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Commit 03ee902f authored by root's avatar root
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Update models

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dataproc/api/models/__pycache__/autoPROC_model.cpython-38.pyc
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dataproc/api/models/__pycache__/ligand_model.cpython-38.pyc
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dataproc/api/models/__pycache__/pipedream_model.cpython-38.pyc
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dataproc/api/models/__pycache__/refinement_model.cpython-38.pyc
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dataproc/api/models/__pycache__/report_model.cpython-38.pyc
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dataproc/api/models/autoPROC_model.py
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− 18
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......@@ -10,18 +10,10 @@ class autoPROC(StructuredNode):
Defines node properties and relationships
Provides data serializer
"""
# Properties
uuid=StringProperty(unique_index=True, default=uuid4)
refinedCell_beta=StringProperty()
refinedCell_b=StringProperty()
wavelength=StringProperty()
refinedCell_a=StringProperty()
refinedCell_alpha=StringProperty()
spaceGroup=StringProperty()
refinedCell_c=StringProperty()
refinedCell_gamma=StringProperty()
@property
def serialize(self):
......@@ -32,13 +24,5 @@ class autoPROC(StructuredNode):
return {
'autoPROC_node_properties': {
'uuid': self.uuid,
'refinedCell_beta': self.refinedCell_beta,
'refinedCell_b': self.refinedCell_b,
'wavelength': self.wavelength,
'refinedCell_a': self.refinedCell_a,
'refinedCell_alpha': self.refinedCell_alpha,
'spaceGroup': self.spaceGroup,
'refinedCell_c': self.refinedCell_c,
'refinedCell_gamma': self.refinedCell_gamma,
},
}
\ No newline at end of file
dataproc/api/models/draft.py 0 → 100644
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'recordTimeStamp': self.recordTimeStamp,
'resolutionEllipsoidAxis13': self.resolutionEllipsoidAxis13,
'resolutionEllipsoidAxis33': self.resolutionEllipsoidAxis33,
'resolutionEllipsoidAxis23': self.resolutionEllipsoidAxis23,
'resolutionEllipsoidValue2': self.resolutionEllipsoidValue2,
'resolutionEllipsoidAxis21': self.resolutionEllipsoidAxis21,
'resolutionEllipsoidAxis31': self.resolutionEllipsoidAxis31,
'resolutionEllipsoidAxis22': self.resolutionEllipsoidAxis22,
'resolutionEllipsoidAxis32': self.resolutionEllipsoidAxis32,
'resolutionEllipsoidValue3': self.resolutionEllipsoidValue3,
'resolutionEllipsoidAxis12': self.resolutionEllipsoidAxis12,
'resolutionEllipsoidValue1': self.resolutionEllipsoidValue1,
'resolutionEllipsoidAxis11': self.resolutionEllipsoidAxis11,
'multiplicity': self.multiplicity,
'resolutionLimitLow': self.resolutionLimitLow,
'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus,
'DanoOverSigDano': self.DanoOverSigDano,
'completenessSpherical': self.completenessSpherical,
'nTotalUniqueObservations': self.nTotalUniqueObservations,
'rMerge': self.rMerge,
'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus,
'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal,
'nTotalObservations': self.nTotalObservations,
'completenessEllipsoidal': self.completenessEllipsoidal,
'anomalousCompleteness': self.anomalousCompleteness,
'anomalousMultiplicity': self.anomalousMultiplicity,
'resolutionLimitHigh': self.resolutionLimitHigh,
'completeness': self.completeness,
'ccHalf': self.ccHalf,
'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus,
'meanIOverSigI': self.meanIOverSigI,
'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical,
'ccAnomalous': self.ccAnomalous,
'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus,
'nTotalObservations': self.nTotalObservations,
'completenessEllipsoidal': self.completenessEllipsoidal,
'anomalousMultiplicity': self.anomalousMultiplicity,
'anomalousCompleteness': self.anomalousCompleteness,
'resolutionLimitHigh': self.resolutionLimitHigh,
'completeness': self.completeness,
'ccHalf': self.ccHalf,
'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus,
'meanIOverSigI': self.meanIOverSigI,
'ccAnomalous': self.ccAnomalous,
'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical,
'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus,
'resolutionLimitLow': self.resolutionLimitLow,
'multiplicity': self.multiplicity,
'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus,
'DanoOverSigDano': self.DanoOverSigDano,
'completenessSpherical': self.completenessSpherical,
