def findTopObjectPath(repositoryPath, topObject):
"""Get topObject absolute file path given the repositoryPath,
where topObject can be of class MemopsRoot or TopObject.
Will find an existing file fitting the TopObject ID.
If none is found returns default file name
"""
suffix = fileSuffix
lenSuffix = lenFileSuffix
sep = separatorFileNameChar
if topObject.root is topObject:
# MemopsRoot
objId = topObject.name
else:
# other TopObject
objId = topObject.guid
# get default file name
topObjectDir = uniIo.joinPath(repositoryPath,
*topObject.packageName.split('.'))
result = uniIo.joinPath(topObjectDir, getTopObjectFile(topObject))
if not os.path.isfile(result):
# default file name is not there. Look for alternative file that fits ID
if os.path.isdir(topObjectDir):
for filename in os.listdir(topObjectDir):
if filename.endswith(suffix):
if filename.split(sep)[-1][:-lenSuffix] == objId:
result = os.path.join(topObjectDir, filename)
break
# return whatever result we have
return result
def parsePulProgName(name, fileLocation=None):
""" Input: pulse program name to be parsed
location of pulse program map file
- if not given use standard file
Output: List of (expName,isReversed) tuples
expName can be either an NmrExpPrototype name
or a RefExperiment name.
isReversed can be True, False, or None (meaning not set).
Caches pulse program parsing map
"""
global pulProgNameMap
# get pulse program name translation map
if fileLocation is None:
if pulProgNameMap is None:
fileLocation = uniIo.joinPath(uniIo.getTopDirectory(), 'data', 'ccp',
'bruker', 'BrukerPulseProgMap.xml')
parseInfo = ccpGenUtil.loadAllParseInfo(fileLocation)
pulProgNameMap = ccpGenUtil.convertParseInfo(parseInfo)
else:
parseInfo = ccpGenUtil.loadAllParseInfo(fileLocation)
pulProgNameMap = ccpGenUtil.convertParseInfo(parseInfo)
# get match result
matchMap = matchName(name, pulProgNameMap, specialCases)
dd = matchMap
return matchMap['matches']
def testNameParsing(dirPath):
""" Frame code to run name testing
"""
# set of imput info
stdInfoFile = uniIo.joinPath(uniIo.getTopDirectory(),
'data', 'ccp', 'bruker', 'BrukerPulseProgMap.xml')
fileNames = os.listdir(dirPath)
fileNames.sort()
parseInfo = ccpGenUtil.loadAllParseInfo(stdInfoFile)
useInfo = ccpGenUtil.convertParseInfo(parseInfo)
# set up mapId:list dictionary
matchByMap = {}
notmatched = []
skipped = []
for expNameMap in parseInfo['expNameMaps']:
matchByMap[id(expNameMap)] = []
# match filenames and store by matchDict
for fname in fileNames:
dd = matchName(fname, useInfo, specialCases)
dd['fname'] = fname
expNameMap = dd.get('expNameMap')
if (dd.get('status') == 'skip'
or not os.path.isfile(uniIo.joinPath(dirPath,fname))):
skipped.append(dd)
elif expNameMap is None:
notmatched.append(dd)
else:
matchByMap[id(expNameMap)].append(dd)
#print fname, dd['matches'], dd['names'], dd['unused']
# print result
print '\nSKIPPED:'
for dd in skipped:
print ' - ', dd['fname'], dd.get('usenames'), dd.get('prefixes'), dd.get('unused')
print '\nNO MATCH:'
for dd in notmatched:
print ' - ', dd['fname'], dd.get('usenames'), dd.get('prefixes'), dd.get('unused')
unused = []
for xmap in parseInfo['expNameMaps']:
ll = matchByMap[id(xmap)]
prototypes = [(x.get('name'), x.get('isReversed')) for x in xmap['expPrototypes']]
if ll:
