def importp(filepath, dependencies=Dependencies()):
"""Add provenance in bulk from a file, such as saved by export().
Named importp as opposed to import because the latter is a reserved word
in Python.
This can serve as a backup, migration tool, or for exchange.
"""
repository = dependencies.getRepository()
importDeps = Dependencies()
importDeps.getConfiguration().database_url = filepath
importRepo = JsonFile(importDeps)
allFiles = importRepo.all()
for pfile in allFiles:
repository.add(pfile)
def __init__(self, dependencies=Dependencies()):
self.filesys = dependencies.getFilesystem()
self.json = dependencies.getSerializer()
self.factory = dependencies.getFileFactory()
self.pictureCache = dependencies.getPictureCache()
url = dependencies.getConfiguration().database_url
self.datafile = os.path.expanduser(url)
def main(global_config, **settings):
""" This function returns a Pyramid WSGI application.
"""
# settings = {}
# settings['reload_all'] = True
# settings['debug_all'] = True
# settings['mako.directories'] = os.path.join(here, 'templates')
config = Configurator(settings=settings)
config.include('pyramid_mako')
config.add_static_view('static', 'static', cache_max_age=10)
config.add_static_view('snapshots',
os.path.expanduser('~/.niprov-snapshots'),
cache_max_age=10)
config.add_route('home', '/')
config.add_route('latest', '/latest')
config.add_route('stats', '/stats')
config.add_route('short', '/id/{id}')
config.add_route('pipeline', '/id/{id}/pipeline')
config.add_route('location', '/locations/{host}*path')
config.add_route('modality', '/modalities/{modality}')
config.add_route('subject', '/subjects/{subject}')
config.add_route('project', '/projects/{project}')
config.add_route('user', '/users/{user}')
config.add_route('search', '/search')
config.add_route('modalities', '/modalities')
config.add_route('projects', '/projects')
config.add_route('users', '/users')
config.add_request_method(lambda r: Dependencies(),
'dependencies',
reify=True)
config.scan()
return config.make_wsgi_app()
def test_reconfigureOrGetConfiguration_with_new_config_returns_it(self):
from niprov.dependencies import Dependencies, Configuration
dependencies = Dependencies()
newSettings = Configuration()
newSettings.verbose = True
outConfig = dependencies.reconfigureOrGetConfiguration(newSettings)
self.assertEqual(newSettings, outConfig)
def export(provenance, medium, form, pipeline=False, dependencies=Dependencies()):
"""Publish or simply return provenance for selected files.
To get provenance on one specific file, pass its path as the 'forFile'
argument. Alternatively, to get all files associated with a certain subject,
use the 'forSubject' argument. If none of these is used, provenance for the
most recently registered files is reported.
Args:
provenance: Niprov BaseFile object or list of such.
medium (str): The medium in which to publish the provenance.
One of:
'stdout' (print the provenance to the terminal),
'direct' (return object to caller),
'file' (write to a text file),
'viewer' (open in the system image viewer).
form (str): The format in which to serialize the provenance.
One of 'json','xml','narrated','simple','dict','picture'.
Returns:
Depends on medium selected.
"""
formatFactory = dependencies.getFormatFactory()
mediumFactory = dependencies.getMediumFactory()
makePipeline = dependencies.getPipelineFactory()
form = formatFactory.create(form)
medium = mediumFactory.create(medium)
if pipeline:
provenance = makePipeline.forFile(provenance)
formattedProvenance = form.serialize(provenance)
return medium.export(formattedProvenance, form)
def discover(root, dependencies=Dependencies()):
"""
Search a directory for image files, and add them to your provenance collection.
Files are only included if they match the filters in the
'discover_file_extensions' settings.
Refer to niprov.add for details on what happens to individual files.
Args:
root (str): The top directory in which to look for new files.
"""
filesys = dependencies.getFilesystem()
filefilter = dependencies.getFileFilter()
listener = dependencies.getListener()
dirs = filesys.walk(root)
stats = {
'total': 0,
'new': 0,
'series-new-file': 0,
'failed': 0,
'new-version': 0
}
for (root, sdirs, files) in dirs:
for filename in files:
filepath = os.path.join(root, filename)
if filefilter.include(filename):
stats['total'] = stats['total'] + 1
p = add(filepath, transient=False, dependencies=dependencies)
stats[p.status] = stats[p.status] + 1
listener.discoveryFinished(nnew=stats['new'],
nadded=stats['series-new-file'],
nfailed=stats['failed'],
ntotal=stats['total'])
def test_reconfigureOrGetConfiguration_with_None_doesnt_affect_config(
self):
from niprov.dependencies import Dependencies
dependencies = Dependencies()
self.assertEqual(dependencies.getListener().verbosity, 'info')
dependencies.reconfigureOrGetConfiguration(None)
self.assertEqual(dependencies.getListener().verbosity, 'info')
def markedForApproval(dependencies=Dependencies()):
"""List files marked for approval by a human.
"""
query = dependencies.getQuery()
listener = dependencies.getListener()
markedFiles = query.byApproval('pending')
listener.filesMarkedForApproval(markedFiles)
return markedFiles
def test_reconfigureOrGetConfiguration_creates_new_dependencies(self):
from niprov.dependencies import Dependencies, Configuration
dependencies = Dependencies()
self.assertEqual(dependencies.getListener().verbosity, 'info')
newSettings = Configuration()
newSettings.verbosity = 'warning'
dependencies.reconfigureOrGetConfiguration(newSettings)
self.assertEqual(dependencies.getListener().verbosity, 'warning')
def approve(filepath, dependencies=Dependencies()):
"""Mark this file as approved.
