def get_similar_projects_by_accession(accession):
"""
get similar projects by accession
:return:
"""
project = Project()
print(project.get_similar_projects_by_accession(accession))
def get_reanalysis_projects_by_accession(accession):
"""
get reanalysis projects by accession
:return:
"""
project = Project()
print(project.get_reanalysis_projects_by_accession(accession))
def get_projects(page_size, page, sort_direction, sort_conditions):
"""
get paged projects
:return:
"""
project = Project()
print(
project.get_projects(page_size, page, sort_direction, sort_conditions))
def get_files_by_project_accession(accession, filter, page_size, page,
sort_direction, sort_conditions):
"""
get files by project accession
:return:
"""
project = Project()
print(
project.get_files_by_accession(accession, filter, page_size, page,
sort_direction, sort_conditions))
def test_search_projects(self):
"""
A test method to search projects
"""
project = Project()
result = project.get_projects(77, 0, "ASC", "submission_date")
assert len(result['_embedded']['projects']) == 77
result = project.get_by_accession("PXD009476")
assert result['accession'] == "PXD009476"
result = project.get_reanalysis_projects_by_accession("PXD000419")
assert result['accession'] == "PXD000419"
result = project.get_files_by_accession("PXD009476", "", 100, 0, "ASC",
"fileName")
assert result['page']['totalElements'] == 113
result = project.get_files_by_accession("PXD009476",
"fileCategory.value==RAW", 100,
0, "ASC", "fileName")
assert result['page']['totalElements'] == 109
result = project.search_by_keywords_and_filters(
"accession:PXD008644", "", 100, 0, "", "ASC", "submission_date")
assert len(result['_embedded']['compactprojects']) == 1
result = project.search_by_keywords_and_filters(
"", "accession==PXD008644", 100, 0, "", "ASC", "submission_date")
assert len(result['_embedded']['compactprojects']) == 1
def createProject(self):
self.destroyProject()
self.project = Project(0.7, 0.9, 0.1, 1000)
self.project.message.connect(self.showMessage,
type=Qt.QueuedConnection)
self.project.stateChanged.connect(self.updateState,
type=Qt.QueuedConnection)
self.view = View(self, self.project)
self.container.layout().addWidget(self.view)
self.enableProjectActions(True)
self.updateShaderMenu()
self.editor.setProject(self.project)
def build_project():
'''Builds the project directory, YAML files, and BDS submission files.'''
# Check if the config file exists
assert os.access(args.config_file, os.R_OK), \
logger.error("Could not find config file '{0}'. Please provide the correct path".format(
args.config_file))
# Get global application path
PATH = os.path.dirname(os.path.realpath(__file__))
project = Project(args, PATH)
project.initialize_project()
project.configure_pipeline()
def search_projects_by_keywords_and_filters(keyword, filter, page_size, page,
date_gap, sort_direction,
sort_fields):
"""
search public pride with keywords and filters
:return:
"""
project = Project()
print(
project.search_by_keywords_and_filters(keyword, filter, page_size,
page, date_gap, sort_direction,
sort_fields))
class ProjectMain(object):
"""doc for Main"""
def __init__(self, config_path=""):
super(ProjectMain, self).__init__()
environment = Environment.get_instance()
environment.init_by_file_name("/.", os.path.basename(os.getcwd()), 1)
configure = Configure.get_instance(environment)
self._project = Project()
def start(self):
logging.info("%s Started." % __name__)
self._project.start()
logging.info("%s Closed." % __name__)
def __init__(self, config_path=""):
super(ProjectMain, self).__init__()
environment = Environment.get_instance()
environment.init_by_file_name("/.", os.path.basename(os.getcwd()), 1)
configure = Configure.get_instance(environment)
self._project = Project()
def action_create_project(self):
self.create_project_window = CreateProjectWindow()
self.create_project_window.exec_()
if self.create_project_window.success:
self.project = Project.load_from_file(
self.create_project_window.project_location)
self.project_file = self.create_project_window.project_location
self.setup_project_tree()
self.action_reset()
def create_project(self):
name = self.project_name.text()
location = self.project_location_selected_label.text()
if not name:
QMessageBox.warning(self, 'Project name',
'Project name is required')
if not location:
QMessageBox.warning(self, 'Project name',
'Project location is required')
proj = Project(location, name)
proj.save()
self.project_location = proj.description_path
self.success = True
self.close()
def __init__(self, browser, base_url):
if browser == "firefox":
self.wd = webdriver.Firefox()
elif browser == "chrome":
self.wd = webdriver.Chrome()
elif browser == "ie":
self.wd = webdriver.Ie()
else:
raise ValueError("Unrecognized browser %s" % browser)
self.wd.implicitly_wait(3)
self.session = SessionHelper(self)
self.action = ProjectAction(self)
self.project = Project(self)
#self.kontact = KontactHelper(self)
self.base_url = base_url
def action_open_file(self):
home_dir = str(Path.home())
filename = QFileDialog.getOpenFileName(
self,
'Open file',
home_dir,
'project files (*.codespace)',
options=QFileDialog.DontUseNativeDialog,
)
if filename and filename[0]:
self.project = Project.load_from_file(filename[0])
self.project_file = filename[0]
self.setup_project_tree()
self.action_reset()
def build_project():
'''Builds the project directory, YAML files, and BDS submission files.'''
