How to use equivalents method in pandera

Best Python code snippet using pandera_python

action.py

Source:action.py

1from entities.abstract_entity import ConceptualEntity2from entities.instrument import Instrument,Pipette3from entities.apparatus import Apparatus,Thermocycler,Centrifuge,Incubator4from entities.container import Well,Container5from property import protocols as pp6from property import actions as ap7from equivalent import abstract_equivalent as ae8from equivalent import protocol_equivalent as pe9from restriction import action_recipes as ar10class Action(ConceptualEntity):11    def __init__(self,properties=[],equivalents=[],restrictions=[]):12        if equivalents == []:13            e = [pe.ActionEquivalent()]14        else:15            e = equivalents16        p = [pp.Actions(Action),17            pp.UsesApparatus(Apparatus),18            pp.UsesInstrument(Instrument)] + properties19        super().__init__(properties=p,equivalents=e,20                        restrictions=restrictions)21class Restriction(Action):22    def __init__(self,properties=[],equivalents=[],restrictions=[]):23        name = self.__class__.__name__24        e = equivalents + [ae.NameEquivalentClass(name)]25        p = properties + [pp.MayUseInstrument(default_value=Pipette),26                          pp.MayUseApparatus(default_value=Thermocycler),27                          pp.MayUseApparatus(default_value=Centrifuge),28                          pp.MayUseApparatus(default_value=Incubator)]29        super().__init__(properties=p,equivalents=e,30                        restrictions=restrictions)31class Purify(Action):32    def __init__(self,properties=[],equivalents=[],restrictions=[]):33        name = self.__class__.__name__34        e = equivalents + [ae.NameEquivalentClass(name)]35        p = properties + [pp.MayUseInstrument(default_value=Pipette),36                          pp.MayUseApparatus(default_value=Centrifuge),37                          pp.MayUseApparatus(default_value=Incubator)]38        super().__init__(properties=p,equivalents=e,39                        restrictions=restrictions)40class Bind(Action):41    def __init__(self,properties=[],equivalents=[],restrictions=[]):42        name = self.__class__.__name__43        e = equivalents + [ae.NameEquivalentClass(name)]44        p = properties + [pp.MayUseInstrument(default_value=Pipette),45                          pp.MayUseApparatus(default_value=Centrifuge)]46        super().__init__(properties=p,equivalents=e,47                        restrictions=restrictions)48class Wash(Action):49    def __init__(self,properties=[],equivalents=[],restrictions=[]):50        name = self.__class__.__name__51        e = equivalents + [ae.NameEquivalentClass(name)]52        p = properties + [pp.MayUseInstrument(default_value=Pipette),53                          pp.MayUseApparatus(default_value=Centrifuge)]54        super().__init__(properties=p,equivalents=e,55                        restrictions=restrictions)56class Elution(Action):57    def __init__(self,properties=[],equivalents=[],restrictions=[]):58        name = self.__class__.__name__59        e = equivalents + [ae.NameEquivalentClass(name)]60        p = properties + [pp.MayUseInstrument(default_value=Pipette),61                          pp.MayUseApparatus(default_value=Centrifuge),62                          pp.MayUseApparatus(default_value=Incubator)]63        super().__init__(properties=p,equivalents=e,64                        restrictions=restrictions)65class Transfer(Action):66    def __init__(self,properties=[],equivalents=[],restrictions=[]):67        name = [self.__class__.__name__.lower(),"dispense"]68        e = equivalents + [ae.NameEquivalentClass(name),69                           pe.TransferEquivalent()]70        p = properties + [ap.Source(Well),71                          ap.Destination(Well),72                          ap.Volume(),73                          pp.MayUseInstrument(default_value=Pipette)]74        r = restrictions + [ar.TransferRecipe()]75        super().__init__(properties=p,equivalents=e,76                        restrictions=restrictions)77class Seal(Action):78    def __init__(self,properties=[],equivalents=[],restrictions=[]):79        name = self.__class__.__name__.lower()80        e = equivalents + [ae.NameEquivalentClass(name)]81        p = properties + [ap.Object(Container)]82        super().