def test_cyana2cing(self):
# SETUP FIRST
projectId = "1pdb"
cyanaDirectory = os.path.join( cingDirTestsData, "cyana", projectId )
self.assertTrue( os.path.exists( cyanaDirectory) and os.path.isdir(cyanaDirectory ) )
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
projectRootPath = os.path.join( cingDirTmp, projectId )
projectRoot = Project.rootPath( projectRootPath )[0] # xeasy_project.cing in /tmp
if os.path.exists( projectRoot ):
nTwarning('Output directory "%s" already exists. It will now be removed.' % projectRoot )
self.failIf( shutil.rmtree(projectRoot), "Failed to remove old project directory." )
project = Project.open(projectRootPath, 'new')
project.cyana2cing( #project=project,
cyanaDirectory=cyanaDirectory,
uplFiles = [projectId],
acoFiles = [projectId,"talos"],
pdbFile = projectId,
nmodels = 2,
copy2sources = True
)
if not project:
nTwarning("No project generated. Aborting further execution.")
sys.exit(0)
project.save()
def test_cyana2cing(self):
# SETUP FIRST
projectId = "1pdb"
cyanaDirectory = os.path.join(cingDirTestsData, "cyana", projectId)
self.assertTrue(
os.path.exists(cyanaDirectory) and os.path.isdir(cyanaDirectory))
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
projectRootPath = os.path.join(cingDirTmp, projectId)
projectRoot = Project.rootPath(projectRootPath)[
0] # xeasy_project.cing in /tmp
if os.path.exists(projectRoot):
nTwarning(
'Output directory "%s" already exists. It will now be removed.'
% projectRoot)
self.failIf(shutil.rmtree(projectRoot),
"Failed to remove old project directory.")
project = Project.open(projectRootPath, 'new')
project.cyana2cing( #project=project,
cyanaDirectory=cyanaDirectory,
uplFiles=[projectId],
acoFiles=[projectId, "talos"],
pdbFile=projectId,
nmodels=2,
copy2sources=True)
if not project:
nTwarning("No project generated. Aborting further execution.")
sys.exit(0)
project.save()
def testRootPath(self):
p = Project('1brv')
self.assertEquals('./1brv.cing', p.rootPath('1brv')[0])
self.assertEquals('1brv', p.rootPath('1brv')[1])
nTmessage("hello")
nTdebug(p.root)
def testRootPath(self):
p = Project('1brv')
self.assertEquals('./1brv.cing', p.rootPath('1brv')[0])
self.assertEquals('1brv', p.rootPath('1brv')[1])
nTmessage("hello")
nTdebug(p.root)
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
