Class BianaSessionManager

Starts a new BIANA Working session ------ pSessionID: identifier for current session object unification_protocol_name: name of the unification protocol to be used while retrieving data from database dbname: name of the mysql database to be used dbhost: host where mysql database resides dbuser: user for the given mysql database dbpassword: password for the given mysql database and host dbport: port for mysql database connection, if None default value is used out_method: is where biana session manager has to inform about changes

Overrides: object.__init__

Method for selecting a user entity set ------ user_entity_set_id: identifier of user entity set to be selected

#! Not called by any other method

Method to print into the biana interface the description of the User Entity ID identified by "user_entity_set_id"

"format" can be txt or html

Returns list of identifiers of selected user entity sets

#! Not called by any other method

Clears selection of user entity sets

#! Not called by any other method

File either contains an identifier per line
or (attribute_name, identifier) couple on each line

- Designated for use from command line scripts
------
file_name: name of the file identifiers will be read from
identifier_description_list: list of identifiers (or (id_type, id_string) tuples in case id_type is "embedded")
id_type: type of the identifiers in the file, if "embedded" then file contains "attribute_name" "identifier" (seperated by tab) instead of just identifier at each line, if "auto" certain regular expressions will be tried to matched for automatic detection

Return auto-detected type of the given id

Works for ids with strict regular format (such as ENSP00123, AC1423234.1, EC0123123, RAW1_HUMAN, Q1234R, ...)

Randomizes network of a given user entity set. ------ user_entity_set_id: id of the user entity set whose network will be randomized type_randomization: randomization type to be used in network randomization, can be one of the following: "random", "preserve_topology", "preserve_topology_and_node_degree", "preserve_degree_distribution", "preserve_degree_distribution_and_node_degree"

create userEntity objects from given externalEntity ids (or get if already existing) then add them to a userEntitySet ------ identifier_description_list: list with external identifiers of the nodes in the set provided by user id_type: either list of attrubutes defined in EXTERNAL_ENTITY_TABLES or "embedded" meaning identifier_description_list is a list of (id_type, identifier) tuple in the form [(type1, id1), (type2, id2), ..., (typeN, idN)] new_user_entity_set_id: identifier of the set provided by the user attribute_restriction_list: list of tuples provided by the user containing external entity attribute restrictons to be applied. They will be used always in the set (network creation, etc) negative_attribute_restriction_list: list of tuples provided by the user containing attributes that may neve appear in the user entity set. They will be used alwyas in the set.

Creates network of given user entity set adding relations of nodes as edges. ------ user_entity_set_id: identifier of user entity set for which network will be created level: level of the network to be created, network will be expanded till that level include_relations_last_level: include relations between the nodes residing at the last level source_database_version_list: list of (biological database, version) tuples relation_type_list: type of the relations to be used in expansion relation_attribute_restriction_list: tuples of (attribute, value) corresponding to restrictions to be applied on attributes of relations use_self_relations: include relations within the node itself expansion_attribute_list: tuples of (attribute, value_dictionary) corresponding to attributes to be used in relation inference between nodes based on shared attributes - value_dictionary is empty if attribute is not parameterizable expansion_relation_type_list: type of relations to be used in shared attribute based relation inference expansion_level: number of relations (edges) to look further while inferring relations based on shared attributes attribute_network_attribute_list: tuples of (attribute, value) corresponding to attributes to be used while associating nodes with common attributes - value_dictionary is empty if attribute is not parameterizable group_relation_type_list: type of relations that are going to be treated as a group (like pathway, complex, cluster..)

Outputs the ontology in XML Format ------ ontology_name: Ontology to be loaded additional_attributes: Not implemented yet. TO DO!!! (Attribute "id" is the visual ID) out_method: output method to be used if None overwritten by instance default output method

Outputs details of participants involved in a given external entry relation ------ external_entity_relation_id: relation identifier for which participant details will be outputted out_method: output method to be used if None overwritten by instance default output method

Called by BianaGUI/showTableDialog.java via output_external_entity_relation_details method

Gets user defined and BIANA defined node external names - adds substitution functionality to helper ------ user_entity_set_id: identifier for the user entity set information for whose user entity will be fetched user_entity_id: user_entity_id for the node for wich defined attributes are obtained attribute: attribute name corresponding to the attributes to be outputed output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute

Gets user defined and BIANA defined user_entity_id external names ------ user_entity_set_id: identifier for the user entity set information for whose user entity will be fetched user_entity_id: user_entity_id for the user_entity_id for wich defined attributes are obtained attribute: attribute name corresponding to the attributes to be outputed output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute

Outputs information of the network of a given user entity set in sif format. User entity id will be taken as the node identifier. ------ output_path: directory in which Cytoscape attribute files will be generated output_prefix: prefix to be added to the begining of Cytoscape attribute files

Outputs information of the network of a given user entity set ------ output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute output_format: format for the output used in case format is "table"; can be "tabulated" or "xml" include_relation_ids: Boolean to whether display or not relation identifiers include_participant_ids: Boolean to whether display or not relation participant identifiers include_relation_type: Boolean to whether display or not types of relations include_relation_sources: Boolean to whether display or not relation sources include_participant_tags: Boolean to whether display or not tags of participants include_relation_tags: Boolean to whether display or not tags of relations value_seperator: string to seperate consequitive values in the same column only_selected: Boolean to decide whether to output only selected nodes or all nodes (and their interactions) include_command_in_rows: Include the command to output individual relation information at each row substitute_node_attribute_if_not_exists: In case the node does not have a value for a given attribute (s.t. uniprotaccession) this flag make it possible to output another attribute (e.g. geneid) in the same column indicated as attribute:value (e.g. geneid:123123) include_unconnected_nodes: Boolean to whether display or not unconnected nodes

Outputs given user entity. Called by output_user_entity_set_details. ------ user_entity_set: Instace of the user entity set, user entities of which will be outputted user_entity_id_list: list of user entities out_method: method to which output information will be directed attributes: list of attribute names corresponding to the attributes to be outputed include_level_info: Boolean. