def __init__(self):
projName = self.__class__.__name__
manager = Manager()
if manager.hasProject(projName):
self.project = manager.loadProject(projName)
else:
self.project = manager.createProject(projName)
# Use graph view as default
settings = self.project.getSettings()
settings.setRunsView(1) # graph view
settings.write()
self.loadWorkflow()
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
copyFiles = self.tkCheckVar.get() != 0
searchLocation = self.searchLocation.get().strip()
manager = Manager()
# If project name is empty we will use the same name as the source
if not projName:
projName = os.path.basename(projLocation)
errorMessage = ''
# Validate that project location is not empty
if not projLocation:
errorMessage = "Project location is empty\n"
# Validate that project location exists
elif not os.path.exists(projLocation):
errorMessage += "Project location does not exist\n"
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
errorMessage += "Project location is not a directory\n"
# Validate that the project location is a scipion project folder
elif not os.path.exists(os.path.join(projLocation, PROJECT_DBNAME)):
errorMessage += "Project location doesn't look like a scipion folder\n"
# Validate that there isn't already a project with the same name
if manager.hasProject(projName):
errorMessage += "Project [%s] already exists\n" % projName
# Validate that search location exists
if searchLocation:
if not os.path.exists(searchLocation):
errorMessage += "Raw files location does not exist\n"
# Validate that search location is a directory
elif not os.path.isdir(searchLocation):
errorMessage += "Raw files location is not a directory\n"
if errorMessage:
showError("Validation error", errorMessage, self.root)
else:
self.parent.importProject(projLocation, copyFiles, projName,
searchLocation)
self.close()
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
copyFiles = self.tkCheckVar.get() != 0
searchLocation = self.searchLocation.get().strip()
manager = Manager()
# If project name is empty we will use the same name as the source
if not projName:
projName = os.path.basename(projLocation)
errorMessage = ''
# Validate that project location is not empty
if not projLocation:
errorMessage = "Project location is empty\n"
# Validate that project location exists
elif not os.path.exists(projLocation):
errorMessage += "Project location does not exist\n"
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
errorMessage += "Project location is not a directory\n"
# Validate that the project location is a scipion project folder
elif not os.path.exists(os.path.join(projLocation, PROJECT_DBNAME)):
errorMessage += "Project location doesn't look like a scipion folder\n"
# Validate that there isn't already a project with the same name
if manager.hasProject(projName):
errorMessage += "Project [%s] already exists\n" % projName
# Validate that search location exists
if searchLocation:
if not os.path.exists(searchLocation):
errorMessage += "Raw files location does not exist\n"
# Validate that search location is a directory
elif not os.path.isdir(searchLocation):
errorMessage += "Raw files location is not a directory\n"
if errorMessage:
showError("Validation error", errorMessage, self.root)
else:
self.parent.importProject(projLocation, copyFiles, projName, searchLocation)
self.close()
n = len(sys.argv)
if n <> 2:
usage("This script accepts 1 parameter: the project name.")
projName = sys.argv[1]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'gui',
'no-tkinter')
sys.path.insert(1, path)
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("There is no project with this name: %s" % pwutils.red(projName))
# the project may be a soft link which may be unavailable to the cluster so get the real path
try:
projectPath = os.readlink(manager.getProjectPath(projName))
except:
projectPath = manager.getProjectPath(projName)
project = Project(projectPath)
project.load()
runs = project.getRuns()
# Now assuming that there is no dependencies between runs
# and the graph is lineal
sys.exit(1)
argc = len(sys.argv)
if argc < 3 or argc > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
protId = sys.argv[2]
n = int(sys.argv[3]) if argc == 4 else 3
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("Unexistent project: %s" % pwutils.red(projName))
project = manager.loadProject(projName)
protExtractParts = project.getProtocol(protId)
protVol = project.getProtocol(1256)
protRelionAllParts = project.getProtocol(1291)
protRelionBestParts = project.getProtocol(1359)
project.launchProtocol(protRelionAllParts, wait=True)
project.launchProtocol(protRelionBestParts, wait=True)
for i in range(n):
protSubSet = project.newProtocol(em.ProtSubSet,
