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Commit 0f835264 authored by Raphael Bourgeas's avatar Raphael Bourgeas
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ADR-Documents/v13_graph_data_model.json 0 → 100644
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dataproc/api/models/__pycache__/dpstep_model.cpython-38.pyc
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dataproc/api/models/__pycache__/structurefactors_model.cpython-38.pyc
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dataproc/api/models/dpstep_model.py
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......@@ -5,29 +5,29 @@ from uuid import uuid4
from neomodel import StructuredNode, StringProperty, IntegerProperty, UniqueIdProperty, RelationshipTo
# Models imports
from api.models.ligandsfitting_model import LigandsFitting
from api.models.refinement_model import Refinement
from api.models.postrefinement_model import PostRefinement
from api.models.reductionscaling_model import ReductionScaling
from api.models.autoPROC_model import autoPROC
from api.models.rhofit_model import Rhofit
from api.models.buster_model import Buster
from api.models.report_model import Report
from api.models.coordinates_model import Coordinates
from api.models.structurefactors_model import StructureFactors
from api.models.pdbfile_model import PDBFile
from api.models.mmciffile_model import mmCIFFile
from api.models.construct_model import Construct
from api.models.reference_model import Reference
from api.models.pipedream_model import GPhLPipedream
from api.models.pipedream_cmd_options_model import PipedreamCmdOptions
from api.models.autoproc_cmd_options_model import AutoprocCmdOptions
from api.models.buster_cmd_options_model import BusterCmdOptions
from api.models.rhofit_cmd_options_model import RhofitCmdOptions
from api.models.started_model import Started
from api.models.completed_model import Completed
from api.models.error_model import Error
from api.models.importation_model import Importation
# from api.models.ligandsfitting_model import LigandsFitting
# from api.models.refinement_model import Refinement
# from api.models.postrefinement_model import PostRefinement
# from api.models.reductionscaling_model import ReductionScaling
# from api.models.autoPROC_model import autoPROC
# from api.models.rhofit_model import Rhofit
# from api.models.buster_model import Buster
# from api.models.report_model import Report
# from api.models.coordinates_model import Coordinates
# # from api.models.structurefactors_model import StructureFactors
# from api.models.pdbfile_model import PDBFile
# from api.models.mmciffile_model import mmCIFFile
# from api.models.construct_model import Construct
# from api.models.reference_model import Reference
# from api.models.pipedream_model import GPhLPipedream
# from api.models.pipedream_cmd_options_model import PipedreamCmdOptions
# from api.models.autoproc_cmd_options_model import AutoprocCmdOptions
# from api.models.buster_cmd_options_model import BusterCmdOptions
# from api.models.rhofit_cmd_options_model import RhofitCmdOptions
# from api.models.started_model import Started
# from api.models.completed_model import Completed
# from api.models.error_model import Error
# from api.models.importation_model import Importation
class DPStep(StructuredNode):
......@@ -41,29 +41,29 @@ class DPStep(StructuredNode):
# name=StringProperty()
# Relationships
is_fitting=RelationshipTo(LigandsFitting, 'IS')
is_refinement=RelationshipTo(Refinement, 'IS')
is_postrefinement=RelationshipTo(PostRefinement, 'IS')
is_reductionscaling=RelationshipTo(ReductionScaling, 'IS')
is_importation=RelationshipTo(Importation, 'IS')
# is_fitting=RelationshipTo(LigandsFitting, 'IS')
# is_refinement=RelationshipTo(Refinement, 'IS')
# is_postrefinement=RelationshipTo(PostRefinement, 'IS')
# is_reductionscaling=RelationshipTo(ReductionScaling, 'IS')
# is_importation=RelationshipTo(Importation, 'IS')
with_autoproc=RelationshipTo(autoPROC, 'WITH')
with_rhofit=RelationshipTo(Rhofit, 'WITH')
with_buster=RelationshipTo(Buster, 'WITH')
with_pipedream=RelationshipTo(GPhLPipedream, 'WITH')
# with_autoproc=RelationshipTo(autoPROC, 'WITH')
# with_rhofit=RelationshipTo(Rhofit, 'WITH')
# with_buster=RelationshipTo(Buster, 'WITH')
# with_pipedream=RelationshipTo(GPhLPipedream, 'WITH')
genereates_report=RelationshipTo(Report, 'GENERATES')
generates_coordinates=RelationshipTo(Coordinates, 'GENERATES')
generates_structurefactors=RelationshipTo(StructureFactors, 'GENERATES')
# genereates_report=RelationshipTo(Report, 'GENERATES')
# generates_coordinates=RelationshipTo(Coordinates, 'GENERATES')
# # generates_structurefactors=RelationshipTo('StructureFactors', 'GENERATES')
has_status_error=RelationshipTo(Error, 'HAS STATUS')
has_status_completed=RelationshipTo(Completed, 'HAS STATUS')
has_status_started=RelationshipTo(Started, 'HAS STATUS')
# has_status_error=RelationshipTo(Error, 'HAS STATUS')
# has_status_completed=RelationshipTo(Completed, 'HAS STATUS')
# has_status_started=RelationshipTo(Started, 'HAS STATUS')
pipedream_cmd_options=RelationshipTo(PipedreamCmdOptions, 'HAS')
autoproc_cmd_options=RelationshipTo(AutoprocCmdOptions, 'HAS')
buster_cmd_options=RelationshipTo(BusterCmdOptions, 'HAS')
rhofit_cmd_options=RelationshipTo(RhofitCmdOptions, 'HAS')
# pipedream_cmd_options=RelationshipTo(PipedreamCmdOptions, 'HAS')
# autoproc_cmd_options=RelationshipTo(AutoprocCmdOptions, 'HAS')
# buster_cmd_options=RelationshipTo(BusterCmdOptions, 'HAS')
# rhofit_cmd_options=RelationshipTo(RhofitCmdOptions, 'HAS')
@property
def serialize(self):
......
