def batch_modify_label(csv_id):
csv_file = CSVFile.query.get_or_404(csv_id)
args = modify_label_list_schema.load(request.json or {})
row_column_dump_schema = CSVFileSchema(
only=['rows', 'columns', 'group_levels'])
for change in args['changes']:
index = change['index']
label = change['label']
context = change['context']
if context == AXIS_NAME_TYPES.ROW:
row = TableRow.query.get_or_404((csv_id, index))
if label == TABLE_ROW_TYPES.INDEX:
csv_file.header_row_index = index
setattr(row, 'row_type', label)
db.session.add(row)
elif context == AXIS_NAME_TYPES.COLUMN:
column = TableColumn.query.get_or_404((csv_id, index))
if label == TABLE_COLUMN_TYPES.INDEX:
csv_file.key_column_index = index
elif label == TABLE_COLUMN_TYPES.GROUP:
csv_file.group_column_index = index
setattr(column, 'column_type', label)
db.session.add(column)
db.session.add(csv_file)
try:
db.session.commit()
return jsonify(row_column_dump_schema.dump(csv_file))
except Exception:
db.session.rollback()
raise
from viime.models import CSVFileSchema, db
csv_file_schema = CSVFileSchema()
def generate_csv_file(data):
csv_file = csv_file_schema.load({
'table': data,
'name': 'test_csv_file.csv'
})
db.session.add(csv_file)
db.session.commit()
return csv_file
def test_no_header(app):
with app.test_request_context():
csv = generate_csv_file("""
a,1,2,3
b,4,5,6
c,7,8,9
""")
db.session.commit()
csv.header_row_index = None
db.session.commit()
assert csv.headers == ['col1', 'col2', 'col3', 'col4']
assert list(csv.indexed_table.columns) == ['col2', 'col3', 'col4']
def _serialize_csv_file(csv_file):
csv_file_schema = CSVFileSchema()
return csv_file_schema.dump(csv_file)
def test_merge_files(client):
csv_file_schema = CSVFileSchema()
csv_file1 = csv_file_schema.load({
'table': 'id,g,col1,col2\nrow1,g,0.5,2.0\nrow2,g,1.5,0\nrow3,h,3,-1.0\n',
'name': 'test_csv_file1.csv'
})
csv_file2 = csv_file_schema.load({
'table': 'id,g,col3,col4\nrow1,g,0.5,2.0\nrow2,g,1.5,0\nrow4,h,3,-1.0\n',
'name': 'test_csv_file2.csv'
})
db.session.add_all([csv_file1, csv_file2])
db.session.flush()
validated1 = ValidatedMetaboliteTable.create_from_csv_file(csv_file1)
validated2 = ValidatedMetaboliteTable.create_from_csv_file(csv_file2)
db.session.add_all([validated1, validated2])
db.session.commit()
resp = client.post(url_for('csv.merge_csv_files'),
json={
'name': 'merge',
'description': '',
'method': 'simple',
'datasets': [csv_file1.id, csv_file2.id]
})
assert resp.status_code == 201
expected_column_types = [{
'column_header': 'nan',
'column_index': 0,
'column_type': 'key',
'subtype': None,
'meta': None
}, {
'column_header': 'g',
'column_index': 1,
'column_type': 'group',
'subtype': None,
'meta': None
}, {
'column_header': 'g_1',
'column_index': 2,
'column_type': 'group',
'subtype': None,
'meta': None
}, {
'column_header': 'col1',
'column_index': 3,
'column_type': 'measurement',
'subtype': None,
'meta': None
}, {
'column_header': 'col2',
'column_index': 4,
'column_type': 'measurement',
'subtype': None,
'meta': None
}, {
'column_header': 'col3',
'column_index': 5,
'column_type': 'measurement',
'subtype': None,
'meta': None
}, {
'column_header': 'col4',
'column_index': 6,
'column_type': 'measurement',
'subtype': None,
'meta': None
}]
expected_row_types = [{
'row_index': 0,
'row_name': 'nan',
'row_type': 'header',
'subtype': None,
'meta': None
}, {
'row_index': 1,
'row_name': 'Data Source',
'row_type': 'metadata',
'subtype': 'categorical',
'meta': dict(levels=[dict(name='DS1', label='test_csv_file1.csv', color='#8dd3c7'),
dict(name='DS2', label='test_csv_file2.csv', color='#ffffb3')])
}, {
'row_index': 2,
'row_name': 'row1',
'row_type': 'sample',
'subtype': None,
'meta': None
}, {
'row_index': 3,
'row_name': 'row2',
'row_type': 'sample',
'subtype': None,
'meta': None
}]
assert resp.json['columns'] == expected_column_types
assert resp.json['rows'] == expected_row_types
# test remerge which shouldn't change a thing
resp = client.post(url_for('csv.remerge_csv_file', csv_id=resp.json['id']))
assert resp.status_code == 200
assert resp.json['columns'] == expected_column_types
assert resp.json['rows'] == expected_row_types