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Merge pull request #21 from oesteban/enh/refactor-json-derivatives
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[ENH] Refactor schema of JSON derivatives
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@oesteban
oesteban authored May 31, 2017
2 parents 93a66fd + e8c391c commit aba6375
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Showing 101 changed files with 1,098 additions and 8,276 deletions.
1 change: 0 additions & 1 deletion circle.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,3 @@ test:
- docker-compose -f dockereve-master/docker-compose.yml up -d
- sleep 60
- python test/testGetPost.py

257 changes: 114 additions & 143 deletions dockereve-master/eve-app/settings.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
import os
import re
from copy import deepcopy

get_mongo_host = re.match('tcp://(.*):(.*)', os.environ['MONGODB_PORT'])

bids_schema = {
# BIDS identification bits
'modality': {
'type': 'string',
'required': True
Expand All @@ -15,9 +18,71 @@
'acq_id': {'type': 'string'},
'task_id': {'type': 'string'},
'run_id': {'type': 'string'},
# BIDS metadata
'AccelNumReferenceLines': {'type': 'integer'},
'AccelerationFactorPE': {'type': 'integer'},
'AcquisitionMatrix': {'type': 'string'},
'CogAtlasID': {'type': 'string'},
'CogPOID': {'type': 'string'},
'CoilCombinationMethod': {'type': 'string'},
'ContrastBolusIngredient': {'type': 'string'},
'ConversionSoftware': {'type': 'string'},
'ConversionSoftwareVersion': {'type': 'string'},
'DelayTime': {'type': 'float'},
'DeviceSerialNumber': {'type': 'string'},
'EchoTime': {'type': 'float'},
'EchoTrainLength': {'type': 'integer'},
'EffectiveEchoSpacing': {'type': 'float'},
'FlipAngle': {'type': 'integer'},
'GradientSetType': {'type': 'string'},
'HardcopyDeviceSoftwareVersion': {'type': 'string'},
'ImageType': {'type': 'string'},
'ImagingFrequency': {'type': 'integer'},
'InPlanePhaseEncodingDirection': {'type': 'string'},
'InstitutionAddress': {'type': 'string'},
'InstitutionName': {'type': 'string'},
'Instructions': {'type': 'string'},
'InversionTime': {'type': 'float'},
'MRAcquisitionType': {'type': 'string'},
'MRTransmitCoilSequence': {'type': 'string'},
'MagneticFieldStrength': {'type': 'integer'},
'Manufacturer': {'type': 'string'},
'ManufacturersModelName': {'type': 'string'},
'MatrixCoilMode': {'type': 'string'},
'MultibandAccelerationFactor': {'type': 'float'},
'NumberOfAverages': {'type': 'integer'},
'NumberOfPhaseEncodingSteps': {'type': 'integer'},
'NumberOfVolumesDiscardedByScanner': {'type': 'float'},
'NumberOfVolumesDiscardedByUser': {'type': 'float'},
'NumberShots': {'type': 'integer'},
'ParallelAcquisitionTechnique': {'type': 'string'},
'ParallelReductionFactorInPlane': {'type': 'float'},
'PartialFourier': {'type': 'boolean'},
'PartialFourierDirection': {'type': 'string'},
'PatientPosition': {'type': 'string'},
'PercentPhaseFieldOfView': {'type': 'integer'},
'PercentSampling': {'type': 'integer'},
'PhaseEncodingDirection': {'type': 'string'},
'PixelBandwidth': {'type': 'integer'},
'ProtocolName': {'type': 'string'},
'PulseSequenceDetails': {'type': 'string'},
'PulseSequenceType': {'type': 'string'},
'ReceiveCoilName': {'type': 'string'},
'RepetitionTime': {'type': 'float'},
'ScanOptions': {'type': 'string'},
'ScanningSequence': {'type': 'string'},
'SequenceName': {'type': 'string'},
'SequenceVariant': {'type': 'string'},
'SliceEncodingDirection': {'type': 'string'},
'SoftwareVersions': {'type': 'string'},
'TaskDescription': {'type': 'string'},
'TotalReadoutTime': {'type': 'float'},
'TotalScanTimeSec': {'type': 'integer'},
'TransmitCoilName': {'type': 'string'},
'VariableFlipAngleFlag': {'type': 'string'},
}

settings_schema = {
prov_schema = {
'version': {
'type': 'string',
'required': True
Expand All @@ -30,6 +95,15 @@
'type': 'string',
'required': True
},
'settings': {
'type': 'dict',
'schema': {
'fd_thres': {'type': 'float'},
'hmc_fsl': {'type': 'boolean'},
'testing': {'type': 'boolean'}
},
},
'mriqc_pred': {'type': 'integer'},
}

