cyclient.table.get_column

cyclient.table.get_column(self,column=None,table=None,verbose=None)

Get the information about a table column.

  • column (string, optional) Specifies the name of a column in the tab le
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • returns information about a table column

cyclient.table.create_column

cyclient.table.create_column(self,columnName=None,listType=None,table=None,ntype=None,verbose=None)

Appends an additional column of attribute values to the current table.

  • columnName (string, optional) The new column name
  • listType (string, optional) Can be one of integer, long, double, or string.
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • ntype (string, optional) Can be one of integer, long, double, string , or list.

cyclient.table.import_url

cyclient.table.import_url(self,caseSensitiveNetworkCollectionKeys=None, caseSensitiveNetworkKeys=None,dataTypeList=None,\ DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\ delimiters=None,delimitersForDataList=None,firstRowAsColumnNames=None,\ KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,\ keyColumnIndex=None,newTableName=None,startLoadRow=None,\ TargetNetworkCollection=None,TargetNetworkList=None,url=None,\ WhereImportTable=None,verbose=None)

Similar to Import Table this uses a long list of input parameters to specify the attributes of the table, the mapping keys, and the destination table for the input.

  • caseSensitiveNetworkCollectionKeys (string, optional) Determines wh ether capitalization is considered in matching and sorting
  • caseSensitiveNetworkKeys (string, optional) Determines whether capi talization is considered in matching and sorting
  • dataTypeList (string, optional) List of column data types ordered b y column index (e.g. "string,int,long,double,boolean,intlist" or jus t "s,i,l,d,b,il")
  • DataTypeTargetForNetworkCollection (string, optional) Select whethe r to import the data as Node Table Columns, Edge Table Columns, or N etwork Table Columns
  • DataTypeTargetForNetworkList (string, optional) The data type of th e targets
  • delimiters (string, optional) The list of delimiters that separate columns in the table.
  • delimitersForDataList (string, optional) The delimiters between ele ments of list columns in the table.
  • firstRowAsColumnNames (string, optional) If the first imported row contains column names, set this to true.
  • KeyColumnForMapping (string, optional) The column in the network to use as the merge key
  • KeyColumnForMappingNetworkList (string, optional) The column in the network to use as the merge key
  • keyColumnIndex (string, optional) The column that contains the key values for this import. These values will be used to match with the key values in the network.
  • newTableName (string, optional) The title of the new table
  • startLoadRow (string, optional) The first row of the input table to load. This allows the skipping of headers that are not part of the import.
  • TargetNetworkCollection (string, optional) The network collection t o use for the table import
  • TargetNetworkList (string, optional) The list of networks into whic h the table is imported
  • url (string) The URL of the file or resource that provides the tabl e or network to be imported.
  • WhereImportTable (string, optional) Determines what network(s) the imported table will be associated with (if any). A table can be impo rted into a Network Collection, Selected networks or to an unassigne d table.

cyclient.table.list_columns

cyclient.table.list_columns(self,table=None,verbose=None)

Returns the list of columns in the table.

  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • returns list of columns in the table.

cyclient.table.rename_column

cyclient.table.rename_column(self,columnName=None,newColumnName=None,table=None,verbose=None)

Changes the name of a specified column in the table.

  • columnName (string) The name of the column that will be renamed.
  • newColumnName (string) The new name of the column.
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.add_row

cyclient.table.add_row(self,keyValue=None,table=None,verbose=None)

Appends an additional row of empty cells to the current table.

  • keyValue (string, optional) Specifies the primary key of a value in the row of a table Note that network, node, and edge tables must ha ve Long values as keys
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.list_tables

cyclient.table.list(self,includePrivate=None,namespace=None,atype=None,verbose=None)

Returns a list of the table SUIDs associated with the passed network parameter.

