def saveProject(self):
if self.saveCcpn:
# Must be saved (and thus also renamed) before it can be packaged
genIo.saveProject(self.ccpnProject,
newPath=os.path.join(self.dataDir,
self.identifier),
newProjectName=self.identifier,
checkValid=True,
removeExisting=True)
genIo.packageProject(self.ccpnProject,
os.path.join(self.dataDir, self.identifier))
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
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
from memops.general import Io as genIo
from ccpnmr.integrator.core import Util as intUtil
if __name__ == '__main__':
""" Make NmrCalc.Run from json file.
"""
# get input arguments
if len(sys.argv) == 3:
projectDir, jsonFile = sys.argv[1:3]
nmrProjectName = None
else:
raise Exception("Usage: projectToJson projectDir jsonFilePath")
try:
memopsRoot = genIo.loadProject(projectDir, suppressGeneralDataDir=True)
jsonObject = json.load(open(jsonFile))
tmpFile = jsonFile + '_tmp'
json.dump(jsonObject, open(tmpFile, 'w'), sort_keys=True, indent=2)
nmrCalcId = intUtil.makeNmrCalc(memopsRoot, jsonObject)
memopsRoot.saveModified()
jsonObject['CCPN.nmrCalcId'] = nmrCalcId
fp = open(jsonFile, 'w')
json.dump(jsonObject, fp, sort_keys=True, indent=2)
fp.close()
except:
traceback.print_exc()
raise
def makeCcpnProject(entryName):
""" Execute conversion to CCPN project
"""
logFileHandle = None
try:
#entryName = casdUtil.getEntryName(info)
orgName = entryName.split('_')[0] + '_Org'
print 'Starting', entryName
logFileHandle = casdUtil.createLogFile(entryName, 'extractEntry')
# get CCPN project from Org data
#orgName = casdUtil.getEntryName(info, isOriginal=True)
path = os.path.join(allDataDir, orgName[1:3], orgName)
ppath = os.path.join(path, orgName)
ff = ppath + '.tgz'
if not (os.path.exists(ppath) or os.path.exists(ff)):
raise Exception("NO original CCPN project in %s" % path)
if not os.path.isdir(ppath):
casdUtil.extractCompressedFile(ff, path, entryName)
if not os.path.exists(ppath):
raise Exception("NO extracted CCPN project in %s" % path)
ccpnProject = genIo.loadProject(ppath, suppressGeneralDataDir=True)
# neutralize any other pending CASD-NMR projects
casdRun = casdUtil.prepareNmrCalcRun(ccpnProject, 'CING')
for run in casdRun.nmrCalcStore.findAllRuns(status='pending'):
if run is not casdRun:
run.status = 'provisional'
#
dataDir = os.path.join(allDataDir, entryName[1:3], entryName)
tmpdir = tempfile.mkdtemp(dir=casdConstants.topTmpDir)
try:
# Extract structure data
tmpstruc = os.path.join(tmpdir, 'structures')
src = casdUtil.getInputFile(entryName, 'structures')
casdUtil.extractCompressedFile(src,
tmpstruc,
entryName,
okExts=('pdb', ))
tmpstruc = casdUtil.getLowestSubDir(tmpstruc,
followDirs=('cns_format', ))
structureFiles = os.listdir(tmpstruc)
# Extract restraint data
tmprestr = os.path.join(tmpdir, 'restraints')
src = casdUtil.getInputFile(entryName,
'restraints',
ignoreErrors=True)
if src:
casdUtil.extractCompressedFile(src, tmprestr, entryName)
tmprestr = casdUtil.getLowestSubDir(
tmprestr, followDirs=('cns_format', ))
restraintFiles = os.listdir(tmprestr)
else:
restraintFiles = ()
print 'WARNING, %s no restraints found at %s' % (entryName,
src)
# read in data
# FormatConverter version
fcw = FormatConverterWrapper(ccpnProject=ccpnProject)
# dataIo version
#fcw = None
if structureFiles:
# NBNB uses Rasmus in-development trunk structure reading.
# WOrks well. Temporarily disabled
# read in structures
pdbFiles = [
x for x in structureFiles if any(
x.endswith(y) for y in casdConstants.pdbEndings)
]
floatFiles = [
x for x in structureFiles if x.endswith('.float')
]
if floatFiles:
# Use only pdb files with names that match float files
stems = set(x[:-6] for x in floatFiles)
pdbFiles = [x for x in pdbFiles if x[:-4] in stems]
pdbPaths = [os.path.join(tmpstruc, x) for x in pdbFiles]
if True:
#if fcw is None:
#Always use dataIo version
# dataIo version
ensemble = StructureIo.getStructureFromFiles(
ccpnProject.findFirstMolSystem(), pdbPaths)
if ensemble is None:
print '### Skipping %s, no structures loaded' % entryName
else:
print '### num files, ensemble', len(
pdbPaths), ensemble.ensembleId
casdRun.newStructureEnsembleData(
name=entryName, structureEnsemble=ensemble)
else:
# FormatConverter version
#fileInfo = fcw.determineFileInfo(pdbPaths[0])
if len(pdbPaths) != 1:
print 'WARNING %s pdb files, only one read. TBD FIX' % len(
pdbPaths)
dataType = 'coordinates'
formatName = 'pseudoPdb'
pdbPath = pdbPaths[0]
print 'Reading structure file', dataType, formatName, pdbPath
fcw.readFile(dataType, formatName, pdbPath)
