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#!/usr/bin/python |
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# -*- coding: UTF-8 -*- |
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from __future__ import print_function |
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from niprov.exceptions import UnknownFileError |
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from niprov.dependencies import Dependencies |
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class Commandline(object): |
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vlevels = ['debug','info','warning','error'] |
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def __init__(self, dependencies=Dependencies()): |
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self.config = dependencies.config |
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self.verbosity = dependencies.config.verbosity |
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assert self.verbosity in self.vlevels, "Unknown verbosity value" |
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def usingCopyAsParent(self, copy): |
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loc = str(copy.location) |
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self.log('warning', 'Used provenance from copy found at '+loc) |
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def fileAdded(self, image): |
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if image.status == 'new': |
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self.log('info', 'New file: {0}'.format(image.path)) |
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if image.status == 'series-new-file': |
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template = 'Added {0} file to series: {1}' |
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nfiles = len(image.provenance['filesInSeries']) |
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self.log('info', template.format(ordinal(nfiles), image.getSeriesId())) |
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if image.status == 'new-version': |
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self.log('info', 'Added new version for: {}'.format(image.path)) |
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def missingDependencyForImage(self, lib, fpath): |
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template = 'Missing python package "{0}" to read file: {1}' |
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self.log('warning', template.format(lib, fpath)) |
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def fileError(self, fpath): |
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import traceback |
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traceback.print_exc() |
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self.log('warning', 'Error inspecting file: {0}'.format(fpath)) |
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def interpretedRecording(self, new, transform, parents): |
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template = ('[provenance] Recorded the command [{1}] to create [{0}] '+ |
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'based on [{2}]') |
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self.log('info', template.format(', '.join(new), transform, |
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', '.join(parents))) |
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def renamedDicom(self, fpath): |
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self.log('info', 'Renamed dicom file: '+fpath) |
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def discoveryFinished(self, nnew, nadded, nfailed, ntotal): |
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self.log('info', 'Discovered {0} new, added {1} to series, failed to read {2}, ' |
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'processed {3} total files.'.format(nnew, nadded, nfailed, ntotal)) |
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def mnefunEventReceived(self, operationName): |
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self.log('info', 'Mnefun operation: '+operationName) |
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def receivedBashCommand(self, command): |
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self.log('info', 'Recording command: \n'+(' '.join(command))) |
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def filesMarkedForApproval(self, images): |
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paths = '\n'.join([img.path for img in images]) |
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self.log('info', 'Files marked for approval: \n{0}'.format(paths)) |
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def exportedToFile(self, fname): |
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self.log('info', 'Exported to file: {0}'.format(fname)) |
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def log(self, level, message, exceptionClass=None): |
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if self.vlevels.index(level) >= self.vlevels.index(self.verbosity): |
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if level == 'error': |
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if exceptionClass is None: |
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raise NiprovError(message) |
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else: |
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raise exceptionClass(message) |
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else: |
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print('[provenance:{0}] {1}'.format(level, message)) |
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def addUnknownParent(self, fpath): |
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self.log('warning', '{0} unknown. Adding to provenance'.format(fpath)) |
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SUFFIXES = {1: 'st', 2: 'nd', 3: 'rd'} |
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def ordinal(num): |
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if 10 <= num % 100 <= 20: |
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suffix = 'th' |
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else: |
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# the second parameter is a default. |
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suffix = SUFFIXES.get(num % 10, 'th') |
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return str(num) + suffix |
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ilogue /
niprov
