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import os |
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from operator import itemgetter |
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from niprov.dependencies import Dependencies |
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class JsonFile(object): |
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"""Stores provenance in a local text file encoded as json. |
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""" |
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def __init__(self, dependencies=Dependencies()): |
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self.filesys = dependencies.getFilesystem() |
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self.json = dependencies.getSerializer() |
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self.factory = dependencies.getFileFactory() |
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self.pictureCache = dependencies.getPictureCache() |
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url = dependencies.getConfiguration().database_url |
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self.datafile = os.path.expanduser(url) |
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def serializeAndWrite(self, images): |
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jsonstr = self.json.serializeList(images) |
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self.filesys.write(self.datafile, jsonstr) |
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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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current = self.all() |
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current.append(image) |
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self.serializeAndWrite(current) |
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self.pictureCache.saveToDisk(for_=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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current = self.all() |
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for r in range(len(current)): |
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if current[r].location.toString() == image.location.toString(): |
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current[r] = image |
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self.serializeAndWrite(current) |
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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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try: |
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jsonstr = self.filesys.read(self.datafile) |
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except IOError: |
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return [] |
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return self.json.deserializeList(jsonstr) |
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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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for image in self.all(): |
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if image.location.toString() == locationString: |
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return image |
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def byLocations(self, listOfLocations): |
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return [f for f in self.all() if f.location.toString() in listOfLocations] |
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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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seriesId = image.getSeriesId() |
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if seriesId is None: |
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return None |
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for image in self.all(): |
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if 'seriesuid' in image.provenance and ( |
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image.provenance['seriesuid'] == seriesId): |
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return image |
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def updateApproval(self, fpath, approvalStatus): |
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img = self.byLocation(fpath) |
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img.provenance['approval'] = approvalStatus |
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self.update(img) |
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def latest(self, n=20): |
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def dateTimeAdded(img): |
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return img.provenance.get('added') |
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sortedImages = sorted(self.all(), key=dateTimeAdded, reverse=True) |
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return sortedImages[:n] |
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def statistics(self): |
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stats = {} |
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images = self.all() |
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stats['count'] = len(images) |
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sizes = [img.provenance['size'] for img in images if 'size' in img.provenance] |
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stats['totalsize'] = sum(sizes) |
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return stats |
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def byId(self, uid): |
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for image in self.all(): |
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if image.provenance['id'] == uid: |
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return image |
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def byParents(self, listOfParentLocations): |
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return [f for f in self.all() if set(listOfParentLocations).intersection( |
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f.provenance.get('parents',[]))] |
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def inquire(self, query): |
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field = query.getFields()[0] |
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matches = [] |
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for image in self.all(): |
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if field.name in image.provenance: |
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if field.all: |
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if not image.provenance[field.name] in matches: |
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matches.append(image.provenance[field.name]) |
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else: |
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if image.provenance[field.name] == field.value: |
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matches.append(image) |
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return matches |
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def search(self, text): |
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fields = ['location','user','subject','project','protocol', |
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'transformation','technique','modality'] |
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matches = [] |
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for image in self.all(): |
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score = 0 |
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for word in text.split(): |
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for field in fields: |
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if field in image.provenance: |
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score += image.provenance[field].count(word) |
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if score > 0: |
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matches.append((image, score)) |
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sortedResults = sorted(matches, key=itemgetter(1), reverse=True) |
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return [i for i, s in sortedResults[:20]] |
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ilogue /
niprov
