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 run_scipion_qc(movie_file):
manager = Manager()
project = manager.loadProject(PROJECT)
path, pattern = os.path.split(movie_file)
add_movies = project.newProtocol(
ProtImportMovies,
filesPath=path,
filesPattern=pattern,
voltage=VOLTAGE,
samplingRate=SAMPLING_RATE,
)
project.launchProtocol(add_movies, wait=True)
align_movies = project.newProtocol(
ProtMovieAlignment,
inputMovies=add_movies.outputMovies,
)
project.launchProtocol(align_movies, wait=True)
find_ctf = project.newProtocol(
ProtCTFFind,
inputMicrographs=align_movies.outputMicrographs,
)
project.launchProtocol(find_ctf, wait=False)
def test_createNoChdir(self):
"""Test the list with several Complex"""
cwd = os.getcwd()
manager = Manager()
projectName = "TestProjectCreate"
project = manager.createProject(projectName, chdir=False)
dataset = DataSet.getDataSet('emx')
prot1 = project.newProtocol(
em.ProtImportParticles,
objLabel='from emx (coordinatesT1)',
importFrom=em.ProtImportParticles.IMPORT_FROM_EMX,
emxFile=dataset.getFile('coordinatesT1'),
alignType=3,
voltage=100,
magnification=10000,
samplingRate=2.46)
project.launchProtocol(prot1, wait=True)
# Execute a copy of prot1
prot2 = project.copyProtocol(prot1)
project.launchProtocol(prot2, wait=True)
# Now restart prot2
prot2.runMode.set(MODE_RESTART)
project.launchProtocol(prot2, wait=True)
#self.assertEqual(cwd, project.getPath())
self.assertEqual(cwd, os.getcwd())
def delete_project(request):
manager = Manager()
if request.is_ajax():
projectName = request.GET.get('projectName')
manager.deleteProject(projectName)
return HttpResponse(mimetype='application/javascript')
def delete_project(request):
manager = Manager()
if request.is_ajax():
projectName = request.GET.get('projectName')
manager.deleteProject(projectName)
return HttpResponse(mimetype='application/javascript')
def delete_project(request):
manager = Manager()
if request.is_ajax():
projectName = getVarFromRequest(request, PROJECT_NAME)
manager.deleteProject(projectName)
return HttpResponse(content_type='application/javascript')
def create_project(request):
manager = Manager()
if request.is_ajax():
projectName = getVarFromRequest(request, PROJECT_NAME)
workflow = getVarFromRequest(request, WORKFLOW)
manager.createProject(projectName, chdir=False, workflow=workflow)
return HttpResponse(content_type='application/javascript')
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()):
try:
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
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def test_create(self):
"""Test the list with several Complex"""
cwd = os.getcwd()
manager = Manager()
projectName = "TestProjectCreate"
project = manager.createProject(projectName)
self.assertNotEqual(cwd, os.getcwd())
self.assertEqual(project.getPath(), os.getcwd())
os.chdir(cwd)
manager.deleteProject(projectName)
def setupTestProject(cls):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(
projName) # Now it will be loaded if exists
cls.outputPath = proj.path
cls.projName = projName
cls.proj = proj
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()
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()):
try:
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
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def setupTestProject(cls):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(projName) # Now it will be loaded if exists
cls.outputPath = proj.path
# Create project does not change the working directory anymore
os.chdir(cls.outputPath)
cls.projName = projName
cls.proj = proj
def getServiceManager(serviceName):
print "getServiceManager"
print "serviceName: ", serviceName
scipionUserData = os.path.join(os.environ['SCIPION_USER_DATA'], serviceName)
manager = Manager(SCIPION_USER_DATA = scipionUserData)
manager.config = os.path.join(os.environ['HOME'], '.config', 'scipion', serviceName)
manager.protocols = os.path.join(manager.config, 'protocols.conf')
manager.hosts = os.path.join(manager.config, 'hosts.conf')
print "config: ", manager.config
print "protocols: ", manager.protocols
print "hosts: ", manager.hosts
return manager
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 _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 project_content(request):
projectName = request.GET.get('projectName', None)
if projectName is None:
projectName = request.POST.get('projectName', None)
project = Manager().loadProject(projectName)
context = contentContext(request, project)
context.update({'mode': None, 'formUrl': 'form'})
