def insert_screening(c, session_id = None): if session_id is None: session_id = core.retrieve_visit_id(cursor, 'cm5952-5') dcg_id = insert_dcgroup(c, session_id) params = mxscreening.get_screening_params() params['dcgid'] = dcg_id params['program_version'] = 'EDNA 1.0' params['short_comments'] = 'ENDAStrategy1' params['comments'] = 'param1 = 1.2, param2 = 2.06' id = mxscreening.insert_screening(c, params.values()) assert id is not None assert id > 0 return id
def insert_screening_input(c): session_id = core.retrieve_visit_id(cursor, 'cm5952-5') s_id = insert_screening(c, session_id) params = mxscreening.get_screening_input_params() params['screening_id'] = s_id params['beamx'] = 20.2 params['beamy'] = 25.6 params['rms_err_lim'] = 2.09 params['min_fraction_indexed'] = 0.10 params['max_fraction_rejected'] = 0.30 params['min_signal2noise'] = 0.98 id = mxscreening.insert_screening_input(c, params.values()) assert id is not None assert id > 0 return id
conn = None cursor = None conf_file = sys.argv[1] if opts.db is None or opts.db == "prod": conn = DBConnection("prod", conf_file=conf_file) elif opts.db == "dev": conn = DBConnection("dev", conf_file=conf_file) elif opts.db == "test": conn = DBConnection("test", conf_file=conf_file) else: exit(1, "ERROR: Invalid database") cursor = conn.get_cursor() # Find the id for the visit visitid = core.retrieve_visit_id(cursor, opts.visit) result = None if visitid is not None or opts.movieid is not None: # EMMovieId, blsessionId,blsampleId,movieFile,p_NOImages,frameLength,totalExposure,magnification,samplePixSize,dosePerFrame,totalDose,runStatus,comments,runDirectory,binning,particleDiameter,pixelSize,boxSize,minResolution,maxResolution, minDefocus, maxDefocus, defocusStepSize, amountAstigmatism, extractSize, starttime, endtime # Store a movie data collection ... params = mxacquisition.get_data_collection_params() params["parentid"] = opts.groupid params["visitid"] = visitid params["sampleid"] = opts.sampleid params["detectorid"] = opts.microscopeid if opts.filename is not None: imgdir = opts.filename[:opts.filename.rfind("/")]
def retrieve_visit_id(c): id = core.retrieve_visit_id(c, 'mx12788-35') assert id == 344095