__init__(properties=p,equivalents=e,83                        restrictions=restrictions)84class Unseal(Action):85    def __init__(self,properties=[],equivalents=[],restrictions=[]):86        name = self.__class__.__name__.lower()87        e = equivalents + [ae.NameEquivalentClass(name)]88        p = properties + [ap.Object(Container)]89        super().__init__(properties=p,equivalents=e,90                        restrictions=restrictions)91class Spin(Action):92    def __init__(self,properties=[],equivalents=[],restrictions=[]):93        name = self.__class__.__name__.lower()94        e = equivalents + [ae.NameEquivalentClass(name)]95        p = properties + [ap.Object(Container),96                          ap.Speed(),97                          ap.Duration(),98                          pp.MayUseApparatus(default_value=Centrifuge)]99        super().__init__(properties=p,equivalents=e,100                        restrictions=restrictions)101class SeperateGel(Action):102    def __init__(self,properties=[],equivalents=[],restrictions=[]):103        name = [self.__class__.__name__.lower(),"gel_separate"]104        e = equivalents + [ae.NameEquivalentClass(name)]105        p = properties + [ap.Source(Well),106                          ap.Duration(),107                          ap.Volume()]108        super().__init__(properties=p,equivalents=e,109                        restrictions=restrictions)110class ColonyPick(Action):111    def __init__(self,properties=[],equivalents=[],restrictions=[]):112        name = [self.__class__.__name__.lower(),"autopick"]113        e = equivalents + [ae.NameEquivalentClass(name)]114        p = properties + [ap.Source(Well),115                          ap.Destination(Well)]116        super().__init__(properties=p,equivalents=e,117                        restrictions=restrictions)118                        119class Incubate(Action):120    def __init__(self,properties=[],equivalents=[],restrictions=[]):121        name = self.__class__.__name__.lower()122        e = equivalents + [ae.NameEquivalentClass(name)]123        p = properties + [ap.Object(Container),124                          ap.Temperature(),125                          ap.Duration(),126                          pp.MayUseApparatus(default_value=Incubator)]127        super().__init__(properties=p,equivalents=e,128                        restrictions=restrictions)129class Thermocycle(Action):130    def __init__(self,properties=[],equivalents=[],restrictions=[]):131        name = self.__class__.__name__.lower()132        e = equivalents + [ae.NameEquivalentClass(name)]133        p = properties + [ap.Object(Container),134                          ap.Cycles(),135                          ap.Temperature(),136                          ap.Duration(),137                          pp.MayUseApparatus(default_value=Thermocycler)]138        super().__init__(properties=p,equivalents=e,139                        restrictions=restrictions)140class Extract(Action): # Source141    def __init__(self,properties=[],equivalents=[],restrictions=[]):142        if equivalents == []:143            e = [pe.ExtractEquivalent()]144        else:145            e = equivalents146        p = properties + [ap.Source(Well)]147        super().__init__(properties=p,equivalents=e,148                        restrictions=restrictions)149class Dispense(Action): # Location150    def __init__(self,properties=[],equivalents=[],restrictions=[]):151        if equivalents == []:152            e = [pe.DispenseEquivalent()]153        else:154            e = equivalents155        p = properties + [ap.Destination(Well)]156        super().__init__(properties=p,equivalents=e,157                        restrictions=restrictions)158class Consolidate(Action):159    def __init__(self,properties=[],equivalents=[],restrictions=[]):160        if equivalents == []:161            e = [pe.ConsolidateEquivalent()]162        else:163            e = equivalents164        super().__init__(properties=properties,equivalents=e,165                        restrictions=restrictions)166class Distribute(Action):167    def __init__(self,properties=[],equivalents=[],restrictions=[]):168        if equivalents == []:169            e = [pe.DistributeEquivalent()]170        else:171            e = equivalents172        super().__init__(properties=properties,equivalents=e,...

