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ISPyBClient2.py
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ISPyBClient2.py
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"""
A client for ISPyB Webservices.
"""
import logging
import gevent
import suds; logging.getLogger("suds").setLevel(logging.INFO)
import os
import itertools
import time
import json
from suds.transport.http import HttpAuthenticated
from suds.client import Client
from suds import WebFault
from suds.sudsobject import asdict
from urllib2 import URLError
from HardwareRepository.BaseHardwareObjects import HardwareObject
from datetime import datetime
from collections import namedtuple
from pprint import pformat
# Production web-services: http://160.103.210.1:8080/ispyb-ejb3/ispybWS/
# Test web-services: http://160.103.210.4:8080/ispyb-ejb3/ispybWS/
# The WSDL root is configured in the hardware object XML file.
#_WS_USERNAME, _WS_PASSWORD have to be configured in the HardwareObject XML file.
_WSDL_ROOT = ''
_WS_BL_SAMPLE_URL = _WSDL_ROOT + 'ToolsForBLSampleWebService?wsdl'
_WS_SHIPPING_URL = _WSDL_ROOT + 'ToolsForShippingWebService?wsdl'
_WS_COLLECTION_URL = _WSDL_ROOT + 'ToolsForCollectionWebService?wsdl'
_WS_AUTOPROC_URL = _WSDL_ROOT + 'ToolsForAutoprocessingWebService?wsdl'
_WS_USERNAME = None
_WS_PASSWORD = None
_CONNECTION_ERROR_MSG = "Could not connect to ISPyB, please verify that " + \
"the server is running and that your " + \
"configuration is correct"
SampleReference = namedtuple('SampleReference', ['code',
'container_reference',
'sample_reference',
'container_code'])
def trace(fun):
def _trace(*args):
log_msg = "lims client " + fun.__name__ + " called with: "
for arg in args[1:]:
try:
log_msg += pformat(arg, indent = 4, width = 80) + ', '
except:
pass
logging.getLogger("ispyb_client").debug(log_msg)
result = fun(*args)
try:
result_msg = "lims client " + fun.__name__ + \
" returned with: " + pformat(result, indent = 4, width = 80)
except:
pass
logging.getLogger("ispyb_client").debug(result_msg)
return result
return _trace
def in_greenlet(fun):
def _in_greenlet(*args, **kwargs):
log_msg = "lims client " + fun.__name__ + " called with: "
for arg in args[1:]:
try:
log_msg += pformat(arg, indent = 4, width = 80) + ', '
except:
pass
logging.getLogger("ispyb_client").debug(log_msg)
task = gevent.spawn(fun, *args)
if kwargs.get("wait", False):
task.get()
return _in_greenlet
def utf_encode(res_d):
for key in res_d.iterkeys():
if isinstance(res_d[key], dict):
utf_encode(res_d)
if isinstance(res_d[key], suds.sax.text.Text):
try:
res_d[key] = res_d[key].encode('utf8', 'ignore')
except:
pass
return res_d
class ISPyBClient2(HardwareObject):
"""
Web-service client for ISPyB.
"""
def __init__(self, name):
HardwareObject.__init__(self, name)
self.ldapConnection=None
self.beamline_name = "unknown"
self.__shipping = None
self.__collection = None
self.__tools_ws = None
self.__translations = {}
self.__disabled = False
self.authServerType = None
self.loginType = None
self.loginTranslate = None
self.ws_username = None
self.ws_password = None
def init(self):
"""
Init method declared by HardwareObject.
