 8 |
trajectory = [] if not trajectory else trajectory |
257 | 8 |
for result_id in trajectory: |
258 | 8 |
traj = Trajectory(opt_id=int(self.id), result_id=int(result_id)) |
259 | 8 |
self.trajectory_obj.append(traj) |
260 |
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# def add_relations(self, trajectory):
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# session = object_session(self)
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# # add many to many relation with results if ids are given not objects
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# if trajectory:
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# session.execute(
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# opt_result_association
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# .insert() # or update
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# .values([(self.id, i) for i in trajectory])
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# )
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# session.commit()
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272 |
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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274 |
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275 |
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276 | 8 |
class GridOptimizationAssociation(Base): |
277 |
"""Association table for many to many"""
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279 | 8 |
__tablename__ = "grid_optimization_association" |
280 |
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281 | 8 |
grid_opt_id = Column(Integer, ForeignKey("grid_optimization_procedure.id", ondelete="cascade"), primary_key=True) |
282 | 8 |
key = Column(String, nullable=False, primary_key=True) |
283 |
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284 |
# not primary key
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285 | 8 |
opt_id = Column(Integer, ForeignKey("optimization_procedure.id", ondelete="cascade")) |
286 |
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287 |
# Index('grid_opt_id', 'key', unique=True)
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288 |
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289 |
# optimization_obj = relationship(OptimizationProcedureORM, lazy="joined")
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290 |
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291 |
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292 | 8 |
class GridOptimizationProcedureORM(ProcedureMixin, BaseResultORM): |
293 |
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294 | 8 |
__tablename__ = "grid_optimization_procedure" |
295 |
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296 | 8 |
id = Column(Integer, ForeignKey("base_result.id", ondelete="cascade"), primary_key=True) |
297 |
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298 | 8 |
def __init__(self, **kwargs): |
299 | 1 |
kwargs.setdefault("version", 1) |
300 | 1 |
kwargs.setdefault("procedure", "gridoptimization") |
301 | 1 |
kwargs.setdefault("program", "qcfractal") |
302 | 1 |
super().__init__(**kwargs) |
303 |
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304 |
# Input data
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305 | 8 |
initial_molecule = Column(Integer, ForeignKey("molecule.id")) |
306 | 8 |
initial_molecule_obj = relationship(MoleculeORM, lazy="select", foreign_keys=initial_molecule) |
307 |
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308 | 8 |
optimization_spec = Column(JSON) |
309 |
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310 |
# Output data
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311 | 8 |
starting_molecule = Column(Integer, ForeignKey("molecule.id")) |
312 | 8 |
starting_molecule_obj = relationship(MoleculeORM, lazy="select", foreign_keys=initial_molecule) |
313 |
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314 | 8 |
final_energy_dict = Column(JSON) # Dict[str, float] |
315 | 8 |
starting_grid = Column(JSON) # tuple |
316 |
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317 | 8 |
grid_optimizations_obj = relationship( |
318 |
GridOptimizationAssociation, |
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lazy="selectin", |
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cascade="all, delete-orphan", |
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backref="grid_optimization_procedure", |
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)
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323 |
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324 | 8 |
@hybrid_property
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325 | 3 |
def grid_optimizations(self): |
326 |
"""calculated property when accessed, not saved in the DB
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327 |
A view of the many to many relation in the form of a dict"""