dataproc/api/models/structurefactors_model.py
+ 10
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......@@ -5,9 +5,9 @@ from uuid import uuid4
from neomodel import StructuredNode, StringProperty, IntegerProperty, UniqueIdProperty, RelationshipTo
# Models imports
# from api.models.dpstep_model import DPStep
from api.models.mtzfile_model import MTZ
from api.models.scalepackfile_model import ScalepackFile
from api.models.dpstep_model import DPStep
# from api.models.mtzfile_model import MTZ
# from api.models.scalepackfile_model import ScalepackFile
from api.models.reference_model import Reference
# from api.models.construct_model import Construct
......@@ -20,24 +20,20 @@ class StructureFactors(StructuredNode):
# Properties
uuid=StringProperty(unique_index=True, default=uuid4)
# processingtype=StringProperty()
gamma=StringProperty()
a=StringProperty()
alpha=StringProperty()
b=StringProperty()
beta=StringProperty()
c=StringProperty()
# rsf_source=StringProperty()
# rsf_filesize=StringProperty()
# rsf_filepath=StringProperty()
symmetry=StringProperty()
# Relationships
is_scalepack=RelationshipTo('ScalepackFile', 'IS')
is_mtz=RelationshipTo('MTZfile', 'IS')
labelled_ref=RelationshipTo('Reference', 'LABELLED_AS')
# is_scalepack=RelationshipTo('ScalepackFile', 'IS')
# is_mtz=RelationshipTo('MTZfile', 'IS')
labelled_ref=RelationshipTo(Reference, 'LABELLED_AS')
# input_as_ref=RelationshipTo('DPStep', 'INPUT_AS_REFERENCE')
# input_of=RelationshipTo('DPStep', 'INPUT')
input_of=RelationshipTo('DPStep', 'INPUT')
# belongs=RelationshipTo('Construct', 'BELONGS')
@property
......@@ -50,16 +46,13 @@ class StructureFactors(StructuredNode):
return {
'structurefactors_node_properties': {
'uuid': self.uuid,
# 'rsf_source': self.rsf_source,
# 'rsf_filesize': self.rsf_filesize,
# 'rsf_filepath': self.rsf_filepath,
# 'datatype': self.datatype,
# 'processingtype': self.processingtype,
'gamma': self.gamma,
'a': self.a,
'b': self.b,
'beta': self.beta,
'c': self.c,
'symmetry': self.symmetry,
'alpha': self.alpha,
},
}
dataproc/api/views/proc_input_view.py
+ 70
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......@@ -61,7 +61,6 @@ def storeProcInput(request):
# structurefactors=storeParseStructureFactors(json_data_reference)
# storeParseStructureFactors(json_data_reference)
# storeParseMTZ(json_data_mtz, structurefactors)
return JsonResponse({"STATUS": "INPUT SUCCESSFULLY REGISTERED"})
......@@ -218,66 +217,65 @@ def storeParseReport(data):
return ({"STATUS": "ERROR OCCURRED WHILE REGISTERING REPORT"})
@csrf_exempt
def storeParseStructureFactors(data):
def storeParseReference():
"""
Creates nodes for
Creates nodes for reference label
"""
logger.info('ENTER FUNCTION')
try:
# structurefactors=StructureFactors(
# # uuid=data['uuid'],
# # datatype=data['datatype'],
# # processingtype=data['processingtype'],
# gamma=data['gamma'],
# a=data['a'],
# alpha=data['alpha'],
# b=data['b'],
# beta=data['beta'],
# c=data['c'])
# # rsf_source=data['rsf_source'],
# # rsf_filesize=data['rsf_filesize'],
# # rsf_filepath=data['rsf_filepath'])
reference=Reference()
reference.save()
reference2=reference.serialize
return reference2
structurefactors=StructureFactors(
gamma=data['gamma'],
a=data['a'],
alpha=data['alpha'],
b=data['b'],
beta=data['beta'],
c=data['c'])
except:
return ({"STATUS": "ERROR OCCURRED WHILE REGISTERING REFERENCE LABEL NODE"})
logger.info(structurefactors)
@csrf_exempt
def storeParseStructureFactors(data, reference):
"""
Creates nodes for Structure factors with relative properties
"""
try:
structurefactors=StructureFactors(
gamma=data['cell']['gamma'],
a=data['cell']['a'],
alpha=data['cell']['alpha'],
b=data['cell']['b'],
beta=data['cell']['beta'],
c=data['cell']['c'],