bold_iqms_schema = {
Expand All @@ -42,6 +116,7 @@
'required': True

},
'dummy_trs': {'type': 'integer'},
'dvars_nstd': {
'type': 'float',
'required': True
Expand Down Expand Up @@ -264,10 +339,6 @@
'type': 'float',
'required': True
},
'mriqc_pred': {
'type': 'integer',
'required': True
},
'qi_1': {
'type': 'float',
'required': True
Expand Down Expand Up @@ -489,153 +560,53 @@
'item_title': 'bold',
'resource_methods': ['GET', 'POST'],
'item_methods': ['GET', 'PATCH', 'PUT', 'DELETE'],
'schema': {
# if modality == bold, the fields below are required
'TaskName': {
'type': 'string',
'required': True
},
'AccelNumReferenceLines': {'type': 'integer'},
'AccelerationFactorPE': {'type': 'integer'},
'AcquisitionMatrix': {'type': 'string'},
'DeviceSerialNumber': {'type': 'string'},
'EchoTime': {'type': 'float'},
'EchoTrainLength': {'type': 'integer'},
'FlipAngle': {'type': 'integer'},
'ImageType': {'type': 'string'},
'ImagingFrequency': {'type': 'integer'},
'InPlanePhaseEncodingDirection': {'type': 'string'},
'InversionTime': {'type': 'float'},
'MRAcquisitionType': {'type': 'string'},
'MagneticFieldStrength': {'type': 'integer'},
'ManufacturerModelName': {'type': 'string'},
'NumberOfAverages': {'type': 'integer'},
'NumberOfPhaseEncodingSteps': {'type': 'integer'},
'PatientPosition': {'type': 'string'},
'PercentPhaseFieldOfView': {'type': 'integer'},
'PercentSampling': {'type': 'integer'},
'PhaseEncodingDirection': {'type': 'string'},
'PixelBandwidth': {'type': 'integer'},
'ProtocolName': {'type': 'string'},
'ReceiveCoilName': {'type': 'string'},
'RepetitionTime': {'type': 'float'},
'ScanOptions': {'type': 'string'},
'ScanningSequence': {'type': 'string'},
'SequenceName': {'type': 'string'},
'SequenceVariant': {'type': 'string'},
'SoftwareVersions': {'type': 'string'},
'TotalScanTimeSec': {'type': 'integer'},
'TransmitCoilName': {'type': 'string'},
'VariableFlipAngleFlag': {'type': 'string'},
'ContrastBolusIngredient': {'type': 'string'},
'Manufacturer': {'type': 'string'},
'HardcopyDeviceSoftwareVersion': {'type': 'string'},
'GradientSetType': {'type': 'string'},
'MRTransmitCoilSequence': {'type': 'string'},
'MatrixCoilMode': {'type': 'string'},
'CoilCombinationMethod': {'type': 'string'},
'PulseSequenceType': {'type': 'string'},
'PulseSequenceDetails': {'type': 'string'},
'NumberShots': {'type': 'integer'},
'ParallelReductionFactorInPlane': {'type': 'float'},
'ParallelAcquisitionTechnique': {'type': 'string'},
'PartialFourier': {'type': 'boolean'},
'PartialFourierDirection': {'type': 'string'},
'EffectiveEchoSpacing': {'type': 'float'},
'TotalReadoutTime': {'type': 'float'},
'SliceEncodingDirection': {'type': 'string'},
'NumberOfVolumesDiscardedByScanner': {'type': 'float'},
'NumberOfVolumesDiscardedByUser': {'type': 'float'},
'DelayTime': {'type': 'float'},
'MultibandAccelerationFactor': {'type': 'float'},
'Instructions': {'type': 'string'},
'TaskDescription': {'type': 'string'},
'CogAtlasID': {'type': 'string'},
'CogPOID': {'type': 'string'},
'InstitutionName': {'type': 'string'},
'InstitutionAddress': {'type': 'string'},
'ConversionSoftware': {'type': 'string'},
'ConversionSoftwareVersion': {'type': 'string'},
} # end of schema
}, # end of bold
'T1w': {
'item_title': 'T1w',
'resource_methods': ['GET', 'POST'],
'item_methods': ['GET', 'PATCH', 'PUT', 'DELETE'],
'schema': {
# if modality == T1w, the fields below are required
'AccelNumReferenceLines': {'type': 'integer'},
'AccelerationFactorPE': {'type': 'integer'},
'AcquisitionMatrix': {'type': 'string'},
'DeviceSerialNumber': {'type': 'string'},
'EchoTime': {'type': 'float'},
'EchoTrainLength': {'type': 'integer'},
'FlipAngle': {'type': 'integer'},
'ImageType': {'type': 'string'},
'ImagingFrequency': {'type': 'integer'},
'InPlanePhaseEncodingDirection': {'type': 'string'},
'InversionTime': {'type': 'float'},
'MRAcquisitionType': {'type': 'string'},
'MagneticFieldStrength': {'type': 'integer'},
'ManufacturerModelName': {'type': 'string'},
'NumberOfAverages': {'type': 'integer'},
'NumberOfPhaseEncodingSteps': {'type': 'integer'},
'PatientPosition': {'type': 'string'},
'PercentPhaseFieldOfView': {'type': 'integer'},
'PercentSampling': {'type': 'integer'},
'PhaseEncodingDirection': {'type': 'string'},
'PixelBandwidth': {'type': 'integer'},
'ProtocolName': {'type': 'string'},
'ReceiveCoilName': {'type': 'string'},
'RepetitionTime': {'type': 'float'},
'ScanOptions': {'type': 'string'},
'ScanningSequence': {'type': 'string'},
'SequenceName': {'type': 'string'},
'SequenceVariant': {'type': 'string'},
'SoftwareVersions': {'type': 'string'},
'TotalScanTimeSec': {'type': 'integer'},
'TransmitCoilName': {'type': 'string'},
'VariableFlipAngleFlag': {'type': 'string'},
'ContrastBolusIngredient': {'type': 'string'},
'Manufacturer': {'type': 'string'},
'HardcopyDeviceSoftwareVersion': {'type': 'string'},
'GradientSetType': {'type': 'string'},
'MRTransmitCoilSequence': {'type': 'string'},
'MatrixCoilMode': {'type': 'string'},
'CoilCombinationMethod': {'type': 'string'},
'PulseSequenceType': {'type': 'string'},
'PulseSequenceDetails': {'type': 'string'},
'NumberShots': {'type': 'integer'},
'ParallelReductionFactorInPlane': {'type': 'float'},
'ParallelAcquisitionTechnique': {'type': 'string'},
'PartialFourier': {'type': 'boolean'},
'PartialFourierDirection': {'type': 'string'},
'EffectiveEchoSpacing': {'type': 'float'},
'TotalReadoutTime': {'type': 'float'},
'SliceEncodingDirection': {'type': 'string'},
'NumberOfVolumesDiscardedByScanner': {'type': 'float'},
'NumberOfVolumesDiscardedByUser': {'type': 'float'},
'DelayTime': {'type': 'float'},
'MultibandAccelerationFactor': {'type': 'float'},
'Instructions': {'type': 'string'},
'TaskDescription': {'type': 'string'},
'CogAtlasID': {'type': 'string'},
'CogPOID': {'type': 'string'},
'InstitutionName': {'type': 'string'},
'InstitutionAddress': {'type': 'string'},
'ConversionSoftware': {'type': 'string'},
'ConversionSoftwareVersion': {'type': 'string'},
} # end of schema
} # end of T1w

