def setDataSourceDataStore(dataSource,
dataUrlPath,
localPath,
dataLocationStore=None,
dataUrl=None):
#
# Get DataLocationStore
#
if not dataLocationStore:
setCurrentStore(dataSource.root, 'DataLocationStore')
dataLocationStore = dataSource.root.currentDataLocationStore
#
# Get (or create) DataUrl
#
# TODO should this search function go elsewhere?
if not dataUrl:
for tmpDataUrl in dataLocationStore.dataUrls:
if tmpDataUrl.url.dataLocation == dataUrlPath:
dataUrl = tmpDataUrl
if not dataUrl:
dataUrlPath = uniIo.normalisePath(dataUrlPath)
dataUrl = dataLocationStore.newDataUrl(url=Implementation.Url(
path=dataUrlPath))
#
# Create a BlockedBinaryMatrix. TODO: could be other classes that are set up this way - rename func and make general,, pass in class?
#
localPath = uniIo.normalisePath(localPath)
blockedBinaryMatrix = dataLocationStore.newBlockedBinaryMatrix(
path=localPath, dataUrl=dataUrl)
"""
TODO Set here as well, or do this later after returning object:
blockSizes Int 0..* Block sizes in dimension order
complexStoredBy ComplexStorage 1..1 The ordering of real and imaginary parts of hypercomplex numbers in the data matrix. See ComplexStorage type for details
hasBlockPadding Boolean 1..1 Are data padded to fill all blocks completely? Alternatively incomplete blocks store only the actual data.
headerSize Int 1..1 Header size in bytes
isBigEndian Boolean 1..1 Are data big-endian (alternative little-endian).
isComplex Boolean 0..* Are numbers complex (if True) or real/integer (if False).
nByte Int 1..1 Number of bytes per number
numPoints Int 0..* number of points for each matrix dimension - also defines dimensionality of matrix. The number of points is the same for real or complex data, in the sense that n complex points require 2n real numbers for storage.
numRecords Int 1..1 Number of matrix records in file. All other information in the object describes a single record.
numberType NumberType 1..1 Type of numbers held in matrix
"""
dataSource.dataStore = blockedBinaryMatrix
return blockedBinaryMatrix
def getRefExpFromOldExpType(project,expType):
refExperiment = None
if oldToNewExpDict.has_key(expType):
(expPrototypeName,refExpName) = oldToNewExpDict[expType]
setCurrentStore(project,'ChemElementStore')
expPrototype = project.findFirstNmrExpPrototype(name = expPrototypeName)
if expPrototype:
refExperiment = expPrototype.findFirstRefExperiment(name = refExpName)
return refExperiment
def __init__(self, parent, project, numDim=None, topText=None, expName=''):
self.parent = parent
self.project = project
self.numDim = numDim
self.topText = topText
self.skip = 1
self.expName = expName
setCurrentStore(project, 'ChemElementStore')
TemporaryBasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Create Experiment',
modal=False,
transient=True)
import Tkinter
from memops.api import Implementation
from memops.gui.Button import Button
from memops.gui.MessageReporter import showInfo
from ccp.general.Util import setCurrentStore
from ccp.gui.ChemCompFrame import ChemCompFrame
from ccp.gui.ChemCompEditor import ChemCompEditPopup
from pdbe.chemComp.Constants import editChemCompDataDir
if (__name__ == '__main__'):
project = Implementation.MemopsRoot(name='edit')
setCurrentStore(project, 'ChemElementStore')
root = Tkinter.Tk()
root.top = root
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
frame = ChemCompFrame(
root, project,
chemCompEntries=('ChemComp', )) #path = editChemCompDataDir,
frame.grid(sticky=Tkinter.NSEW)
def getSelected():
chemComp = frame.getSelectedChemComp()
def initialiseWorkflow(
self,
ccpnProject=None, # One of these top three is obligatory!
ccpnProjectTgz=None,
identifier=None,
useGui=False,
overwrite=True,
initializeObjects=True, # Set to False if don't want to automatically set NmrProject and constraint stuff. Should probably do this differently anyway! More options...
verbose=True):
self.verbose = verbose
#
# Need either an existing CCPN project or an identifier for it - note that this
# can be set as part of the class if required.
#
if not hasattr(self, 'identifier') and identifier:
self.identifier = identifier
if not ccpnProject and not self.identifier and not ccpnProjectTgz:
raise self.WorkFlowError(
"No CCPN project or identifier given - aborting workflow.")