# Check if the config file exists
assert os.access(args.config_file, os.R_OK), \
logger.error("Could not find config file '{0}'. Please provide the correct path".format(
args.config_file))
# Get global application path
PATH = os.path.dirname(os.path.realpath(__file__))
project = Project(args, PATH)
project.initialize_project()
project.configure_pipeline()
def main():
# H_1 parameters
action = request.args.get('action', '')
on = request.args.get('on', '')
gsid = request.args.get('gsid', '')
# TODO
email = request.args.get('email', '')
# H_2 credentials
# HIGHLIGHT 需開啟 Google Sheets API、Google Drive API
gsheets = load_gsheets()
db = load_firestore()
bucket = load_storage()
# H_3 action
if on == 'team':
target = Team(gsheets=gsheets, db=db, bucket=bucket)
elif on == 'project':
target = Project(gsheets=gsheets, db=db)
elif on == 'survey':
target = Survey(gsheets=gsheets, db=db, bucket=bucket)
elif on == 'module':
target = SurveyModule(gsheets=gsheets, db=db)
elif on == 'recode_module':
target = SurveyModule(gsheets=gsheets, db=db, module='recode')
if on:
if action == 'create' and email:
return target.create(email=email)
elif action == 'update' and gsid:
return target.update(gsid=gsid)
elif action == 'delete' and gsid:
return target.delete(gsid=gsid)
elif on == 'survey' and action == 'update_respondents' and gsid:
return target.update_respondents(gsid=gsid)
elif on == 'survey' and action == 'transfer' and gsid:
return target.transfer(gsid=gsid)
elif on == 'survey' and action == 'update_download_files' and gsid:
return target.update_download_files(gsid=gsid)
elif on == 'survey' and action == 'delete_all_responses' and gsid:
return target.delete_all_responses(gsid=gsid)
return '失敗了....'