'nTotalUniqueObservations': self.nTotalUniqueObservations,
'rMerge': self.rMerge,
'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus,
'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal,
'DanoOverSigDano': self.DanoOverSigDano,
'completenessSpherical': self.completenessSpherical,
'rMerge': self.rMerge,
'nTotalUniqueObservations': self.nTotalUniqueObservations,
'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus,
'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal,
'multiplicity': self.multiplicity,
'resolutionLimitLow': self.resolutionLimitLow,
'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus,
'ccHalf': self.ccHalf,
'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus,
'meanIOverSigI': self.meanIOverSigI,
'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical,
'ccAnomalous': self.ccAnomalous,
'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus,
'nTotalObservations': self.nTotalObservations,
'completenessEllipsoidal': self.completenessEllipsoidal,
'anomalousCompleteness': self.anomalousCompleteness,
'anomalousMultiplicity': self.anomalousMultiplicity,
'resolutionLimitHigh': self.resolutionLimitHigh,
'completeness': self.completeness,
'refinedCell_beta': self.refinedCell_beta,
'refinedCell_b': self.refinedCell_b,
'wavelength': self.wavelength,
'refinedCell_a': self.refinedCell_a,
'refinedCell_alpha': self.refinedCell_alpha,
'spaceGroup': self.spaceGroup,
'refinedCell_c': self.refinedCell_c,
'refinedCell_gamma': self.refinedCell_gamma,
\ No newline at end of file
dataproc/api/models/ligand_model.py
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− 54
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......@@ -16,33 +16,6 @@ class Ligand(StructuredNode):
# Properties
uuid=StringProperty(unique_index=True, default=uuid4)
id=StringProperty()
ligandomin=StringProperty()
mogulzbond=StringProperty()
ligandbmin=StringProperty()
mogulring=StringProperty()
moguldihe=StringProperty()
ligandbavg=StringProperty()
mogulangl=StringProperty()
mogulbond=StringProperty()
ligandbmax=StringProperty()
ligandid=StringProperty()
ligandomax=StringProperty()
ligandcc=StringProperty()
mogulzangl=StringProperty()
molprobitypercentile=StringProperty()
ramaoutlierpercent=StringProperty()
cbetadeviations=StringProperty()
ramafavoredpercent=IntegerProperty()
poorrotamers=IntegerProperty()
rmsbonds=IntegerProperty()
rmsangles=IntegerProperty()
clashpercentile=StringProperty()
poorrotamerspercent=IntegerProperty()
clashscore=IntegerProperty()
ramafavored=StringProperty()
molprobityscore=IntegerProperty()
ramaoutlier=StringProperty()
# Relationships
associated=RelationshipTo(Dataset, 'ASSOCIATED')
......@@ -58,32 +31,5 @@ class Ligand(StructuredNode):
'ligand_node_properties': {
'uuid': self.uuid,
'id': self.id,
'ligandomin': self.ligandomin,
'mogulzbond': self.mogulzbond,
'ligandbmin': self.ligandbmin,
'mogulring': self.mogulring,
'moguldihe': self.moguldihe,
'ligandbavg': self.ligandbavg,
'mogulangl': self.mogulangl,
'mogulbond': self.mogulangl,
'ligandbmax': self.ligandbmax,
'ligandid': self.ligandid,
'ligandomax': self.ligandomax,
'ligandcc': self.ligandcc,
'mogulzangl': self.mogulzangl,
'molprobitypercentile': self.molprobitypercentile,
'ramaoutlierpercent': self.ramaoutlierpercent,
'cbetadeviations': self.cbetadeviations,
'ramafavoredpercent': self.ramafavoredpercent,
'poorrotamers': self.poorrotamers,
'rmsbonds': self.rmsbonds,
'rmsangles': self.rmsangles,
'clashpercentile': self.clashpercentile,
'poorrotamerspercent': self.poorrotamerspercent,
'clashscore': self.clashscore,
'ramafavored': self.ramafavored,
'molprobityscore': self.molprobityscore,
'ramaoutlier': self.ramaoutlier,
}
},
dataproc/api/models/pipedream_model.py
+ 7
− 7
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......@@ -12,13 +12,13 @@ class GPhLPipedream(StructuredNode):
"""
# Properties
command=StringProperty()
jsonversion=StringProperty()
runby=StringProperty()
runfrom=StringProperty()
command=StringProperty(max_length=500)
jsonversion=StringProperty(max_length=500)
runby=StringProperty(max_length=500)
runfrom=StringProperty(max_length=500)
jobid=StringProperty(unique_index=True, default=uuid4)
output=StringProperty()
version=StringProperty()
output=StringProperty(max_length=500)
version=StringProperty(max_length=500)
@property
def serialize(self):
......@@ -33,7 +33,7 @@ class GPhLPipedream(StructuredNode):
'jsonversion': self.jsonversion,
'runby': self.runby,
'runfrom': self.runfrom,
'jobid': self.uuid,
'jobid': self.jobid,
'output': self.output,
'version': self.version,
},
......
