def test_cfgNewConfigDef():
ch = ExpConfigHandler(pathscheme='test1')
#ch.addNewConfig("/home/scholer/Documents/labfluence_data_testsetup/.labfluence/templates.yml", "templates")
# I have added the following to the 'exp' config:
# config_define_new:
# templates: ./.labfluence/templates.yml
logger.info("ch.get('exp_subentry_template'): %s", ch.get('exp_subentry_template'))
def notestExpConfig1():
ch = ExpConfigHandler(pathscheme='test1')
logger.info("ch.HierarchicalConfigHandler.Configs: %s", ch.HierarchicalConfigHandler.printConfigs())
path = "/home/scholer/Documents/labfluence_data_testsetup/2013_Aarhus/RS102 Strep-col11 TR annealed with biotin"
cfg = ch.loadExpConfig(path)
if cfg is None:
logger.info("cfg is None; using empty dict.")
cfg = dict()
cfg['test_key'] = datetime.now().strftime("%Y%m%d-%H%M%S") # you can use strptime to parse a formatted date string.
logger.info("Saving config for path '%s'", path)
ch.saveExpConfig(path)
def test_configTypeChain():
#ch2 = ExpConfigHandler('../test/config/system_config.yml')
ch2 = self.Confighandler
logger.info('ch2.Configs:\n{}'.format(ch2.Configs))
ch2.Configs
ch2.Configs['system']['user_config_path'] = os.path.join(
configtestdir, 'user_config.yml')
ch2.saveConfigs()
ch3 = ExpConfigHandler('../test/config/system_config.yml')
logger.info('ch3.Configs:\n{}'.format(ch3.Configs))
def setUp():
scriptdir = os.path.dirname(os.path.abspath(__file__))
configtestdir = os.path.join(scriptdir, '../test/config')
paths = [
os.path.join(configtestdir, cfg)
for cfg in ('system_config.yml', 'user_config.yml',
'exp_config.yml')
]
self.Confighandler = ch = ExpConfigHandler(*paths)
logger.info("End ch confighandler init...")
def printPaths():
logger.info("os.path.curdir: %s", os.path.curdir)
logger.info("os.path.realpath(curdir) : %s",
os.path.realpath(os.path.curdir))
logger.info("os.path.abspath(__file__): %s",
os.path.abspath(__file__))
#print "os.path.curdir: {}".format(os.path.curdir)
printPaths()
return ch
def __init__(self, confighandler=None):
#self.ActiveExperiments = list() # Probably better to use a property attribute
#self.RecentExperiments = list()
logger.info(
">>>>>>>>>>>>>> Starting init of LabfluenceGUI >>>>>>>>>>>>>>>>")
self.Confighandler = confighandler or ExpConfigHandler(
pathscheme='default1')
#self.Confighandler.Singletons.setdefault('app', self)
self.Confighandler.Singletons['app'] = self
if 'experimentmanager' not in self.Confighandler.Singletons:
print "LabfluenceGUI.__init__ >> Instantiating new ExperimentManager!"
self.Confighandler.Singletons[
'experimentmanager'] = ExperimentManager(
confighandler=self.Confighandler, autoinit=('localexps', ))
#self.init_ui()
self.tkroot = LabfluenceTkRoot(confighandler)
logger.debug("self.tkroot initialized")
self.Controllers = dict()
self.ExpNotebooks = dict()
self.init_bindings()
self.init_fonts()
self.connect_controllers()
def confighandler1():
ch = ExpConfigHandler(pathscheme='test1')
return ch
def test_registerEntryChangeCallback():
logger.info(">>>>>>>>>>>> starting test_registerEntryChangeCallback(): >>>>>>>>>>>>>>>>>>>>")
#registerEntryChangeCallback invokeEntryChangeCallback
ch = ExpConfigHandler(pathscheme='test1')
ch.setkey('testkey', 'random string')
def printHej(who, *args):
logger.info("hi %s, other args: %s", who, args)
def printNej():
logger.info("no way!")