"""
self.authServerType = self.getProperty('authServerType') or "ldap"
if self.authServerType == "ldap":
# Initialize ldap
self.ldapConnection=self.getObjectByRole('ldapServer')
if self.ldapConnection is None:
logging.getLogger("HWR").debug('LDAP Server is not available')
self.loginType = self.getProperty("loginType") or "proposal"
self.loginTranslate = self.getProperty("loginTranslate") or True
self.session_hwobj = self.getObjectByRole('session')
self.beamline_name = self.session_hwobj.beamline_name
self.ws_username = self.getProperty('ws_username')
if not self.ws_username:
self.ws_username = _WS_USERNAME
self.ws_password = self.getProperty('ws_password')
if not self.ws_password:
self.ws_password = _WS_PASSWORD
try:
# ws_root is a property in the configuration xml file
if self.ws_root:
global _WSDL_ROOT
global _WS_BL_SAMPLE_URL
global _WS_SHIPPING_URL
global _WS_COLLECTION_URL
global _WS_SCREENING_URL
global _WS_AUTOPROC_URL
_WSDL_ROOT = self.ws_root.strip()
_WS_BL_SAMPLE_URL = _WSDL_ROOT + \
'ToolsForBLSampleWebService?wsdl'
_WS_SHIPPING_URL = _WSDL_ROOT + \
'ToolsForShippingWebService?wsdl'
_WS_COLLECTION_URL = _WSDL_ROOT + \
'ToolsForCollectionWebService?wsdl'
_WS_AUTOPROC_URL = _WSDL_ROOT + \
'ToolsForAutoprocessingWebService?wsdl'
t1 = HttpAuthenticated(username = self.ws_username,
password = self.ws_password)
t2 = HttpAuthenticated(username = self.ws_username,
password = self.ws_password)
t3 = HttpAuthenticated(username = self.ws_username,
password = self.ws_password)
t4 = HttpAuthenticated(username = self.ws_username,
password = self.ws_password)
try:
self.__shipping = Client(_WS_SHIPPING_URL, timeout = 3,
transport = t1, cache = None)
self.__collection = Client(_WS_COLLECTION_URL, timeout = 3,
transport = t2, cache = None)
self.__tools_ws = Client(_WS_BL_SAMPLE_URL, timeout = 3,
transport = t3, cache = None)
self.__autoproc_ws = Client(_WS_AUTOPROC_URL, timeout = 3,
transport = t4, cache = None)
# ensure that suds do not create those files in tmp
self.__shipping.set_options(cache=None)
self.__collection.set_options(cache=None)
self.__tools_ws.set_options(cache=None)
self.__autoproc_ws.set_options(cache=None)
except URLError:
logging.getLogger("ispyb_client")\
.exception(_CONNECTION_ERROR_MSG)
return
except:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
return
# Add the porposal codes defined in the configuration xml file
# to a directory. Used by translate()
try:
proposals = self.session_hwobj['proposals']
for proposal in proposals:
code = proposal.code
self.__translations[code] = {}
try:
self.__translations[code]['ldap'] = proposal.ldap
except AttributeError:
pass
try:
self.__translations[code]['ispyb'] = proposal.ispyb
except AttributeError:
pass
try:
self.__translations[code]['gui'] = proposal.gui
except AttributeError:
pass
except IndexError:
pass
def get_login_type(self):
return self.loginType
def translate(self, code, what):
"""
Given a proposal code, returns the correct code to use in the GUI,
or what to send to LDAP, user office database, or the ISPyB database.
"""
try:
translated = self.__translations[code][what]
except KeyError:
translated = code
return translated
def clear_daily_email(self):
raise NotImplementedException("Depricated ?")
def send_email(self):
raise NotImplementedException("Depricated ?")
@trace
def get_proposal_by_username(self, username):
proposal_code = ""
proposal_number = 0
empty_dict = {'Proposal': {}, 'Person': {}, 'Laboratory': {}, 'Session': {}, 'status': {'code':'error'}}
if not self.__shipping:
logging.getLogger("ispyb_client").\
warning("Error in get_proposal: Could not connect to server," + \
" returning empty proposal")
return empty_dict
try:
try:
person = self.__shipping.service.findPersonByLogin(username, os.environ["SMIS_BEAMLINE_NAME"])
except WebFault, e:
logging.getLogger("ispyb_client").warning(e.message)
person = {}
try:
proposal = self.__shipping.service.findProposalByLoginAndBeamline(username, os.environ["SMIS_BEAMLINE_NAME"])
if not proposal:
logging.getLogger("ispyb_client").warning("Error in get_proposal: No proposal has been found to the user, returning empty proposal")
return empty_dict
proposal_code = proposal.code
proposal_number = proposal.number
except WebFault, e:
logging.getLogger("ispyb_client").warning(e.message)
proposal = {}
try:
lab = self.__shipping.service.findLaboratoryByCodeAndNumber(proposal_code, proposal_number)
except WebFault, e:
logging.getLogger("ispyb_client").warning(e.message)
lab = {}
try:
res_sessions = self.__collection.service.\
findSessionsByProposalAndBeamLine(proposal_code,
proposal_number,
os.environ["SMIS_BEAMLINE_NAME"])
sessions = []
# Handels a list of sessions
for session in res_sessions:
if session is not None :
try:
session.startDate = \
datetime.strftime(session.startDate,
"%Y-%m-%d %H:%M:%S")
session.endDate = \
datetime.strftime(session.endDate,
"%Y-%m-%d %H:%M:%S")
except:
pass
sessions.append(utf_encode(asdict(session)))
except WebFault, e:
logging.getLogger("ispyb_client").warning(e.message)
sessions = []
except URLError:
logging.getLogger("ispyb_client").warning(_CONNECTION_ERROR_MSG)
return empty_dict
logging.getLogger("ispyb_client").info( str(sessions) )
return {'Proposal': utf_encode(asdict(proposal)),
'Person': utf_encode(asdict(person)),
'Laboratory': utf_encode(asdict(lab)),
'Session': sessions,
'status': {'code':'ok'}}
@trace
def get_proposal(self, proposal_code, proposal_number):
"""
Returns the tuple (Proposal, Person, Laboratory, Session, Status).