dataproc/api/models/refinement_model.py
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− 22
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......@@ -13,17 +13,6 @@ class Refinement(StructuredNode):
# Properties
uuid=StringProperty(unique_index=True, default=uuid4)
WilsonB=StringProperty()
Rfree=IntegerProperty()
MeanB=StringProperty()
type=StringProperty()
step=StringProperty()
RMSbonds=IntegerProperty()
RMSangles=IntegerProperty()
R=IntegerProperty()
WatersPresent=StringProperty()
selectedmodel=StringProperty()
refinementprotocol=StringProperty()
@property
def serialize(self):
......@@ -34,17 +23,6 @@ class Refinement(StructuredNode):
return {
'postrefinement_node_properties': {
'uuid': self.uuid,
'WilsonB': self.WilsonB,
'Rfree': self.Rfree,
'MeanB': self.MeanB,
'type': self.type,
'step': self.step,
'RMSbonds': self.RMSbonds,
'RMSangles': self.RMSangles,
'R': self.R,
'WatersPresent': self.WatersPresent,
'selectedmodel': self.selectedmodel,
'refinementprotocol': self.refinementprotocol,
},
}
dataproc/api/models/report_model.py
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− 11
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......@@ -11,15 +11,115 @@ from api.models.summaryhtml_model import SummaryHtml
class Report(StructuredNode):
"""
'''
Defines node properties and relationships
Provides data serializer
"""
'''
# Properties
report_path=StringProperty()
report_source=StringProperty()
report_size=StringProperty()
uuid=StringProperty(unique_index=True, default=uuid4)
# GPhL_pipedream report properties
command=StringProperty(max_length=700)
jsonversion=StringProperty(max_length=700)
runby=StringProperty(max_length=700)
runfrom=StringProperty(max_length=700)
jobid=StringProperty(unique_index=True, default=uuid4)
gphlpipedream_output=StringProperty(max_length=700)
version=StringProperty(max_length=700)
# Ligands fitting (Rhofit) report properties
ligandomin=StringProperty()
mogulzbond=StringProperty()
ligandbmin=StringProperty()
mogulring=StringProperty()
moguldihe=StringProperty()
ligandbavg=StringProperty()
mogulangl=StringProperty()
mogulbond=StringProperty()
ligandbmax=StringProperty()
ligandid=StringProperty()
ligandomax=StringProperty()
ligandcc=StringProperty()
mogulzangl=StringProperty()
molprobitypercentile=StringProperty()
ramaoutlierpercent=StringProperty()
cbetadeviations=StringProperty()
ramafavoredpercent=StringProperty()
poorrotamers=IntegerProperty()
rmsbonds=IntegerProperty()
rmsangles=IntegerProperty()
clashpercentile=StringProperty()
poorrotamerspercent=IntegerProperty()
clashscore=IntegerProperty()
ramafavored=StringProperty()
molprobityscore=IntegerProperty()
ramaoutliers=StringProperty()
closecontacts=StringProperty()
chain=StringProperty()
contactscore=StringProperty()
ligandstrain=StringProperty()
poorfit=StringProperty()
output=StringProperty()
correlationcoefficient=StringProperty()
rhofitscore=StringProperty()
# Refinement/Post-refinement report properties
WilsonB=StringProperty()
Rfree=IntegerProperty()
MeanB=StringProperty()
type=StringProperty()
step=StringProperty()
RMSbonds=IntegerProperty()
RMSangles=IntegerProperty()