#
# Set day/time when workflow was run
#
self.timeFlag = self.getTimeString()
#
# Set CCPN project - this is obligatory, and the CCPN project is unpacked if
# tgz file. Is this smart? Should I always start from a loaded project?
# And always pack it (temporary file) if have to send off? Probably best!
#
self.ccpnProject = None
if ccpnProject:
self.ccpnProject = ccpnProject
elif ccpnProjectTgz:
self.ccpnProject = self.unpackCcpnProjectTgz(ccpnProjectTgz)
else:
try:
tmpCcpnProject = loadProject(self.identifier)
except:
tmpCcpnProject = None
if tmpCcpnProject:
if not overwrite:
print(" Warning: using existing project!")
self.ccpnProject = tmpCcpnProject
else:
print(" Warning: overwriting existing project!")
shutil.rmtree(self.identifier)
if not self.ccpnProject:
self.ccpnProject = Implementation.MemopsRoot(
name=self.identifier)
#
# Set other CCPN objects (if required)
#
if initializeObjects:
# NMR project
setCurrentStore(self.ccpnProject, 'NmrProject')
self.nmrProject = self.ccpnProject.currentNmrProject
nmrConstraintStores = self.ccpnProject.sortedNmrConstraintStores()
if not nmrConstraintStores:
self.nmrConstraintStore = None
else:
if len(nmrConstraintStores) > 1:
raise self.WorkFlowError(
"Only one NMR constraint store allowed for running workflow. Please modify input."
)
self.nmrConstraintStore = nmrConstraintStores[0]
# TODO nmrEntry?
#
# Set graphical interface, if required
#
self.useGui = useGui
if useGui:
import Tkinter
self.guiRoot = Tkinter.Tk()
else:
self.guiRoot = None
#
# Run other <programShortCode>__init__
#
for program in programList:
programInit = '%s__init__' % program.lower()
if hasattr(self, programInit):
getattr(self, programInit)()
def findDataStoringFromFilepath(project,
fullFilePath,
preferDataUrls=None,
dataLocationStore=None,
keepDirectories=1):
""" Get DataUrl and relative filePath from normalised absolute filePath
Uses heuristics to select compatible DataUrl from existing ones.
sisterObjects is a collection of objects with a dataStore link -
DataUrls in use for sisterObjects are given preference in the
heuristics.
uses dataLocationStore or current dataLocationStore
If no compatible DataUrl is found the routine returns dataUrl None
and the file name plus the lowest keepDirectories directories
as the filePath
"""
# NB fullFilePath *must* be absolute her for code to work properly
#
if not os.path.isabs(fullFilePath):
raise ApiError(
"findDataStoringFromFilepath called with non-absolute file name %s"
% fullFilePath)
# get DataLocationStore
if not dataLocationStore:
setCurrentStore(project, 'DataLocationStore')
dataLocationStore = project.currentDataLocationStore
# get DataUrl that match fullFilePath
dataUrls = []
for dataUrl in dataLocationStore.dataUrls:
dirPath = uniIo.normalisePath(dataUrl.url.path)
if fullFilePath.startswith(dirPath):
lenPath = len(dirPath)
ss = fullFilePath
while len(ss) > lenPath:
ss, junk = uniIo.splitPath(ss)
if ss == dirPath:
# DataUrl path matches file path
dataUrls.append(dataUrl)
# process result
if dataUrls:
if preferDataUrls:
# look for DataUrls that are in use with related objects
ll = [x for x in dataUrls if x in preferDataUrls]
if ll:
dataUrls = ll
if len(dataUrls) == 1:
# only one DataUrl - use it
dataUrl = dataUrls[0]
else:
# use DataUrl with longest path
ll = [(len(dataUrl.url.path), dataUrl) for dataUrl in dataUrls]
ll.sort()
dataUrl = ll[-1][1]
# get filePath
ss = uniIo.joinPath(dataUrl.url.path,
'') # removes file separator from end
filePath = fullFilePath[len(ss) + 1:]
else:
dataUrl = None
ll = []
ss = fullFilePath
for dummy in range(keepDirectories + 1):
ss, name = os.path.split(ss)
ll.append(name)
ll.reverse()
filePath = uniIo.joinPath(*ll)
#
return (dataUrl, filePath)