def loadField(h5, resNode):
longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
try:
creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
except:
from pyphant.core.Helpers import emd52dict
emd5dict = emd52dict(resNode._v_title)
creator = emd5dict['creator']
machine = emd5dict['machine']
data = scipy.array(resNode.data.read())
def loads(inputList):
if type(inputList)==type([]):
try:
return map(lambda s: eval(s),inputList)
except:
return map(lambda s: unicode(s, 'utf-8'),inputList)
else:
return map(loads,inputList)
if data.dtype.char == 'S':
data = scipy.array(loads(data.tolist()))
attributes = {}
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key]=h5.getNodeAttr(resNode.data,key)
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError, e:
error = None
def loadField(h5, resNode):
longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
try:
creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
except:
from pyphant.core.Helpers import emd52dict
emd5dict = emd52dict(resNode._v_title)
creator = emd5dict['creator']
machine = emd5dict['machine']
data = scipy.array(resNode.data.read())
def loads(inputList):
if type(inputList) == type([]):
try:
return map(lambda s: eval(s), inputList)
except:
return map(lambda s: unicode(s, 'utf-8'), inputList)
else:
return map(loads, inputList)
if data.dtype.char == 'S':
data = scipy.array(loads(data.tolist()))
attributes = {}
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key] = h5.getNodeAttr(resNode.data, key)
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError, e:
error = None
def __init__(self, emd5, cursor, type):
self.cursor = cursor
self.emd5 = emd5
self.emd5dict = emd52dict(emd5)
self.emd5dict['id'] = emd5
self.select_query = "SELECT %s FROM km_%s WHERE %s_id=?"\
% ('%s', type, type)
self.update_query = "UPDATE km_%s SET %s=? WHERE %s_id=?"\
% (type, '%s', type)
self.attr_query = "SELECT key, value FROM km_attributes WHERE dc_id=?"
def __init__(self, emd5, cursor, type):
self.cursor = cursor
self.emd5 = emd5
self.emd5dict = emd52dict(emd5)
self.emd5dict['id'] = emd5
self.select_query = "SELECT %s FROM km_%s WHERE %s_id=?"\
% ('%s', type, type)
self.update_query = "UPDATE km_%s SET %s=? WHERE %s_id=?"\
% (type, '%s', type)
self.attr_query = "SELECT key, value FROM km_attributes WHERE dc_id=?"
def loadField(h5, resNode):
longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
try:
creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
except:
from pyphant.core.Helpers import emd52dict
emd5dict = emd52dict(resNode._v_title)
creator = emd5dict['creator']
machine = emd5dict['machine']
data = scipy.array(resNode.data.read())
def loads(inputList):
if type(inputList) == type([]):
try:
return map(lambda s: eval(s), inputList)
except:
return map(lambda s: unicode(s, 'utf-8'), inputList)
else:
return map(loads, inputList)
if data.dtype.char == 'S':
data = scipy.array(loads(data.tolist()))
attributes = {}
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key] = h5.getNodeAttr(resNode.data, key)
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError:
error = None
try:
mask = scipy.array(resNode.mask.read())
except tables.NoSuchNodeError:
mask = None
unit = eval(unicode(h5.getNodeAttr(resNode, "unit"), 'utf-8'))
try:
dimTable = resNode.dimensions
dimensions = [
loadField(
h5,
h5.getNode(
"/results/result_" + DataContainer.parseId(row['id'])[0]
)
)
for row in dimTable.iterrows()
]
except tables.NoSuchNodeError:
dimensions = DataContainer.INDEX
result = DataContainer.FieldContainer(data, unit, error, mask,
dimensions, longname, shortname,
attributes)
result.creator = creator
result.machine = machine
result.seal(resNode._v_title)
return result
def loadSummary(self, dcId=None):
"""
Extracts meta data about a given DataContainer and returns it
as a dictionary.
dcId -- emd5 of the DC to summarize. If the emd5 belongs to an
IndexMarker object, u'IndexMarker' is returned.
If dcId == None, a dictionary that maps emd5s to summaries
is returned, where IndexMarker objects are ignored.