# NBNB TODO 1) How to set up trying true PDB before pseudoPdb?
# 2) How to read several files into an ensemble?
# 3) How to get hold of the new ensemble for putting in NmrCalc
else:
print '### Skipping %s, no structure file' % entryName
# Make NmrCalc object for shift list
# NBNB consider later: if we are reading in assigned peaks,
# shifts may change. NBNB
shiftLists = casdRun.nmrCalcStore.nmrProject.findAllMeasurementLists(
className='ShiftList')
if len(shiftLists) == 1:
casdRun.newMeasurementListData(
name='Shiftlist', measurementList=shiftLists.pop())
else:
print 'WARNING. %s shift lists found, should be s' % len(
shiftLists)
# Restraints reading
if restraintFiles:
if fcw is None:
# NBNB TBD dataIo restraint reading to go here
#for rfile in restraintFiles:
# fileInfo = casdUtil.getFileInfo(tmprestr, rfile)
pass
else:
# FormatConverter version
restraintLists = []
for rfile in restraintFiles:
rpath = os.path.join(tmprestr, rfile)
fileInfo = fcw.determineFileInfo(rpath)
dataType = fileInfo.get('dataType')
formatName = fileInfo.get('formatName')
if dataType is None or formatName is None:
print 'Skipping unidentified restraint file', dataType, formatName, rfile
elif dataType not in (
'distanceConstraints',
'dihedralConstraints',
'rdcConstraints',
):
print 'Skipping wrong type of restraint file', dataType, formatName, rfile
else:
print 'Reading restraint file', dataType, formatName, rfile
fcw.readFile(dataType, formatName, rpath)
if fcw.conversionSuccess:
print("Successful restraint file read:\n%s" %
fcw.conversionInfo)
restraintLists.append(fcw.ccpnObjectOrList)
else:
print("Failed restraint file read:\n%s" %
fcw.conversionInfo)
if restraintLists:
print("Found restraint lists: %s" %
len(restraintLists))
casdRun.newConstraintStoreData(
constraintLists=restraintLists,
name='Restraintlists')
# linkResonances
print '### linking resonances'
linkingInfo = fcw.linkAllResonancesToAtoms()
finally:
shutil.rmtree(tmpdir, ignore_errors=True)
pass
# rename and package project
ccpnOutputDir = os.path.join(dataDir, entryName)
genIo.saveProject(ccpnProject,
newPath=ccpnOutputDir,
newProjectName=entryName,
checkValid=True,
removeExisting=True)
genIo.packageProject(ccpnProject, ccpnOutputDir)
shutil.rmtree(ccpnOutputDir)
ccpnOutputPath = ccpnOutputDir + '.tgz'
print 'SUCCESS, %s saved to %s' % (entryName, ccpnOutputPath)
return ccpnOutputPath
except:
print 'ERROR for %s' % (entryName)
traceback.print_exc(file=sys.stdout)
finally:
if logFileHandle is not None:
logFileHandle.close()
sys.stdout = sys.__stdout__
def __init__(self,
guiParent,
project,
callback=None,
help_msg='',
help_url='',
dismiss_text='',
modal=False,
*args,
**kw):
self.project = project
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
self.modal = modal
self.did_save = False
Frame.__init__(self, guiParent, *args, **kw)
projDir = Io.getUserDataPath(self.project)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Project Name:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.proj_name_entry = Entry(
guiParent,
text=self.project.name,
returnCallback=self.updateInfo,
leaveCallback=self.updateInfo,
tipText='The name used for the project save directory')
self.proj_name_entry.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(guiParent, text='Project Directory:')
label.grid(row=row, column=0, sticky=Tkinter.E)
label = self.proj_dir_label = Label(guiParent, text=projDir)
label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
guiParent,
text='Note: Project Directory = Save Location + Project Name')
label.grid(row=row, column=1, sticky=Tkinter.W)
text = 'Save binary data with project'
tipText = 'Copy data files (e.g. for spectra) into new project directory if not already in current project directory: careful, this can take some time'
row = row + 1
self.dataCheckButton = CheckButton(guiParent,
text=text,
tipText=tipText)
self.dataCheckButton.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
guiParent.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiParent, text='Save Location')
labelFrame.grid(row=row, column=0, columnspan=2, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
directory = os.path.dirname(projDir)
self.proj_dir_select = FileSelect(
labelFrame,
directory=directory,
select_dir_callback=self.selectDir,
change_dir_callback=self.updateInfo,
should_change_dir_callback=self.shouldChangeDir,
getRowColor=self.getEntryColor,
show_file=False)
self.proj_dir_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = ['Save']
tipTexts = ['Save project with specified name in specified directory']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def getOldData(oldPath, oldTag, currentVersionStr, oldName=None):