}
}


my_settings['DOMAIN']['bold']['schema'].update(bids_schema)
my_settings['DOMAIN']['bold']['schema'].update(settings_schema)
my_settings['DOMAIN']['bold']['schema'].update(bold_iqms_schema)
my_settings['DOMAIN']['bold']['schema'] = deepcopy(bold_iqms_schema)
my_settings['DOMAIN']['bold']['schema'].update(
{
'bids_meta': {
'type': 'dict',
'required': True,
'schema': deepcopy(bids_schema)
},
'provenance': {
'type': 'dict',
'required': True,
'schema': deepcopy(prov_schema)
}
}
)

my_settings['DOMAIN']['bold']['schema']['bids_meta']['schema'].update({
'TaskName': {
'type': 'string',
'required': True
},
})


my_settings['DOMAIN']['T1w']['schema'].update(bids_schema)
my_settings['DOMAIN']['T1w']['schema'].update(settings_schema)
my_settings['DOMAIN']['T1w']['schema'].update(t1w_iqms_schema)
my_settings['DOMAIN']['T1w']['schema'] = deepcopy(t1w_iqms_schema)
my_settings['DOMAIN']['T1w']['schema'].update(
{
'bids_meta': {
'type': 'dict',
'required': True,
'schema': deepcopy(bids_schema)
},
'provenance': {
'type': 'dict',
'required': True,
'schema': deepcopy(prov_schema)
}
}
)
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