JsonFile.bySubject() - Code Metrics - Inspection of "Context dependencies related bug fix" - ilogue/niprov - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#127)

by Jasper

created 2016-04-12 22:15 UTC

JsonFile.bySubject() B

↳ Parent: JsonFile

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Metric	Value
cc	5
dl	0
loc	12
rs	8.5454

import os
from operator import itemgetter
from niprov.dependencies import Dependencies


class JsonFile(object):
    """Stores provenance in a local text file encoded as json.
    """

    def __init__(self, dependencies=Dependencies()):
        self.filesys = dependencies.getFilesystem()
        self.json = dependencies.getSerializer()
        self.factory = dependencies.getFileFactory()
        url = dependencies.getConfiguration().database_url
        self.datafile = os.path.expanduser(url)

    def serializeAndWrite(self, images):
        jsonstr = self.json.serializeList(images)
        self.filesys.write(self.datafile, jsonstr)

    def add(self, image):
        """Add the provenance for one file to storage.

        Args:
            image (:class:`.BaseFile`): Image file to store.
        """
        current = self.all()
        current.append(image)
        self.serializeAndWrite(current)

    def update(self, image):
        """Save changed provenance for this file..

        Args:
            image (:class:`.BaseFile`): Image file that has changed.
        """
        current = self.all()
        for r in range(len(current)):
            if current[r].location.toString() == image.location.toString():
                current[r] = image
        self.serializeAndWrite(current)

    def all(self):
        """Retrieve all known provenance from storage.

        Returns:
            list: List of provenance for known files.
        """
        try:
            jsonstr = self.filesys.read(self.datafile)
        except IOError:
            return []
        return self.json.deserializeList(jsonstr)

    def knowsByLocation(self, locationString):
        """Whether the file at this path has provenance associated with it.

        Returns:
            bool: True if provenance is available for that path.
        """
        try:
            self.byLocation(locationString)
        except IndexError:
            return False
        return True

    def knows(self, image):
        """Whether this file has provenance associated with it.

        Returns:
            bool: True if provenance is available for this image.
        """
        try:
            self.byLocation(image.path)
        except IndexError:
            return False
        return True

    def knowsSeries(self, image):
        """Whether the series that this file is part of has provenance 
        associated with it.

        Args:
            image (:class:`.BaseFile`): File for which the series is sought.

        Returns:
            bool: True if provenance is available for this series.
        """
        try:
            self.getSeries(image)
        except IndexError:
            return False
        return True

    def byLocation(self, locationString):
        """Get the provenance for a file at the given location. 

        In the case of a dicom series, this returns the provenance for the 
        series.

        Args:
            locationString (str): Location of the image file.

        Returns:
            dict: Provenance for one image file.
        """
        for image in self.all():
            if image.location.toString() == locationString:
                return image
            elif 'filesInSeries' in image.provenance and (
                locationString in image.provenance['filesInSeries']):
                return image
        else:
            raise IndexError('No file with that path known.')

    def byLocations(self, listOfLocations):
        return [f for f in self.all() if f.location.toString() in listOfLocations]

    def bySubject(self, subject):
        """Get the provenance for all files of a given participant. 

        Args:
            subject (str): The name or other ID string.

        Returns:
            list: List of provenance for known files imaging this subject.
        """
        all = self.all()
        imagesWithSubject = [f for f in all if 'subject' in f.provenance]
        return [f for f in imagesWithSubject if f.provenance['subject']==subject]

    def getSeries(self, image):
        """Get the object that carries provenance for the series that the image 
        passed is in. 

        Args:
            image (:class:`.DicomFile`): File that is part of a series.

        Returns:
            :class:`.DicomFile`: Image object that caries provenance for the series.
        """
        if image.getSeriesId() is None:
            raise IndexError('Image has no series id.')
        seriesId = image.getSeriesId()
        for image in self.all():
            if 'seriesuid' in image.provenance and (
                image.provenance['seriesuid'] == seriesId):
                return image
        else:
            raise IndexError('No provenance record for that series.')

    def byApproval(self, approvalStatus):
        matches = []
        for image in self.all():
            if 'approval' in image.provenance:
                if image.provenance['approval'] == approvalStatus:
                    matches.append(image)
        return matches

    def updateApproval(self, fpath, approvalStatus):
        img = self.byLocation(fpath)
        img.provenance['approval'] = approvalStatus
        self.update(img)

    def latest(self, n=20):
        def dateTimeAdded(img):
            return img.provenance.get('added')
        sortedImages = sorted(self.all(), key=dateTimeAdded, reverse=True)
        return sortedImages[:n]

    def statistics(self):
        stats = {}
        images = self.all()
        stats['count'] = len(images)
        sizes = [img.provenance['size'] for img in images if 'size' in img.provenance]
        stats['totalsize'] = sum(sizes)
        return stats

    def byId(self, uid):
        for image in self.all():
            if image.provenance['id'] == uid:
                return image
        else:
            raise IndexError('No file with that path known.')

    def byParents(self, listOfParentLocations):
        return [f for f in self.all() if set(listOfParentLocations).intersection(
            f.provenance.get('parents',[]))]

       