"""
if dcId == None:
summary = {}
for group in self.handle.walkGroups(where="/results"):
currDcId = group._v_attrs.TITLE
if len(currDcId) > 0:
tmp = self.loadSummary(currDcId)
if tmp == 'IndexMarker':
summary[im_id] = im_summary
else:
summary[currDcId] = tmp
elif self.isIndexMarker(dcId):
return u'IndexMarker'
else:
summary = {}
summary['id'] = dcId
resNode, uriType = self.getNodeAndTypeFromId(dcId)
summary['longname'] = utf82uc(
self.handle.getNodeAttr(resNode, "longname"))
summary['shortname'] = utf82uc(
self.handle.getNodeAttr(resNode, "shortname"))
summary.update(emd52dict(dcId))
try:
summary['machine'] = utf82uc(
self.handle.getNodeAttr(resNode, "machine"))
summary['creator'] = utf82uc(
self.handle.getNodeAttr(resNode, "creator"))
except:
pass # machine, creator set by emd52dict(dcId) before
attributes = {}
if uriType == 'field':
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key] = self.handle.getNodeAttr(
resNode.data, key)
unit = eval(utf82uc(self.handle.getNodeAttr(resNode, "unit")))
summary['unit'] = unit
dimTable = resNode.dimensions
def filterIndexMarker(emd5):
if self.isIndexMarker(emd5):
return im_id
else:
return emd5
dimensions = [filterIndexMarker(row['id']) \
for row in dimTable.iterrows()]
summary['dimensions'] = dimensions
elif uriType == 'sample':
for key in resNode._v_attrs._v_attrnamesuser:
if key not in PyTablesPersister._reservedAttributes:
attributes[key] = self.handle.getNodeAttr(resNode, key)
columns = []
for resId in self.handle.getNodeAttr(resNode, "columns"):
nodename = "/results/" + resId
columnId = self.handle.getNodeAttr(nodename, "TITLE")
columns.append(columnId)
summary['columns'] = columns
summary['attributes'] = attributes
return summary
def loadSummary(self, dcId=None):
"""
Extracts meta data about a given DataContainer and returns it
as a dictionary.
dcId -- emd5 of the DC to summarize. If the emd5 belongs to an
IndexMarker object, u'IndexMarker' is returned.
If dcId == None, a dictionary that maps emd5s to summaries
is returned, where IndexMarker objects are ignored.
"""
if dcId is None:
summary = {}
for group in self.handle.walkGroups(where="/results"):
currDcId = group._v_attrs.TITLE
if len(currDcId) > 0:
tmp = self.loadSummary(currDcId)
if tmp == 'IndexMarker':
summary[im_id] = im_summary
else:
summary[currDcId] = tmp
elif self.isIndexMarker(dcId):
return u'IndexMarker'
else:
summary = {}
summary['id'] = dcId
resNode, uriType = self.getNodeAndTypeFromId(dcId)
summary['longname'] = utf82uc(self.handle.getNodeAttr(resNode,
"longname"))
summary['shortname'] = utf82uc(
self.handle.getNodeAttr(resNode, "shortname")
)
summary.update(emd52dict(dcId))
try:
summary['machine'] = utf82uc(
self.handle.getNodeAttr(resNode, "machine")
)
summary['creator'] = utf82uc(
self.handle.getNodeAttr(resNode, "creator")
)
except:
pass # machine, creator set by emd52dict(dcId) before
attributes = {}
if uriType == 'field':
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key] = self.handle.getNodeAttr(
resNode.data, key
)
unit = eval(utf82uc(self.handle.getNodeAttr(resNode, "unit")))
summary['unit'] = unit
dimTable = resNode.dimensions
def filterIndexMarker(emd5):
if self.isIndexMarker(emd5):
return im_id
else:
return emd5
dimensions = [filterIndexMarker(row['id']) \
for row in dimTable.iterrows()]
summary['dimensions'] = dimensions
elif uriType == 'sample':
for key in resNode._v_attrs._v_attrnamesuser:
if key not in PyTablesPersister._reservedAttributes:
attributes[key] = self.handle.getNodeAttr(resNode, key)
columns = []
for resId in self.handle.getNodeAttr(resNode, "columns"):
nodename = "/results/" + resId
columnId = self.handle.getNodeAttr(nodename, "TITLE")
columns.append(columnId)
summary['columns'] = columns
summary['attributes'] = attributes
return summary