def bsveSearchAnalysis(self, params):
currentUser = self.getCurrentUser()
datasetName = params['datasetName']
bsveSearchParams = params['bsveSearchParams']
analysis = findAnalysisByName(currentUser, 'bsve search')
# TODO in case can't find analysis?
try:
bsveSearchParams = json.loads(bsveSearchParams)
except ValueError:
raise RestException('bsveSearchParams is invalid JSON.')
minerva_metadata = {
'dataset_type': 'geojson',
'source_type': 'bsve_search',
'bsve_search_params': bsveSearchParams,
'original_type': 'json'
}
datasetResource = Dataset()
dataset = datasetResource.constructDataset(datasetName,
minerva_metadata,
'created by bsve search')
params = {
'bsveSearchParams': bsveSearchParams
}
# TODO change token to job token
user, token = self.getCurrentUser(returnToken=True)
kwargs = {
'params': params,
'user': currentUser,
'dataset': dataset,
'analysis': analysis,
'token': token
}
job = self.model('job', 'jobs').createLocalJob(
title='bsve search: %s' % datasetName,
user=currentUser,
type='bsve.search',
public=False,
kwargs=kwargs,
module='girder.plugins.minerva.jobs.bsve_search_worker',
async=True)
addJobOutput(job, dataset)
self.model('job', 'jobs').scheduleJob(job)
return job
def bsveSearchAnalysis(self, params):
currentUser = self.getCurrentUser()
datasetName = params['datasetName']
bsveSearchParams = params['bsveSearchParams']
analysis = findAnalysisByName(currentUser, 'bsve search')
# TODO in case can't find analysis?
try:
bsveSearchParams = json.loads(bsveSearchParams)
except ValueError:
raise RestException('bsveSearchParams is invalid JSON.')
minerva_metadata = {
'dataset_type': 'geojson',
'source_type': 'bsve_search',
'bsve_search_params': bsveSearchParams,
'original_type': 'json'
}
datasetResource = Dataset()
dataset = datasetResource.constructDataset(datasetName,
minerva_metadata,
'created by bsve search')
params = {
'bsveSearchParams': bsveSearchParams
}
# TODO change token to job token
user, token = self.getCurrentUser(returnToken=True)
kwargs = {
'params': params,
'user': currentUser,
'dataset': dataset,
'analysis': analysis,
'token': token
}
job = self.model('job', 'jobs').createLocalJob(
title='bsve search: %s' % datasetName,
user=currentUser,
type='bsve.search',
public=False,
kwargs=kwargs,
module='girder.plugins.minerva.jobs.bsve_search_worker',
async=True)
addJobOutput(job, dataset)
self.model('job', 'jobs').scheduleJob(job)
return job
def bsveMMWRAnalysis(self, params):
currentUser = self.getCurrentUser()
datasetName = params['datasetName']
count = int(params.get('count', 1000))
analysis = findAnalysisByName(currentUser, 'MMWR data import')
# TODO in case can't find analysis?
minerva_metadata = {
'dataset_type': 'geojson',
'source_type': 'mmwr_data_import',
'original_type': 'json'
}
datasetResource = Dataset()
dataset = datasetResource.constructDataset(
datasetName,
minerva_metadata,
'created by MMWR data import'
)
params = {
'count': count
}
# TODO change token to job token
user, token = self.getCurrentUser(returnToken=True)
kwargs = {
'params': params,
'user': currentUser,
'dataset': dataset,
'analysis': analysis,
'token': token
}
job = self.model('job', 'jobs').createLocalJob(
title='MMWR import: %s' % datasetName,
user=currentUser,
type='bsve.mmwr',
public=False,
kwargs=kwargs,
module='girder.plugins.minerva.jobs.soda_import_worker',
async=True)
addJobOutput(job, dataset)
self.model('job', 'jobs').scheduleJob(job)
return job
def bsveMMWRAnalysis(self, params):
currentUser = self.getCurrentUser()
datasetName = params['datasetName']
count = int(params.get('count', 1000))
analysis = findAnalysisByName(currentUser, 'MMWR data import')
# TODO in case can't find analysis?
minerva_metadata = {
'dataset_type': 'geojson',
'source_type': 'mmwr_data_import',
'original_type': 'json'
}
datasetResource = Dataset()
dataset = datasetResource.constructDataset(
datasetName,
minerva_metadata,
'created by MMWR data import'
)
params = {
'count': count
}
# TODO change token to job token
user, token = self.getCurrentUser(returnToken=True)
kwargs = {
'params': params,
'user': currentUser,
'dataset': dataset,
'analysis': analysis,
'token': token
}
job = self.model('job', 'jobs').createLocalJob(
title='MMWR import: %s' % datasetName,
user=currentUser,
type='bsve.mmwr',
public=False,
kwargs=kwargs,
module='girder.plugins.minerva.jobs.soda_import_worker',
async=True)
addJobOutput(job, dataset)
self.model('job', 'jobs').scheduleJob(job)
return job
def bsveSearchAnalysis(self, params):
currentUser = self.getCurrentUser()
datasetName = params['datasetName']
bsveSearchParams = params['bsveSearchParams']
analysis = findAnalysisByName(currentUser, 'bsve search')
# TODO in case can't find analysis?
try:
bsveSearchParams = json.loads(bsveSearchParams)
except ValueError:
raise RestException('bsveSearchParams is invalid JSON.')
datasetFolder = findDatasetFolder(currentUser, currentUser)
# TODO
# try findOne earlier
# all throughout utility
# create a new dataset in the dataset folder with this name
# TODO in case of duplicates?
dataset = (self.model('item').createItem(datasetName, currentUser,
datasetFolder,
'created by bsve search'))
params = {
'bsveSearchParams': bsveSearchParams
}
# create a local job with bsve search
# tie in the dataset id with the local job
# TODO would we rather create the dataset at the end of the bsve search?
# TODO change token to job token
user, token = self.getCurrentUser(returnToken=True)
kwargs = {
'params': params,
'user': currentUser,
'dataset': dataset,
'analysis': analysis,
'token': token
}
job = self.model('job', 'jobs').createLocalJob(
title='bsve search: %s' % datasetName,
user=currentUser,
type='bsve.search',
public=False,
kwargs=kwargs,
module='girder.plugins.minerva.jobs.bsve_search_worker',
async=True)
if 'meta' in dataset:
metadata = dataset['meta']
else:
metadata = {}
minerva_metadata = {
'dataset_id': dataset['_id'],
'source': 'bsve_search',
'bsve_search_params': bsveSearchParams,
'original_type': 'json'
}
metadata['minerva'] = minerva_metadata
self.model('item').setMetadata(dataset, metadata)
self.model('job', 'jobs').scheduleJob(job)
return minerva_metadata