genetic.py

Source:genetic.py

1from entities.abstract_entity import PhysicalEntity2from equivalent import physcial_equivalent as pe3from property.property import HasPart,HasSequence4# -------------- DNA --------------5class DNA(PhysicalEntity):6    def __init__(self,equivalents=[],properties=[]):7        if equivalents == []:8            r = [pe.DNARoleEquivalent()]9        else:10            r = equivalents11        p = properties + [HasPart(PhysicalEntity),HasSequence()]12        super().__init__(equivalents=r,properties=p)13class Promoter(DNA):14    def __init__(self,equivalents=[]):15        if equivalents == []:16            r = [pe.PromoterRoleEquivalent()]17        else:18            r = equivalents19        super().__init__(equivalents=r)20class RBS(DNA):21    def __init__(self,equivalents=[]):22        if equivalents == []:23            r = [pe.RBSRoleEquivalent()]24        else:25            r = equivalents26        super().__init__(equivalents=r)27class CDS(DNA):28    def __init__(self,equivalents=[]):29        if equivalents == []:30            r = [pe.CDSRoleEquivalent()]31        else:32            r = equivalents33        super().__init__(equivalents=r)34class Terminator(DNA):35    def __init__(self,equivalents=[]):36        if equivalents == []:37            r = [pe.TerminatorRoleEquivalent()]38        else:39            r = equivalents40        super().__init__(equivalents=r)41class Gene(DNA):42    def __init__(self,equivalents=[]):43        if equivalents == []:44            r = [pe.GeneRoleEquivalent()]45        else:46            r = equivalents47        super().__init__(equivalents=r)48class Operator(DNA):49    def __init__(self,equivalents=[]):50        if equivalents == []:51            r = [pe.OperatorRoleEquivalent()]52        else:53            r = equivalents54        super().__init__(equivalents=r)55class EngineeredRegion(DNA):56    def __init__(self,equivalents=[]):57        if equivalents == []:58            r = [pe.EngineeredRegionRoleEquivalent()]59        else:60            r = equivalents61        super().__init__(equivalents=r)62class EngineeredTag(DNA):63    def __init__(self,equivalents=[]):64        if equivalents == []:65            r = [pe.EngineeredTagRoleEquivalent()]66        else:67            r = equivalents68        super().__init__(equivalents=r)69class StartCodon(DNA):70    def __init__(self,equivalents=[]):71        if equivalents == []:72            r = [pe.StartCodonRoleEquivalent()]73        else:74            r = equivalents75        super().__init__(equivalents=r)76class Tag(DNA):77    def __init__(self,equivalents=[]):78        if equivalents == []:79            r = [pe.TagRoleEquivalent()]80        else:81            r = equivalents82        super().__init__(equivalents=r)83class NonCovBindingSite(DNA):84    def __init__(self,equivalents=[]):85        if equivalents == []:86            r = [pe.NonCovBindingSiteRoleEquivalent()]87        else:88            r = equivalents89        super().__init__(equivalents=r)90class EngineeredGene(DNA):91    def __init__(self,equivalents=[]):92        if equivalents == []:93            r = [pe.EngineeredGeneRoleEquivalent()]94        else:95            r = equivalents96        super().__init__(equivalents=r)97# -------------- Complex --------------98class Complex(PhysicalEntity):99    def __init__(self,equivalents=[]):100        if equivalents == []:101            r = [pe.ComplexRoleEquivalent()]102        else:103            r = equivalents104        super().__init__(equivalents=r)105# -------------- RNA --------------106class RNA(PhysicalEntity):107    def __init__(self,equivalents=[]):108        if equivalents == []:109            r = [pe.RNARoleEquivalent()]110        else:111            r = equivalents112        super().__init__(equivalents=r)113class mRNA(RNA):114    def __init__(self,equivalents=[]):115        if equivalents == []:116            r = [pe.mRNARoleEquivalent()]117        else:118            r = equivalents119        super().__init__(equivalents=r)120class sgRNA(RNA):121    def __init__(self,equivalents=[]):122        if equivalents == []:123            r = [pe.sgRNARoleEquivalent()]124        else:125            r = equivalents...

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