Containing the data from the coresponding tables in the database
the status of the database operations are returned in Status.
:param proposal_code: The proposal code
:type proposal_code: str
:param proposal_number: The proposal number
:type propsoal_number: int
:returns: The dict (Proposal, Person, Laboratory, Sessions, Status).
:rtype: dict
"""
if self.__shipping:
try:
try:
person = self.__shipping.service.\
findPersonByProposal(proposal_code,
proposal_number)
if not person:
person = {}
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
person = {}
try:
proposal = self.__shipping.service.\
findProposal(proposal_code,
proposal_number)
if proposal:
proposal.code = proposal_code
else:
return {'Proposal': {},
'Person': {},
'Laboratory': {},
'Session': {},
'status': {'code':'error'}}
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
proposal = {}
try:
lab = None
#lab = self.__shipping.service.findLaboratoryByCodeAndNumber(proposal_code, proposal_number)
lab = self.__shipping.service.findLaboratoryByProposal(proposal_code, proposal_number)
if not lab:
lab = {}
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
lab = {}
try:
res_sessions = self.__collection.service.\
findSessionsByProposalAndBeamLine(proposal_code,
proposal_number,
self.beamline_name)
sessions = []
# Handels a list of sessions
for session in res_sessions:
if session is not None :
try:
session.startDate = \
datetime.strftime(session.startDate,
"%Y-%m-%d %H:%M:%S")
session.endDate = \
datetime.strftime(session.endDate,
"%Y-%m-%d %H:%M:%S")
except:
pass
sessions.append(utf_encode(asdict(session)))
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
sessions = []
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
return {'Proposal': {},
'Person': {},
'Laboratory': {},
'Session': {},
'status': {'code':'error'}}
return {'Proposal': utf_encode(asdict(proposal)),
'Person': utf_encode(asdict(person)),
'Laboratory': utf_encode(asdict(lab)),
'Session': sessions,
'status': {'code':'ok'}}
else:
logging.getLogger("ispyb_client").\
exception("Error in get_proposal: Could not connect to server," + \
" returning empty proposal")
return {'Proposal': {},
'Person': {},
'Laboratory': {},
'Session': {},
'status': {'code':'error'}}
@trace
def get_proposal_by_username(self, username):
proposal_code = ""
proposal_number = 0
empty_dict = {'Proposal': {}, 'Person': {}, 'Laboratory': {}, 'Session': {}, 'status': {'code':'error'}}
if not self.__shipping:
logging.getLogger("ispyb_client").\
warning("Error in get_proposal: Could not connect to server," + \
" returning empty proposal")
return empty_dict
try:
try:
person = self.__shipping.service.findPersonByLogin(username, self.beamline_name)
except WebFault, e:
logging.getLogger("ispyb_client").warning(str(e))
person = {}
try:
proposal = self.__shipping.service.findProposalByLoginAndBeamline(username, self.beamline_name)
if not proposal:
logging.getLogger("ispyb_client").warning("Error in get_proposal: No proposal has been found to the user, returning empty proposal")
return empty_dict
proposal_code = proposal.code
proposal_number = proposal.number
except WebFault, e:
logging.getLogger("ispyb_client").warning(str(e))
proposal = {}
try:
lab = self.__shipping.service.findLaboratoryByCodeAndNumber(proposal_code, proposal_number)
except WebFault, e:
logging.getLogger("ispyb_client").warning(str(e))
lab = {}
try:
res_sessions = self.__collection.service.\
findSessionsByProposalAndBeamLine(proposal_code,
proposal_number,
self.beamline_name)
sessions = []
# Handels a list of sessions
for session in res_sessions:
if session is not None :
try:
session.startDate = \
datetime.strftime(session.startDate,
"%Y-%m-%d %H:%M:%S")
session.endDate = \
datetime.strftime(session.endDate,
"%Y-%m-%d %H:%M:%S")
except:
pass
sessions.append(utf_encode(asdict(session)))
except WebFault, e:
logging.getLogger("ispyb_client").warning(str(e))
sessions = []
except URLError:
logging.getLogger("ispyb_client").warning(_CONNECTION_ERROR_MSG)
return empty_dict
logging.getLogger("ispyb_client").info( str(sessions) )
return {'Proposal': utf_encode(asdict(proposal)),
'Person': utf_encode(asdict(person)),
'Laboratory': utf_encode(asdict(lab)),
'Session': sessions,
'status': {'code':'ok'}}
@trace
def get_session_local_contact(self, session_id):
"""
Retrieves the person entry associated with the session id <session_id>
:param session_id:
:type session_id: int
:returns: Person object as dict.
