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:param filelike: path to a file (str) or a file-like object
:param specfile: name of an ms-run file present in ``self.info``
:param compress: bool, True to use zip file compression
""""""
aux.writeJsonZipfile(filelike, self.sic[specfile], compress)"
1937,"def _writeRmc(self, filelike, specfile):
""""""Writes the ``.rmc`` container entry of the specified specfile as an
human readable and pretty formatted xml string.
:param filelike: path to a file (str) or a file-like object
:param specfile: name of an ms-run file present in ``self.info``
""""""
xmlString = ETREE.tostring(self.rmc[specfile], pretty_print=True)
filelike.write(xmlString)"
1938,"def load(self, specfiles=None, rm=False, ci=False, smi=False, sai=False,
si=False):
""""""Import the specified datatypes from ``mrc`` files on the hard disk.
:param specfiles: the name of an ms-run file or a list of names. If None
all specfiles are selected.
:type specfiles: None, str, [str, str]
:param rm: bool, True to import ``mrc_rm`` (run metadata)
:param ci: bool, True to import ``mrc_ci`` (chromatogram items)
:param smi: bool, True to import ``mrc_smi`` (spectrum metadata items)
:param sai: bool, True to import ``mrc_sai`` (spectrum array items)
:param si: bool, True to import ``mrc_si`` (spectrum items)
""""""
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
#Select only specfiles which are present in the ``self.info``.
selectedSpecfiles = list()
for specfile in specfiles:
if specfile not in self.info:
warntext = 'Error while calling ""MsrunContainer.load()"": ""%s"" '\
'not present in MsrunContainer.info' % specfile
warnings.warn(warntext)
else:
selectedSpecfiles.append(specfile)
datatypes = self._processDatatypes(rm, ci, smi, sai, si)
if len(datatypes) == 0:
datatypes = ['rm', 'ci', 'smi', 'sai', 'si']
for specfile in selectedSpecfiles:
msrunInfo = self.info[specfile]
specfilePath = msrunInfo['path']
if 'rm' in datatypes:
rmPath = aux.joinpath(specfilePath, specfile+'.mrc_rm')
with open(rmPath, 'rb') as openfile:
xmlString = openfile.read()
self.rmc[specfile] = ETREE.fromstring(xmlString)
msrunInfo['status']['rm'] = True
if 'ci' in datatypes:
ciPath = aux.joinpath(specfilePath, specfile+'.mrc_ci')
self.cic[specfile] = aux.loadBinaryItemContainer(ciPath,
Ci.jsonHook)
msrunInfo['status']['ci'] = True
if 'smi' in datatypes:
smiPath = aux.joinpath(specfilePath, specfile+'.mrc_smi')
with zipfile.ZipFile(smiPath, 'r') as containerZip:
#Convert the zipfile data into a str object,necessary since
#containerZip.read() returns a bytes object.
jsonString = io.TextIOWrapper(containerZip.open('data'),
encoding='utf-8'
).read()
self.smic[specfile] = json.loads(jsonString,
object_hook=Smi.jsonHook
)
msrunInfo['status']['smi'] = True
if 'sai' in datatypes:
saiPath = aux.joinpath(specfilePath, specfile+'.mrc_sai')
self.saic[specfile] = aux.loadBinaryItemContainer(saiPath,
Sai.jsonHook
)
msrunInfo['status']['sai'] = True
if 'si' in datatypes:
siPath = aux.joinpath(specfilePath, specfile+'.mrc_si')
with zipfile.ZipFile(siPath, 'r') as containerZip:
#Convert the zipfile data into a str object, necessary since
#containerZip.read() returns a bytes object.
jsonString = io.TextIOWrapper(containerZip.open('data'),
encoding='utf-8'
).read()
self.sic[specfile] = json.loads(jsonString,
object_hook=Si.jsonHook
)
msrunInfo['status']['si'] = True"
1939,"def _reprJSON(self):
""""""Returns a JSON serializable represenation of a ``Ci`` class instance.
Use :func:`maspy.core.Ci._fromJSON()` to generate a new ``Ci`` instance
from the return value.