print '\nMATCH:', xmap.get('namesStartWith'), xmap.get('hasnames'), xmap.get('hasprefixes')
print ' ', prototypes
for dd in ll:
if dd.get('unused'):
ss = ' NB - '
else:
ss = ' - '
print ss, dd['fname'], dd.get('usenames'), dd.get('prefixes'), dd.get('unused')
for xmap in unused:
print '\nUNUSED', xmap.get('namesStartWith'), xmap.get('hasnames'), xmap.get('hasprefixes')
print ' ', [(x.get('name'), x.get('isReversed')) for x in xmap['expPrototypes']]
def getCcpForgeUrls(molType, ccpCode, sourceName=None):
"""
Creates the URL info for ChemComp(Coord) downloads from CcpForge
"""
ccpForgeUrl = "http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&root=ccpn-chemcomp&pathrev=MAIN&path=/"
checkOutDir = "~checkout~"
archiveDir = "ccpn-chemcomp/data/pdbe/chemComp/archive/"
#%2Acheckout%2A%2Fccpn-chemcomp%2Fdata%2Fpdbe%2FchemComp%2Farchive%2FChemComp%2Fprotein%2Fprotein%252B004%252Bpdbe_ccpnRef_2010-09-23-14-41-20-237_00001.xml&revision=1.1
if not sourceName:
fileType = 'ChemComp'
subPath = getChemCompArchiveXmlFilePath("", molType, ccpCode)
else:
fileType = 'ChemCompCoord'
subPath = getChemCompCoordArchiveXmlFilePath("", sourceName, molType,
ccpCode)
# wb104: 15 Dec 2010: need to use joinPath because otherwise does not
# work on Windows, but cannot stick ccpForgeUrl in joinPath() because
# that would convert http:// to http:/
ccpForgeDirUrl = ccpForgeUrl + uniIo.joinPath(archiveDir, fileType,
subPath)
ccpForgeDownloadUrl = ccpForgeUrl + uniIo.joinPath(checkOutDir, archiveDir,
fileType, subPath)
return (fileType, ccpForgeDirUrl, ccpForgeDownloadUrl)
def getDataPath(*args):
"""
Gives location of data path. Extra args are added on as extra directories
Result ends with the last arg (which might be either a file or a dictionary)
"""
dataPath = uniIo.joinPath(uniIo.getTopDirectory(), 'data', *args)
return dataPath
def getChemCompArchiveXmlFilePath(chemCompPath, molType, ccpCode):
chemCompXmlFilePath = uniIo.joinPath(chemCompPath, molType)
if molType == 'other':
chemCompXmlFilePath = uniIo.joinPath(chemCompXmlFilePath, ccpCode[0])
return chemCompXmlFilePath
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 prepareLocalExecution(nmrCalcRun, targetDir):
""" return [procArgs, targetDir, logFile list for later, local execution
And carry out any preliminary commands
"""
# Set up parameters for program call
shellParObj = nmrCalcRun.findFirstRunParameter(name='programCall')
if shellParObj is None:
raise Exception("Parameter name=programCall not found")
else:
shellCall = shellParObj.textValue
executeScript = os.path.join(os.path.expandvars(programBin), shellCall)
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
if fileNameObj is None:
raise Exception("no 'fileNameSetup' parameter found")
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
procargs = [executeScript, '-f', filePath]
algObj = nmrCalcRun.findFirstRunParameter(name='MDAlgorithm')
if 'XPLOR' in algObj.textValue.upper():
# copy xplor template files
for fname in ('sa.inp', 'generate.inp', 'generate_template.inp'):
src = os.path.join(os.path.expandvars(unioXplor), fname)
shutil.copy2(src, targetDir)
#
return (procargs, targetDir)
def configParameter(keyWord):
"""Get configuration parameter corresponding to 'keyWord'.
NBNB TBD this should go to a configuration file to get its data
The format of this file is still up for grabs.