return render_to_response('project_content/project_content.html', context)
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 getServiceManager(serviceName):
print "getServiceManager"
print "serviceName: ", serviceName
scipionUserData = os.path.join(os.environ['SCIPION_USER_DATA'],
serviceName)
manager = Manager(SCIPION_USER_DATA=scipionUserData)
serviceConf = os.path.join(os.environ['HOME'], '.config', 'scipion',
serviceName)
manager.config = os.path.join(serviceConf, 'scipion.conf')
manager.protocols = os.path.join(serviceConf, 'protocols.conf')
manager.hosts = os.path.join(serviceConf, 'hosts.conf')
print "config: ", manager.config
print "protocols: ", manager.protocols
print "hosts: ", manager.hosts
return manager
def projects(request):
from pyworkflow.utils.utils import prettyDate
manager = Manager()
projects = manager.listProjects()
for p in projects:
p.pTime = prettyDate(p.mTime)
if 'projectName' in request.session: request.session['projectName'] = ""
if 'projectPath' in request.session: request.session['projectPath'] = ""
context = {'projects': projects,
'projects_css': getResourceCss('projects'),
'project_utils_js': getResourceJs('project_utils'),
}
context = base_grid(request, context)
return render_to_response('projects.html', context)
def project_content(request):
projectName = getVarFromRequest(request, PROJECT_NAME)
mode = getVarFromRequest(request, MODE)
project = Manager().loadProject(projectName, chdir=False)
context = contentContext(request, project)
context.update({'mode': mode, 'formUrl': 'form'})
if mode == MODE_WORKFLOW:
context.update({'nowest': True})
return render_to_response('project_content/project_content.html', context)
def projects(request):
from pyworkflow.utils.utils import prettyDate
manager = Manager()
projects = manager.listProjects()
for p in projects:
p.pTime = prettyDate(p.mTime)
if 'projectName' in request.session: request.session['projectName'] = ""
if 'projectPath' in request.session: request.session['projectPath'] = ""
context = {
'projects': projects,
'projects_css': getResourceCss('projects'),
'project_utils_js': getResourceJs('project_utils'),
}
context = base_grid(request, context)
return render_to_response('projects.html', context)
def _writeSubset(self, subset):
""" Generated the output of this subset. """
newSubsetName = 'outputParticles_%03d' % self._counter
self.info("Creating new subset: %s" % newSubsetName)
subset.write()
self._defineOutputs(**{newSubsetName: subset})
self._defineTransformRelation(self.inputParticles, subset)
# The following is required to commit the changes to the database
self._store(subset)
subset.close()
from pyworkflow.manager import Manager
manager = Manager()
project = manager.loadProject(self.getProject().getName())
input2D = self.input2dProtocol.get()
copyProt = project.copyProtocol(project.getProtocol(input2D.getObjId()))
copyProt.inputParticles.set(project.getProtocol(self.getObjId()))
copyProt.inputParticles.setExtended(newSubsetName)
project.scheduleProtocol(copyProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(copyProt.getObjId())
def getServiceManager(serviceName):
global SERVICE_MANAGERS
manager = SERVICE_MANAGERS.get(serviceName, None)
if manager is None:
print "...Creating new cached Manager"
scipionUserData = os.environ['SCIPION_USER_DATA']
servicePath = '' if serviceName is None else serviceName
scipionUserData = os.path.join(scipionUserData, servicePath)
manager = Manager(SCIPION_USER_DATA=scipionUserData)
serviceConf = os.path.join(os.environ['HOME'], '.config', 'scipion',
servicePath)
manager.config = os.path.join(serviceConf, 'scipion.conf')
manager.protocols = os.path.join(serviceConf, 'protocols.conf')
manager.hosts = os.path.join(serviceConf, 'hosts.conf')
SERVICE_MANAGERS[serviceName] = manager
return manager
def data_content(request):
projectName = request.GET.get('projectName', None)
manager = Manager()
request.session['projectPath'] = manager.getProjectPath(projectName)
project = loadProject(request)
context = {'projectName': projectName,
'editTool': getResourceIcon('edit_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'data_content_utils': getResourceJs('data_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css':getResourceCss('project_content'),
'view':'data'
}
context = base_flex(request, context)
return render_to_response('data_content/data_content.html', context)
def data_content(request):
projectName = getVarFromRequest(request, PROJECT_NAME)
manager = Manager()
request.session[CTX_PROJECT_PATH] = manager.getProjectPath(projectName)
