def upgrade075(project, restore):
"""
Upgrade project from 075 or earlier conventions
return upgraded project or None on error
"""
io.message('upgrade075: converting from CING version {0}\n', project.version)
# 0.75 version had moleculeNames stored in molecules attribute
# >=0.76 version molecules is a ProjectList instance
project.moleculeNames = project.molecules
# store the project file and reopen to have correct settings
project._save2json()
pr = classes.Project._restoreFromJson(project.path(cing.cingPaths.project))
if pr == None:
io.error('upgrade075: conversion from version %s failed on read\n', project.version)
return None
for molName in pr.moleculeNames:
pathName = pr.path(cing.directories.molecules, molName) # old reference, versions 0.48-0.75
if pr.version <= 0.48:
pathName = pr.path('Molecules', molName) # old reference
# end if
io.debug('upgrade075: trying molecule conversion from {0}\n', pathName)
if not pathName.exists():
io.error('upgrade075: old molecule pathName "{0}" does not exist\n', pathName)
return None
mol = openMol_075(pathName)
if not mol:
io.error('upgrade075: conversion from version {0} failed on molecule {1}\n', project.version, molName)
return None
pathName.removedir()
# Save molecule to new format
mol.save(pr.molecules.path(molName))
#end for
# restore
pr.restore()
# Save to consolidate
pr.save()
return cing.Legacy.Legacy100.upgrade100.upgrade100(pr, restore)
def setup_DummyProject():
global theProject
os.chdir(cdefs.cingDefinitions.tmpdir)
print('Now in %s' % cdefs.cingDefinitions.tmpdir)
theProject = Project.new(TEST)
# create a molecule
mol = molecule.Molecule(TEST)
theProject.appendMolecule(mol)
c = mol.addChain('A')
c.addResidue('ALA', 1, Nterminal = True)
c.addResidue('VAL', 2)
c.addResidue('PHE', 3)
c.addResidue('ARG', 4)
c.addResidue('GLU', 5, Cterminal = True)
c = mol.addChain('B')
c.addResidue('DG', 1, Nterminal = True)
c.addResidue('DA', 2)
c.addResidue('DT', 3)
c.addResidue('DC', 4, Cterminal = True)
c = mol.addChain('C')
c.addResidue('RGUA', 1, convention=constants.INTERNAL_0, Nterminal = True)
c.addResidue('RADE', 2, convention=constants.INTERNAL_0)
c.addResidue('URA', 3, convention=constants.INTERNAL_0) # not RTHY normally of course.
c.addResidue('RTHY', 4, convention=constants.INTERNAL_0)
c.addResidue('RCYT', 5, convention=constants.INTERNAL_0, Cterminal = True)
c = mol.addChain('D')
for i in range(1,11):
c.addResidue('HOH', i )
# end for
c = mol.addChain('E') # Unknown residue to CING
c.addResidue('ACE', 1)
c = mol.addChain('F') # Ions are also other
c.addResidue('CA2P', 1)
for residue in mol.allResidues():
residue.addAllAtoms()
# end for
mol.updateAll()
io.message('{0}\n',mol.format())
def upgradeProject2Json( name, restore ):
"""Upgrade the project from project.xml to project.json file
Convert several parameters to new Adict types
"""
io.debug('upgradeToJson: restoring {0}\n', name)
root, newName, ext = Project.rootPath(name)
if not root:
io.error('upgradeToJson: unable to open Project "{0}" because root is [{1}]\n', name, root)
return None
if not root.exists():
io.error('upgradeToJson: unable to open Project "{0}" because root [{1}] was not found\n', name, root)
return None
#end if
pfile = root / 'project.xml' # Name in all versions <= 1.0
# Check if we find the xml file
if pfile.exists():
io.message('==> Upgrading cing project; please stand by\n')
#GWV: 20140203: cannot do an update method() -> errors in partioning restraints. Do not understand
pr = xmlTools.xML2obj(pfile)
if pr is None:
io.error('upgradeToJson: parsing from project file "{0}" failed\n', pfile)
return None
try:
# <= 0.75 version have string
pr.version = float(pr.version.strip('abcdefghijklmnopqrtsuvw ()!@#$%^&*').split()[0])
except:
pass
# change to Time object
pr.created = io.Time.fromString(pr.created)
pr.lastSaved = io.Time(disk.modtime(pfile))
# change types of names list
for listName in 'moleculeNames peakListNames distanceListNames dihedralListNames rdcListNames'.split():
#print 'listName>>',listName, (listName in pr)
if listName in pr:
pr[listName] = [n for n in pr[listName]]
# update from old status type
status = Adict()
for key in constants.VALIDATION_KEYS:
sdict = StatusDict(key)
status[key] = sdict
# if not isinstance(sdict, StatusDict):
# sdict = StatusDict(key)
if key in pr.status:
# print 'upgrade2json> key=', key
# not certain if we get dict or NTdict; this circumvent unwanted keys of NTdict
for k,v in pr.status[key].items():
#print 'upgrade2json>> k,v', k,v
sdict[k] = v
#print '>>>\n', sdict.formatItems()
#end if
#end for
#end for
# update the status from old definitions;
for (key, statusName) in [
(constants.SHIFTX_KEY, 'shiftxStatus'),
(constants.PROCHECK_KEY,'procheckStatus'),
(constants.DSSP_KEY, 'dsspStatus'),
(constants.WHATIF_KEY, 'whatifStatus'),
(constants.WATTOS_KEY, 'wattosStatus'),
(constants.VASCO_KEY, 'vascoStatus'),
(constants.X3DNA_KEY, 'x3dnaStatus')
]:
sdict = status[key]
if statusName in pr:
#print 'upgrade2json> statusName=', statusName
# not certain if we get dict or NTdict; this circumvent unwanted keys of NTdict
for k,v in pr[statusName].items():
#print 'upgrade2json>> k,v=', k,v
sdict[k] = v
#print '>>>\n', sdict.formatItems()
#end if
#LEGACY names
pr[statusName] = sdict
#end for
# update some fields if present
for sdict in status.values():
if 'molecule' in sdict and isinstance(sdict['molecule'], tuple):
sdict['molecule'] = pid.Pid.new('Molecule:' + sdict['molecule'][0])
if 'moleculeName' in sdict and isinstance(sdict['molecule'], tuple):
sdict['molecule'] = pid.Pid.new('Molecule:' + sdict['moleculeName'][0])
del sdict['moleculeName']
if 'runVersion' in sdict:
sdict['version'] = sdict['runVersion']
del sdict['runVersion']
if 'smlFile' in sdict:
del sdict['smlFile']
# sdict['date'] = io.Time(1360158182.7) # Wed Feb 6 13:43:02 2013
sdict['date'] = io.Time(pr.lastSaved) # make a copy because otherwise the json handler breaks
sdict['version'] = 0.95 # old version
#end for
# make this the new status dict
pr.status = status
#print '>>>>>\n', pr.status.queeny.formatItems()
pr._save2json()
# have to make the directory because we have not yet fully initialised all directories at this stage
pr._updateProjectPaths()
disk.rename(pfile, pr.path() / cdefs.directories.version1 / 'project.xml' )
#now we should be able to open it again
return Project.open( name, status = constants.PROJECT_OLD, restore = restore )
else:
io.error('upgradeToJson: missing Project file "{0}"\n', pfile)
return None