def __init__(self, project_file):
super().__init__()
self.last_go_to_definition = time.time()
self.next_instruction = None
self.project_file = project_file
self.editor_windows = {}
self.setupUi(self)
self.move_window_to_center()
self.setup_editor()
if project_file:
self.project = Project.load_from_file(project_file)
self.setup_project_tree()
self.setup_display()
self.setup_emulator()
self.setup_keyboard()
self.setup_doors()
self.setup_antenna()
self.setup_hardware()
# menu buttons
self.actionCreateProject.triggered.connect(self.action_create_project)
self.actionOpenBinFile.triggered.connect(self.action_open_file)
self.actionStep.triggered.connect(self.action_step)
self.actionRun.triggered.connect(self.action_run)
self.actionReset.triggered.connect(self.action_reset)
# speed combobox
self.speed_multiplier = 1
self.speed_changed()
self.speed.currentIndexChanged.connect(self.speed_changed)
from project.project import Project
import random
import string
def random_string(prefix, maxlen):
symbols = string.ascii_letters + string.digits + string.punctuation + " " * 5
return prefix + "".join(
[random.choice(symbols) for i in range(random.randrange(maxlen))])
Testdata = Project(name=random_string("name", 5),
discription=random_string("header", 5))
class Window(QMainWindow):
def __init__(self):
super(Window, self).__init__()
self.project = None
self.view = None
self.lastProjectDirectory = None
self.lastProjectFile = None
self.recentProjectFiles = list()
self.lastImportDirectory = None
self.loadSettings()
self.setWindowTitle("Point Cloud Tagger")
self.createActions()
self.createMenus()
self.createToolBars()
self.createContainer()
self.createEditor()
self.createStatusBar()
def loadSettings(self):
try:
with io.open(Path(__file__).parent / 'app.json', 'r') as f:
data = json.load(f)
if 'lastProjectDirectory' in data:
self.lastProjectDirectory = data['lastProjectDirectory']
if 'recentProjectFiles' in data:
self.recentProjectFiles = data['recentProjectFiles']
if 'lastImportDirectory' in data:
self.lastImportDirectory = data['lastImportDirectory']
except:
pass
def saveSettings(self):
data = dict()
data['lastProjectDirectory'] = self.lastProjectDirectory
data['recentProjectFiles'] = self.recentProjectFiles
data['lastImportDirectory'] = self.lastImportDirectory
with io.open(Path(__file__).parent / 'app.json', 'w') as f:
json.dump(data, f, indent=' ')
def createActions(self):
# root = QFileInfo(__file__).absolutePath()
self.newAct = QAction(
# QIcon(root + '/icons/new.png'),
"&New",
self,
shortcut=QKeySequence.New,
statusTip="Start new project",
triggered=self.newProject)
self.openAct = QAction(
# QIcon(root + '/icons/open.png'),
"&Open",
self,
shortcut=QKeySequence.Open,
statusTip="Open project",
triggered=self.openProject)
self.saveAct = QAction(
# QIcon(root + '/icons/save.png'),
"&Save",
self,
shortcut=QKeySequence.Save,
statusTip="Save project",
triggered=self.saveProject,
enabled=False)
self.saveAsAct = QAction(
# QIcon(root + '/icons/saveas.png'),
"Save &As...",
self,
shortcut=QKeySequence.SaveAs,
statusTip="Save project under new name",
triggered=self.saveProjectAs,
enabled=False)
self.closeAct = QAction(
# QIcon(root + '/icons/close.png'),
"&Close",
self,
shortcut=QKeySequence.Close,
statusTip="Close project",
triggered=self.closeProject,
enabled=False)
self.importAct = QAction(
# QIcon(root + '/icons/import.png'),
"Import MVE Scene",
self,
statusTip="Import MVE scene",
triggered=self.importMVEScene,
enabled=False)
self.exportSelectionAct = QAction(
