def create_project(request): manager = Manager() if request.is_ajax(): projectName = request.GET.get('projectName') manager.createProject(projectName) return HttpResponse(mimetype='application/javascript')
def create_project(request): manager = Manager() if request.is_ajax(): projectName = request.GET.get('projectName') manager.createProject(projectName) return HttpResponse(mimetype='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')
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 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 __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()
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))
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: print "Error saving the workflow: ", ex ProjectWindow.close(self, e)
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()
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()
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)
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) else: print "\nCreating project...." projName = os.path.basename(cwd) projDir = os.path.dirname(cwd) proj = manager.createProject(projName, location=projDir) elif 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: # Print any exception print("ERROR: At pw_project.py loading Project %s.\n" " Message: %s\n" % (projPath, e))
""" % 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: %s Usage: scipion python new-session-aarhus.py workflow.json PROJECT_FOLDER """ % error) sys.exit(1) n = len(sys.argv) if n < 2 or n > 3: usage("Incorrect number of input parameters") scipionProjPath = sys.argv[2] if n == 3 else None jsonFn = os.path.abspath(sys.argv[1]) now = datetime.now() projName = "scipion-%s" % now.strftime('%Y%m%d-%H%M%S') print("Creating project: ", projName) # Create a new project manager = Manager() proj = manager.createProject(projName, location=scipionProjPath) projPath = manager.getProjectPath(projName) proj.loadProtocols(jsonFn) projWindow = ProjectWindow(projPath) projWindow.show()
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] if ext in ACCEPTED_EXTENSIONS: full_path = os.path.join(args.directory, os.listdir(args.directory)[0])