"""
rootDir = uniIo.normalisePath(uniIo.os.getcwd())
if keyWord == 'repositories':
# list of (name,urlPath) pairs
return []
elif keyWord == 'packageLocators':
# list of (packageName, repositoryName) Triplets
# If the packageName appears more than once, the named repositories
# are added in the order given
return [
('ccp.molecule.ChemComp', 'userData'),
('ccp.molecule.ChemComp', 'refData'),
('ccp.molecule.ChemCompCharge', 'refData'),
('ccp.molecule.ChemCompCoord', 'refData'),
('ccp.molecule.ChemCompLabel', 'userData'),
('ccp.molecule.ChemCompLabel', 'refData'),
('ccp.molecule.ChemElement', 'refData'),
('ccp.molecule.StereoChemistry', 'refData'),
('ccp.nmr.NmrExpPrototype', 'userData'),
('ccp.nmr.NmrExpPrototype', 'refData'),
('ccp.nmr.NmrReference', 'refData'),
('ccpnmr.AnalysisProfile', 'generalData'),
('ccpnmr.AnalysisProfile', 'refData'),
]
else:
return None
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 __init__(self):
""" parameters are mandatoryInitParams, optionalInitParams
and the special optional
"""
for tag in TextWriter_py_2_1.mandatoryAttributes:
if not hasattr(self, tag):
raise MemopsError(" TextWriter lacks mandatory %s attribute" %
tag)
super(TextWriter, self).__init__()
# special parameters: optional with default values
if self.rootFileName is None:
self.rootFileName = ImpConstants.rootPackageDirName
if self.rootDirName is None:
self.rootDirName = uniIo.getTopDirectory()
self.fp = None
self.fileName = ''
self.indent = 0
self.indents = []
self.errorMsg = ''
self.previousLineEmpty = False # used so that do not print out two '\n' in a row
def prepareLocalExecution(nmrCalcRun, targetDir):
""" return [procArgs, targetDir, logFile list for later, local execution
And carry out any preliminary commands
"""
# Set up parameters for program call
shellParObj = nmrCalcRun.findFirstRunParameter(name='programCall')
if shellParObj is None:
raise Exception("Parameter name=programCall not found")
else:
shellCall = shellParObj.textValue
executeScript = os.path.join(os.path.expandvars(programBin), shellCall)
executeScript2 = os.path.join(os.path.expandvars(programBin), 'cyanatable')
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
if fileNameObj is None:
raise Exception("no 'fileNameSetup' parameter found")
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
procargs = [executeScript, filePath]
procargs2 = [executeScript2]
#
return (procargs, targetDir, procargs2)
def setLicenses(directory=None,
licenseDir='license',
warnSkippedFiles=(not 0),
mode='act'):
""" wrapper - set license header for 'directory' and all subdirectories
licenseDir is the relative path from 'directory'
to the directory with license texts
"""
# necessary as the first directory may be a relative directory name,
# playing havoc with import commands
firstLookupDir = sys.path[0]
sys.path[0] = ''
try:
global testInfo
testInfo = {}
if directory is None:
directory = uniIo.getTopDirectory()
else:
directory = os.path.abspath(directory)
doSetLicenses(directory, licenseDir, None, 0, warnSkippedFiles, mode)
if mode == 'test':
print showTestInfo()
finally:
sys.path[0] = firstLookupDir
def read(nmrCalcRun, dataDir):
""" Read Output files for Unio run
Input:
nmrCalcRun: NmrCalc.Run
dataDir: directory directly containing program output.
"""
fileNames = stdFileNames.copy()
# make summary text element
summary = ""
for tag in ('overview', ):
path = uniIo.joinPath(dataDir, fileNames[tag])
if os.path.isfile(path):
txt = open(path).read()
else:
txt = 'WARNING, file % not found' % fileNames[tag]
summary += ('-' * 80 +
"\nFROM FILE : %s\n----------------\n%s\n\n\n" %
(fileNames[tag], txt))
nmrCalcRun.newRunParameter(name='summary',
ioRole='output',
textValue=summary)
# Get MolSystem
molResidueData = (
nmrCalcRun.findFirstData(className='MolResidueData', ioRole='input')
or nmrCalcRun.findFirstData(className='MolSystemData', ioRole='input'))
molSystem = molResidueData.molSystem
# read pdb structures
path = uniIo.joinPath(dataDir, fileNames['pdbBundle'])
if os.path.isfile(path):
ensemble = StructureIo.getStructureFromFile(molSystem, path)
# make EnsembleData
nmrCalcRun.newStructureEnsembleData(name='result',
ioRole='output',
structureEnsemble=ensemble,
details="Unio calculated structures")
# Make Nmr.StructureCalculation
nmrProject = nmrCalcRun.nmrCalcStore.nmrProject
nmrCalcRun.structureGeneration = nmrProject.newStructureGeneration(
generationType='denovo', name='UNIO', structureEnsemble=ensemble)
def getChemCompOrCoordXmlFile(repository, fileSearchString, fileSearchPath,
className, identifier, showError, copyFile):
result = None
if showError is None:
showError = uniIo.printError
# Try to find file...
import glob
fileNameMatches = glob.glob(
uniIo.joinPath(fileSearchPath, fileSearchString))
if fileNameMatches:
if len(fileNameMatches) > 1:
errorText = "Error: multiple matches found for %s %s - taking last one." % (
className, identifier)
showError("Multiple %s matches" % className, errorText)
filePath = fileNameMatches[-1]
(fileDir, fileName) = os.path.split(filePath)
#
# Copy file if found...
#
if os.path.exists(filePath):
if copyFile:
savePath = repository.getFileLocation('ccp.molecule.%s' %
className)
if not os.path.exists(savePath):
os.makedirs(savePath)
import shutil
saveFilePath = uniIo.joinPath(savePath, fileName)
shutil.copy(filePath, saveFilePath)
result = saveFilePath
print " %s file %s copied to %s..." % (className, fileName,
savePath)
else:
result = filePath
return result
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 oldwrite(nmrCalcRun, topDir=None):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
topDir: optional destination directory.