R=IntegerProperty()
WatersPresent=StringProperty()
selectedmodel=StringProperty()
refinementprotocol=StringProperty()
# AutoPROC report properties (includes AutoProcscaling, AutoProcScalingStatistics and AutoProc (cf pipdream_summary.json))
recordTimeStamp=StringProperty()
resolutionEllipsoidAxis13=StringProperty()
resolutionEllipsoidAxis33=StringProperty()
resolutionEllipsoidAxis23=StringProperty()
resolutionEllipsoidValue2=StringProperty()
resolutionEllipsoidAxis21=StringProperty()
resolutionEllipsoidAxis31=StringProperty()
resolutionEllipsoidAxis22=StringProperty()
resolutionEllipsoidAxis32=StringProperty()
resolutionEllipsoidValue3=StringProperty()
resolutionEllipsoidAxis12=StringProperty()
resolutionEllipsoidValue1=StringProperty()
resolutionEllipsoidAxis11=StringProperty()
multiplicity=StringProperty()
resolutionLimitLow=StringProperty()
rMeasWithinIPlusIMinus=StringProperty()
DanoOverSigDano=StringProperty()
completenessSpherical=StringProperty()
nTotalUniqueObservations=StringProperty()
rMerge=StringProperty()
rPimWithinIPlusIMinus=StringProperty()
anomalousCompletenessEllipsoidal=StringProperty()
nTotalObservations=StringProperty()
completenessEllipsoidal=StringProperty()
anomalousCompleteness=StringProperty()
anomalousMultiplicity=StringProperty()
resolutionLimitHigh=StringProperty()
completeness=StringProperty()
ccHalf=StringProperty()
rPimAllIPlusIMinus=StringProperty()
meanIOverSigI=StringProperty()
anomalousCompletenessSpherical=StringProperty()
ccAnomalous=StringProperty()
rMeasAllIPlusIMinus=StringProperty()
refinedCell_beta=StringProperty()
refinedCell_b=StringProperty()
wavelength=StringProperty()
refinedCell_a=StringProperty()
refinedCell_alpha=StringProperty()
spaceGroup=StringProperty()
refinedCell_c=StringProperty()
refinedCell_gamma=StringProperty()
# Relationships
is_statisticalreport=RelationshipTo(StatisticalReport, 'IS')
......@@ -29,14 +129,113 @@ class Report(StructuredNode):
@property
def serialize(self):
"""
'''
Serializer for node properties
"""
'''
return {
'node_properties': {
'report_path': self.report_path,
'report_source': self.report_source,
'report_size': self.report_size,
# GPhL_pipedream report properties
'command': self.command,
'jsonversion': self.jsonversion,
'runby': self.runby,
'runfrom': self.runfrom,
'jobid': self.jobid,
'gphlpipedream_output': self.gphlpipedream_output,
'version': self.version,
# Ligands fitting (Rhofit) report properties
'ligandomin': self.ligandomin,
'mogulzbond': self. mogulzbond,
'ligandbmin': self.ligandbmin,
'mogulring': self.mogulring,
'moguldihe': self.moguldihe,
'ligandbavg': self.ligandbavg,
'mogulangl': self.mogulangl,
'mogulbond': self.mogulbond,
'ligandbmax': self.ligandbmax,
'ligandid': self.ligandid,
'ligandomax': self.ligandomax,
'ligandcc': self.ligandcc,
'mogulzangl': self.mogulzangl,
'molprobitypercentile': self.molprobitypercentile,
'ramaoutlierpercent': self.ramaoutlierpercent,
'cbetadeviations': self.cbetadeviations,
'ramafavoredpercent': self.ramafavoredpercent,
'poorrotamers': self.poorrotamers,
'rmsbonds': self.rmsbonds,
'rmsangles': self.rmsangles,
