def changeExtension(self, extension=None):
"""
Change to a new extension.
:param extension: can be "mini", "3d", "tissue", "plant"
"""
self.removeDocksWidgets()
filename = 'oalab.py'
conf = path(get_openalea_home_dir()) / filename
if extension in ["mini", "3d", "tissue", "plant"]:
filename = ('oalab_' + extension + '.py')
conf = path(get_openalea_home_dir()) / filename
if not conf.exists():
with conf.open('w') as f:
# TODO : auto generate config file
# f.write(self._config.generate_config_file())
if extension == "mini":
f.write(config_file_mini)
elif extension == "3d":
f.write(config_file_3d)
elif extension == "tissue":
f.write(config_file_tissue)
elif extension == "plant":
f.write(config_file_plant)
else:
f.write(config_file_default)
self.session.load_config_file(filename=filename,
path=get_openalea_home_dir())
self.setWidgets(self.controller)
def changeExtension(self, extension=None):
"""
Change to a new extension.
:param extension: can be "mini", "3d", "tissue", "plant"
"""
self.removeDocksWidgets()
filename = 'oalab.py'
conf = path(get_openalea_home_dir()) / filename
if extension in ["mini", "3d", "tissue", "plant"]:
filename = ('oalab_' + extension + '.py')
conf = path(get_openalea_home_dir()) / filename
if not conf.exists():
with conf.open('w') as f:
# TODO : auto generate config file
# f.write(self._config.generate_config_file())
if extension == "mini":
f.write(config_file_mini)
elif extension == "3d":
f.write(config_file_3d)
elif extension == "tissue":
f.write(config_file_tissue)
elif extension == "plant":
f.write(config_file_plant)
else:
f.write(config_file_default)
self.session.load_config_file(filename=filename, path=get_openalea_home_dir())
self.setWidgets(self.controller)
def add_data(self,
data_id="",
path="",
site="",
exec_data=False,
cache_data=False,
*args,
**kwargs):
# FIRST: FORMAT INPUT:
ind = {
"data_id": data_id,
"path": path,
"site": site,
"exec_data": exec_data,
"cache_data": cache_data
}
try:
index_path = os.path.join(self.path, str(data_id + '.json'))
with open(index_path, 'a+') as fp:
json.dump(ind, fp)
fp.write("\n")
except:
index_path = os.path.join(settings.get_openalea_home_dir(),
'index_default.json')
print('Fail to open index files. - Now write index in : ',
index_path)
with open(index_path, 'a+') as fp:
json.dump(ind, fp)
fp.write("\n")
def launch_lab(plugin_class):
from openalea.oalab.gui.splittablewindow import OALabMainWin
from openalea.core.settings import get_openalea_home_dir
from openalea.core.path import path as Path
from openalea.core.service.introspection import alias
from openalea.oalab.gui.utils import qicon
plugin = plugin_class()
lab_class = plugin()
layout_path = Path(get_openalea_home_dir()) / '%s.oaui' % lab_class.name
OALabMainWin.DEFAULT_LAYOUT_PATH = layout_path
OALabMainWin.DEFAULT_LAYOUT = lab_class.layout
OALabMainWin.DEFAULT_MENU_NAMES = lab_class.menu_names
OALabMainWin.LAB = lab_class
if hasattr(lab_class, "start"):
lab_class.start()
win = OALabMainWin(lab=lab_class)
win.setWindowIcon(qicon(lab_class.icon))
if hasattr(lab_class, 'connect_applet'):
win.appletSet.connect(lab_class.connect_applet)
win.emit_applet_set()
if hasattr(lab_class, "initialize"):
lab_class.initialize()
win.initialize()
win.setWindowTitle('OpenAleaLab "%s"' % alias(plugin))
win.showMaximized()
win.raise_()
return win
def launch_lab(plugin_class):
from openalea.oalab.gui.splittablewindow import OALabMainWin
from openalea.core.settings import get_openalea_home_dir
from openalea.core.path import path as Path
from openalea.core.service.introspection import alias
