def sync_score_row(legacy_row): # Build the object using the minimimum fields count_adult = legacy_row[8] count_larva = legacy_row[9] if count_adult == -1: count_adult = None if count_larva == -1: count_larva = None machine_call = legacy_row[15] if machine_call: selected_for_scoring = True else: selected_for_scoring = False new_score = DevstarScore( experiment=get_experiment(legacy_row[0], legacy_row[1]), area_adult=legacy_row[5], area_larva=legacy_row[6], area_embryo=legacy_row[7], count_adult=count_adult, count_larva=count_larva, is_bacteria_present=legacy_row[16], selected_for_scoring=selected_for_scoring, gi_score_larva_per_adult=legacy_row[17], gi_score_survival=legacy_row[18] ) # Clean the object to populate the fields derived from other fields new_score.clean() ############### # SANITY CHECKS ############### errors = [] new_allele = new_score.experiment.worm_strain.allele if (new_allele != legacy_row[2]): # Deal with case of legacy database using zc310 instead of zu310 if (legacy_row[2] == 'zc310' and new_allele == 'zu310'): pass # Deal with some case sensitivity issues in legacy database # (e.g. see experiment 32405, where the allele is capitalized). # Can't do lower() in all cases because "N2" should always be # capitalized. elif new_allele == legacy_row[2].lower(): pass else: errors.append('allele mismatch') # Deal with case of some experiments having the wrong RNAiPlateID # in the legacy database's RawDataWithScore table. This field is # redundant with the RawData table, and RawData is more trustworthy; # however it is still worthwhile to perform this check in order # to find the mismatches, and to confirm manually that each one # makes sense. new_lp = new_score.experiment.library_stock.plate_id legacy_lp = legacy_row[4].replace('_', '-').replace('zc310', 'zu310') if (legacy_lp != new_lp and new_score.experiment.plate_id not in (461, 8345) and ('vidal-' not in new_lp or legacy_lp != new_lp.split('vidal-')[1])): errors.append('RNAi plate mismatch: {} {}') if new_score.count_embryo != legacy_row[10]: errors.append('embryo count mismatch') if (new_score.embryo_per_adult and legacy_row[8] and legacy_row[8] != -1 and int(new_score.embryo_per_adult) != legacy_row[11]): errors.append('embryo per adult mismatch') if (new_score.larva_per_adult and legacy_row[9] and legacy_row[9] != -1 and int(new_score.larva_per_adult) != legacy_row[12]): errors.append('larva per adult mismatch') if (new_score.survival and not compare_floats_for_equality( new_score.survival, legacy_row[13]) and legacy_row[13] != 0): errors.append('invalid survival') if (new_score.lethality and not compare_floats_for_equality( new_score.lethality, legacy_row[14]) and legacy_row[13] != 0): errors.append('invalid lethality') if errors: raise CommandError( 'DevstarScore for {}:{} had these errors: {}' .format(legacy_row[0], legacy_row[1], errors)) return update_or_save_object( command, new_score, recorded_scores, fields_to_compare, alternate_pk={'experiment': new_score.experiment})
def sync_score_row(legacy_row): # Build the object using the minimimum fields count_adult = legacy_row[8] count_larva = legacy_row[9] if count_adult == -1: count_adult = None if count_larva == -1: count_larva = None machine_call = legacy_row[15] if machine_call: selected_for_scoring = True else: selected_for_scoring = False new_score = DevstarScore(experiment=get_experiment( legacy_row[0], legacy_row[1]), area_adult=legacy_row[5], area_larva=legacy_row[6], area_embryo=legacy_row[7], count_adult=count_adult, count_larva=count_larva, is_bacteria_present=legacy_row[16], selected_for_scoring=selected_for_scoring, gi_score_larva_per_adult=legacy_row[17], gi_score_survival=legacy_row[18]) # Clean the object to populate the fields derived from other fields new_score.clean() ############### # SANITY CHECKS ############### errors = [] new_allele = new_score.experiment.worm_strain.allele if (new_allele != legacy_row[2]): # Deal with case of legacy database using zc310 instead of zu310 if (legacy_row[2] == 'zc310' and new_allele == 'zu310'): pass # Deal with some case sensitivity issues in legacy database # (e.g. see experiment 32405, where the allele is capitalized). # Can't do lower() in all cases because "N2" should always be # capitalized. elif new_allele == legacy_row[2].lower(): pass else: errors.append('allele mismatch') # Deal with case of some experiments having the wrong RNAiPlateID # in the legacy database's RawDataWithScore table. This field is # redundant with the RawData table, and RawData is more trustworthy; # however it is still worthwhile to perform this check in order # to find the mismatches, and to confirm manually that each one # makes sense. new_lp = new_score.experiment.library_stock.plate_id legacy_lp = legacy_row[4].replace('_', '-').replace('zc310', 'zu310') if (legacy_lp != new_lp and new_score.experiment.plate_id not in (461, 8345) and ('vidal-' not in new_lp or legacy_lp != new_lp.split('vidal-')[1])): errors.append('RNAi plate mismatch: {} {}') if new_score.count_embryo != legacy_row[10]: errors.append('embryo count mismatch') if (new_score.embryo_per_adult and legacy_row[8] and legacy_row[8] != -1 and int(new_score.embryo_per_adult) != legacy_row[11]): errors.append('embryo per adult mismatch') if (new_score.larva_per_adult and legacy_row[9] and legacy_row[9] != -1 and int(new_score.larva_per_adult) != legacy_row[12]): errors.append('larva per adult mismatch') if (new_score.survival and not compare_floats_for_equality( new_score.survival, legacy_row[13]) and legacy_row[13] != 0): errors.append('invalid survival') if (new_score.lethality and not compare_floats_for_equality( new_score.lethality, legacy_row[14]) and legacy_row[13] != 0): errors.append('invalid lethality') if errors: raise CommandError( 'DevstarScore for {}:{} had these errors: {}'.format( legacy_row[0], legacy_row[1], errors)) return update_or_save_object( command, new_score, recorded_scores, fields_to_compare, alternate_pk={'experiment': new_score.experiment})