def argsAndkwargs(arg1, arg2, hej, der, **kwargs):
logger.info("%s, %s, %s, %s, %s", arg1, arg2, hej, der, kwargs)
ch.registerEntryChangeCallback('app_active_experiments', printHej, ('morten', ))
ch.registerEntryChangeCallback('app_recent_experiments', printNej)
ch.registerEntryChangeCallback('app_recent_experiments', argsAndkwargs, ('word', 'up'), dict(hej='tjubang', der='sjubang', my='cat'))
ch.ChangedEntriesForCallbacks.add('app_active_experiments')
ch.ChangedEntriesForCallbacks.add('app_recent_experiments')
logger.info("Round one:")
ch.invokeEntryChangeCallback('app_active_experiments')
ch.invokeEntryChangeCallback() # invokes printNej and argsAndkwargs
logger.info("Round two:")
ch.invokeEntryChangeCallback('app_active_experiments') # still invokes printHej
ch.invokeEntryChangeCallback() # does not invoke anything...
logger.info("<<<<<<<<<<<<< completed test_registerEntryChangeCallback(): <<<<<<<<<<<<<<<<<<<<")
def test_addNewConfig():
ch = ExpConfigHandler(pathscheme='test1')
ch.addNewConfig("/home/scholer/Documents/labfluence_data_testsetup/.labfluence/templates.yml", "templates")
logger.info("ch.get('exp_subentry_template'): %s", ch.get('exp_subentry_template'))
def __init__(self, pathscheme=None, enableHierarchy=False, readfiles=False):
ExpConfigHandler.__init__(self, pathscheme=pathscheme, enableHierarchy=False, readfiles=False)
expconfigyaml = r"""
exp_series_dir_fmt: '{expid} {exp_titledesc}'
exp_series_regex: (?P<expid>RS[0-9]{3})[_ ]+(?P<exp_titledesc>.+)
exp_subentry_dir_fmt: '{expid}{subentry_idx} {subentry_titledesc} ({datetime:%Y%m%d})'
exp_subentry_regex: (?P<date1>[0-9]{8})?[_ ]*(?P<expid>RS[0-9]{3})-?(?P<subentry_idx>[^_
])[_ ]+(?P<subentry_titledesc>.+?)\s*(\((?P<date2>[0-9]{8})\))?$
exp_subentry_regex_old: (?P<date1>[0-9]{8})?[_ ]*(?P<expid>RS[0-9]{3})-?(?P<subentry_idx>[^_ ])[_ ]+(?P<subentry_titledesc>.+?)\s?(\((?P<date2>[0-9]{8})\))?$
exp_subentryid_fmt: '{expid}{subentry_idx}'
expid_fmt: RS{exp_series_index:03d}
expid_regex: RS(?P<exp_series_index>[0-9]{3,4})
journal_entry_fmt: '[{datetime:%Y%m%d %H:%M:%S}] {text}'
journal_subentry_token_fmt_obsolete: '<p id="{}"></p>'
journal_date_format: '%Y%m%d'
local_exp_ignoreDirs:
- equipment_data_sync
- 2008-2010_Aarhus
- 2011_Aarhus
- 2012_Aarhus
- 2012_Harvard
local_exp_rootDir: .
local_exp_subDir: ./2013_Aarhus
wiki_exp_root_spaceKey: ~scholer
wiki_exp_root_pageId: '524296'
wiki_exp_archive_pageId: '524308'
wiki_exp_new_subentry_token: <h2>Results and discussion</h2>
wiki_exp_new_subentry_insert_regex_fmt: (?P<before_insert><h2>Experimental section</h2>.*?)(?P<after_insert><h4>{expid}[_-]?[{next_subentry_idx}-z].*?</h4>|<h[1-3]>.*?</h[1-3]>|$)
wiki_journal_entry_insert_regex_fmt: '(?P<before_insert><h2>Experimental section</h2>.*?<h4>{expid}{subentry_idx}.*?</h4>.*?)(?P<after_insert><h[1-4]>.+?</h[1-4]>|$)'
wiki_subentry_parse_regex_fmt: '(?P<exp_section_header><h2>Experimental section</h2>).*?(?P<subentry_header><h4>{expid}{subentry_idx}.+?</h4>)(?P<subentry_xhtml>.*?)(?P<next_header><h[1-4]>.+?</h[1-4]>|$)'
wiki_templates_pageIds:
exp_page: '524303'
exp_subentry: '524306'
wiki_template_string_interpolation_mode: 'old'
wiki_template_string_interpolation_mode_comment: can be 'new', 'old' and 'template'. 'new' is curly-braced based string.format; 'old' is %-based moduli substitution and 'template' uses string templates only.