# project = loadProject(request)
context = {CTX_PROJECT_NAME: projectName,
'editTool': getResourceIcon('edit_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'data_content_utils': getResourceJs('data_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css': getResourceCss('project_content'),
'view': 'data'
}
context = base_flex(request, context)
return render_to_response('data_content/data_content.html', context)
def projects(request):
from pyworkflow.utils.utils import prettyDate
manager = Manager()
projectsList = manager.listProjects()
for p in projectsList:
p.pTime = prettyDate(p.mTime)
if CTX_PROJECT_NAME in request.session:
request.session[CTX_PROJECT_NAME] = ""
if CTX_PROJECT_PATH in request.session:
request.session[CTX_PROJECT_PATH] = ""
context = {
'projects': projectsList,
'projects_css': getResourceCss('projects'),
'project_utils_js': getResourceJs('project_utils'),
'workflows': json.dumps(getWorkflowsList())
}
context = base_grid(request, context)
return render_to_response('projects.html', context)
def __init__(self, config, **kwargs):
try:
title = '%s (%s on %s)' % (Message.LABEL_PROJECTS,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
title = Message.LABEL_PROJECTS
settings = ProjectSettings()
self.generalCfg = settings.getConfig()
self.config = config
ProjectBaseWindow.__init__(self, title, minsize=(400, 550), **kwargs)
self.viewFuncs = {VIEW_WIZARD: BoxWizardView}
self.manager = Manager()
self.switchView(VIEW_WIZARD)
def check_project_id(request):
result = 0
projectName = request.GET.get('code', None)
serviceName = request.GET.get('serviceName', None)
try:
if serviceName is None:
project = Manager().loadProject(projectName)
else:
manager = getServiceManager(serviceName)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
result = 1
except Exception:
pass
return HttpResponse(result, mimetype='application/javascript')
def __init__(self, **kwargs):
# Load global configuration
settings = ProjectSettings()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
fileMenu = menu.addSubMenu('File')
fileMenu.addSubMenu('Browse files',
'browse',
icon='fa-folder-open.png')
fileMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.png')
confMenu = menu.addSubMenu('Configuration')
confMenu.addSubMenu('General', 'general')
confMenu.addSubMenu('Hosts', 'hosts')
confMenu.addSubMenu('Protocols', 'protocols')
confMenu.addSubMenu('User', 'user')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help',
'online_help',
icon='fa-external-link.png')
helpMenu.addSubMenu('About', 'about', icon='fa-question-circle.png')
self.menuCfg = menu
self.generalCfg = settings.getConfig()
try:
title = '%s (%s on %s)' % (Message.LABEL_PROJECTS,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
title = Message.LABEL_PROJECTS
ProjectBaseWindow.__init__(self, title, minsize=(750, 500), **kwargs)
self.manager = Manager()
self.switchView(VIEW_PROJECTS)
if n > 3:
usage("Incorrect number of input parameters")
delete = '--delete' in sys.argv
arg1 = sys.argv[1]
if n > 1 and arg1 != '--delete':
customUserData = arg1
else:
customUserData = os.environ['SCIPION_USER_DATA']
print "Loading projects from:\n", customUserData
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
for projInfo in manager.listProjects():
projName = projInfo.getName()
proj = manager.loadProject(projName)
settings = proj.getSettings()
leftTime = proj.getLeftTime()
if (leftTime is not None and
leftTime.days < 0):
if delete:
print "Deleting: %s (%s) " % (projName, leftTime)
manager.deleteProject(projName)
else:
print "Should delete: %s (%s)" % (projName, leftTime)
""" % 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)
""" % error
sys.exit(1)
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()
from pyworkflow.gui.project import ProjectWindow
import pyworkflow.utils as pwutils
if __name__ == '__main__':
# Add callback for remote debugging if available.
try:
from rpdb2 import start_embedded_debugger
from signal import signal, SIGUSR2
signal(SIGUSR2, lambda sig, frame: start_embedded_debugger('a'))
except ImportError:
pass
if len(sys.argv) > 1:
manager = Manager()
projName = os.path.basename(sys.argv[1])
# Handle special name 'here' to create a project
# from the current directory
if projName == 'here':
cwd = os.environ['SCIPION_CWD']
print "\nYou are trying to create a project here:", pwutils.cyan(cwd)
if os.listdir(cwd):
print pwutils.red('\nWARNING: this folder is not empty!!!')
key = raw_input("\nDo you want to create a project here? [y/N]?")
if key.lower().strip() != 'y':
print "\nAborting..."
sys.exit(0)
if n < 2 or n > 3:
usage("Incorrect number of input parameters")
jsonFn = os.path.abspath(sys.argv[1])
now = datetime.now()
tempSpace = "editor-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(os.environ['SCIPION_USER_DATA'],
'tmp', tempSpace)
pwutils.makePath(os.path.join(customUserData, 'projects'))
print "Loading projects from:\n", customUserData
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
projName = os.path.basename(jsonFn)
proj = manager.createProject(projName)
projPath = manager.getProjectPath(projName)
proj.loadProtocols(jsonFn)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Writing protocols to: ", jsonFn
proj.getRunsGraph() # Build project runs graph
proj.exportProtocols(proj.getRuns(), jsonFn)
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
ALL_RELATIONS = 'all'
def usage(error):
print """
ERROR: %s
""" % error
sys.exit(1)
delete = '--delete' in sys.argv
# Create a new project
manager = Manager()
missing = []
for projName in os.listdir(manager.PROJECTS):
entry = manager.getProjectPath(projName)
#print " entry: ", entry, " islink: ", os.path.islink(entry), " exists: ", os.path.exists(entry)
if os.path.islink(entry) and not os.path.exists(entry):
missing.append(entry)
if missing:
print "Missing projects:"
print " \n".join(missing)
if delete:
for entry in missing:
print "Removing: ", entry
n = len(sys.argv)
if n < 2 or n > 5:
usage("Incorrect number of input parameters")
fromLocation = sys.argv[1]
projName = fromLocation.rsplit('/', 1)[-1] if n < 3 else sys.argv[2]
jsonFile = None if n < 4 else os.path.abspath(sys.argv[3])
location = None if n < 5 else sys.argv[4]
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))
project = manager.createProject(projName, location=location)
# copy sqlite and make links of runs
pwutils.copyFile(os.path.join(fromLocation, PROJECT_DBNAME), project.path)
fromRuns = os.path.join(fromLocation, PROJECT_RUNS)
for r in os.listdir(fromRuns):
print " %s,%s" % (os.path.join(fromRuns,
r), os.path.join(project.runsPath, r))
pwutils.createAbsLink(os.path.join(fromRuns, r),
os.path.join(project.runsPath, r))
now = datetime.now()
tempSpace = "loading-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(os.environ['SCIPION_USER_DATA'],
'tmp', tempSpace)
projectsDir = os.path.join(customUserData, 'projects')
pwutils.makePath(projectsDir)
print "Loading projects from:\n", projectsDir
projName = os.path.basename(pathToProj)
pwutils.createAbsLink(pathToProj, os.path.join(projectsDir, projName))
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
proj = manager.loadProject(projName)
projPath = manager.getProjectPath(projName)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
print "Error: ", ex
ProjectWindow.close(self, e)
projWindow = EditorProjectWindow(projPath)
projWindow.show()
N: the number of times to repeat the workflow.
""" % error
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)
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)
Usage: scipion python export_particles.py PROJECT PROCOTOL
PROJECT: provide the project name
PROCOTOL: provide the protocol id to be used as input.
""" % error
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]
manager = Manager()
if not manager.hasProject(projName):
usage("Unexistent project: %s" % pwutils.red(projName))
project = manager.loadProject(projName)
prot = project.getProtocol(protId)
if prot is None:
usage("Unexistent protocol: %s" % protId)
outputParticles = getattr(prot, 'outputParticles', None)
if outputParticles is None:
usage("Protocol does not have 'outputParticles'")
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)
sys.exit(1)
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()
print "ERROR: ", msg
print "\nUSAGE: scipion tutorial [TUTORIAL_NAME]"
print "\nwhere TUTORIAL_NAME can be:"
print "\n".join([' %s' % k for k in ALL_TUTORIALS.keys()])
if pwutils.envVarOn('SCIPION_DEBUG'):
# Add callback for remote debugging if available.
try:
from rpdb2 import start_embedded_debugger
from signal import signal, SIGUSR2
signal(SIGUSR2, lambda sig, frame: start_embedded_debugger('a'))
except ImportError:
pass
if len(sys.argv) == 2:
manager = Manager()
tutorialName = sys.argv[1]
if not tutorialName in ALL_TUTORIALS:
printUsage("Invalid tutorial '%s'." % tutorialName)
else:
# Instanciate the proper tutorial class
tutorial = ALL_TUTORIALS[tutorialName]()
projWindow = ProjectWindow(tutorial.project.getName())
projWindow.show()
else:
msg = 'Too many arguments.' if len(sys.argv) > 2 else ''
printUsage(msg)
from pyworkflow.gui.project import ProjectWindow
if __name__ == '__main__':
# Add callback for remote debugging if available.
try:
from rpdb2 import start_embedded_debugger
from signal import signal, SIGUSR2
signal(SIGUSR2, lambda sig, frame: start_embedded_debugger('a'))
except ImportError:
pass
if len(sys.argv) > 1:
manager = Manager()
projName = os.path.basename(sys.argv[1])
if projName == 'last': # Get last project
projects = manager.listProjects()
if not projects:
sys.exit("No projects yet, cannot open the last one.")