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328 |
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329 | 1 |
return self._grid_optimizations(self.grid_optimizations_obj) |
330 |
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331 | 8 |
@staticmethod
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332 | 3 |
def _grid_optimizations(grid_optimizations_obj): |
333 |
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334 | 1 |
if not grid_optimizations_obj: |
335 |
return {} |
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336 |
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337 | 1 |
if not isinstance(grid_optimizations_obj, list): |
338 | 1 |
grid_optimizations_obj = [grid_optimizations_obj] |
339 |
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340 | 1 |
ret = {} |
341 | 1 |
try: |
342 | 1 |
for obj in grid_optimizations_obj: |
343 | 1 |
ret[obj.key] = str(obj.opt_id) |
344 |
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345 | 1 |
except Exception as err: |
346 |
# raises exception of first access!!
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347 | 1 |
pass
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348 |
# print(err)
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349 |
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350 | 1 |
return ret |
351 |
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352 | 8 |
@grid_optimizations.setter
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353 | 3 |
def grid_optimizations(self, dict_values): |
354 |
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355 | 1 |
return dict_values |
356 |
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357 | 8 |
__table_args__ = (Index("ix_grid_optmization_program", "program"),) # todo: needed for procedures? |
358 |
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359 | 8 |
__mapper_args__ = { |
360 |
"polymorphic_identity": "grid_optimization_procedure", |
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361 |
# to have separate select when querying BaseResultsORM
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362 |
"polymorphic_load": "selectin", |
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363 |
}
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364 |
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365 | 8 |
def update_relations(self, grid_optimizations=None, **kwarg): |
366 |
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367 | 1 |
self.grid_optimizations_obj = [] |
368 | 1 |
for key, opt_id in grid_optimizations.items(): |
369 | 1 |
obj = GridOptimizationAssociation(grid_opt_id=int(self.id), opt_id=int(opt_id), key=key) |
370 | 1 |
self.grid_optimizations_obj.append(obj) |
371 |
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372 |
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373 |
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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374 |
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375 |
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376 | 8 |
class OptimizationHistory(Base): |
377 |
"""Association table for many to many"""
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378 |
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379 | 8 |
__tablename__ = "optimization_history" |
380 |
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381 | 8 |
torsion_id = Column(Integer, ForeignKey("torsiondrive_procedure.id", ondelete="cascade"), primary_key=True) |
382 | 8 |
opt_id = Column(Integer, ForeignKey("optimization_procedure.id", ondelete="cascade"), primary_key=True) |
383 | 8 |
key = Column(String, nullable=False, primary_key=True) |
384 | 8 |
position = Column(Integer, primary_key=True) |
385 |
# Index('torsion_id', 'key', unique=True)
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386 |
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387 |
# optimization_obj = relationship(OptimizationProcedureORM, lazy="joined")
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388 |
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389 |
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390 | 8 |
class TorsionInitMol(Base): |
391 |
"""
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392 |
Association table for many to many relation
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393 |
"""
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394 |
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395 | 8 |
__tablename__ = "torsion_init_mol_association" |
396 |
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397 | 8 |
torsion_id = Column( |
398 |
"torsion_id", Integer, ForeignKey("torsiondrive_procedure.id", ondelete="cascade"), primary_key=True |
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399 |
)
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400 | 8 |
molecule_id = Column("molecule_id", Integer, ForeignKey("molecule.id", ondelete="cascade"), primary_key=True) |
401 |
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402 |
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403 | 8 |
class TorsionDriveProcedureORM(ProcedureMixin, BaseResultORM): |
404 |
"""