"""
targetDir = intIo.createTargetDir(nmrCalcRun, topDir=topDir)
# write Properties file
propDict, dummy = intIo.makeParameterDict(nmrCalcRun)
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
open(propFile,'w').write(json.dumps(propDict, sort_keys=True,
indent=intIo.propIndent))
# Write data file
# get file
inpFile = propDict.get('INPUT_FILE')
if inpFile:
talosInputFile = uniIo.joinPath(targetDir, inpFile)
else:
raise Exception("No code=INPUT_FILE RunParameter in nmrCalcRun")
# Get shiftList
shiftList = intUtil.getMeasurementList(nmrCalcRun)
if shiftList is None:
raise Exception("Run must have exactly one shift list, %s found" % len(ll))
# Get residues
ll = list(nmrCalcRun.findAllData(className='MolResidueData'))
if len(ll) == 1:
obj = ll.pop()
residues = list(obj.residues)
residues.sort(key=operator.attrgetter('seqId'))
if len(set(obj.chainCodes)) != 1:
raise Exception("Run MolResidueData did not have a (single) chain" )
else:
raise Exception("Run must have excactly one MolResidueData, %s found" % len(ll))
#
talosIo.writeShiftFile(open(talosInputFile,'w'), residues, shiftList,
propDict.get('minShiftQuality'))
def getProjectFile(repositoryPath, projectName=None):
"""Get project file given the repositoryPath and optionally the projectName
(if none given then determined from repositoryPath)
"""
if not projectName:
projectName = os.path.basename(repositoryPath)
implDirectory = getImplementationDirectory(repositoryPath)
return uniIo.joinPath(implDirectory, projectName + fileSuffix)
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
open(propFile, 'w').write(
json.dumps(jsonDict, sort_keys=True, indent=intIo.propIndent))
# Write program setup file
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
if fileNameObj is not None:
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
writeSetupFile(filePath, jsonDict)
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
print 'About to write', propFile
open(propFile, 'w').write(
json.dumps(jsonDict, sort_keys=True, indent=intIo.propIndent))
# Write program setup file
fileNameObj = nmrCalcRun.findFirstRunParameter(name='fileNameSetup')
importJsonName = 'cyana2ccpn.json'
if fileNameObj is not None:
# write init.cya
initFile = uniIo.joinPath(targetDir, initFileName)
rmsdrange = jsonDict['RunParameter'].pop('rmsdrange')
seqFile = jsonDict['RunParameter'].pop('fileNameSequence')
text = """# Cyana init file - Generated by CcpNmr Integrator
rmsdrange:=%s
cyanalib
read seq %s
""" % (rmsdrange, seqFile)
open(initFile, 'w').write(text)
# write main command file
filePath = uniIo.joinPath(targetDir, fileNameObj.textValue)
importFilePath = uniIo.joinPath(targetDir, importJsonName)
writeSetupFile(filePath, jsonDict)
writeImportJson(importFilePath, jsonDict)
def getDetails(self, fullfile):
details = ''
if os.path.isfile(fullfile):
format = self.formatPulldown.getText()
detailsDir = os.path.dirname(fullfile)
detailsFile = uniIo.joinPath(detailsDir, details_file_dict[format])
if os.path.exists(detailsFile):
fp = open(detailsFile)
details = fp.read().strip().replace('\n',
' ').replace('\r', ' ')
fp.close()
return (details, )
def getDataStoringFromFilepath(memopsRoot,
fullFilePath,
preferDataUrls=None,
dataLocationStore=None,
keepDirectories=1):
# make absolute,, normalised path
fullFilePath = uniIo.normalisePath(fullFilePath, makeAbsolute=True)
dataUrl, filePath = findDataStoringFromFilepath(memopsRoot, fullFilePath,
preferDataUrls,
dataLocationStore,
keepDirectories)
if dataUrl is None:
urlPath = uniIo.normalisePath((fullFilePath[:-len(filePath)]))
dataLocationStore = memopsRoot.currentDataLocationStore
dataUrl = dataLocationStore.newDataUrl(url=Implementation.Url(
path=urlPath))
dataUrl.name = 'auto-%s' % dataUrl.serial
#
return (dataUrl, filePath)
def resetPackageLocators(project):
carbDataPath = uniIo.normalisePath(
os.path.join(os.path.abspath('..'), 'data'))
print 'Location of local carbohydrate ChemComps: [%s]' % carbDataPath
carbDataUrl = Implementation.Url(path=carbDataPath)
carbDataRepos = project.newRepository(name='carbData', url=carbDataUrl)
chemPackLoc = project.findFirstPackageLocator(
targetName='ccp.molecule.ChemComp')
chemPackLoc.addRepository(carbDataRepos)
def write(nmrCalcRun, targetDir):
""" Write input files for Program run
Input:
nmrCalcRun: NmrCalc.Run
targetDir: destination directory.