# QIcon(root + '/icons/import.png'),
"Export Selection",
self,
statusTip="Export selection to ply",
triggered=self.exportSelection,
enabled=False)
self.exportViewsAct = QAction(
# QIcon(root + '/icons/import.png'),
"Export Views",
self,
statusTip="Export views to png",
triggered=self.exportViews,
enabled=False)
self.exitAct = QAction(
# QIcon(root + '/icons/quit.png'),
"&Quit",
self,
shortcut=QKeySequence.Quit,
statusTip="Close the application",
triggered=self.close)
self.aboutAct = QAction("&About",
self,
statusTip="Show the application's About box",
triggered=self.about)
cameraGroup = QActionGroup(self)
self.orthoCameraAct = QAction(
# QIcon(root + '/icons/camera-ortho.png'),
"Orthographic",
cameraGroup,
shortcut="O",
statusTip="Orthographic camera",
triggered=self.toggleOrthoCamera,
checkable=True,
checked=False,
enabled=False)
self.perspectiveCameraAct = QAction(
# QIcon(root + '/icons/camera-perpective.png'),
"Perspective",
cameraGroup,
shortcut="P",
statusTip="Perspective camera",
triggered=self.togglePerspectiveCamera,
checkable=True,
checked=True,
enabled=False)
self.viewCameraAct = QAction(
# QIcon(root + '/icons/camera-view.png'),
"View",
cameraGroup,
shortcut="[",
statusTip="Views camera",
triggered=self.toggleViewCamera,
checkable=True,
checked=False,
enabled=False)
self.toggleAxisAct = QAction(
# QIcon(root + '/icons/axis.png'),
"Axis",
self,
statusTip="Show/hide axis",
triggered=self.toggleAxis,
checkable=True,
checked=True,
enabled=False)
self.togglePlaneAct = QAction(
# QIcon(root + '/icons/plane.png'),
"Plane",
self,
statusTip="Show/hide plane",
triggered=self.togglePlane,
checkable=True,
checked=True,
enabled=False)
self.toggleLocationAct = QAction(
# QIcon(root + '/icons/location.png'),
"Location",
self,
statusTip="Show/hide location",
triggered=self.toggleLocation,
checkable=True,
checked=True,
enabled=False)
self.toggleBBoxAct = QAction(
# QIcon(root + '/icons/bbox.png'),
"BBox",
self,
statusTip="Show/hide box",
triggered=self.toggleBBox,
checkable=True,
checked=True,
enabled=False)
self.togglePhotoAct = QAction(
# QIcon(root + '/icons/photo.png'),
"Picture",
self,
shortcut="]",
statusTip="Show/hide picture",
triggered=self.togglePicture,
checkable=True,
checked=True,
enabled=False)
self.preselectAct = QAction(
"Build/apply selection",
self,
statusTip="Build index and apply saved selection",
triggered=self.preselect,
enabled=False)
self.editorAct = QAction("Scene editor",
self,
statusTip="Open scene editor",
triggered=self.showEditor,
enabled=False)
def createMenus(self):
fileMenu = self.menuBar().addMenu("&File")
fileMenu.addAction(self.newAct)
fileMenu.addAction(self.openAct)
fileMenu.addAction(self.saveAct)
fileMenu.addAction(self.saveAsAct)
fileMenu.addAction(self.closeAct)
fileMenu.addSeparator()
fileMenu.addAction(self.importAct)
fileMenu.addSeparator()
fileMenu.addAction(self.exportSelectionAct)
fileMenu.addAction(self.exportViewsAct)
fileMenu.addSeparator()
self.recentMenu = fileMenu.addMenu("Recent...")
self.updateRecentMenu()
fileMenu.addSeparator()
fileMenu.addAction(self.exitAct)
viewMenu = self.menuBar().addMenu("&View")
viewMenu.addAction(self.orthoCameraAct)
viewMenu.addAction(self.perspectiveCameraAct)
viewMenu.addAction(self.viewCameraAct)
viewMenu.addSeparator()
viewMenu.addAction(self.toggleAxisAct)
viewMenu.addAction(self.togglePlaneAct)
viewMenu.addAction(self.toggleLocationAct)
viewMenu.addAction(self.toggleBBoxAct)
viewMenu.addAction(self.togglePhotoAct)
viewMenu.addSeparator()
self.shaderMenu = viewMenu.addMenu("Cloud shaders...")