1			import os
2			from operator import itemgetter
3			from niprov.dependencies import Dependencies
4
5
6			class JsonFile(object):
7			"""Stores provenance in a local text file encoded as json.
8			"""
9
10			def __init__(self, dependencies=Dependencies()):
11			self.filesys = dependencies.getFilesystem()
12			self.json = dependencies.getSerializer()
13			self.factory = dependencies.getFileFactory()
14			url = dependencies.getConfiguration().database_url
15			self.datafile = os.path.expanduser(url)
16
17			def serializeAndWrite(self, images):
18			jsonstr = self.json.serializeList(images)
19			self.filesys.write(self.datafile, jsonstr)
20
21			def add(self, image):
22			"""Add the provenance for one file to storage.
23
24			Args:
25			image (:class:`.BaseFile`): Image file to store.
26			"""
27			current = self.all()
28			current.append(image)
29			self.serializeAndWrite(current)
30
31			def update(self, image):
32			"""Save changed provenance for this file..
33
34			Args:
35			image (:class:`.BaseFile`): Image file that has changed.
36			"""
37			current = self.all()
38			for r in range(len(current)):
39			if current[r].location.toString() == image.location.toString():
40			current[r] = image
41			self.serializeAndWrite(current)
42
43			def all(self):
44			"""Retrieve all known provenance from storage.
45
46			Returns:
47			list: List of provenance for known files.
48			"""
49			try:
50			jsonstr = self.filesys.read(self.datafile)
51			except IOError:
52			return []
53			return self.json.deserializeList(jsonstr)
54
55			def knowsByLocation(self, locationString):
56			"""Whether the file at this path has provenance associated with it.
57
58			Returns:
59			bool: True if provenance is available for that path.
60			"""
61			try:
62			self.byLocation(locationString)
63			except IndexError:
64			return False
65			return True
66
67			def knows(self, image):
68			"""Whether this file has provenance associated with it.
69
70			Returns:
71			bool: True if provenance is available for this image.
72			"""
73			try:
74			self.byLocation(image.path)
75			except IndexError:
76			return False
77			return True
78
79			def knowsSeries(self, image):
80			"""Whether the series that this file is part of has provenance
81			associated with it.
82
83			Args:
84			image (:class:`.BaseFile`): File for which the series is sought.
85
86			Returns:
87			bool: True if provenance is available for this series.
88			"""
89			try:
90			self.getSeries(image)
91			except IndexError:
92			return False
93			return True
94
95			def byLocation(self, locationString):
96			"""Get the provenance for a file at the given location.
97
98			In the case of a dicom series, this returns the provenance for the
99			series.
100
101			Args:
102			locationString (str): Location of the image file.
103
104			Returns:
105			dict: Provenance for one image file.
106			"""
107			for image in self.all():
108			if image.location.toString() == locationString:
109			return image
110			elif 'filesInSeries' in image.provenance and (
111			locationString in image.provenance['filesInSeries']):
112			return image
113			else:
114			raise IndexError('No file with that path known.')
115
116			def byLocations(self, listOfLocations):
117			return [f for f in self.all() if f.location.toString() in listOfLocations]
118
119			def bySubject(self, subject):
120			"""Get the provenance for all files of a given participant.
121
122			Args:
123			subject (str): The name or other ID string.
124
125			Returns:
126			list: List of provenance for known files imaging this subject.
127			"""
128			all = self.all()
129			imagesWithSubject = [f for f in all if 'subject' in f.provenance]
130			return [f for f in imagesWithSubject if f.provenance['subject']==subject]
131
132			def getSeries(self, image):
133			"""Get the object that carries provenance for the series that the image
134			passed is in.
135
136			Args:
137			image (:class:`.DicomFile`): File that is part of a series.
138
139			Returns:
140			:class:`.DicomFile`: Image object that caries provenance for the series.
141			"""
142			if image.getSeriesId() is None:
143			raise IndexError('Image has no series id.')
144			seriesId = image.getSeriesId()
145			for image in self.all():
146			if 'seriesuid' in image.provenance and (
147			image.provenance['seriesuid'] == seriesId):
148			return image
149			else:
150			raise IndexError('No provenance record for that series.')
151
152			def byApproval(self, approvalStatus):
153			matches = []
154			for image in self.all():
155			if 'approval' in image.provenance:
156			if image.provenance['approval'] == approvalStatus:
157			matches.append(image)
158			return matches
159
160			def updateApproval(self, fpath, approvalStatus):
161			img = self.byLocation(fpath)
162			img.provenance['approval'] = approvalStatus
163			self.update(img)
164
165			def latest(self, n=20):
166			def dateTimeAdded(img):
167			return img.provenance.get('added')
168			sortedImages = sorted(self.all(), key=dateTimeAdded, reverse=True)
169			return sortedImages[:n]
170
171			def statistics(self):
172			stats = {}
173			images = self.all()
174			stats['count'] = len(images)
175			sizes = [img.provenance['size'] for img in images if 'size' in img.provenance]
176			stats['totalsize'] = sum(sizes)
177			return stats
178
179			def byId(self, uid):
180			for image in self.all():
181			if image.provenance['id'] == uid:
182			return image
183			else:
184			raise IndexError('No file with that path known.')
185
186			def byParents(self, listOfParentLocations):
187			return [f for f in self.all() if set(listOfParentLocations).intersection(
188			f.provenance.get('parents',[]))]
189
190
191
192

ilogue / niprov

Pull Request — master (#127)

JsonFile.bySubject() B

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