  • includePrivate (string, optional) A boolean value determining wheth er to return private as well as public tables
  • namespace (string, optional) An optional argument to contrain outpu t to a single namespace, or ALL
  • atype (string, optional) One of ''network'', ''node'', ''edge'', ''u nattached'', ''all'', to constrain the type of table listed
  • returns list of the table SUIDs associated with the passed network parameter.

cyclient.table.get_value

cyclient.table.get_value(self,column=None,keyValue=None,table=None,verbose=None)

Returns the value from a cell as specified by row and column ids.

  • column (string, optional) Specifies the name of a column in the tab le
  • keyValue (string, optional) Specifies a row of a table using the pr imary key as the indentifier
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • returns value from a cell as specified by row and column ids

cyclient.table.merge

cyclient.table.merge(self,DataTypeTargetForNetworkCollection=None, dataTypeTargetForNetworkList=None,mergeType=None,SourceMergeColumns=None,\ SourceMergeKey=None,SourceTable=None,TargetKeyNetworkCollection=None,\ TargetMergeKey=None,TargetNetworkCollection=None,TargetNetworkList=None,\ UnassignedTable=None,WhereMergeTable=None,verbose=None)

Merge tables together joining around a designated key column. Depending on the arguments, might merge into multiple local tables.

  • DataTypeTargetForNetworkCollection (string, optional) The collectio n of networks where the merged table will reside
  • dataTypeTargetForNetworkList (string, optional)
  • mergeType (string, optional) A choice between ''Copy Columns'' and ''Link To Columns'' that determines if replicates are created
  • SourceMergeColumns (string, optional) A list of columns that will b e brought into the merged table
  • SourceMergeKey (string, optional) The name of the columns that exis ts in both tables and is used to correlate rows
  • SourceTable (string, optional) The name of the table used as the ba se data in the merge
  • TargetKeyNetworkCollection (string, optional) The name of the prima ry column about which the merge is made
  • TargetMergeKey (string, optional)
  • TargetNetworkCollection (string, optional) The group of networks th at will be merged into the source table
  • TargetNetworkList (string, optional) The list of networks where the merged table will be added
  • UnassignedTable (string, optional)
  • WhereMergeTable (string, optional) The destination path of the resu ltant merged table. The choices are ''Network Collection'', ''Select ed Networks'', or ''All Unassigned Tables''.

cyclient.table.list_rows

cyclient.table.list_rows(self,rowList=None,table=None,verbose=None)

Returns the list of primary keys for each of the rows in the specified table.

  • rowList (string, optional) Specifies a list of rows. The pattern CO LUMN:VALUE sets this parameter to any rows that contain the specifie d column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLU MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values. This parameter can also be set to all to include all rows.
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.delete_row

cyclient.table.delete_row(self,keyValue=None,table=None,verbose=None)

Deletes a row from a table.Requires the table name or SUID and the row key.

  • keyValue (string) Specifies the primary key of a value in the row o f a table
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.import_file

cyclient.table.import_file(self,caseSensitiveNetworkCollectionKeys=None, caseSensitiveNetworkKeys=None,dataTypeList=None,\ DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\ delimiters=None,delimitersForDataList=None,afile=None,firstRowAsColumnNames=None,\ KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,keyColumnIndex=None,\ newTableName=None,startLoadRow=None,TargetNetworkCollection=None,\ TargetNetworkList=None,WhereImportTable=None,verbose=None)

This uses a long list of input parameters to specify the attributes of the table, the mapping keys, and the destination table for the input.

