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Merge pull request #520 from oesteban/enh/508
[ENH] Integration testing for MRIQCWebAPI
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| #!/bin/bash | ||
| # | ||
| # Balance nipype testing workflows across CircleCI build nodes | ||
| # | ||
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| # Setting # $ help set | ||
| set -e # Exit immediately if a command exits with a non-zero status. | ||
| set -u # Treat unset variables as an error when substituting. | ||
| set -x # Print command traces before executing command. | ||
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| # Exit if build_only tag is found | ||
| if [ "$(grep -qiP 'build[ _]?only' <<< "$GIT_COMMIT_MSG"; echo $? )" == "0" ]; then | ||
| exit 0 | ||
| fi | ||
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| # Exit if docs_only tag is found | ||
| if [ "$(grep -qiP 'docs[ _]?only' <<< "$GIT_COMMIT_MSG"; echo $? )" == "0" ]; then | ||
| echo "Building [docs_only], nothing to do." | ||
| exit 0 | ||
| fi | ||
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| MODALITY=T1w | ||
| NRECORDS=4 | ||
| if [ "$CIRCLE_NODE_INDEX" == "1" ]; then | ||
| MODALITY=bold | ||
| NRECORDS=9 | ||
| fi | ||
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| echo "Checking records in MRIQC Web API" | ||
| docker run -i --entrypoint="/usr/local/miniconda/bin/python" \ | ||
| ${DOCKER_IMAGE}:${DOCKER_TAG} \ | ||
| /root/src/mriqc/mriqc/bin/mriqcwebapi_test.py \ | ||
| ${MODALITY} ${NRECORDS} \ | ||
| --webapi-addr $( hostname -I | awk '{print $1}' ) --webapi-port ${MRIQC_API_PORT} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| # @Author: oesteban | ||
| # @Date: 2015-11-19 16:44:27 | ||
| from __future__ import print_function, division, absolute_import, unicode_literals | ||
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| def get_parser(): | ||
| """Build parser object""" | ||
| from argparse import ArgumentParser | ||
| from argparse import RawTextHelpFormatter | ||
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| parser = ArgumentParser(description='MRIQCWebAPI: Check entries', | ||
| formatter_class=RawTextHelpFormatter) | ||
| parser.add_argument('modality', action='store', choices=['T1w', 'bold'], | ||
| help='number of expected items in the database') | ||
| parser.add_argument('expected', action='store', type=int, | ||
| help='number of expected items in the database') | ||
| parser.add_argument( | ||
| '--webapi-addr', action='store', default='34.201.213.252', type=str, | ||
| help='IP address where the MRIQC WebAPI is listening') | ||
| parser.add_argument( | ||
| '--webapi-port', action='store', default=80, type=int, | ||
| help='port where the MRIQC WebAPI is listening') | ||
| return parser | ||
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| def main(): | ||
| """Entry point""" | ||
| from requests import get | ||
| from mriqc import MRIQC_LOG | ||
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| # Run parser | ||
| opts = get_parser().parse_args() | ||
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| endpoint = 'http://{}:{}/{}'.format(opts.webapi_addr, | ||
| opts.webapi_port, | ||
| opts.modality) | ||
| MRIQC_LOG.info('Sending GET: %s', endpoint) | ||
| resp = get(endpoint).json() | ||
| MRIQC_LOG.info('There are %d records in database', resp['_meta']['total']) | ||
| assert opts.expected == resp['_meta']['total'] | ||
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| if __name__ == '__main__': | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,198 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
| # vi: set ft=python sts=4 ts=4 sw=4 et: | ||
| from __future__ import print_function, division, absolute_import, unicode_literals | ||
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| from nipype import logging | ||
| from nipype.interfaces.base import (Bunch, traits, isdefined, TraitedSpec, | ||
| BaseInterfaceInputSpec, File, Str) | ||
| from niworkflows.interfaces.base import SimpleInterface | ||
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| IFLOGGER = logging.getLogger('interface') | ||
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| SECRET_KEY = """\ | ||
| ZUsBaabr6PEbav5DKAHIODEnwpwC58oQTJF7KWvDBPUmBIVFFtw\ | ||
| Od7lQBdz9r9ulJTR1BtxBDqDuY0owxK6LbLB1u1b64ZkIMd46\ | ||
| """ | ||
|
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| # metadata whitelist | ||
| META_WHITELIST = [ | ||
| 'AccelNumReferenceLines', | ||
| 'AccelerationFactorPE', | ||
| 'AcquisitionMatrix', | ||
| 'CogAtlasID', | ||
| 'CogPOID', | ||
| 'CoilCombinationMethod', | ||
| 'ContrastBolusIngredient', | ||
| 'ConversionSoftware', | ||
| 'ConversionSoftwareVersion', | ||
| 'DelayTime', | ||
| 'DeviceSerialNumber', | ||
| 'EchoTime', | ||
| 'EchoTrainLength', | ||
| 'EffectiveEchoSpacing', | ||
| 'FlipAngle', | ||
| 'GradientSetType', | ||
| 'HardcopyDeviceSoftwareVersion', | ||
| 'ImageType', | ||
| 'ImagingFrequency', | ||
| 'InPlanePhaseEncodingDirection', | ||
| 'InstitutionAddress', | ||
| 'InstitutionName', | ||
| 'Instructions', | ||
| 'InversionTime', | ||
| 'MRAcquisitionType', | ||
| 'MRTransmitCoilSequence', | ||
| 'MagneticFieldStrength', | ||
| 'Manufacturer', | ||
| 'ManufacturersModelName', | ||
| 'MatrixCoilMode', | ||
| 'MultibandAccelerationFactor', | ||
| 'NumberOfAverages', | ||
| 'NumberOfPhaseEncodingSteps', | ||
| 'NumberOfVolumesDiscardedByScanner', | ||