self.shaderMenu.setEnabled(False)
self.updateShaderMenu()
toolsMenu = self.menuBar().addMenu("&Tools")
toolsMenu.addAction(self.preselectAct)
toolsMenu.addSeparator()
toolsMenu.addAction(self.editorAct)
self.menuBar().addSeparator()
helpMenu = self.menuBar().addMenu("&Help")
helpMenu.addAction(self.aboutAct)
def updateRecentMenu(self):
self.recentMenu.clear()
if len(self.recentProjectFiles) > 0:
for file in self.recentProjectFiles:
def openRecent(filename):
return lambda: self.openProject(filename)
if len(file) > 30:
name = "..." + file[-30:]
else:
name = file
self.recentMenu.addAction(name, openRecent(file))
else:
self.recentMenu.addSection("No project yet")
def updateShaderMenu(self):
self.shaderActions = dict()
self.shaderMenu.clear()
items = sorted(
set([
file.stem
for file in (Path(__file__).parent / 'shaders').iterdir()
if file.is_file()
]))
group = QActionGroup(self)
for item in items:
def setShader(name):
return lambda: self.setCloudShader(name)
checked = False
if self.project:
checked = self.project.cloudShaderName == item
action = QAction(item,
group,
triggered=setShader(item),
checkable=True,
checked=checked)
self.shaderActions[item] = action
self.shaderMenu.addAction(action)
def createToolBars(self):
# self.fileToolBar = self.addToolBar("File")
# self.fileToolBar.addAction(self.newAct)
# self.fileToolBar.addAction(self.openAct)
# self.fileToolBar.addAction(self.saveAct)
# viewToolBar = self.addToolBar("View")
# cameraMenu = QMenu("Camera", self)
# cameraMenu.addAction(self.orthoCameraAct)
# cameraMenu.addAction(self.perspectiveCameraAct)
# cameraMenu.addAction(self.viewCameraAct)
# cameraButton = QToolButton(text="Camera", popupMode=QToolButton.InstantPopup)
# cameraButton.setMenu(cameraMenu)
# viewToolBar.addWidget(cameraButton)
# viewToolBar.addAction(self.toggleAxisAct)
# viewToolBar.addAction(self.togglePlaneAct)
# viewToolBar.addAction(self.toggleLocationAct)
# viewToolBar.addAction(self.toggleBBoxAct)
# viewToolBar.addAction(self.togglePhotoAct)
pass
def createContainer(self):
self.container = QWidget(self)
self.container.setStyleSheet("QOpenGLWidget { background: black; }")
self.container.setLayout(QVBoxLayout())
self.setCentralWidget(self.container)
def createEditor(self):
self.editor = Editor(self)
self.editor.changed.connect(self.renderProject,
type=Qt.QueuedConnection)
def createStatusBar(self):
self.statusBar().showMessage("Initialized")
def closeEvent(self, event):
self.destroyProject()
event.accept()
def enableProjectActions(self, enabled):
actions = [
self.saveAct,
self.saveAsAct,
self.closeAct,
self.importAct,
self.exportSelectionAct,
self.exportViewsAct,
self.orthoCameraAct,
self.perspectiveCameraAct,
self.viewCameraAct,
self.toggleAxisAct,
self.togglePlaneAct,
self.toggleLocationAct,
self.toggleBBoxAct,
self.togglePhotoAct,
self.shaderMenu,
self.preselectAct,
self.editorAct,
]
for action in actions:
action.setEnabled(enabled)
def createProject(self):
self.destroyProject()
self.project = Project(0.7, 0.9, 0.1, 1000)
self.project.message.connect(self.showMessage,
type=Qt.QueuedConnection)
self.project.stateChanged.connect(self.updateState,
type=Qt.QueuedConnection)
self.view = View(self, self.project)
self.container.layout().addWidget(self.view)
self.enableProjectActions(True)
self.updateShaderMenu()
self.editor.setProject(self.project)
def destroyProject(self):
self.editor.setProject(None)
self.enableProjectActions(False)
if self.view:
self.container.layout().removeWidget(self.view)
self.view.close()
self.view = None
if self.project:
self.project.message.disconnect(self.showMessage)
self.project.stateChanged.disconnect(self.updateState)
self.project = None
@Slot(str)
def showMessage(self, message):
self.statusBar().showMessage(message)
@Slot()
def updateState(self):
if not self.project:
return
self.orthoCameraAct.setChecked(self.project.cameraMode == 'ortho')
self.perspectiveCameraAct.setChecked(
self.project.cameraMode == 'perspective')
self.viewCameraAct.setChecked(self.project.cameraMode == 'view')
self.toggleAxisAct.setChecked(self.project.showAxis)
self.togglePlaneAct.setChecked(self.project.showPlane)
self.toggleLocationAct.setChecked(self.project.showLocation)
self.toggleBBoxAct.setChecked(self.project.showBBox)
