def main(root):
# find or create NmrProject
nmrProject = root.findFirstNmrProject()
if not nmrProject:
nmrProject = root.newNmrProject(name='testNmr')
# create experiment, including expDimRefs
dd = {}
dd['sf'] = (800, 81)
dd['isotopeCode'] = ('1H', '15N')
experiment = createExperiment(nmrProject,
name='testNmr',
numDim=2,
expDimRefDict=dd)
# set refExperiment
setRefExperiment(experiment, expPrototypeSynonym='15N HSQC/HMQC')
# create dataSource, including freqDataDims and dataDimRefs
dd = {}
dd['isComplex'] = (False, False)
dd['numPoints'] = (2048, 1024)
dd['numPointsOrig'] = (2048, 1024)
dd['valuePerPoint'] = (3.93, 0.99)
dd['refPoint'] = (1024, 512)
dd['refValue'] = (4.72, 117.4)
dataSource = createDataSource(experiment,
name='testSpec',
numDim=2,
dataDimDict=dd)
# create peakList
peakList = dataSource.newPeakList()
# create dataLocationStore
dataLocationStore = root.findFirstDataLocationStore()
if not dataLocationStore:
dataLocationStore = root.newDataLocationStore(name='testStore')
# create dataStore
from memops.api.Implementation import Url
dd = {}
dd['path'] = 'myHsqcData.spc'
dd['dataUrl'] = dataLocationStore.newDataUrl(url=Url(
path='/usr/myaccount/mydata'))
dd['blockSizes'] = (256, 128)
dd['headerSize'] = 0
dd['isBigEndian'] = True
dd['isComplex'] = (False, False)
dd['nByte'] = 4
dd['numPoints'] = [
dataDim.numPoints for dataDim in dataSource.sortedDataDims()
]
dd['numberType'] = 'float'
dataStore = dataLocationStore.newBlockedBinaryMatrix(**dd)
dataSource.dataStore = dataStore
root.saveModified()
def fixImplementation(topObj, delayDataDict):
""" Add generalData repository, packageLocator for AnalysisProfile with
repositories link, and set
NB when this is called PAckageLocators and Repositories
have already had their child links and crosslinks set.
"""
from memops.universal import Io as uniIo
from memops.api.Implementation import Url
import os.path
emptyDict = {}
emptyList = []
doGet = delayDataDict.get
urlPath = uniIo.normalisePath(os.path.expanduser('~/.ccpn/data'))
repositories = doGet(topObj).get('repositories')
for refData in repositories:
if refData.name == 'refData':
break
else:
raise ApiError("refData repository not found")
genData = topObj.newRepository(name='generalData', url=Url(path=urlPath))
topObj.__dict__['repositories']['generalData'] = genData
profileLocator = topObj.newPackageLocator(targetName='ccpnmr.AnalysisProfile',
repositories=(genData, refData))
topObj.__dict__['packageLocators']['ccpnmr.AnalysisProfile'] = profileLocator
def saveProject(project, name='test', subDir='data'):
# Find the backup repository and set the right path for it.
backupRepos = project.findFirstRepository(name='backup')
backupPath = uniIo.joinPath(os.getcwd(), subDir, name + '_backup')
# Create a URL for the backup repository.
backupRepos.url = Url(path=backupPath)
# Do the same for the repository containing the data in the project.
projectRepos = project.findFirstRepository(name='userData')
newPath = uniIo.joinPath(os.getcwd(), subDir, name)
# And also for the URL of this data.
projectRepos.url = Url(path=newPath)
# This saves the project to the path specified by the URL for the
# 'userData' repository.
project.saveModified()
def setRepositoryPath(project, repositoryName, path):
from memops.api.Implementation import Url
repository = project.findFirstRepository(name=repositoryName)
if repository:
if path != repository.url.path:
# TBD: should we copy anything over from old url?
url = Url(path=normalisePath(path))
repository.url = url
def setDir(self):
directory = self.dir_entry.get()
if not directory:
showWarning('No directory',
'No directory specified, not setting backup directory',
parent=self)
return
if not os.path.abspath(directory):
directory = joinPath(os.getcwd(), directory)
if os.path.exists(directory):
if not os.path.isdir(directory):
showWarning('Path not directory',
'Path "%s" exists but is not a directory' %
directory,
parent=self)
return
else:
if showYesNo(
'Directory does not exist',
'Directory "%s" does not exist, should it be created?' %
directory,
parent=self):
os.mkdir(directory)
else:
showWarning(
'Directory not created',
'Directory "%s" not created so not setting backup directory'
% directory,
parent=self)
return
repository = self.project.findFirstRepository(name='backup')
if not repository:
showWarning(
'No backup repository',
'No backup repository found (something wrong somewhere)',
parent=self)
return
url = repository.url
if url.path != directory:
repository.url = Url(path=normalisePath(directory))
fp.write('refpt %5.4f\n' % self.refpt[i])
fp.write('nuc %s\n' % self.nuc[i])
if self.pointValues[i]:
fp.write('params')
for value in self.pointValues[i]:
fp.write(' %5.4f' % value)
fp.write('\n')
fp.close()
if (__name__ == '__main__'):
import sys
if (len(sys.argv) != 2):
print 'Error: required argument: <parFile>'
sys.exit(1)
parFile = sys.argv[1]
params = AzaraParams(parFile)
from memops.api.Implementation import MemopsRoot, Url
from ccp.util.Spectrum import createExperiment
r = MemopsRoot()
l = r.newDataLocationStore(name='testDLS')
d = l.newDataUrl(name='testDataUrl', url=Url(path='/Users/wb104/edl387'))
n = r.newNmrProject(name='testNmrProject')
e = createExperiment(n, name='testExpt', numDim=params.ndim, sf=params.sf, isotopeCodes=params.nuc)
s = params.createDataSource(e, name='testSpectrum', dataUrl=d)
print 'Project: [%s]\n' % project
# Find the right repository that contains the project data.
projectRepos = project.findFirstRepository(name='userData')
# Specify a new location to save the project in.
newPath = uniIo.normalisePath(
os.path.join(os.path.abspath('.'), 'newDir', 'newSubDir'))
# Make a new Url pointing to the new location and link it to the
# 'userData' repository.
projectRepos.url = Url(path=newPath)
# Print the location of all project repositories.
print 'Repositories:\n%s' % ('\n'.join(
repos.name + ': ' + repos.url.path
for repos in project.sortedRepositories()))
carbDataPath = uniIo.normalisePath(
os.path.join(os.path.abspath('..'), 'data'))
print '\nLocation of local carbohydrate ChemComps: [%s]' % carbDataPath
carbDataUrl = Url(path=carbDataPath)
carbDataRepos = project.newRepository(name='carbData', url=carbDataUrl)