wiki_allow_template_caching: true
wiki_default_newpage_template: 'exp_page'
"""
userconfigyaml = """
app_active_experiments:
- RS102
- RS134
- RS135
app_recent_experiments:
- RS103
crypt_iv: Ko8E4tmJP7SCgLla
wiki_serverparams:
baseurl: http://10.14.40.245:8090
wiki_username: scholer
wiki_lims_pageid: '917542'
"""
# Consider switching to using the 'test1' config, even for this...
# Well, on the other hand... The fake objects are not supposed to touch anything, used for testing.
configyamls = dict(user=userconfigyaml, exp=expconfigyaml)
for cfg, yml in configyamls.items():
newconfig = yaml.load(yml)
self.Configs.setdefault(cfg, dict()).update(newconfig) # 1-liner, replacing the four below:
#if cfg in self.Configs:
# self.Configs[cfg].update(newconfig)
#else:
# self.Configs[cfg] = newconfig
logger.debug("Config '%s' loaded (using hard-coded test configuration...).", cfg)
self.__expconfigs = dict()
def setUp():
self.Confighandler = ch = ExpConfigHandler(pathscheme='test1')
def setUp():
self.Confighandler = ch = ExpConfigHandler(pathscheme='test1')
self.Pathfinder = pf = PathFinder(VERBOSE=10)
logging.getLogger("tkui.mainframe").setLevel(logging.DEBUG)
logging.getLogger(__name__).setLevel(logging.DEBUG)
logger.debug("Loggers setting to debug level...")
pathscheme = argsns.pathscheme or 'test1'
logger.info( "Enabling testing environment..." )
confighandler = FakeConfighandler(pathscheme=pathscheme)
# set basedir for exp:
confighandler.ConfigPaths['exp'] = os.path.join('tests', 'test_data', 'test_filestructure', 'labfluence_data_testsetup', '.labfluence.yml')
server = FakeConfluenceServer(confighandler=confighandler)
else:
logger.debug(" >>>>>> Initiating real confighandler and server... >>>>>>")
pathscheme = argsns.pathscheme or 'default1'
confighandler = ExpConfigHandler(pathscheme='default1')
try:
logger.debug("Confighandler instantiated, Initiating server... >>>>>>")
# setting autologin=False during init should defer login attempt...
server = ConfluenceXmlRpcServer(autologin=False, confighandler=confighandler)
server._autologin = True
except socket.error as e:
logger.error( "Socket error during server init ('%s'). This should not happen; autologin is shielded by try-clause.", e)
server = None
confighandler.Singletons['server'] = server
logger.debug(" >>>>>> Server instantiated, initiating ExperimentManager... >>>>>> ")
manager = ExperimentManager(confighandler=confighandler, autoinit=('localexps', ))
confighandler.Singletons['experimentmanager'] = manager
logger.debug(" >>>>>> ExperimentManager instantiated, starting LabfluenceApp... >>>>>>")
def main():
##############################
###### Parse arguments: ######
##############################
#argsns = parser.parse_args() # produces a namespace, not a dict.
argsns = parse_args()
#######################################
### Set up standard logging system ####
#######################################
loghandlers = init_logging(argsns, prefix="labfluence_cmd")
############################
#### Set up logging: ####
############################
#logfmt = "%(levelname)s %(name)s:%(lineno)s %(funcName)s() > %(message)s"
#try:
# loglevel = int(argsns.loglevel)
#except ValueError:
# loglevel = argsns.loglevel.upper()
##logfmt = "%(levelname)s:%(name)s: %(funcName)s() :: %(message)s"
#if argsns.debug is None:
# #and 'all' in argsns.debug:
# logging.basicConfig(level=loglevel, format=logfmt)
## argsns.debug is a list (possibly empty)
#elif argsns.debug:
## argsns.debug is a non-empty list
# logging.basicConfig(level=loglevel, format=logfmt)
# for mod in argsns.debug:
# logger.info("Enabling logging debug messages for module: %s", mod)
# logging.getLogger(mod).setLevel(logging.DEBUG)
#else:
# # argsns.debug is an empty list
# logging.basicConfig(level=min(logging.DEBUG, loglevel), format=logfmt)
#logging.getLogger("__main__").setLevel(logging.DEBUG)
#
#if argsns.logtofile or True: # always log for now...