symmetry=data['symmetry'])
structurefactors.save()
# structurefactors2=structurefactors.serialize
# structurefactors2=structurefactors.serialize
# connectStructureFactorsRef(structurefactors2['structurefactors_node_properties']['uuid'], ref['ref_node_properties']['uuid'])
logger.info('SAVE DATA')
return structurefactors.serialize
structurefactors2=structurefactors.serialize
connectStructureFactorsRef(structurefactors2['structurefactors_node_properties']['uuid'], reference['ref_node_properties']['uuid'])
return ({"STATUS": "STRUCTURE FACTORS REGISTERED"})
except:
return ({"STATUS": "ERROR OCCURRED WHILE REGISTERING RC"})
# @csrf_exempt
# def storeParseMTZ(data, structurefactors):
# """
# Creates nodes for
# """
# try:
# mtz=MTZ(datatype=data['datatype'])
# mtz.save()
@csrf_exempt
def storeParseDPStep():
# mtz2=mtz.serialize
# # connectStructureFactorsMTZ(structurefactors['structurefactors_node_properties']['uuid'], mtz2['mtz_node_properties']['uuid'])
"""
Creates nodes for dpstep label
"""
# return ({"STATUS": "MTZ DATATYPE REGISTERED"})
try:
dpstep=DPStep()
dpstep.save()
dpstep2=dpstep.serialize
return dpstep2
# except:
# return ({"STATUS": "ERROR OCCURRED WHILE REGISTERING RC"})
except:
return ({"STATUS": "ERROR OCCURRED WHILE REGISTERING DPSTEP LABEL NODE"})
@csrf_exempt
def storeParseRC(data, report):
......@@ -513,17 +511,24 @@ def connectStructureFactorsRef(data1, data2):
"""
Create a relationship between a SF (Structure factors) and Reference node.
"""
logger.info('ENTER FUNCTION')
try:
logger.info('TRY FUNCTION')
structurefactors=StructureFactors.nodes.get(uuid=data1)
ref=Reference.nodes.get(uuid=data2)
return JsonResponse({"STATUS": structurefactors.labelled.connect(ref)}, safe=False)
logger.info(structurefactors)
logger.info(ref)
return JsonResponse({"STATUS": structurefactors.labelled_ref.connect(ref)}, safe=False)
except:
return JsonResponse({"STATUS": "ERROR OCCURRED WHILE CONNECTING STRUCTURE FACTORS TO REFERENCE"}, safe=False)
@csrf_exempt
def connectStructureFactorsMTZ(data1, data2):
def connectStructureFactorsDPStep(data1, data2):
"""
Create a relationship between a SF (Structure factors) and MTZ node.
......@@ -531,8 +536,23 @@ def connectStructureFactorsMTZ(data1, data2):
try:
structurefactors=StructureFactors.nodes.get(uuid=data1)
mtz=MTZ.nodes.get(uuid=data2)
return JsonResponse({"STATUS": structurefactors.is_mtz.connect(mtz)}, safe=False)
dpstep=DPStep.nodes.get(uuid=data2)
return JsonResponse({"STATUS": structurefactors.input_of.connect(dpstep)}, safe=False)
except:
return JsonResponse({"STATUS": "ERROR OCCURRED WHILE CONNECTING STRUCTURE FACTORS TO MTZ"}, safe=False)
return JsonResponse({"STATUS": "ERROR OCCURRED WHILE CONNECTING STRUCTURE FACTORS TO DPSTEP"}, safe=False)
# @csrf_exempt
# def connectStructureFactorsMTZ(data1, data2):
# """
# Create a relationship between a SF (Structure factors) and MTZ node.
# """
# try:
# structurefactors=StructureFactors.nodes.get(uuid=data1)
# mtz=MTZ.nodes.get(uuid=data2)
# return JsonResponse({"STATUS": structurefactors.is_mtz.connect(mtz)}, safe=False)
# except:
# return JsonResponse({"STATUS": "ERROR OCCURRED WHILE CONNECTING STRUCTURE FACTORS TO MTZ"}, safe=False)
dataproc/requirements.txt 0 → 100644
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asgiref==3.2.10
Django==3.0.8
django-neomodel==0.0.4
neo4j-driver==1.7.2
neobolt==1.7.17
neomodel==3.3.2
neotime==1.7.4
pytz==2020.1
six==1.15.0
sqlparse==0.3.1
djangorestframework==3.12.2
requirements.txt
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asgiref==3.2.10
Django==3.0.8
django-neomodel==0.0.4
neo4j-driver==4.3.1
neomodel==4.0.4
neotime==1.7.4
pytz==2021.1
six==1.16
sqlparse==0.3.1
......
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