def sync_score_row(legacy_row):
legacy_score_code = legacy_row[2]
legacy_scorer = legacy_row[3]
experiment = get_experiment(legacy_row[0], tile_to_well(legacy_row[1]))
score_code = get_score_code(legacy_score_code)
scorer = get_user(legacy_scorer)
timestamp = get_timestamp_from_ymd(legacy_row[4], legacy_row[5])
if not timestamp:
raise CommandError(
'ERROR: score of experiment {}, well {} '
'could not be converted to a proper datetime'
.format(legacy_row[0], legacy_row[1]))
new_score = ManualScore(
experiment=experiment,
score_code=score_code,
scorer=scorer,
timestamp=timestamp)
return update_or_save_object(
command, new_score, recorded_scores, fields_to_compare,
alternate_pk={'experiment': new_score.experiment,
'score_code': new_score.score_code,
'scorer': new_score.scorer,
'timestamp': new_score.timestamp})
def sync_score_row(legacy_row):
legacy_score_code = legacy_row[2]
legacy_scorer = legacy_row[3]
experiment = get_experiment(legacy_row[0], tile_to_well(legacy_row[1]))
score_code = get_score_code(legacy_score_code)
scorer = get_user(legacy_scorer)
timestamp = get_timestamp_from_ymd(legacy_row[4], legacy_row[5])
if not timestamp:
raise CommandError(
'ERROR: score of experiment {}, well {} '
'could not be converted to a proper datetime'.format(
legacy_row[0], legacy_row[1]))
new_score = ManualScore(experiment=experiment,
score_code=score_code,
scorer=scorer,
timestamp=timestamp)
return update_or_save_object(command,
new_score,
recorded_scores,
fields_to_compare,
alternate_pk={
'experiment': new_score.experiment,
'score_code': new_score.score_code,
'scorer': new_score.scorer,
'timestamp': new_score.timestamp
})
def sync_score_row(legacy_row):
legacy_score_code = legacy_row[2]
legacy_scorer = legacy_row[3]
gene = legacy_row[9]
screen = legacy_row[10]
# Skip some scores entirely (see criteria above)
skip_entirely = ('alejandro', 'katy')
skip_ENH = ('eliana', 'lara')
if ((legacy_scorer == 'Julie' and legacy_score_code != -2)
or (legacy_scorer in skip_entirely)
or (screen == 'ENH' and legacy_scorer in skip_ENH)):
command.stderr.write(
'FYI: Skipping a {} {} score of {} by {}\n'.format(
gene, screen, legacy_score_code, legacy_scorer))
return True
# Convert some scorers to hueyling (see criteria above)
if legacy_scorer == 'Julie' or legacy_scorer == 'expPeople':
command.stderr.write(
'FYI: Converting a {} score by {} to hueyling\n'.format(
legacy_score_code, legacy_scorer))
legacy_scorer = 'hueyling'
# Convert some score codes (see criteria above)
if legacy_score_code == -6:
command.stderr.write('FYI: Converting score from -6 to -7\n')
legacy_score_code = -7
# Following raise exceptions if improperly formatted or not found
experiment = get_experiment(legacy_row[0], tile_to_well(legacy_row[1]))
score_code = get_score_code(legacy_score_code)
scorer = get_user(legacy_scorer)
timestamp = get_timestamp(legacy_row[5], legacy_row[6], legacy_row[7],
legacy_row[8], legacy_row[4])
if not timestamp:
raise CommandError(
'ERROR: score of {} could not be converted to a proper '
'datetime'.format(experiment))
new_score = ManualScore(experiment=experiment,
score_code=score_code,
scorer=scorer,
timestamp=timestamp)
return update_or_save_object(command,
new_score,
recorded_scores,
fields_to_compare,
alternate_pk={
'experiment': new_score.experiment,
'score_code': new_score.score_code,
'scorer': new_score.scorer,
'timestamp': new_score.timestamp
})
def sync_score_row(legacy_row):
legacy_score_code = legacy_row[2]
legacy_scorer = legacy_row[3]
gene = legacy_row[9]
screen = legacy_row[10]
# Skip some scores entirely (see criteria above)
skip_entirely = ('alejandro', 'katy')
skip_ENH = ('eliana', 'lara')
if ((legacy_scorer == 'Julie' and legacy_score_code != -2) or
(legacy_scorer in skip_entirely) or
(screen == 'ENH' and legacy_scorer in skip_ENH)):
command.stderr.write(
'FYI: Skipping a {} {} score of {} by {}\n'
.format(gene, screen, legacy_score_code, legacy_scorer))
return True
# Convert some scorers to hueyling (see criteria above)
if legacy_scorer == 'Julie' or legacy_scorer == 'expPeople':
command.stderr.write(
'FYI: Converting a {} score by {} to hueyling\n'
.format(legacy_score_code, legacy_scorer))
legacy_scorer = 'hueyling'
# Convert some score codes (see criteria above)
if legacy_score_code == -6:
command.stderr.write('FYI: Converting score from -6 to -7\n')
legacy_score_code = -7
# Following raise exceptions if improperly formatted or not found
experiment = get_experiment(legacy_row[0], tile_to_well(legacy_row[1]))
score_code = get_score_code(legacy_score_code)
scorer = get_user(legacy_scorer)
timestamp = get_timestamp(legacy_row[5], legacy_row[6], legacy_row[7],
legacy_row[8], legacy_row[4])
if not timestamp:
raise CommandError(
'ERROR: score of {} could not be converted to a proper '
'datetime'.format(experiment))
new_score = ManualScore(
experiment=experiment,
score_code=score_code,
scorer=scorer,
timestamp=timestamp)
return update_or_save_object(
command, new_score, recorded_scores, fields_to_compare,
alternate_pk={'experiment': new_score.experiment,
'score_code': new_score.score_code,
'scorer': new_score.scorer,
'timestamp': new_score.timestamp})
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})