Update models

dataproc/api/models/autoPROC_model.py

@@ -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

+
+'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

@@ -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

@@ -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

@@ -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

@@ -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