| 'NumberOfVolumesDiscardedByUser', | ||
| 'NumberShots', | ||
| 'ParallelAcquisitionTechnique', | ||
| 'ParallelReductionFactorInPlane', | ||
| 'PartialFourier', | ||
| 'PartialFourierDirection', | ||
| 'PatientPosition', | ||
| 'PercentPhaseFieldOfView', | ||
| 'PercentSampling', | ||
| 'PhaseEncodingDirection', | ||
| 'PixelBandwidth', | ||
| 'ProtocolName', | ||
| 'PulseSequenceDetails', | ||
| 'PulseSequenceType', | ||
| 'ReceiveCoilName', | ||
| 'RepetitionTime', | ||
| 'ScanOptions', | ||
| 'ScanningSequence', | ||
| 'SequenceName', | ||
| 'SequenceVariant', | ||
| 'SliceEncodingDirection', | ||
| 'SoftwareVersions', | ||
| 'TaskDescription', | ||
| 'TaskName', | ||
| 'TotalReadoutTime', | ||
| 'TotalScanTimeSec', | ||
| 'TransmitCoilName', | ||
| 'VariableFlipAngleFlag', | ||
| 'acq_id', | ||
| 'modality', | ||
| 'run_id', | ||
| 'subject_id', | ||
| 'task_id', | ||
| ] | ||
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| PROV_WHITELIST = [ | ||
| 'version', | ||
| 'md5sum', | ||
| 'software', | ||
| 'settings' | ||
| ] | ||
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| class UploadIQMsInputSpec(BaseInterfaceInputSpec): | ||
| in_iqms = File(exists=True, mandatory=True, desc='the input IQMs-JSON file') | ||
| address = Str(mandatory=True, desc='ip address listening') | ||
| port = traits.Int(mandatory=True, desc='MRIQCWebAPI service port') | ||
| email = Str(desc='set sender email') | ||
| strict = traits.Bool(False, usedefault=True, | ||
| desc='crash if upload was not succesfull') | ||
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| class UploadIQMs(SimpleInterface): | ||
| """ | ||
| Upload features to MRIQCWebAPI | ||
| """ | ||
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| input_spec = UploadIQMsInputSpec | ||
| output_spec = TraitedSpec | ||
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| def _run_interface(self, runtime): | ||
| email = None | ||
| if isdefined(self.inputs.email): | ||
| email = self.inputs.email | ||
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| response = upload_qc_metrics( | ||
| self.inputs.in_iqms, | ||
| self.inputs.address, | ||
| self.inputs.port, | ||
| ) | ||
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| if response.status_code == 201: | ||
| IFLOGGER.info('QC metrics successfully uploaded.') | ||
| return runtime | ||
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| errmsg = 'QC metrics failed to upload. Status %d: %s' % ( | ||
| response.status_code, response.text) | ||
| IFLOGGER.warn(errmsg) | ||
| if self.inputs.strict: | ||
| raise RuntimeError(response.text) | ||
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| return runtime | ||
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| def upload_qc_metrics(in_iqms, addr, port, email=None): | ||
| """ | ||
| Upload qc metrics to remote repository. | ||
| :param str in_iqms: Path to the qc metric json file as a string | ||
| :param str email: email address to be included with the metric submission | ||
| :param bool no_sub: Flag from settings indicating whether or not metrics should be submitted. | ||
| If False, metrics will be submitted. If True, metrics will not be submitted. | ||
| :param str mriqc_webapi: the default mriqcWebAPI url | ||
| :param bool upload_strict: the client should fail if it's strict mode | ||
| :return: either the response object if a response was successfully sent | ||
| or it returns the string "No Response" | ||
| :rtype: object | ||
| """ | ||
| from json import load, dumps | ||
| import requests | ||
| from io import open | ||
| from copy import deepcopy | ||
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| with open(in_iqms, 'r') as input_json: | ||
| in_data = load(input_json) | ||
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| # Extract metadata and provenance | ||
| meta = in_data.pop('bids_meta') | ||
| prov = in_data.pop('provenance') | ||
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| # At this point, data should contain only IQMs | ||
| data = deepcopy(in_data) | ||
|
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| # Check modality | ||
| modality = meta.get('modality', 'None') | ||
| if modality not in ('T1w', 'bold'): | ||
| errmsg = ('Submitting to MRIQCWebAPI: image modality should be "bold" or "T1w", ' | ||
| '(found "%s")' % modality) | ||
| return Bunch(status_code=1, text=errmsg) | ||
|
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| # Filter metadata values that aren't in whitelist | ||
| data['bids_meta'] = {k: meta[k] for k in META_WHITELIST if k in meta} | ||
| # Filter provenance values that aren't in whitelist | ||
| data['provenance'] = {k: prov[k] for k in PROV_WHITELIST if k in prov} | ||
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| if email: | ||
| data['email'] = email | ||
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| headers = {'token': SECRET_KEY, "Content-Type": "application/json"} | ||
| try: | ||
| # if the modality is bold, call "bold" endpointt | ||
| response = requests.post( | ||
| 'http://{}:{}/{}'.format(addr, port, modality), | ||
| headers=headers, data=dumps(data)) | ||
| except requests.ConnectionError as err: | ||
| errmsg = 'QC metrics failed to upload due to connection error shown below:\n%s' % err | ||
| return Bunch(status_code=1, text=errmsg) | ||
|
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| return response |
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