def get_population_flags(list_only=False, dictionary=False, table=False):
"""Return all population flags available in the PopFlags class.
:list_only: Return a simple text list instead of a list of Phenotype
objects.
:dictionary: Return a dictionary of population=>ID
:table: Return a pretty table for printing.
"""
flags = _ref.PopFlag.__dict__['__members__']
if list_only:
return [i for i in flags.values()]
elif dictionary:
return {k: v for k, v in flags.items()}
elif table:
return _tb(
[['FLAG', 'Label']] + [[int(v), k] for k, v in flags.items()],
headers='firstrow', tablefmt='grid'
)
else:
return flags
def get_populations(list_only=False, dictionary=False, table=False):
"""Return all populatons from the Population table.
:list_only: Return a simple text list instead of a list of Phenotype
objects.
:dictionary: Return a dictionary of population=>ID
:table: Return a pretty table for printing.
"""
s, _ = _db.get_session()
q = s.query(t.Population).all()
if list_only:
return [i.population for i in q]
elif dictionary:
return {i.population: i.id for i in q}
elif table:
ids = [i.id for i in q]
pops = [i.population for i in q]
return _tb({'ID': ids, 'Population': pops}, headers='keys',
tablefmt='grid')
else:
return q
def get_phenotypes(list_only=False, dictionary=False, table=False):
"""Return all phenotypes from the Phenotype table.
:list_only: Return a simple text list instead of a list of Phenotype
objects.
:dictionary: Return a dictionary of phenotype=>ID
:table: Return a pretty table for printing.
"""
s, _ = _db.get_session()
q = s.query(t.Phenotype).order_by('phenotype').all()
if list_only:
return [i.phenotype for i in q]
elif dictionary:
return {i.phenotype: i.id for i in q}
elif table:
ids = [i.id for i in q]
phenos = [i.phenotype for i in q]
return _tb({'ID': ids, 'Phenotype': phenos}, headers='keys',
tablefmt='grid')
else:
return q
def get_phenotype_categories(list_only=False, dictionary=False, table=False):
"""Return all phenotype categories from the PhenoCats table.
:list_only: Return a simple text list instead of a list of Phenotype
objects.
:dictionary: Return a dictionary of phenotype=>ID
:table: Return a pretty table for printing.
"""
s, _ = _db.get_session()
q = s.query(t.PhenoCats).order_by('category').all()
if list_only:
return [i.category for i in q]
elif dictionary:
return {i.category: i.id for i in q}
elif table:
ids = [i.id for i in q]
cats = [i.category for i in q]
aliases = [i.alias for i in q]
return _tb({'ID': ids, 'Category': cats, 'Alias': aliases},
headers='keys', tablefmt='grid')
else:
return q
def display_columns(self, display_as='table', write=False):
"""Return all columns in the table nicely formatted.
Display choices:
table: A formatted grid-like table
tab: A tab delimited non-formatted version of table
list: A string list of column names
Args:
display_as: {table,tab,list}
write: If true, print output to console, otherwise return
string.
Returns:
A formatted string or None
"""
cols = self.columns
if display_as == 'table':
out = _tb(
[['Column', 'Description', 'Type']] +\
[[k, v[1], v[0]] for k, v in cols.items()],
headers='firstrow', tablefmt='grid'
)
elif display_as == 'tab':
out = '\n'.join(
['\t'.join(['Column', 'Description', 'Type'])] +\
['\t'.join([k, v[1], v[0]]) for k, v in cols.items()],
)
elif display_as == 'list':
out = '\n'.join([i[1] for i in cols.values()])
else:
raise Exception("'display_as' must be one of {table,tab,list}")
if write:
print(out)
else:
return out