self.togglePhotoAct.setChecked(self.project.showPicture)
def newProject(self):
self.createProject()
self.project.create()
self.lastProjectFile = None
def openProject(self, filename=None):
if not filename:
(filename, ftype) = QFileDialog.getOpenFileName(
self,
"Choose project file",
dir=self.lastProjectDirectory,
filter="Projects (*.prj)",
options=QFileDialog.DontResolveSymlinks
| QFileDialog.HideNameFilterDetails)
if filename:
self.lastProjectDirectory = str(Path(filename).parent)
self.createProject()
progress = QProgressDialog('', None, 0, 100, self)
try:
self.project.load(filename, progress)
self.lastProjectFile = filename
if filename in self.recentProjectFiles:
self.recentProjectFiles.remove(filename)
self.recentProjectFiles.insert(0, filename)
self.updateRecentMenu()
self.updateShaderMenu()
self.editor.setProject(self.project)
self.saveSettings()
except BaseException as e:
progress.close()
raise e
def saveProject(self):
if not self.lastProjectFile:
self.saveProjectAs()
return
self.project.save(self.lastProjectFile)
def saveProjectAs(self):
(filename, ftype) = QFileDialog.getSaveFileName(
self,
"Choose project file",
dir=self.lastProjectDirectory,
filter="Projects (*.prj)",
options=QFileDialog.DontResolveSymlinks
| QFileDialog.HideNameFilterDetails)
if filename:
if not filename.endswith('.prj'):
filename += '.prj'
self.project.save(filename)
self.lastProjectFile = filename
if filename in self.recentProjectFiles:
self.recentProjectFiles.remove(filename)
self.recentProjectFiles.insert(0, filename)
self.updateRecentMenu()
self.saveSettings()
def closeProject(self):
self.destroyProject()
def importMVEScene(self):
(filename, ftype) = QFileDialog.getOpenFileName(
self,
"Choose MVE scene",
dir=self.lastImportDirectory,
filter="MVE Scene (synth_0.out)",
options=QFileDialog.DontResolveSymlinks)
if filename:
directory = str(Path(filename).parent)
self.lastImportDirectory = directory
progress = QProgressDialog('', None, 0, 100, self)
try:
self.project.importmve(directory, progress)
self.view.update()
self.saveSettings()
except BaseException as e:
progress.close()
raise e
def exportSelection(self):
(filename, ftype) = QFileDialog.getSaveFileName(
self,
"Choose ply file",
dir=self.lastProjectDirectory,
filter="Meshes (*.ply)",
options=QFileDialog.DontResolveSymlinks
| QFileDialog.HideNameFilterDetails)
if filename:
if not filename.endswith('.ply'):
filename += '.ply'
progress = QProgressDialog('', None, 0, 100, self)
try:
self.project.exportply(filename, progress)
except BaseException as e:
progress.close()
raise e
def exportViews(self):
filename, ok = QInputDialog.getText(self, "View Image Filename",
"Png filename")
if ok and len(filename) > 0:
progress = QProgressDialog('', None, 0, 100, self)
try:
self.project.exportviews(self.view.context(), filename,
progress)
except BaseException as e:
progress.close()
raise e
def preselect(self):
progress = QProgressDialog('', None, 0, 100, self)
try:
self.project.preselect(progress)
except BaseException as e:
progress.close()
raise e
def showEditor(self):
dock = QDockWidget("Scene Parameters", self)
dock.setAllowedAreas(Qt.RightDockWidgetArea)
dock.setFixedWidth(640)
dock.setWidget(self.editor)
self.addDockWidget(Qt.RightDockWidgetArea, dock)
def toggleOrthoCamera(self):
if not self.orthoCameraAct.isChecked():
return
self.project.setCameraMode('ortho')
def togglePerspectiveCamera(self):
if not self.perspectiveCameraAct.isChecked():
return
self.project.setCameraMode('perspective')
def toggleViewCamera(self):
if not self.viewCameraAct.isChecked():
return
self.project.setCameraMode('view')
def toggleAxis(self):
self.project.toggleAxis()
def togglePlane(self):
self.project.togglePlane()
def toggleLocation(self):
self.project.toggleLocation()
def toggleBBox(self):
self.project.toggleBBox()
def togglePicture(self):
self.project.togglePicture()
def setCloudShader(self, name):
if not self.project:
return
self.editor.loadShader(name)
self.project.setCloudShader(name)
self.shaderActions[name].setChecked(True)
def renderProject(self):
if not self.project:
return
self.project.redraw.emit()
def about(self):
QMessageBox.about(
self, "About Application",
"The <b>3D Tagger</b> can load point-clouds from MVE scenes, tag points and export result."
)