Args:
filepath (str): Path to the tracked file that has been found valid.
"""
loc = dependencies.getLocationFactory().completeString(filepath)
repository = dependencies.getRepository()
repository.updateApproval(loc, 'granted')
def search(text, dependencies=Dependencies()):
"""
Search for files with the given text in their provenance fields.
Args:
text (str): Words to look for.
Returns:
list: List of BaseFile objects
"""
return dependencies.getRepository().search(text)
def test_Changing_storage_setting_changes_repository_provided(self):
from niprov.dependencies import Dependencies
from niprov.jsonfile import JsonFile
from niprov.mongo import MongoRepository
dependencies = Dependencies()
with patch('niprov.mongo.pymongo'):
dependencies.config.database_type = 'file'
self.assertIsInstance(dependencies.getRepository(), JsonFile)
dependencies.config.database_type = 'MongoDB'
self.assertIsInstance(dependencies.getRepository(),
MongoRepository)
def renameDicoms(dicomdir, dependencies=Dependencies()):
""" Add the .dcm extension to any non-hidden files without extension.
Args:
dicomdir (str): Directory in which to rename files.
"""
listener = dependencies.getListener()
for f in glob.glob(os.path.join(dicomdir, '*')):
if '.' not in os.path.basename(f):
listener.renamedDicom(f)
shutil.move(f, f + '.dcm')
def selectApproved(files, dependencies=Dependencies()):
"""Return only files that have approval status 'granted'.
Args:
files (list): List of paths of files to check for approval status.
"""
repository = dependencies.getRepository()
location = dependencies.getLocationFactory()
selection = []
for filepath in files:
locationString = location.completeString(filepath)
img = repository.byLocation(locationString)
if img.provenance.get('approval') == 'granted':
selection.append(img.path)
return selection
def markForApproval(files, reset=False, dependencies=Dependencies()):
"""Mark a list of files for approval by a human.
Args:
files (list): List of paths of files tracked by niprov to mark for
approval.
reset (bool): Also mark files that have already been approved. False
by default.
"""
repository = dependencies.getRepository()
location = dependencies.getLocationFactory()
for filepath in files:
loc = location.completeString(filepath)
if not reset:
image = repository.byLocation(loc)
if image is None:
raise ValueError('Unknown file: ' + filepath)
if image.provenance.get('approval') == 'granted':
continue
repository.updateApproval(loc, 'pending')
def test_provides_LocationFactory(self):
from niprov.dependencies import Dependencies
from niprov.locationfactory import LocationFactory
dependencies = Dependencies()
self.assertIsInstance(dependencies.getLocationFactory(),
LocationFactory)
def test_Filefactory_provided(self):
from niprov.dependencies import Dependencies
from niprov.files import FileFactory
dependencies = Dependencies()
self.assertIsInstance(dependencies.getFileFactory(), FileFactory)
def test_provides_PipelineFactory(self):
from niprov.dependencies import Dependencies
from niprov.pipelinefactory import PipelineFactory
dependencies = Dependencies()
self.assertIsInstance(dependencies.getPipelineFactory(),
PipelineFactory)
def __init__(self):
self.config = Configuration()
self.deps = Dependencies(self.config)
def test_provides_FormatFactory(self):
from niprov.dependencies import Dependencies
from niprov.formatfactory import FormatFactory
dependencies = Dependencies()
self.assertIsInstance(dependencies.getFormatFactory(), FormatFactory)
def test_Changing_setting_directly_affects_component_setting(self):
from niprov.dependencies import Dependencies
dependencies = Dependencies()
self.assertEqual(dependencies.getListener().verbosity, 'info')
dependencies.config.verbosity = 'warning'
self.assertEqual(dependencies.getListener().verbosity, 'warning')
def __init__(self, dependencies=Dependencies()):
self.dependencies = dependencies
def test_provides_MediumFactory(self):
from niprov.dependencies import Dependencies
from niprov.mediumfactory import MediumFactory
dependencies = Dependencies()
self.assertIsInstance(dependencies.getMediumFactory(), MediumFactory)
def print_(provenance, pipeline=False, dependencies=Dependencies()):
"""Shortcut for export(medium='stdout', form='simple').
"""
return export(provenance, medium='stdout', form='simple',
pipeline=pipeline, dependencies=dependencies)
def __init__(self, dependencies=Dependencies()):
self.libs = dependencies.getLibraries()
self.listener = dependencies.getListener()
self.dependencies = dependencies
def test_provides_Externals(self):
from niprov.dependencies import Dependencies
from niprov.externals import Externals
dependencies = Dependencies()
self.assertIsInstance(dependencies.getExternals(), Externals)
def backup(dependencies=Dependencies()):
"""Shortcut for export(medium='file', form='json') for all provenance.
"""
provenance = dependencies.getQuery().all()
return export(provenance, medium='file', form='json',
dependencies=dependencies)
def __init__(self, dependencies=Dependencies()):
self.files = dependencies.getRepository()
def view(provenance, pipeline=False, dependencies=Dependencies()):
"""Shortcut for export(medium='viewer', form='picture').
"""
return export(provenance, medium='viewer', form='picture',
pipeline=pipeline, dependencies=dependencies)
def __init__(self, dependencies=Dependencies()):
self.fileExtension = 'txt'