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
jsonFile = None if n < 3 else os.path.abspath(sys.argv[2])
location = None if n < 4 else sys.argv[3]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'gui',
'no-tkinter')
sys.path.insert(1, path)
# Create a new project
manager = Manager()
if manager.hasProject(projName):
usage("There is already a project with this name: %s" %
pwutils.red(projName))
if jsonFile is not None and not os.path.exists(jsonFile):
usage("Unexistent json file: %s" % pwutils.red(jsonFile))
project = manager.createProject(projName, location=location)
if jsonFile is not None:
protDict = project.loadProtocols(jsonFile)
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize, family=fontName, weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize, family=fontName, weight='bold')
self.manager = Manager()
btn = HotButton(self, text=Message.LABEL_CREATE_PROJECT, font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
project = self.manager.loadProject(p.getName(), chdir=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
frame = self.createProjectLabel(parent, p, color=colors[i%2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def createProjectLabel(self, parent, projInfo, color):
frame = tk.Frame(parent, bg=color)
label = tk.Label(frame, text=projInfo.projName, anchor='nw', bg=color,
justify=tk.LEFT, font=self.projNameFont, cursor='hand1', width=50)
label.grid(row=0, column=0, padx=2, pady=2, sticky='nw')
label.bind('<Button-1>', lambda e: self.openProject(projInfo.projName))
dateMsg = '%s%s %s%s' % (Message.LABEL_MODIFIED, prettyDate(projInfo.mTime),
Message.LABEL_CREATED, prettyTime(projInfo.cTime, time=False))
dateLabel = tk.Label(frame, text=dateMsg, font=self.projDateFont, bg=color)
dateLabel.grid(row=1, column=0, sticky='nw')
delLabel = tk.Label(frame, text=Message.LABEL_DELETE_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
delLabel.grid(row=1, column=1, padx=10)
delLabel.bind('<Button-1>', lambda e: self.deleteProject(projInfo.projName))
mvLabel = tk.Label(frame, text=Message.LABEL_RENAME_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
mvLabel.grid(row=1, column=2)
mvLabel.bind('<Button-1>', lambda e: self.renameProject(projInfo.projName))
return frame
def createNewProject(self, projName, projLocation):
self.manager.createProject(projName, location=projLocation)
self.createProjectList(self.text)
self.openProject(projName)
def _onCreateProject(self, e=None):
projWindow = ProjectCreateWindow("Create project", self)
projWindow.show()
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([os.environ['SCIPION_PYTHON'], script, projName])
def deleteProject(self, projName):
if askYesNo(Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT, self.root):
self.manager.deleteProject(projName)
self.createProjectList(self.text)
def renameProject(self, projName):
newName = askString("Rename project %s" % projName, "Enter new name:", self.root)
if not newName or newName == projName:
return
if self.manager.hasProject(newName):
showError("Rename cancelled",
"Project name already exists: %s" % newName, self.root)
return
self.manager.renameProject(projName, newName)
self.createProjectList(self.text)
""" % error
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
jsonFile = None if n < 3 else os.path.abspath(sys.argv[2])
location = None if n < 4 else sys.argv[3]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'gui', 'no-tkinter')
sys.path.insert(1, path)
# Create a new project
manager = Manager()
if manager.hasProject(projName):
usage("There is already a project with this name: %s"
% pwutils.red(projName))
if jsonFile is not None and not os.path.exists(jsonFile):
usage("Unexistent json file: %s" % pwutils.red(jsonFile))
project = manager.createProject(projName, location=location)
if jsonFile is not None:
protDict = project.loadProtocols(jsonFile)
help='Scipion processes to run in parallel')
parser.add_argument('project', type=str, help='Scipion project')
parser.add_argument('directory', type=str, help='Directory to monitor')
args = parser.parse_args()
PROJECT = args.project
VOLTAGE = args.voltage
SAMPLING_RATE = args.sampling_rate
PROCESSES = args.processes
POOL = Pool(processes=PROCESSES)
# Create or load project
manager = Manager()
if manager.hasProject(PROJECT):
project = manager.loadProject(PROJECT)
else:
project = manager.createProject(PROJECT)
# First, start up watchdog
event_handler = MyEventHandler()
observer = Observer()
observer.schedule(event_handler, path=args.directory, recursive=False)
observer.start()
print('Watchdog started; to exit, press Control-C')
# Second, run all existing files
for f in os.listdir(args.directory):
try:
ext = os.path.splitext(f)[1].split('.')[1]