"""
#intIo.writeDataFiles(nmrCalcRun, targetDir)
jsonDict = intIo.makeJsonDict(nmrCalcRun)
# write properties file
propFile = uniIo.joinPath(targetDir, intIo.propFileName)
print 'About to write', propFile
open(propFile, 'w').write(
json.dumps(jsonDict, sort_keys=True, indent=intIo.propIndent))
def getPossibleProjectFiles(repositoryPath):
"""Get the possible project files given the repositoryPath
"""
if os.path.isdir(repositoryPath):
implDirectory = getImplementationDirectory(repositoryPath)
if os.path.isdir(implDirectory):
files = os.listdir(implDirectory)
files = [
uniIo.joinPath(implDirectory, file) for file in files
if file.endswith(fileSuffix)
]
return files
return []
def __init__(self, **kw):
"""To make this work under python 2.1 we need to inline the inits
of several other files.
"""
# set input attributes
for (tag, val) in kw.items():
if not hasattr(self, tag):
setattr(self, tag, val)
# in-line set xml settings (in lieu of Language init)
settings = TextWriter_py_2_1.settings['xmlmodel']
for (tag, val) in settings.items():
if not hasattr(self, tag):
setattr(self, tag, val)
# in-line version of TextWriter init
for tag in TextWriter_py_2_1.mandatoryAttributes:
if not hasattr(self, tag):
raise MemopsError(" TextWriter lacks mandatory %s attribute" %
tag)
# special parameters: optional with default values
if self.rootFileName is None:
self.rootFileName = ImpConstants.rootPackageDirName
if self.rootDirName is None:
self.rootDirName = uniIo.getTopDirectory()
# process self.includePackageNames, including container names
inclNames = self.includePackageNames
if inclNames:
for name in inclNames:
ll = name.split('.')
for ii in range(1, len(ll)):
ss = '.'.join(ll[:ii])
if ss not in inclNames:
inclNames.append(ss)
self.fp = None
self.fileName = ''
self.indent = 0
self.indents = []
self.errorMsg = ''
self.previousLineEmpty = False # used so that do not print out two '\n' in a row
def changeDataStoreUrl(dataStore, newPath):
""" Change the url for this dataStore, so at the end we have
dataStore.dataUrl.url.path = newPath. This changes all dataUrls
with the same old path if the old path does not exist and the
new one does.
"""
newPath = uniIo.normalisePath(newPath, makeAbsolute=True)
oldDataUrl = dataStore.dataUrl
oldUrl = oldDataUrl.url
oldPath = oldUrl.dataLocation
oldExists = os.path.exists(oldPath)
if newPath != oldPath:
dataLocationStore = dataStore.dataLocationStore
newUrl = Implementation.Url(
path=newPath) # TBD: should use oldUrl.clone(path=newPath)
# first check if have a dataUrl with this path
newDataUrl = dataLocationStore.findFirstDataUrl(url=newUrl)
if not newDataUrl:
# if old path exists and there is more than one dataStore with
# this dataUrl then create new one
dataUrlStores = dataLocationStore.findAllDataStores(
dataUrl=oldDataUrl)
if oldExists and len(dataUrlStores) > 1:
newDataUrl = dataLocationStore.newDataUrl(name=oldDataUrl.name,
url=newUrl)
# if have found or have created newDataUrl then set dataStore to point to it
# else just change url of oldDataUrl (which could affect other dataStores)
if newDataUrl:
dataStore.dataUrl = newDataUrl
else:
oldDataUrl.url = newUrl
# if old path does not exist and new path exists then change urls of
# all data urls which have old path to new path (there might be none)
if not oldExists:
newExists = os.path.exists(newPath)
if newExists:
for dataUrl in dataLocationStore.dataUrls:
if dataUrl.url == oldUrl:
dataUrl.url = newUrl
def loadProject(parent, path, projectName=None):
path = uniIo.normalisePath(path)
askdir = lambda title, prompt, initial_value: askDir(
title, prompt, initial_value, parent=parent, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title, prompt, initial_value, parent=parent, extra_dismiss_text='Skip')
project = genIo.loadProject(path,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
# now check dataStores
# delete those that are not used
# and otherwise check path to see if exists
dataStores = []
