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Entity ID table importer

IMPORTER
Typing name :  TASK.gws_gena.EntityIDTableImporter Brick :  gws_gena v

Import file to Entity ID table

EntityIDTableImporter class

Allows to import a csv or xls file and create a EntityIDTable resource object.

Your File must have at least:

  • a column with the ID of the entity For example:
id name
CHEBI:57972 L-alanine

Input

File

Output

Entity ID table
Generic table of entity IDs (e.g. CheBI IDs, Rhea IDs, EC Numbers, User-defined IDs, ...)

Configuration

file_format

Optional

File format

Type : stringAllowed values : auto  xlsx  xls  csv  tsv  tab  txt  Default value : auto

delimiter

Optional

Delimiter character. Only for parsing CSV files

Type : stringAllowed values : auto  tab  space  ,  ;  Default value : auto

header

Optional

Row to use as the column names. By default the first row is used (i.e. header=0). Set header=-1 to not read column names.

Type : int

format_header_names

Optional

If true, the column and row names are formatted to remove special characters and spaces (only '_' are allowed).

Type : bool

index_column

OptionalAdvanced parameter

Column to use as the row names. By default no index is used (i.e. index_column=-1).

Type : intDefault value : -1

decimal

OptionalAdvanced parameter

Character to recognize as decimal point (e.g. use ‘,’ for European/French data).

Type : stringDefault value : .

nrows

OptionalAdvanced parameter

Number of rows to import. Useful to read piece of data.

Type : int

comment

OptionalAdvanced parameter

Character used to comment lines. Set empty to disable comment lines.

Type : stringDefault value : #

encoding

OptionalAdvanced parameter

Encoding of the file, 'auto' for automatic detection.

Type : stringDefault value : auto

metadata_columns

OptionalAdvanced parameter

Columns data to use to tag the rows of the table

Type : ListMaximum occurrences number : -1

column

OptionalAdvanced parameter

Metadata column to use to tag rows

Type : string

keep_in_table

OptionalAdvanced parameter

Set True to keep the column in the final table; False otherwise

Type : boolDefault value : true

id_column

Optional

The column containing the IDs entities

Type : stringDefault value : id

name_column

Optional

The column containing the names of the entities

Type : string

id_type

Optional

The expected ID type

Type : stringAllowed values :   chebi  rhea