def insert_phenotypes_from_file(conn, phenotypeFile, populationID):
"""Inserts phenotypes into database
This function inserts phenotypes from a file into a database
:param conn: psycopg2 connection
:type conn: connection object
:param phenotypeFile: absolute path to input file
:type phenotypeFile: string
:param populationID: :ref:`population_id <population_class>`
:type populationID: integer
:return: list of phenotype_id
:rtype: list of integers
"""
maize282popID = find.find_population(conn, 'Maize282')
# Read through just the first column of the CSV, ignoring any column
phenotypeRawData = pd.read_csv(phenotypeFile, index_col=0)
insertedPhenoIDs = []
for key, value in tqdm(phenotypeRawData.iteritems(), desc="Phenotypes"):
# print("***********KEY**************:")
# print(key)
traitID = find.find_trait(conn, key)
for line_name, traitval in tqdm(value.iteritems(), desc="Traits"):
lineID = find.find_line(conn, line_name, maize282popID)
if lineID is None:
newline = line(line_name, maize282popID)
lineID = insert_line(conn, newline)
pheno = phenotype(lineID, traitID, traitval)
# print(pheno)
insertedPhenoID = insert_phenotype(conn, pheno)
insertedPhenoIDs.append(insertedPhenoID)
return insertedPhenoIDs
def insert_lines_from_file(conn, lineFile, populationID):
linelist = ph.parse_lines_from_file(lineFile)
insertedLineIDs = []
for linename in linelist:
lineobj = line(linename, populationID)
insertedLineID = insert_line(conn, lineobj)
insertedLineIDs.append(insertedLineID)
return insertedLineIDs
def insert_phenotypes_from_file(conn, phenotypeFile, populationID):
phenotypeRawData = pd.read_csv(phenotypeFile, index_col=0)
insertedPhenoIDs = []
for key, value in phenotypeRawData.iteritems():
print("***********KEY**************:")
print key
traitID = find_trait(conn, key)
for index, traitval in value.iteritems():
print("index:")
print(index)
lineID = find_line(conn, index, maize282popID)
if lineID is None:
newline = line(index, maize282popID)
lineID = insert_line(conn, newline)
print("trait value:")
print(traitval)
pheno = phenotype(lineID, traitID, traitval)
insertedPhenoID = insert_phenotype(conn, pheno)
insertedPhenoIDs.append(insertedPhenoID)
return insertedPhenoIDs
def insert_lines_from_file(conn, lineFile, populationID):
"""Inserts lines into database from a file
This function inserts a lines into a database from a file
:param conn: psycopg2 connection
:type conn: connection object
:param lineFile: absolute path to input file
:type lineFile: string
:param populationID: :ref:`population <population_class>`
:type populationID: integer
:return: list of population_id
:rtype: list of integers
"""
linelist = ph.parse_lines_from_file(lineFile)
insertedLineIDs = []
for linename in tqdm(linelist, desc="Lines"):
lineobj = line(linename, populationID)
insertedLineID = insert_line(conn, lineobj)
insertedLineIDs.append(insertedLineID)
return insertedLineIDs
def new_line():
data = request.get_json()
print 'adding new line to day', request.get_json()['day_id'], 'line', request.get_json()['line_id']
now = datetime.datetime.now()
date = '%s/%s/%s' % (now.month, now.day, now.year)
d = day.query.get(int(data['day_id']))
if (current_user.is_authenticated and current_user.id == d.user_id):
l = line(text='<br>',
date=date,
date_complete=date,
check=False,
important=False,
parent_id=data['line_id'],
user_id=d.user_id,
book_id=d.book_id,
day_id=d.id,
shape=0)
db.session.add(l)
db.session.commit()
print 'commited session'
return jsonify(id = l.id)
return jsonify(id = 0)
print("[ INSERT ]\t(%s)\t%s" % (insertedSpeciesID, str(soybeanSpecies)))
mySpecies = species('maize', 'Zea mays', None, None)
insertedSpeciesID = insert.insert_species(conn, mySpecies)
print("[ INSERT ]\t(%s)\t%s" % (insertedSpeciesID, str(mySpecies)))
maizeSpeciesID = find.find_species(conn, 'maize')
print("[ FIND ]\t(%s)\t%s" % (maizeSpeciesID, '< species: maize >'))
# ADD A HARD-CODED POPULATION TO DB USING insert_population()
myPopulation = population('Maize282', maizeSpeciesID)
insertedPopulationID = insert.insert_population(conn, myPopulation)
print("[ INSERT ]\t(%s)\t%s" % (insertedPopulationID, str(myPopulation)))
maize282popID = find.find_population(conn, 'Maize282')
print("[ FIND ]\t(%s)\t%s" % (maize282popID, '< population: Maize282 >'))
# ADD A HARD-CODED LINE TO DB USING insert_line()
myLine = line(line_name='282set_B73', line_population=maize282popID)
insertedLineID = insert.insert_line(conn, myLine)
print("[ INSERT ]\t(%s)\t%s" % (insertedLineID, str(myLine)))
B73lineID = find.find_line(conn, '282set_B73', maize282popID)
print("[ FIND ]\t(%s)\t%s" % (B73lineID, '< line: Maize282 >'))
# ADD NEW HARD-CODED GENOTYPE_VERSION TO DB
myGenotypeVersion = genotype_version(genotype_version_name='B73 RefGen_v4_AGPv4_Maize282',
genotype_version=315, reference_genome=B73lineID, genotype_version_population=maize282popID)
B73_agpv4_maize282_versionID = insert.insert_genotype_version(conn, myGenotypeVersion)
print("[ INSERT ]\t(%s)\t%s" % (B73_agpv4_maize282_versionID, str(myGenotypeVersion)))
# ADD ALL CHROMOSOMES FOR A SPECIES TO DB
insertedChromosomeIDs = insert.insert_all_chromosomes_for_species(conn, 10, maizeSpeciesID)
print("[ INSERT ]\t%s\t%s" % (insertedChromosomeIDs, '\t10 (sID: %s)' % maizeSpeciesID))
check=False,
important=False,
date="null",
parent_id=2,
text="the '+' adds a child line to the current point",
),
],
]
for points in liners:
l = points[0]
lines.append(
line(text=l['text'],
date=b.date,
date_complete=b.date,
check=l['check'],
important=l['important'],
parent_id=0,
user_id=u.id,
book_id=b.id,
day_id=d['id'],
shape=l['shape']))
db.session.add(lines[-1])
db.session.commit()
pid = lines[-1].id
for point in points[1:]:
l = point
lines.append(
line(text=l['text'],
date=b.date,
date_complete=b.date,
check=l['check'],
important=l['important'],
def __init__(self):
"""Creates the lines object"""
self.red_line = line("red")
self.green_line = line("green")
self.blue_line = line("blue")