from openalea.oalab.gui.utils import qicon
plugin = plugin_class()
lab_class = plugin()
layout_path = Path(get_openalea_home_dir()) / '%s.oaui' % lab_class.name
OALabMainWin.DEFAULT_LAYOUT_PATH = layout_path
OALabMainWin.DEFAULT_LAYOUT = lab_class.layout
OALabMainWin.DEFAULT_MENU_NAMES = lab_class.menu_names
OALabMainWin.LAB = lab_class
if hasattr(lab_class, "start"):
lab_class.start()
win = OALabMainWin(lab=lab_class)
win.setWindowIcon(qicon(lab_class.icon))
if hasattr(lab_class, 'connect_applet'):
win.appletSet.connect(lab_class.connect_applet)
win.emit_applet_set()
if hasattr(lab_class, "initialize"):
lab_class.initialize()
win.initialize()
win.setWindowTitle('OpenAleaLab "%s"' % alias(plugin))
win.showMaximized()
win.raise_()
return win
def add_wf_item(self, item, *args, **kwargs):
try:
prov_path = os.path.join(self.localpath,
str(item["workflow"]) + '.json')
with open(prov_path, 'a+') as fp:
json.dump(item, fp, indent=4)
except:
prov_path = path(settings.get_openalea_home_dir()
) / 'provenance' / 'wf_provenance.json'
print('Fail to open prov files. - Now write prov in : ', prov_path)
with open(prov_path, 'a+') as fp:
json.dump(item, fp, indent=4)
def add_execution_item(self, item, *args, **kwargs):
try:
prov_path = os.path.join(self.localpath,
str(item["workflow_id"]) + '.json')
with open(prov_path, 'a+') as fp:
json.dump(item, fp)
fp.write("\n")
except:
prov_path = os.path.join(settings.get_openalea_home_dir(),
'provenance', 'execution_provenance.json')
print('Fail to open prov files. - Now write prov in : ', prov_path)
with open(prov_path, 'a+') as fp:
json.dump(item, fp)
fp.write("\n")
# -*- coding: utf-8 -*-
from openalea.core.path import path
from openalea.core import settings
import os
from os.path import expanduser
REMOTE_SITE = False
# Files
SITE_PATH = path(settings.get_openalea_home_dir()) / 'index'
# Mongo
MONGO_ADDR='127.0.0.1'
MONGO_PORT = 27017
# remote db
MONGO_SSH_IP='127.0.0.1'
home = expanduser("~")
SSH_PKEY = os.path.join(home, ".ssh", "id_rsa")
SSH_USERNAME="******"
# cassandra
CASSANDRA_SSH_IP = "134.158.247.62"
CASSANDRA_ADDR = "localhost"
CASSANDRA_PORT = 9042
def get_database_name():
db_fn = path(settings.get_openalea_home_dir())/'provenance.sq3'
return db_fn
# -*- coding: utf-8 -*-
from openalea.core.path import path
from openalea.core import settings
import os
from os.path import expanduser
# PATHS
# files infos
PROVENANCE_PATH = path(settings.get_openalea_home_dir()) / 'provenance'
TMP_PATH = path(settings.get_openalea_home_dir()) / "execution_data"
CACHE_PATH = path(settings.get_openalea_home_dir()) / "cached_data"
# infos about provenance db
REMOTE_PROV = False
# Mongo
MONGO_ADDR = '127.0.0.1'
MONGO_PORT = 27017
# cassandra
REMOTE_INDEX = True
CASSANDRA_SSH_IP = "134.158.247.62"
CASSANDRA_PORT = 9042
# SSH
PROVDB_SSH_ADDR = ""
home = expanduser("~")
SSH_PKEY = os.path.join(home, ".ssh", "id_rsa")
SSH_USERNAME = "******"
# REMOTE_DB_ADDR=('127.0.0.1', 27017)
# -*- coding: utf-8 -*-
from openalea.core.path import path
from openalea.core import settings
import os
from os.path import expanduser
REMOTE_PROV = False
# Files
PROVENANCE_PATH = path(settings.get_openalea_home_dir()) / 'provenance'
# Mongo
MONGO_ADDR = '127.0.0.1'
MONGO_PORT = 27017
# remote db
MONGO_SSH_IP = '127.0.0.1'
home = expanduser("~")
SSH_PKEY = os.path.join(home, ".ssh", "id_rsa")
SSH_USERNAME = "******"
# cassandra
CASSANDRA_SSH_IP = "134.158.247.62"
CASSANDRA_ADDR = "localhost"
CASSANDRA_PORT = 9042
def get_database_name():
db_fn = path(settings.get_openalea_home_dir()) / 'provenance.sq3'
return db_fn
