def __init__(self, path):
"""Create a project associated with a given path"""
# To create a Project, a path is required
self.name = path
self.shortName = os.path.basename(path)
self.path = os.path.abspath(path)
self._isLink = os.path.islink(path)
self.pathList = [] # Store all related paths
self.dbPath = self.__addPath(PROJECT_DBNAME)
self.logsPath = self.__addPath(PROJECT_LOGS)
self.runsPath = self.__addPath(PROJECT_RUNS)
self.tmpPath = self.__addPath(PROJECT_TMP)
self.uploadPath = self.__addPath(PROJECT_UPLOAD)
self.settingsPath = self.__addPath(PROJECT_SETTINGS)
self.configPath = self.__addPath(PROJECT_CONFIG)
self.runs = None
self._runsGraph = None
self._transformGraph = None
self._sourceGraph = None
self.address = ''
self.port = pwutils.getFreePort()
self.mapper = None
self.settings = None
# Host configuration
self._hosts = None
self._protocolViews = None
# Creation time should be stored in project.sqlite when the project
# is created and then loaded with other properties from the database
self._creationTime = None
# Time stamp with the last run has been updated
self._lastRunTime = None
def __init__(self, path):
"""Create a project associated with a given path"""
# To create a Project, a path is required
self.name = path
self.shortName = os.path.basename(path)
self.path = os.path.abspath(path)
self.pathList = [] # Store all related paths
self.dbPath = self.__addPath(PROJECT_DBNAME)
self.logsPath = self.__addPath(PROJECT_LOGS)
self.runsPath = self.__addPath(PROJECT_RUNS)
self.tmpPath = self.__addPath(PROJECT_TMP)
self.uploadPath = self.__addPath(PROJECT_UPLOAD)
self.settingsPath = self.__addPath(PROJECT_SETTINGS)
self.configPath = self.__addPath(PROJECT_CONFIG)
self.runs = None
self._runsGraph = None
self._transformGraph = None
self._sourceGraph = None
self.address = ''
self.port = pwutils.getFreePort()
self.mapper = None
self.settings = None
# Host configuration
self._hosts = None
self._protocolViews = None
def __init__(self, volfile, sendEnd=True, **kwargs):
if volfile.endswith('.mrc'):
volfile += ':mrc'
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@')
else:
file = volfile
if ':' in file:
file = file[0:file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists" % file)
self.volfile = volfile
self.voxelSize = self.kwargs.get('voxelSize', None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName = self.kwargs.get('ChimeraServer', 'ChimeraServer')
self.address = ''
self.port = getFreePort()
serverfile = pw.join('em', 'chimera_server.py')
command = CommandView(
"chimera --script '%s %s %s' &" %
(serverfile, self.port, serverName),
env=getChimeraEnviron(),
).show()
self.authkey = 'test'
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol, sendEnd)
self.initListenThread()
def __init__(self, volfile, sendEnd=True,**kwargs):
if volfile.endswith('.mrc'):
volfile += ':mrc'
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@');
else :
file = volfile
if ':' in file:
file = file[0: file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists"%file)
self.volfile = volfile
self.voxelSize = self.kwargs.get('voxelSize', None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName=self.kwargs.get('ChimeraServer','ChimeraServer')
self.address = ''
self.port = getFreePort()
serverfile = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'em', 'chimera_server.py')
command = CommandView("chimera --script '%s %s %s' &" %
(serverfile, self.port,serverName),
env=getChimeraEnviron(),).show()
self.authkey = 'test'
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol,sendEnd)
self.initListenThread()
def __init__(self, volfile, sendEnd=True, **kwargs):
if volfile.endswith(".mrc"):
volfile += ":mrc"
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if "@" in volfile:
[index, file] = volfile.split("@")
else:
file = volfile
if ":" in file:
file = file[0 : file.rfind(":")]
if not os.path.exists(file):
raise Exception("File %s does not exists" % file)
self.volfile = volfile
self.voxelSize = self.kwargs.get("voxelSize", None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName = self.kwargs.get("ChimeraServer", "ChimeraServer")
self.address = ""
self.port = getFreePort()
serverfile = os.path.join(os.environ["SCIPION_HOME"], "pyworkflow", "em", "chimera_server.py")
command = CommandView(
"chimera --script '%s %s %s' &" % (serverfile, self.port, serverName), env=getChimeraEnviron()
).show()
self.authkey = "test"
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol, sendEnd)
self.initListenThread()
def initProtocolTCPServer(protocol):
address = ''
port = getFreePort()
server = MySocketServer((address, port), ProtocolTCPRequestHandler)
server.protocol = protocol
server_thread = threading.Thread(target=server.serve_forever)
server_thread.start()
return port
def __init__(self, dataview, vol, viewParams={}, **kwargs):
#print 'on pair'
self.dataview = dataview
self.showjPort = getFreePort()
self.dataview._viewParams[showj.CHIMERA_PORT] = self.showjPort
self.dataview._viewParams[showj.MODE] = showj.MODE_MD
self.dataview._viewParams[showj.INVERTY] = ''
ChimeraClientView.__init__(self, vol.getFileName(), showProjection=True, showjPort=self.showjPort, voxelSize=vol.getSamplingRate())
def initProtocolTCPServer(protocol):
address = ''
port = getFreePort()
server = MySocketServer((address, port), ProtocolTCPRequestHandler)
server.protocol = protocol
server_thread = threading.Thread(target=server.serve_forever)
server_thread.daemon = True
server_thread.start()
return port
def __init__(self, dataview, vol, viewParams={}, **kwargs):
self.dataview = dataview
self.showjPort = getFreePort()
self.dataview._viewParams[showj.CHIMERA_PORT] = self.showjPort
self.dataview._viewParams[showj.MODE] = showj.MODE_MD
self.dataview._viewParams[showj.INVERTY] = ''
ChimeraClientView.__init__(self, vol.getFileName(), showProjection=True,
showjPort=self.showjPort,
voxelSize=vol.getSamplingRate())