# # based on http://docs.python.org/2/howto/logging-cookbook.html
# if not os.path.exists('logs'):
# os.mkdir('logs')
# if argsns.testing:
# fh = logging.FileHandler('logs/labfluence_cmd_testing.log')
# else:
# fh = logging.FileHandler('logs/labfluence_cmd_debug.log')
# fh.setLevel(logging.DEBUG)
# formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# fh.setFormatter(formatter)
# logging.getLogger('').addHandler(fh) # logging.root == logging.getLogger('')
####################################################################################
# Set up confighandler, etc (depending on whether testing mode is requested...) ####
####################################################################################
if argsns.testing:
logging.getLogger(
"model.model_testdoubles.fake_confighandler").setLevel(
logging.DEBUG)
logging.getLogger("model.model_testdoubles.fake_server").setLevel(
logging.DEBUG)
logging.getLogger(__name__).setLevel(logging.DEBUG)
pathscheme = argsns.pathscheme or 'test1'
logger.info("Enabling testing environment...:")
confighandler = FakeConfighandler(pathscheme=pathscheme)
# set basedir for exp:
confighandler.ConfigPaths['exp'] = os.path.join(
'tests', 'test_data', 'test_filestructure',
'labfluence_data_testsetup', '.labfluence.yml')
confserver = FakeConfluenceServer(confighandler=confighandler)
else:
pathscheme = argsns.pathscheme or 'default1'
confighandler = ExpConfigHandler(pathscheme=pathscheme)
try:
confserver = ConfluenceXmlRpcServer(autologin=True,
confighandler=confighandler)
except socket.error:
print "This should not happen; autologin is shielded by try-clause. Perhaps network issues?"
exit(1)
confighandler.Singletons['server'] = confserver
# Test if default func is defined after parsing:
func = getattr(argsns, 'func', None)
if func:
logger.debug("Executing function %s with argsns %s", func, argsns)
ret = func(argsns)
else:
logger.error("No func specified...?")
#logging.getLogger("tkui.views.lims_frame").setLevel(logging.DEBUG)
logging.getLogger(__name__).setLevel(logging.DEBUG)
logger.debug("Loggers setting to debug level...")
pathscheme = argsns.pathscheme or 'test1'
logger.info("Enabling testing environment...")
confighandler = FakeConfighandler(pathscheme=pathscheme)
# set basedir for exp:
confighandler.ConfigPaths['exp'] = os.path.join(
'tests', 'test_data', 'test_filestructure',
'labfluence_data_testsetup', '.labfluence.yml')
server = FakeConfluenceServer(confighandler=confighandler)
else:
logger.debug(
">>>>>> Initiating real confighandler and server... >>>>>>")
pathscheme = argsns.pathscheme or 'default1'
confighandler = ExpConfigHandler(pathscheme=argsns.pathscheme)
logger.debug(
"<<<<< Confighandler instantiated, Initiating server... >>>>>")
# setting autologin=False during init should defer login attempt...
server = ConfluenceXmlRpcServer(autologin=False,
confighandler=confighandler)
server._autologin = True
# Init server and application:
confighandler.Singletons['server'] = server
logger.debug("<<<<< Server instantiated, starting LimsApp... >>>>>")
limsapp = LimsApp(confighandler)
logger.debug("LimsApp instantiated, adding files: %s", argsns.files)
limsapp.FilesToAdd = argsns.files
#limsapp.addEntriesForFiles(argsns.files)
import argparse
parser = argparse.ArgumentParser(
description="Script for persisting server data.")
parser.add_argument('--outputfn',
help="Start labfluence in testing environment.")