:rtype: dict
"""
if self.__shipping:
try:
person = self.__shipping.service.\
findPersonBySessionIdLocalContact(session_id)
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
person = {}
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
person = {}
if person is None:
return {}
else:
utf_encode(asdict(person))
else:
logging.getLogger("ispyb_client").\
exception("Error in get_session_local_contact: Could not get " + \
"local contact")
return {}
def _ispybLogin (self, loginID, psd):
# to do, check how it is done in EMBL
return True, "True"
def login (self,loginID, psd, ldap_connection=None):
if ldap_connection is None:
ldap_connection = self.ldapConnection
login_name=loginID
prpopsal_code = ""
prpopsal_number = ""
# For porposal login, split the loginID to code and numbers
if self.loginType == "proposal" :
proposal_code = "".join(itertools.takewhile(lambda c: not c.isdigit(), loginID))
proposal_number = loginID[len(proposal_code):]
# if translation of the loginID is needed, need to be tested by ESRF
if self.loginTranslate is True:
login_name=self.translate(proposal_code,'ldap')+str(proposal_number)
# Authentication
if self.authServerType == 'ldap':
logging.getLogger('HWR').debug('LDAP login')
ok, msg=ldap_connection.login(login_name,psd)
elif self.authServerType == 'ispyb':
logging.getLogger('HWR').debug('ISPyB login')
ok, msg=self._ispybLogin(login_name,psd)
else:
raise Exception ("Authentication server type is not defined")
if not ok:
msg="%s." % msg.capitalize()
# refuse Login
return {'status':{ "code": "error", "msg": msg }, 'Proposal': None, 'session': None}
# login succeed, get proposal and sessions
#logging.getLogger('HWR').debug('Logged in: querying ISPyB database...')
if self.loginType == "proposal":
# get the proposal ID
prop=self.get_proposal(proposal_code,proposal_number)
elif self.loginType =="user":
prop=self.get_proposal_by_username(loginID)
# Check if everything went ok
prop_ok=True
try:
prop_ok=(prop['status']['code']=='ok')
except KeyError:
prop_ok=False
if not prop_ok:
#todo
msg = "Couldn't contact the ISPyB database server: you've been logged as the local user.\nYour experiments' information will not be stored in ISPyB"
return {'status':{ "code": "ispybDown", "msg": msg }, 'Proposal': None, 'session': None}
