py4cytoscape.tables.load_table_data_from_file

load_table_data_from_file(file, first_row_as_column_names=False, start_load_row=1, delimiters='\\,,\t', data_key_column_index=1, table='node', table_key_column='shared name', network=None, base_url='http://127.0.0.1:1234/v1')[source]

Loads data into Cytoscape tables from a tabular file.

This function loads data into Cytoscape node/edge/network tables provided a common key, e.g., name. The tabular file may or may not contain a list of column names as the first row of the file. If not, Cytoscape will pick a name for each column. The data rows can start right after the column name row, or can be offset by some number of lines (which will be ignored). The delimiter that separates column names or data values can be specified. Existing columns with the same names will keep original type but values will be overwritten. Note that because the columns may or may not be named, the column used as a key is specified by its ordinal position amongst the other columns (i.e., the leftmost column is 1).

Note

To load a table file from cloud storage, use the file’s URL and the sandbox_url_to function to download the file to a sandbox, and then use load_table_data_from_file to load it from there.

Parameters

  • file (str) – Name of tabular file in any of the supported formats (e.g., .txt, .csv, .xls, .tsv, etc)

  • first_row_as_column_names (bool) – True if first row contributes column names but no data values; defaults to False

  • start_load_row (int) – 1-based row to start reading data … after column name row, if present; defaults to 1

  • delimiters (str) – comma-separated list of characters that can separate columns … , is a comma, is a tab; defaults to ‘,, ‘

  • data_key_column_index (int) – 1-based column number in tabular file to use a merge key

  • table (str) – name of Cytoscape table to load data into, e.g., node, edge or network; default is “node”

  • table_key_column (str) – name of column in Cytoscape table to use as merge key … must be a column in the root network (i.e., global to all networks in the collection)

  • network (SUID or str or None) – Name or SUID of a network. Default is the “current” network active in Cytoscape.

  • base_url (str) – Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of py4cytoscape.

Returns

SUIDs of tables merged into

Return type

list

Raises

  • CyError – if network name or SUID doesn’t exist, file doesn’t exist, or other parameters are incorrect

  • requests.exceptions.RequestException – if can’t connect to Cytoscape or Cytoscape returns an error

Examples

>>> load_table_data_from_file('data/defaultnode_table.xlsx', first_row_as_column_names=True)
{'mappedTables': [460222, 460260]}
>>> load_table_data_from_file('data/defaultedge_table.csv', first_row_as_column_names=True, table='edge')
{'mappedTables': [460222, 460260]}
>>> load_table_data_from_file('data/defaultnode_table.txt', first_row_as_column_names=True, data_key_column_index=2, table_key_column='COMMON')
{'mappedTables': [460222, 460260]}