'clashpercentile': self.clashpercentile,
'poorrotamerspercent': self.poorrotamerspercent,
'clashscore': self.clashscore,
'ramafavored': self.ramafavored,
'molprobityscore': self.molprobityscore,
'ramaoutliers': self.ramaoutlers,
'closecontacts': self.closecontacts,
'chain': self.chain,
'contactscore': self.contactscore,
'ligandstrain': self.ligandstrain,
'poorfit': self.poorfit,
'output': self.output,
'correlationcoefficient': self.correlationcoefficient,
'rhofitscore': self.rhofitscore,
# Refinement/Post-refinement report properties
'WilsonB': self.WilsonB,
'Rfree': self.Rfree,
'MeanB': self.MeanB,
'type': self.type,
'step': self.step,
'RMSbonds': self.RMSbonds,
'RMSangles': self.RMSangles,
'R': self.R,
'WatersPresent': self.WatersPresent,
'selectedmodel': self.selectedmodel,
'refinementprotocol': self.refinementprotocol,
# AutoPROC report properties (includes AutoProcscaling, AutoProcScalingStatistics and AutoProc (cf pipdream_summary.json))
'recordTimeStamp': self.recordTimeStamp,
'resolutionEllipsoidAxis13': self.resolutionEllipsoidAxis13,
'resolutionEllipsoidAxis33': self.resolutionEllipsoidAxis33,
'resolutionEllipsoidAxis23': self.resolutionEllipsoidAxis23,
'resolutionEllipsoidValue2': self.resolutionEllipsoidValue2,
'resolutionEllipsoidAxis21': self.resolutionEllipsoidAxis21,
'resolutionEllipsoidAxis31': self.resolutionEllipsoidAxis31,
'resolutionEllipsoidAxis22': self.resolutionEllipsoidAxis22,
'resolutionEllipsoidAxis32': self.resolutionEllipsoidAxis32,
'resolutionEllipsoidValue3': self.resolutionEllipsoidValue3,
'resolutionEllipsoidAxis12': self.resolutionEllipsoidAxis12,
'resolutionEllipsoidValue1': self.resolutionEllipsoidValue1,
'resolutionEllipsoidAxis11': self.resolutionEllipsoidAxis11,
'multiplicity': self.multiplicity,
'resolutionLimitLow': self.resolutionLimitLow,
'rMeasWithinIPlusIMinus': self.rMeasWithinIPlusIMinus,
'DanoOverSigDano': self.DanoOverSigDano,
'completenessSpherical': self.completenessSpherical,
'nTotalUniqueObservations': self.nTotalUniqueObservations,
'rMerge': self.rMerge,
'rPimWithinIPlusIMinus': self.rPimWithinIPlusIMinus,
'anomalousCompletenessEllipsoidal': self.anomalousCompletenessEllipsoidal,
'nTotalObservations': self.nTotalObservations,
'completenessEllipsoidal': self.completenessEllipsoidal,
'anomalousCompleteness': self.anomalousCompleteness,
'anomalousMultiplicity': self.anomalousMultiplicity,
'resolutionLimitHigh': self.resolutionLimitHigh,
'completeness': self.completeness,
'ccHalf': self.ccHalf,
'rPimAllIPlusIMinus': self.rPimAllIPlusIMinus,
'meanIOverSigI': self.meanIOverSigI,
'anomalousCompletenessSpherical': self.anomalousCompletenessSpherical,
'ccAnomalous': self.ccAnomalous,
'rMeasAllIPlusIMinus': self.rMeasAllIPlusIMinus,
'refinedCell_beta': self.refinedCell_beta,
'refinedCell_b': self.refinedCell_b,
'wavelength': self.wavelength,
'refinedCell_a': self.refinedCell_a,
'refinedCell_alpha': self.refinedCell_alpha,
'spaceGroup': self.spaceGroup,
'refinedCell_c': self.refinedCell_c,
'refinedCell_gamma': self.refinedCell_gamma,
},
}
\ No newline at end of file
}
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