# logging.getLogger('HWR').debug('Proposal is fine, get sessions from ISPyB...')
# logging.getLogger('HWR').debug(prop)
proposal=prop['Proposal']
todays_session=self.get_todays_session(prop)
# logging.getLogger('HWR').debug(todays_session)
return {'status':{ "code": "ok", "msg": msg }, 'Proposal': proposal,
'session': todays_session,
"local_contact": self.get_session_local_contact(todays_session['session']['sessionId']),
"person": prop['Person'],
"laboratory": prop['Laboratory']}
def get_todays_session(self, prop):
try:
sessions=prop['Session']
except KeyError:
sessions=None
# Check if there are sessions in the proposal
todays_session=None
if sessions is None or len(sessions)==0:
pass
else:
# Check for today's session
for session in sessions:
beamline=session['beamlineName']
start_date="%s 00:00:00" % session['startDate'].split()[0]
end_date="%s 23:59:59" % session['endDate'].split()[0]
try:
start_struct=time.strptime(start_date,"%Y-%m-%d %H:%M:%S")
except ValueError:
pass
else:
try:
end_struct=time.strptime(end_date,"%Y-%m-%d %H:%M:%S")
except ValueError:
pass
else:
start_time=time.mktime(start_struct)
end_time=time.mktime(end_struct)
current_time=time.time()
# Check beamline name
if beamline==self.beamline_name:
# Check date
if current_time>=start_time and current_time<=end_time:
todays_session=session
break
new_session_flag= False
if todays_session is None:
# a newSession will be created, UI (Qt, web) can decide to accept the newSession or not
new_session_flag= True
current_time=time.localtime()
start_time=time.strftime("%Y-%m-%d 00:00:00", current_time)
end_time=time.mktime(current_time)+60*60*24
tomorrow=time.localtime(end_time)
end_time=time.strftime("%Y-%m-%d 07:59:59", tomorrow)
# Create a session
new_session_dict={}
new_session_dict['proposalId']=prop['Proposal']['proposalId']
new_session_dict['startDate']=start_time
new_session_dict['endDate']=end_time
new_session_dict['beamlineName']=self.beamline_name
new_session_dict['scheduled']=0
new_session_dict['nbShifts']=3
new_session_dict['comments']="Session created by the BCM"
session_id=self.create_session(new_session_dict)
new_session_dict['sessionId']=session_id
todays_session=new_session_dict
localcontact=None
logging.getLogger('HWR').debug('create new session')
else:
session_id=todays_session['sessionId']
logging.getLogger('HWR').debug('getting local contact for %s' % session_id)
localcontact=self.get_session_local_contact(session_id)
is_inhouse = self.session_hwobj.is_inhouse(prop['Proposal']["code"], prop['Proposal']["number"])
return {"session": todays_session,"new_session_flag":new_session_flag, "is_inhouse": is_inhouse}
@trace
def store_data_collection(self, *args, **kwargs):
try:
return self._store_data_collection(*args, **kwargs)
except gevent.GreenletExit:
# aborted by user ('kill')
raise
except:
# if anything else happens, let upper level process continue
# (not a fatal error), but display exception still
logging.exception("Could not store data collection")
return (0,0,0)
def _store_data_collection(self, mx_collection, beamline_setup = None):
"""
Stores the data collection mx_collection, and the beamline setup
if provided.
:param mx_collection: The data collection parameters.
:type mx_collection: dict
:param beamline_setup: The beamline setup.
:type beamline_setup: dict
:returns: None
"""
if self.__disabled:
return (0,0,0)
if self.__collection:
data_collection = ISPyBValueFactory().\
from_data_collect_parameters(self.__collection, mx_collection)
if beamline_setup:
lims_beamline_setup = ISPyBValueFactory.\
from_bl_config(self.__collection, beamline_setup)
lims_beamline_setup.synchrotronMode = \
data_collection.synchrotronMode
self.store_beamline_setup(mx_collection['sessionId'],
lims_beamline_setup )
detector_params = \
ISPyBValueFactory().detector_from_blc(beamline_setup,
mx_collection)
detector = self.find_detector(*detector_params)
detector_id = 0
if detector:
detector_id = detector.detectorId
data_collection.detectorId = detector_id
collection_id = self.__collection.service.\
storeOrUpdateDataCollection(data_collection)
return (collection_id, detector_id)
else:
logging.getLogger("ispyb_client").\
exception("Error in store_data_collection: could not connect" + \
" to server")
@trace
def store_beamline_setup(self, session_id, beamline_setup):
"""
Stores the beamline setup dict <beamline_setup>.
:param session_id: The session id that the beamline_setup
should be associated with.
:type session_id: int
:param beamline_setup: The dictonary with beamline settings.
:type beamline_setup: dict
:returns beamline_setup_id: The database id of the beamline setup.
:rtype: str
"""
blSetupId = None
if self.__collection:
session = {}
try:
session = self.get_session(session_id)
except:
logging.getLogger("ispyb_client").exception(\
"ISPyBClient: exception in store_beam_line_setup")
else:
if session is not None:
try:
blSetupId = self.__collection.service.\
storeOrUpdateBeamLineSetup(beamline_setup)
session['beamLineSetupId'] = blSetupId
self.update_session(session)
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
except URLError:
logging.getLogger("ispyb_client").\
exception(_CONNECTION_ERROR_MSG)
else:
logging.getLogger("ispyb_client").\
exception("Error in store_beamline_setup: could not connect" + \
" to server")
return blSetupId
#@trace
@in_greenlet
def update_data_collection(self, mx_collection, wait=False):
"""
Updates the datacollction mx_collection, this requires that the
collectionId attribute is set and exists in the database.
:param mx_collection: The dictionary with collections parameters.