import os
from memops.universal import Io as uniIo
from memops.metamodel.Util import topologicalSortSubgraph
# find old implementation top directory and change temporarily to it.
currentTopDir = uniIo.getTopDirectory()
ss1, lastdir = os.path.split(currentTopDir)
ss2, newTag = os.path.split(ss1)
prevTopDir = os.path.join(ss2, oldTag, lastdir)
uniIo.setTopDirectory(prevTopDir)
# NB these things are put inside the function to avoid problems with
# the uniIo.setTopDirectory approach
def getCurrentVersionStr():
""" Encapsulated to get import out of main. Hoping to fix import problem.
"""
from memops.general.Constants import currentModelVersion
return str(currentModelVersion)
def downlinkTagsByImport(root, sorter=topologicalSortSubgraph):
""" downlink tags from MemopsRoot object for leafPackages in import order
This is the post-v2.0 version
"""
leafPackages = []
packages = [root.metaclass.container.topPackage()]
for pp in packages:
childPackages = pp.containedPackages
if childPackages:
packages.extend(childPackages)
else:
leafPackages.append(pp)
# sort leafPackages by import (imported before importing)
leafPackages = sorter(leafPackages, 'accessedPackages')
tags = []
for pp in leafPackages:
cc = pp.topObjectClass
if cc is not None:
pr = cc.parentRole
if pr is not None:
tags.append(pr.otherRole.name)
#
return tags
try:
# get old version as string
oldVersionStr = getCurrentVersionStr()
from memops.general import Io as oldIo
# post-version-2 behaviour - get repository dir and project name
if oldName is None:
head, tail = os.path.split(oldPath)
oldName = os.path.splitext(tail)[0]
oldPath = os.path.dirname(os.path.dirname(head))
# get root Object and force load all contents
oldRoot = oldIo.loadProject(oldPath, projectName=oldName)
if oldVersionStr != currentVersionStr:
# We do have to convert - force load all TopObjects
tags = downlinkTagsByImport(oldRoot)
for tag in tags:
for topObj in getattr(oldRoot, tag):
if not topObj.isLoaded:
topObj.load()
finally:
# set path back to current
uniIo.setTopDirectory(currentTopDir)
return (oldRoot, oldVersionStr, tags)
atomNameMap = {
'HN':'H',
}
if __name__ == '__main__':
""" Hack for rough creation, given that neither comaptibility nor PDB load works
"""
pdbFile = '6628.pdb'
talosFile = '6628.tab'
molName = 'myMol'
chainCode = 'A'
workingDir = os.getcwd()
project = genIo.newProject('IsdInputTest')
nmrProject = project.newNmrProject(name=molName)
shiftList = nmrProject.newShiftList(name=molName)
project.newAnalysisProject(name='dummy', nmrProject=nmrProject)
# read Talos project
path = uniIo.joinPath(workingDir, talosFile)
if os.path.isfile(path):
# get sequence data
seqReader = TalosSequenceFile(path)
seqReader.read()
seqData = [(x.code1Letter, x.seqCode, x.seqInsertCode)
for x in seqReader.sequences[-1].elements]
del seqReader
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:
# find DataUrls involved
dataUrls = set(dataStore.dataUrl for dataStore in badDataStores)
startDir = project.packageLocator.findFirstRepository(
).url.dataLocation
for dataUrl in dataUrls:
if not dataUrl.dataStores.difference(badDataStores):
# all DataStores for this DataUrl are bad
# we can make changes without affecting 'good' DataStores
# Look for an obvious place the data may have moved to
dataStores = dataUrl.sortedDataStores()
fullPaths = [dataStore.fullPath for dataStore in dataStores]
baseDir, newPaths = uniIo.suggestFileLocations(
fullPaths, startDir=startDir)
if baseDir is not None:
# We have a file location that fits all missing files.
# Change dataStores to use it
print 'WARNING, resetting data locations to: \n%s\n' % baseDir
ccpGenIo.changeDataStoreUrl(dataStores[0], baseDir)
for ii, dataStore in enumerate(dataStores):
dataStore.path = newPaths[ii]
if [
dataStore for dataStore in dataStores
if not os.path.exists(dataStore.fullPath)
]:
popup = DataLocationPopup(parent, project, modal=True)
popup.destroy()
return project