def display_controls(compounds,
outfile,
show_all=False,
message=True,
style='screen'):
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
writer = csv.DictWriter(outfile, fieldnames=display_fields)
if style == 'file':
writer.writerow(display_header)
# sort, then group by compound
compounds.sort(key=lambda c: c.sort_by_compound())
for compound_id, compound_group in groupby(compounds,
lambda c: c.COMPOUND_id):
grp = list(compound_group)
show_group = any(c.qa_ok is False for c in grp) or show_all
if show_group and style == 'screen':
writer.writerow(display_header)
for cmpnd in grp:
if cmpnd.qa_ok is False or show_all:
d = cmpnd.display(message)
writer.writerow(
dict((k, fmt(d.get(k))) for k in display_fields))
if show_group and style == 'screen':
writer.writerow(display_empty)
def display_specimens(compounds,
outfile,
show_all=False,
message=True,
style='screen'):
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
writer = csv.DictWriter(outfile, fieldnames=display_fields)
if style == 'file':
writer.writerow(display_header)
# sort, then group by compound
compounds.sort(key=lambda c: c.sort_by_compound())
for compound_id, compound_group in groupby(compounds,
lambda c: c.COMPOUND_id):
if style == 'screen':
writer.writerow(display_header)
# within each compound, group by label
for label, label_group in groupby(compound_group,
lambda c: c.sample_label):
# the 'show_for_qa' method should provide the logic for
# whether to display each compound
for cmpnd in label_group:
if show_all or cmpnd.show_for_qa():
d = cmpnd.display(message)
writer.writerow(
dict((k, fmt(d.get(k))) for k in display_fields))
if style == 'screen':
writer.writerow(display_empty)
def display_results(patient_samples, outfile, style='screen', grouped=True):
"""
For the resulting, we would like the compounds to be divided
in three worksheets: worksheet 1: compound_ids 1-7, worksheet
2: compound_ids 8-14, worksheet 3: compound ids 15-20.
"""
compound_ids, compound_codes = map(list, zip(*COMPOUND_CODES))
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
# create headers for the first row
rows = [dict(label='label')]
rows[0].update(dict(
(i, '%s-%s' % (i, code)) for i, code in COMPOUND_CODES))
for samples in patient_samples:
d = dict(label=samples[0].row_label())
d.update(dict((s.COMPOUND_id, fmt(s.result)) for s in samples))
rows.append(d)
# print the results grouped by worksheet if grouped is True
colgroups = [(0, 7), (7, 14), (14, None)] if grouped else [(0, None)]
for first, last in colgroups:
compounds = list(islice(compound_ids, first, last))
writer = csv.DictWriter(outfile,
fieldnames=['label'] + compounds,
extrasaction='ignore')
for d in rows:
writer.writerow(d)
if style == 'screen' and (first, last) != colgroups[-1]:
writer.writerow({})
def display_results(patient_samples, outfile, style = 'screen', grouped = True):
"""
For the resulting, we would like the compounds to be divided
in three worksheets: worksheet 1: compound_ids 1-7, worksheet
2: compound_ids 8-14, worksheet 3: compound ids 15-20.
"""
compound_ids, compound_codes = map(list, zip(*COMPOUND_CODES))
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
# create headers for the first row
rows =[ dict(label = 'label')]
rows[0].update(dict((i, '%s-%s' % (i, code)) for i, code in COMPOUND_CODES))
for samples in patient_samples:
d = dict(label = samples[0].row_label())
d.update(dict((s.COMPOUND_id, fmt(s.result)) for s in samples))
rows.append(d)
# print the results grouped by worksheet if grouped is True
colgroups = [(0, 7), (7, 14), (14, None)] if grouped else [(0, None)]
for first, last in colgroups:
compounds = list(islice(compound_ids, first, last))
writer = csv.DictWriter(
outfile, fieldnames = ['label'] + compounds, extrasaction = 'ignore')
for d in rows:
writer.writerow(d)
if style == 'screen' and (first, last) != colgroups[-1]:
writer.writerow({})
def display_controls(compounds, outfile, show_all = False, message = True, style = 'screen'):
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
writer = csv.DictWriter(outfile, fieldnames = display_fields)
if style == 'file':
writer.writerow(display_header)
# sort, then group by compound
compounds.sort(key = lambda c: c.sort_by_compound())
for compound_id, compound_group in groupby(compounds, lambda c: c.COMPOUND_id):
grp = list(compound_group)
show_group = any(c.qa_ok is False for c in grp) or show_all
if show_group and style == 'screen':
writer.writerow(display_header)
for cmpnd in grp:
if cmpnd.qa_ok is False or show_all:
d = cmpnd.display(message)
writer.writerow(dict((k, fmt(d.get(k))) for k in display_fields))
if show_group and style == 'screen':
writer.writerow(display_empty)
def display_specimens(compounds, outfile, show_all = False, message = True, style = 'screen'):
nullchar = choose_nullchar[style]
fmt = lambda s: '%.2f' % s if isinstance(s, float) else (s or nullchar)
writer = csv.DictWriter(outfile, fieldnames = display_fields)
if style == 'file':
writer.writerow(display_header)
# sort, then group by compound
compounds.sort(key = lambda c: c.sort_by_compound())
for compound_id, compound_group in groupby(compounds, lambda c: c.COMPOUND_id):
if style == 'screen':
writer.writerow(display_header)
# within each compound, group by label
for label, label_group in groupby(compound_group, lambda c: c.sample_label):
# the 'show_for_qa' method should provide the logic for
# whether to display each compound
for cmpnd in label_group:
if show_all or cmpnd.show_for_qa():
d = cmpnd.display(message)
writer.writerow(dict((k, fmt(d.get(k))) for k in display_fields))
if style == 'screen':
writer.writerow(display_empty)