for dataLocationStore in project.dataLocationStores:
for dataStore in dataLocationStore.dataStores:
if isinstance(dataStore,
NumericMatrix) and not dataStore.nmrDataSources:
print 'deleting dataStore %s with path %s' % (
dataStore, dataStore.fullPath)
dataStore.delete()
elif isinstance(
dataStore,
MimeTypeDataStore) and not dataStore.nmrDataSourceImages:
print 'deleting dataStore %s with path %s' % (
dataStore, dataStore.fullPath)
dataStore.delete()
else:
dataStores.append(dataStore)
badDataStores = [
dataStore for dataStore in dataStores
if not os.path.exists(dataStore.fullPath)
]
if badDataStores:
popup = DataLocationPopup(parent, project, modal=True)
popup.destroy()
return project
def getObjFileName(self, metaObj, absoluteName=True, addSuffix=False):
""" Get filename for metaObj
If absoluteName is True the file name is absolute
otherwise it is relative to the relevant baseDir
"""
# absoulte or relative path
if absoluteName:
pathList = [self.rootDirName, self.baseDirName]
else:
pathList = []
if metaObj.container is None:
# Root package only
pathList.append(ImpConstants.modellingPackageName)
if self.codeDirName:
pathList.append(self.codeDirName)
pathList.append(self.rootFileName)
else:
# any other object
ll = metaObj.qualifiedName().split('.')
if self.codeDirName:
ll[1:1] = [self.codeDirName]
pathList.extend(ll)
# special handling for ModelElements that may correspond to directories:
if (isinstance(metaObj, MetaModel.MetaPackage) and
(metaObj.containedPackages or not self.classesInPackage)):
pathList.append(self.packageFile)
elif not isinstance(metaObj.container, MetaModel.MetaPackage):
raise MemopsError(
" file names not implemented for objects of type %s" %
(metaObj.__class__.__name__, ))
# add suffix
if addSuffix and self.fileSuffix:
pathList[-1] = '%s.%s' % (pathList[-1], self.fileSuffix)
#
return uniIo.joinPath(*pathList)
def fullLoadValidationStore(topObj):
"""hard load ValidationStore from old location
"""
from memops.format.xml import Util as xmlUtil
from memops.universal import Io as uniIo
from memops.format.xml import XmlIO
root = topObj.memopsRoot
locator = (
root.findFirstPackageLocator(targetName='ccp.molecule.Validation')
or root.findFirstPackageLocator(targetName='any'))
repository = locator.findFirstRepository()
#repository = topObj.activeRepositories[0]
fileLocation = repository.getFileLocation(
'ccp.molecule.StructureValidation')
filePath = uniIo.joinPath(fileLocation, xmlUtil.getTopObjectFile(topObj))
XmlIO.loadFromStream(open(filePath),
topObject=topObj,
topObjId=topObj.guid,
partialLoad=False)
###################
# Main of program #
###################
if __name__ == "__main__":
#
# Variables...
#
dataDir = 'data/'
sequenceFileName = 'fasta.seq'
currentDir = os.path.abspath('.')
projectDir = uniIo.joinPath((currentDir,'local'))
projectName = 'testImportSequence'
#
# Make sure the projectDir exists and delete existing data
#
if not os.path.exists(projectDir):
os.mkdir(projectDir)
projectPath = os.path.join(projectDir,projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
#
# Create a CCPN project. This sets default save locations in the
#
# Make sure it saves the information in the projectDir
# To do this on the Python level you have to reset the path
# for the urls that indicate the directory locations for the
# saved files...
#
# Alternatively create the project in the right directory to
# start with - see convertCns2Pdb
#
for repository in ccpnProject.repositories:
if repository.name in ('userData','backup'):
(oldUrlPath,baseName) = uniIo.splitPath((repository.url.path))
newUrlPath = uniIo.joinPath(projectDir,baseName)
repository.url = Implementation.Url(path = newUrlPath)
#
# Create main Tk window for popups
#
gui = Tkinter.Tk()
#
# Create an NmrView class and read in the files... create an experiment
# for the peak list beforehand and pass in the parameters.
#