  • caseSensitiveNetworkCollectionKeys (string, optional) Determines wh ether capitalization is considered in matching and sorting
  • caseSensitiveNetworkKeys (string, optional) Determines whether capi talization is considered in matching and sorting
  • dataTypeList (string, optional) List of column data types ordered b y column index (e.g. "string,int,long,double,boolean,intlist" or jus t "s,i,l,d,b,il")
  • DataTypeTargetForNetworkCollection (string, optional) Select whethe r to import the data as Node Table Columns, Edge Table Columns, or N etwork Table Columns
  • DataTypeTargetForNetworkList (string, optional) The data type of th e targets
  • delimiters (string, optional) The list of delimiters that separate columns in the table.
  • delimitersForDataList (string, optional) The delimiters between ele ments of list columns in the table.
  • afile (string) The path to the file that contains the table or netwo rk to be imported.
  • firstRowAsColumnNames (string, optional) If the first imported row contains column names, set this to true.
  • KeyColumnForMapping (string, optional) The column in the network to use as the merge key
  • KeyColumnForMappingNetworkList (string, optional) The column in the network to use as the merge key
  • keyColumnIndex (string, optional) The column that contains the key values for this import. These values will be used to match with the key values in the network.
  • newTableName (string, optional) The title of the new table
  • startLoadRow (string, optional) The first row of the input table to load. This allows the skipping of headers that are not part of the import.
  • TargetNetworkCollection (string, optional) The network collection t o use for the table import
  • TargetNetworkList (string, optional) The list of networks into whic h the table is imported
  • WhereImportTable (string, optional) Determines what network(s) the imported table will be associated with (if any). A table can be impo rted into a Network Collection, Selected networks or to an unassigne d table.

cyclient.table.export

cyclient.table.export(self,options=None,OutputFile=None,table=None,verbose=None)

Creates a file with name and writes the table there.

  • options (string, optional) The format of the output file.
  • OutputFile (string, optional) The path of the file to export the ta ble to. Note that the file will be overwritten if it exists.
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.create_table

cyclient.table.create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None)

Adds a new table to the network.

  • keyColumn (string, optional) Specifies the name of a column in the table
  • keyColumnType (string, optional) The syntactical type of the value used in the key

  • title (string, optional) The name of the table used in the current network

  • returns table SUID

cyclient.table.delete_column

cyclient.table.delete_column(self,column=None,table=None,verbose=None)

Remove a column from a table, specified by its name. Returns the name of the column removed.

  • column (string, optional) Specifies the name of a column in the tab le
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.set_title

cyclient.table.set_title(self,table=None,title=None,verbose=None)

Changes the visible identifier of a single table.

  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • title (string, optional) The name of the table used in the current network

cyclient.table.destroy

cyclient.table.destroy(self,table=None,verbose=None)

Removes the specified table from the network.

  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.

cyclient.table.get_row

cyclient.table.get_row(self,keyValue=None,table=None,verbose=None)

Returns the values in each column of a row of a table.

  • keyValue (string, optional) Specifies a row of a table using the pr imary key as the indentifier
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • returns values in each column of a row of a table

cyclient.table.set_values

cyclient.table.set_values(self,columnName=None,rowList=None,table=None,value=None,verbose=None)

Set all the values in the specified list of rows with a single value.

  • columnName (string, optional) Specifies the name of a column in the table
  • rowList (string, optional) Specifies a list of rows. The pattern CO LUMN:VALUE sets this parameter to any rows that contain the specifie d column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLU MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values. This parameter can also be set to all to include all rows.
  • table (string, optional) Specifies a table by table name. If the pr efix SUID: is used, the table corresponding the SUID will be returne d.
  • value (string, optional) The value to set the columns in the select ed rows to. This should be a string value, which will be converted t o the appropriate column type.

cyclient.table.getTable

cyclient.table.getTable(self,columns=None, table=None, network = "current", namespace='default', verbose=VERBOSE)

Gets tables from cytoscape.

  • table table to retrieve eg. node
  • columns columns to retrieve in list format
  • network (string, optional) Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

  • namespace (string, optional) Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.

  • returns a pandas dataframe

cyclient.table.loadTableData

cyclient.table.loadTableData(self,df, df_key='index',table="node", table_key_column = "name", network="current",namespace="default",verbose=False)

Loads tables into cytoscape.

  • df a pandas dataframe to load
  • df_key key column in df, default="index"
  • table target table, default="node"
  • table_key_column table key column, default="name"
  • network (string, optional) Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.
  • namespace (string, optional) Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.

  • verbose print more information

  • returns output of put request

cyclient.table.getTableCount

cyclient.table.getTableCount(verbose=None)

Returns the number of global tables.

  • verbose print more

  • returns 200: successful operation