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405 |
A torsion drive procedure
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406 |
"""
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407 |
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408 | 8 |
__tablename__ = "torsiondrive_procedure" |
409 |
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410 | 8 |
id = Column(Integer, ForeignKey("base_result.id", ondelete="cascade"), primary_key=True) |
411 |
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412 | 8 |
def __init__(self, **kwargs): |
413 | 8 |
kwargs.setdefault("version", 1) |
414 | 8 |
self.procedure = "torsiondrive" |
415 | 8 |
self.program = "torsiondrive" |
416 | 8 |
super().__init__(**kwargs) |
417 |
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418 |
# input data (along with the mixin)
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419 |
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420 |
# ids of the many to many relation
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421 | 8 |
initial_molecule = column_property( |
422 |
select([func.array_agg(TorsionInitMol.molecule_id)]).where(TorsionInitMol.torsion_id == id) |
|
423 |
)
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424 |
# actual objects relation M2M, never loaded here
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425 | 8 |
initial_molecule_obj = relationship(MoleculeORM, secondary=TorsionInitMol.__table__, uselist=True, lazy="noload") |
426 |
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427 | 8 |
optimization_spec = Column(JSON) |
428 |
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429 |
# Output data
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430 | 8 |
final_energy_dict = Column(JSON) |
431 | 8 |
minimum_positions = Column(JSON) |
432 |
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433 | 8 |
optimization_history_obj = relationship( |
434 |
OptimizationHistory, |
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435 |
cascade="all, delete-orphan", # backref="torsiondrive_procedure", |
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436 |
order_by=OptimizationHistory.position, |
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437 |
collection_class=ordering_list("position"), |
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438 |
lazy="selectin", |
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439 |
)
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440 |
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441 | 8 |
@hybrid_property
|
442 | 3 |
def optimization_history(self): |
443 |
"""calculated property when accessed, not saved in the DB
|
|
444 |
A view of the many to many relation in the form of a dict"""
|
|
445 |
|
|
446 | 8 |
return self._optimization_history(self.optimization_history_obj) |
447 |
|
|
448 | 8 |
@staticmethod
|
449 | 3 |
def _optimization_history(optimization_history_obj): |
450 |
|
|
451 | 8 |
if not optimization_history_obj: |
452 | 8 |
return {} |
453 |
|
|
454 | 8 |
if not isinstance(optimization_history_obj, list): |
455 | 8 |
optimization_history_obj = [optimization_history_obj] |
456 |
|
|
457 | 8 |
ret = {} |
458 | 8 |
try: |
459 | 8 |
for opt_history in optimization_history_obj: |
460 | 8 |
if opt_history.key in ret: |
461 | 8 |
ret[opt_history.key].append(str(opt_history.opt_id)) |
462 |
else: |
|
463 | 8 |
ret[opt_history.key] = [str(opt_history.opt_id)] |
464 |
|
|
465 | 8 |
except Exception as err: |
466 |
# raises exception of first access!!
|
|
467 | 8 |
pass
|
468 |
# print(err)
|
|
469 |
|
|
470 | 8 |
return ret |
471 |
|
|
472 | 8 |
@optimization_history.setter
|
473 | 3 |
def optimization_history(self, dict_values): |
474 |
"""A private copy of the opt history as a dict
|
|
475 |
Key: list of optimization procedures"""
|
|
476 |
|
|
477 | 8 |
return dict_values |
478 |
|
|
479 | 8 |
__table_args__ = (Index("ix_torsion_drive_program", "program"),) # todo: needed for procedures? |
480 |
|
|
481 | 8 |
__mapper_args__ = { |
482 |
"polymorphic_identity": "torsiondrive_procedure", |
|
483 |
# to have separate select when querying BaseResultsORM
|
|
484 |
"polymorphic_load": "selectin", |
|
485 |
}
|
|
486 |
|
|
487 | 8 |
def update_relations(self, initial_molecule=None, optimization_history=None, **kwarg): |
488 |
|
|
489 |
# update torsion molecule relation
|
|
490 | 8 |
self._update_many_to_many( |
491 |
TorsionInitMol.__table__, "torsion_id", "molecule_id", self.id, initial_molecule, self.initial_molecule |
|
492 |
)
|
|
493 |
|
|
494 | 8 |
self.optimization_history_obj = [] |
495 | 8 |
for key in optimization_history: |
496 | 8 |
for opt_id in optimization_history[key]: |
497 | 8 |
opt_history = OptimizationHistory(torsion_id=int(self.id), opt_id=int(opt_id), key=key) |
498 | 8 |
self.optimization_history_obj.append(opt_history) |
499 |
|
|
500 |
# No need for the following because the session is committed with parent save
|
|
501 |
# session.add_all(self.optimization_history_obj)
|
|
502 |
# session.add(self)
|
|
503 |
# session.commit()
|
|
504 |
|
|
505 |
|
|
506 |
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
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