:type mx_collection: dict
:returns: None
"""
if self.__disabled:
return
if self.__collection:
if 'collection_id' in mx_collection:
try:
# Update the data collection group
self.store_data_collection_group(mx_collection)
data_collection = ISPyBValueFactory().\
from_data_collect_parameters(self.__collection, mx_collection)
self.__collection.service.\
storeOrUpdateDataCollection(data_collection)
except WebFault:
logging.getLogger("ispyb_client").\
exception("ISPyBClient: exception in update_data_collection")
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
else:
logging.getLogger("ispyb_client").error("Error in update_data_collection: " + \
"collection-id missing, the ISPyB data-collection is not updated.")
else:
logging.getLogger("ispyb_client").\
exception("Error in update_data_collection: could not connect" + \
" to server")
@trace
def update_bl_sample(self, bl_sample):
"""
Creates or stos a BLSample entry.
:param sample_dict: A dictonary with the properties for the entry.
:type sample_dict: dict
"""
if self.__disabled:
return {}
if self.__tools_ws:
try:
status = self.__tools_ws.service.\
storeOrUpdateBLSample(bl_sample)
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
status = {}
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
return status
else:
logging.getLogger("ispyb_client").\
exception("Error in update_bl_sample: could not connect to server")
#@in_greenlet
def store_image(self, image_dict):
"""
Stores the image (image parameters) <image_dict>
:param image_dict: A dictonary with image pramaters.
:type image_dict: dict
:returns: None
"""
if self.__disabled:
return
if self.__collection:
if 'dataCollectionId' in image_dict:
try:
image_id = self.__collection.service.storeOrUpdateImage(image_dict)
return image_id
except WebFault:
logging.getLogger("ispyb_client").\
exception("ISPyBClient: exception in store_image")
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
else:
logging.getLogger("ispyb_client").error("Error in store_image: " + \
"data_collection_id missing, could not store image in ISPyB")
else:
logging.getLogger("ispyb_client").\
exception("Error in store_image: could not connect to server")
def __find_sample(self, sample_ref_list, code = None, location = None):
"""
Returns the sample with the matching "search criteria" <code> and/or
<location> with-in the list sample_ref_list.
The sample_ref object is defined in the head of the file.
:param sample_ref_list: The list of sample_refs to search.
:type sample_ref: list
:param code: The vial datamatrix code (or bar code)
:param type: str
:param location: A tuple (<basket>, <vial>) to search for.
:type location: tuple
"""
for sample_ref in sample_ref_list:
if code and location:
if sample_ref.code == code and \
sample_ref.container_reference == location[0] and \
sample_ref.sample_reference == location[1]:
return sample_ref
elif code:
if sample_ref.code == code:
return sample_ref
elif location:
if sample_ref.container_reference == location[0] and \
sample_ref.sample_reference == location[1]:
return sample_ref
return None
@trace
def get_samples(self, proposal_id, session_id):
response_samples = None
if self.__tools_ws:
try:
response_samples = self.__tools_ws.service.\
findSampleInfoLightForProposal(proposal_id,
self.beamline_name)
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
else:
logging.getLogger("ispyb_client").\
exception("Error in get_samples: could not connect to server")
return response_samples
@trace
def get_session_samples(self, proposal_id, session_id, sample_refs):
"""
Retrives the list of samples associated with the session <session_id>.
The samples from ISPyB is cross checked with the ones that are
currently in the sample changer.
The datamatrix code read by the sample changer is used in case
of conflict.
:param proposal_id: ISPyB proposal id.
:type proposal_id: int
:param session_id: ISPyB session id to retreive samples for.
:type session_id: int
:param sample_refs: The list of samples currently in the
sample changer. As a list of sample_ref
objects
:type sample_refs: list (of sample_ref objects).
:returns: A list with sample_ref objects.
:rtype: list
"""
if self.__tools_ws:
sample_references = []
session = self.get_session(session_id)
response_samples = []
for sample_ref in sample_refs:
sample_reference = SampleReference(*sample_ref)
sample_references.append(sample_reference)
try:
response_samples = self.__tools_ws.service.\
findSampleInfoLightForProposal(proposal_id,
self.beamline_name)
except WebFault, e:
logging.getLogger("ispyb_client").exception(str(e))
except URLError:
logging.getLogger("ispyb_client").exception(_CONNECTION_ERROR_MSG)
samples = []
for sample in response_samples:
try:
loc = [None, None]
try:
loc[0]=int(sample.containerSampleChangerLocation)
except:
pass
try:
loc[1]=int(sample.sampleLocation)
except:
pass
# Unmatched sample, just catch and do nothing