argsns = parser.parse_args()
outputfn = argsns.outputfn or "fakeserver_testdata_large.yml"
outputfn = os.path.join(os.path.dirname(__file__), outputfn)
logfmt = "%(levelname)s:%(name)s:%(lineno)s %(funcName)s():\n%(message)s\n"
logfmt = "%(levelname)s:%(name)s:%(lineno)s %(funcName)s(): %(message)s\n"
logging.basicConfig(level=logging.INFO, format=logfmt)
logging.getLogger("__main__").setLevel(logging.DEBUG)
ch = ExpConfigHandler(pathscheme='test1')
server = ConfluenceXmlRpcServer(confighandler=ch)
### IMPORT PAGES and attachment (info) ###
pagesummaries = server.getPages('~scholer')
pages, comments, attachments = dict(), dict(), dict()
for i, summary in enumerate(pagesummaries):
print("Retrieving page {} of {}".format(i, len(pagesummaries)))
pid = summary['id']
if pid in pages:
logger.warning(
"Duplicate pageId! - This is already in the pages dict: '%s'",
pid)
p = server.getPage(pid)
if p:
def __init__(self,
pathscheme=None,
enableHierarchy=False,
readfiles=False):
ExpConfigHandler.__init__(self,
pathscheme=pathscheme,
enableHierarchy=False,
readfiles=False)
expconfigyaml = r"""
exp_series_dir_fmt: '{expid} {exp_titledesc}'
exp_series_regex: (?P<expid>RS[0-9]{3})[_ ]+(?P<exp_titledesc>.+)
exp_subentry_dir_fmt: '{expid}{subentry_idx} {subentry_titledesc} ({datetime:%Y%m%d})'
exp_subentry_regex: (?P<date1>[0-9]{8})?[_ ]*(?P<expid>RS[0-9]{3})-?(?P<subentry_idx>[^_
])[_ ]+(?P<subentry_titledesc>.+?)\s*(\((?P<date2>[0-9]{8})\))?$
exp_subentry_regex_old: (?P<date1>[0-9]{8})?[_ ]*(?P<expid>RS[0-9]{3})-?(?P<subentry_idx>[^_ ])[_ ]+(?P<subentry_titledesc>.+?)\s?(\((?P<date2>[0-9]{8})\))?$
exp_subentryid_fmt: '{expid}{subentry_idx}'
expid_fmt: RS{exp_series_index:03d}
expid_regex: RS(?P<exp_series_index>[0-9]{3,4})
journal_entry_fmt: '[{datetime:%Y%m%d %H:%M:%S}] {text}'
journal_subentry_token_fmt_obsolete: '<p id="{}"></p>'
journal_date_format: '%Y%m%d'
local_exp_ignoreDirs:
- equipment_data_sync
- 2008-2010_Aarhus
- 2011_Aarhus
- 2012_Aarhus
- 2012_Harvard
local_exp_rootDir: .
local_exp_subDir: ./2013_Aarhus
wiki_exp_root_spaceKey: ~scholer
wiki_exp_root_pageId: '524296'
wiki_exp_archive_pageId: '524308'
wiki_exp_new_subentry_token: <h2>Results and discussion</h2>
wiki_exp_new_subentry_insert_regex_fmt: (?P<before_insert><h2>Experimental section</h2>.*?)(?P<after_insert><h4>{expid}[_-]?[{next_subentry_idx}-z].*?</h4>|<h[1-3]>.*?</h[1-3]>|$)
wiki_journal_entry_insert_regex_fmt: '(?P<before_insert><h2>Experimental section</h2>.*?<h4>{expid}{subentry_idx}.*?</h4>.*?)(?P<after_insert><h[1-4]>.+?</h[1-4]>|$)'
wiki_subentry_parse_regex_fmt: '(?P<exp_section_header><h2>Experimental section</h2>).*?(?P<subentry_header><h4>{expid}{subentry_idx}.+?</h4>)(?P<subentry_xhtml>.*?)(?P<next_header><h[1-4]>.+?</h[1-4]>|$)'
wiki_templates_pageIds:
exp_page: '524303'
exp_subentry: '524306'
wiki_template_string_interpolation_mode: 'old'
wiki_template_string_interpolation_mode_comment: can be 'new', 'old' and 'template'. 'new' is curly-braced based string.format; 'old' is %-based moduli substitution and 'template' uses string templates only.
wiki_allow_template_caching: true
wiki_default_newpage_template: 'exp_page'
"""
userconfigyaml = """
app_active_experiments:
- RS102
- RS134
- RS135
app_recent_experiments:
- RS103
crypt_iv: Ko8E4tmJP7SCgLla
wiki_serverparams:
baseurl: http://10.14.40.245:8090
wiki_username: scholer
wiki_lims_pageid: '917542'
"""
# Consider switching to using the 'test1' config, even for this...
# Well, on the other hand... The fake objects are not supposed to touch anything, used for testing.
configyamls = dict(user=userconfigyaml, exp=expconfigyaml)
for cfg, yml in configyamls.items():
newconfig = yaml.load(yml)
self.Configs.setdefault(cfg, dict()).update(
newconfig) # 1-liner, replacing the four below:
#if cfg in self.Configs:
# self.Configs[cfg].update(newconfig)
#else:
# self.Configs[cfg] = newconfig
logger.debug(
"Config '%s' loaded (using hard-coded test configuration...).",
cfg)
self.__expconfigs = dict()