synapse_io¶

Module: `synapse_io`¶

Input/output functions to read and write Synapse tables.

Authors:

Arno Klein, 2015 (arno@sagebase.org) http://binarybottle.com

Functions¶

mhealthx.synapse_io.copy_synapse_table(synapse_table_id, synapse_project_id, table_name='', remove_columns=[], username='', password='')¶

Copy Synapse table to another Synapse project.

synapse_table_id : string: Synapse ID for table to copy
synapse_project_id : string: copy table to project with this Synapse ID
table_name : string: schema name of table
remove_columns : list of strings: column headers for columns to be removed
username : string: Synapse username (only needed once on a given machine)
password : string: Synapse password (only needed once on a given machine)

table_data : Pandas DataFrame: Synapse table contents
table_name : string: schema name of table
synapse_project_id : string: Synapse ID for project within which table is to be written

>>> from mhealthx.synapse_io import copy_synapse_table
>>> synapse_table_id = 'syn4590865'
>>> synapse_project_id = 'syn4899451'
>>> table_name = 'Copy of ' + synapse_table_id
>>> remove_columns = ['audio_audio.m4a', 'audio_countdown.m4a']
>>> username = ''
>>> password = ''
>>> table_data, table_name, synapse_project_id = copy_synapse_table(synapse_table_id, synapse_project_id, table_name, remove_columns, username, password)

mhealthx.synapse_io.extract_rows(synapse_table, save_path=None, limit=None, username='', password='')¶

Extract rows from a Synapse table.

synapse_table : string or Schema: a synapse ID or synapse table Schema object
save_path : string: save rows as separate files in this path, unless empty or None
limit : integer or None: limit to number of rows returned by the query
username : string: Synapse username (only needed once on a given machine)
password : string: Synapse password (only needed once on a given machine)

rows : list of pandas Series: each row of a Synapse table
row_files: list of strings: file names corresponding to each of the rows

>>> from mhealthx.synapse_io import extract_rows
>>> import synapseclient
>>> syn = synapseclient.Synapse()
>>> syn.login()
>>> synapse_table = 'syn4590865'
>>> save_path = '.'
>>> limit = 3
>>> username = ''
>>> password = ''
>>> rows, row_files = extract_rows(synapse_table, save_path, limit, username='', password='')

mhealthx.synapse_io.feature_file_to_synapse_table(feature_file, raw_feature_file, source_file_id, provenance_activity_id, command, command_line, synapse_table_id, username='', password='')¶

Upload files and file handle IDs to Synapse.

feature_file : string: path to file to upload to Synapse
raw_feature_file : string: path to file to upload to Synapse
source_file_id : string: Synapse file handle ID to source file used to generate features
provenance_activity_id : string: Synapse provenance activity ID
command : string: name of command run to generate raw feature file
command_line : string: full command line run to generate raw feature file
synapse_table_id : string: Synapse table ID for table to store file handle IDs, etc.
username : string: Synapse username (only needed once on a given machine)
password : string: Synapse password (only needed once on a given machine)

>>> from mhealthx.synapse_io import feature_file_to_synapse_table
>>> feature_file = '/Users/arno/Local/wav/test1.wav'
>>> raw_feature_file = '/Users/arno/Local/wav/test1.wav'
>>> source_file_id = ''
>>> provenance_activity_id = ''
>>> command_line = 'SMILExtract -C blah -I blah -O blah'
>>> synapse_table_id = 'syn4899451'
>>> username = ''
>>> password = ''
>>> feature_file_to_synapse_table(feature_file, raw_feature_file, source_file_id, provenance_activity_id, command_line, synapse_table_id, username, password)

mhealthx.synapse_io.read_files_from_row(synapse_table, row, column_name, out_path=None, username='', password='')¶

Read data from a row of a Synapse table.

synapse_table : string or Schema: a synapse ID or synapse table Schema object
row : pandas Series or string: row of a Synapse table converted to a Series or csv file
column_name : string: name of file handle column
out_path : string or None: a local path in which to store downloaded files. If None, stores them in (~/.synapseCache)
username : string: Synapse username (only needed once on a given machine)
password : string: Synapse password (only needed once on a given machine)

row : pandas Series: same as passed in: row of a Synapse table as a file or Series
filepath : string: downloaded file (full path)

>>> from mhealthx.synapse_io import extract_rows, read_files_from_row
>>> import synapseclient
>>> syn = synapseclient.Synapse()
>>> syn.login()
>>> synapse_table = 'syn4590865'
>>> save_path = '.'
>>> limit = 3
>>> username = ''
>>> password = ''
>>> rows, row_files = extract_rows(synapse_table, save_path, limit, username='', password='')
>>> column_name = 'audio_audio.m4a' #, 'audio_countdown.m4a']
>>> out_path = '.'
>>> for i in range(3):
>>>     row = rows[i]
>>>     row, filepath = read_files_from_row(synapse_table, row, column_name, out_path, username, password)
>>>     print(row)

mhealthx.synapse_io.write_synapse_table(table_data, synapse_project_id, table_name='', username='', password='')¶

Write data to a Synapse table.

table_data : Pandas DataFrame: Synapse table contents
synapse_project_id : string: Synapse ID for project within which table is to be written
table_name : string: schema name of table
username : string: Synapse username (only needed once on a given machine)
password : string: Synapse password (only needed once on a given machine)

>>> from mhealthx.synapse_io import read_synapse_table_files, write_synapse_table
>>> in_synapse_table_id = 'syn4590865'
>>> synapse_project_id = 'syn4899451'
>>> column_names = []
>>> download_limit = None
>>> out_path = '.'
>>> username = ''
>>> password = ''
>>> table_data, files = read_synapse_table_files(in_synapse_table_id, column_names, download_limit, out_path, username, password)
>>> table_name = 'Contents of ' + in_synapse_table_id
>>> write_synapse_table(table_data, synapse_project_id, table_name, username, password)

synapse_io¶

Module: synapse_io¶

Functions¶

Module: `synapse_io`¶