def addFilesToCombineArchive(archive_path, file_names, entry_locations,
file_formats, master_attributes,
out_archive_path):
""" Add multiple files to an existing COMBINE archive on disk and save the result as a new archive.
:param archive_path: The path to the archive.
:param file_names: List of extra files to add.
:param entry_locations: List of destination locations for the files in the output archive.
:param file_format: List of formats for the resp. files.
:param master_attributes: List of true/false values for the resp. master attributes of the files.
:param out_archive_path: The path to the output archive.
"""
import tecombine, tempfile
input_archive = tecombine.CombineArchive()
if not input_archive.initializeFromArchive(archive_path):
raise RuntimeError('Failed to initialize archive')
tempfiles = []
output_archive = tecombine.CombineArchive()
description = input_archive.getMetadataForLocation('.')
if description:
output_archive.addMetadata('.', description)
for entry in (input_archive.getEntry(k)
for k in range(input_archive.getNumEntries())):
fhandle, fname = tempfile.mkstemp()
tempfiles.append(fname)
input_archive.extractEntry(entry.getLocation(), fname)
if not entry.getLocation() in entry_locations:
output_archive.addFile(fname, entry.getLocation(),
entry.getFormat(), entry.getMaster())
# add the extra files
for file_name, entry_location, file_format, master in zip(
file_names, entry_locations, file_formats, master_attributes):
output_archive.addFile(file_name, entry_location, file_format, master)
# if the archive already exists, clear it
if os.path.exists(out_archive_path):
if os.path.isfile(out_archive_path):
os.remove(out_archive_path)
elif os.path.isdir(out_archive_path):
raise RuntimeError(
'Tried to write archive to {}, which is a directory.'.format(
out_archive_path))
else:
raise RuntimeError(
'Could not write archive to {}.'.format(out_archive_path))
# write archive
output_archive.writeToFile(out_archive_path)
# delete temp files
for t in tempfiles:
os.remove(t)
def createCombineArchive(archive_path, file_names, entry_locations, file_formats, master_attributes, description=None):
""" Create a new COMBINE archive containing the provided entries and locations.
:param archive_path: The path to the archive.
:param file_names: List of extra files to add.
:param entry_locations: List of destination locations for the files in the output archive.
:param file_format: List of formats for the resp. files.
:param master_attributes: List of true/false values for the resp. master attributes of the files.
:param out_archive_path: The path to the output archive.
:param description: A libcombine description structure to be assigned to the combine archive, if desired.
"""
import tecombine
output_archive = tecombine.CombineArchive()
if description is not None:
output_archive.addMetadata('.', description)
# add the extra files
for file_name, entry_location, file_format, master in zip(file_names, entry_locations, file_formats, master_attributes):
output_archive.addFile(file_name, entry_location, file_format, master)
# if the archive already exists, clear it
if os.path.exists(archive_path):
if os.path.isfile(archive_path):
os.remove(archive_path)
elif os.path.isdir(archive_path):
raise RuntimeError('Tried to write archive to {}, which is a directory.'.format(archive_path))
else:
raise RuntimeError('Could not write archive to {}.'.format(archive_path))
# write archive
output_archive.writeToFile(archive_path)
def exportToCombine(self, outfile):
""" Export Omex instance as combine archive.
:param outfile: A path to the output file"""
import phrasedml
phrasedml.clearReferencedSBML()
archive = libcombine.CombineArchive()
description = libcombine.OmexDescription()
description.setAbout(self.about)
description.setDescription(self.description)
time_now = libcombine.OmexDescription.getCurrentDateAndTime()
description.setCreated(time_now)
# TODO: pass in creator
if self.creator is not None:
creator = libcombine.VCard()
creator.setFamilyName(self.creator['last_name'])
creator.setGivenName(self.creator['first_name'])
creator.setEmail(self.creator['email'])
creator.setOrganization(self.creator['organization'])
description.addCreator(creator)
archive.addMetadata('.', description)
# Write out to temporary files
# TODO: can add content via strings now
workingDir = tempfile.mkdtemp(suffix="_sedml")
files = [] # Keep a list of files to remove
def addAssetToArchive(asset, format):
""" Helper to add asset of given format. """
fname = os.path.join(workingDir,
os.path.normpath(asset.getLocation()))
dname = os.path.dirname(fname)
if not os.path.exists(dname):
os.makedirs(dname)
with open(fname, 'w') as f:
files.append(fname)
f.write(t.getContent())
archive.addFile(fname, asset.getLocation(),
libcombine.KnownFormats.lookupFormat(format),
asset.getMaster())
try:
for t in self.getSedmlAssets():
addAssetToArchive(t, 'sedml')
for t in self.getSbmlAssets():
addAssetToArchive(t, 'sbml')
archive.writeToFile(outfile)
finally:
# put this in finally to make sure files are removed even under Exception
for f in files:
os.remove(f)
def fromFile(cls, path):
""" Initialize from a combine archive.
:param path: The path to the omex file
"""
if not os.path.isfile(path):
raise IOError('No such file: {}'.format(path))
omex = libcombine.CombineArchive()
if not omex.initializeFromArchive(path):
raise IOError('Could not read COMBINE archive.')
return inlineOmexImporter(omex)
def extractFileFromCombineArchive(archive_path, entry_location):
""" Extract a single file from a COMBINE archive and return it as a string.
"""
import tecombine
archive = tecombine.CombineArchive()
if not archive.initializeFromArchive(archive_path):
raise RuntimeError('Failed to initialize archive')
try:
entry = archive.getEntryByLocation(entry_location)
except:
raise RuntimeError('Could not find entry {}'.format(entry_location))
return archive.extractEntryToString(entry_location)
def fromFile(cls, path):
""" Initialize from a combine archive.
:param path: The path to the omex file
"""
if not os.path.isfile(path):
raise IOError('No such file: {}'.format(path))
d = None
if not os.access(os.getcwd(), os.W_OK):
d = os.getcwd()
os.chdir(tempfile.gettempdir())
omex = libcombine.CombineArchive()
if not omex.initializeFromArchive(path):
raise IOError('Could not read COMBINE archive.')
importer = inlineOmexImporter(omex)
# if d is not None:
# os.chdir(d)
return importer