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import pymongo, copy |
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from datetime import timedelta |
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from niprov.dependencies import Dependencies |
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class MongoRepository(object): |
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def __init__(self, dependencies=Dependencies()): |
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self.config = dependencies.getConfiguration() |
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self.factory = dependencies.getFileFactory() |
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client = pymongo.MongoClient(self.config.database_url) |
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self.db = client.get_default_database() |
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def byLocation(self, locationString): |
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"""Get the provenance for a file at the given location. |
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In the case of a dicom series, this returns the provenance for the |
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series. |
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Args: |
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locationString (str): Location of the image file. |
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Returns: |
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dict: Provenance for one image file. |
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""" |
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record = self.db.provenance.find_one({'location':locationString}) |
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return self.inflate(record) |
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def byLocations(self, listOfLocations): |
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records = self.db.provenance.find({'location':{'$in':listOfLocations}}) |
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return [self.inflate(record) for record in records] |
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def knowsByLocation(self, locationString): |
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"""Whether the file at this location has provenance associated with it. |
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Returns: |
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bool: True if provenance is available for that path. |
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""" |
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return self.db.provenance.find_one( |
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{'location':locationString}) is not None |
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def knows(self, image): |
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"""Whether this file has provenance associated with it. |
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Returns: |
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bool: True if provenance is available for this image. |
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""" |
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return self.knowsByLocation(image.location.toString()) |
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def getSeries(self, image): |
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"""Get the object that carries provenance for the series that the image |
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passed is in. |
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Args: |
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image (:class:`.DicomFile`): File that is part of a series. |
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Returns: |
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:class:`.DicomFile`: Image object that caries provenance for the series. |
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""" |
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seriesUid = image.getSeriesId() |
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record = self.db.provenance.find_one({'seriesuid':seriesUid}) |
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return self.inflate(record) |
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def knowsSeries(self, image): |
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"""Whether this file is part of a series for which provenance |
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is available. |
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Args: |
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image (:class:`.BaseFile`): File for which the series is sought. |
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Returns: |
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bool: True if provenance is available for this series. |
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""" |
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seriesUid = image.getSeriesId() |
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if seriesUid is None: |
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return False |
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return self.db.provenance.find_one({'seriesuid':seriesUid}) is not None |
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def add(self, image): |
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"""Add the provenance for one file to storage. |
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Args: |
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image (:class:`.BaseFile`): Image file to store. |
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""" |
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self.db.provenance.insert_one(self.deflate(image)) |
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def update(self, image): |
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"""Save changed provenance for this file.. |
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Args: |
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image (:class:`.BaseFile`): Image file that has changed. |
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""" |
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self.db.provenance.update({'location':image.location.toString()}, |
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self.deflate(image)) |
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def updateApproval(self, locationString, approvalStatus): |
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self.db.provenance.update({'location':locationString}, |
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{'$set': {'approval': approvalStatus}}) |
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def all(self): |
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"""Retrieve all known provenance from storage. |
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Returns: |
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list: List of provenance for known files. |
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""" |
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records = self.db.provenance.find() |
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return [self.inflate(record) for record in records] |
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def bySubject(self, subject): |
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"""Get the provenance for all files of a given participant. |
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Args: |
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subject (str): The name or other ID string. |
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Returns: |
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list: List of provenance for known files imaging this subject. |
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""" |
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records = self.db.provenance.find({'subject':subject}) |
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return [self.inflate(record) for record in records] |
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def byApproval(self, approvalStatus): |
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records = self.db.provenance.find({'approval':approvalStatus}) |
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return [self.inflate(record) for record in records] |
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def latest(self): |
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records = self.db.provenance.find().sort('added', -1).limit(20) |
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return [self.inflate(record) for record in records] |
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def statistics(self): |
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grps = self.db.provenance.aggregate( |
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[{'$group': |
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{ |
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'_id': None, |
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'totalsize': { '$sum': '$size' }, |
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'count': { '$sum': 1 } |
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} |
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}]) |
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groups = list(grps) |
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if len(list(groups)) == 0: |
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return {'count':0} |
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return list(groups)[0] |
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def byId(self, uid): |
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record = self.db.provenance.find_one({'id':uid}) |
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return self.inflate(record) |
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def byParents(self, listOfParentLocations): |
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records = self.db.provenance.find({'parents':{ |
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'$in':listOfParentLocations}}) |
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return [self.inflate(record) for record in records] |
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def deflate(self, img): |
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record = copy.deepcopy(img.provenance) |
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if 'duration' in record: |
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record['duration'] = record['duration'].total_seconds() |
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return record |
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def inflate(self, record): |
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if 'duration' in record: |
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record['duration'] = timedelta(seconds=record['duration']) |
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return self.factory.fromProvenance(record) |
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ilogue /
niprov