projName = projects[0].projName
projPath = manager.getProjectPath(projName)
try:
projWindow = ProjectWindow(projPath)
except Exception as e:
sys.exit(e)
projWindow.show()
else:
print "usage: pw_project.py PROJECT_NAME"
def _createScipionProject(self, projName, projPath, scipionProjPath):
manager = Manager()
project = manager.createProject(projName, location=scipionProjPath)
self.lastProt = None
pattern = self._getConfValue(PATTERN)
smtpServer = self._getConfValue(SMTP_SERVER, '')
smtpFrom = self._getConfValue(SMTP_FROM, '')
smtpTo = self._getConfValue(SMTP_TO, '')
doMail = self._getValue(EMAIL_NOTIFICATION)
doPublish = self._getValue(HTML_REPORT)
protImport = project.newProtocol(em.ProtImportMovies,
objLabel='Import movies',
filesPath=projPath,
filesPattern=pattern,
sphericalAberration=self._getConfValue(CS),
dataStreaming=True)
# Should I publish html report?
if doPublish == 1:
publish = self._getConfValue('HTML_PUBLISH')
print("\n\nReport available at URL: %s/%s\n\n"
%('http://scipion.cnb.csic.es/scipionbox',projName))
else:
publish = ''
protMonitor = project.newProtocol(em.ProtMonitorSummary,
objLabel='Summary Monitor',
doMail=doMail,
emailFrom=smtpFrom,
emailTo=smtpTo,
smtp=smtpServer,
publishCmd=publish)
def _saveProtocol(prot, movies=True, monitor=True):
if movies:
prot.inputMovies.set(self.lastProt)
prot.inputMovies.setExtended('outputMovies')
project.saveProtocol(prot)
self.lastProt = prot
if monitor:
protMonitor.inputProtocols.append(prot)
_saveProtocol(protImport, movies=False)
useMC2 = self._getValue(MOTIONCOR2)
useMC = self._getValue(MOTIONCORR) or useMC2
useOF = self._getValue(OPTICAL_FLOW)
useSM = self._getValue(SUMMOVIE)
useCTF = self._getValue(CTFFIND4)
useGCTF = self._getValue(GCTF)
kwargs = {}
frames = self._getValue(FRAMES_RANGE).split()
if frames:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = frames[0]
kwargs['alignFrameN'] = kwargs['sumFrameN'] = frames[1]
if useMC:
# Create motioncorr
from pyworkflow.em.packages.motioncorr import ProtMotionCorr
protMC = project.newProtocol(ProtMotionCorr,
objLabel='Motioncorr',
useMotioncor2=useMC2,
**kwargs)
_saveProtocol(protMC)
if useOF:
# Create Optical Flow protocol
from pyworkflow.em.packages.xmipp3 import XmippProtOFAlignment
protOF = project.newProtocol(XmippProtOFAlignment,
objLabel='Optical Flow',
doSaveMovie=useSM,
**kwargs)
_saveProtocol(protOF)
if useSM:
# If OF write the movie, then we need to reset frames count
if frames and useOF:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = 1
kwargs['alignFrameN'] = kwargs['sumFrameN'] = 0
from pyworkflow.em.packages.grigoriefflab import ProtSummovie
protSM = project.newProtocol(ProtSummovie,
objLabel='Summovie',
cleanInputMovies=useOF,
numberOfThreads=1,
**kwargs)
_saveProtocol(protSM)
lastBeforeCTF = self.lastProt
if useCTF:
from pyworkflow.em.packages.grigoriefflab import ProtCTFFind
protCTF = project.newProtocol(ProtCTFFind,
objLabel='Ctffind',
numberOfThreads=1)
protCTF.inputMicrographs.set(lastBeforeCTF)
protCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protCTF, movies=False)
if useGCTF:
from pyworkflow.em.packages.gctf import ProtGctf
protGCTF = project.newProtocol(ProtGctf,
objLabel='Gctf')
protGCTF.inputMicrographs.set(lastBeforeCTF)
protGCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protGCTF, movies=False)
project.saveProtocol(protMonitor)
os.system('%s project %s &' % (pw.getScipionScript(), projName))
self.windows.close()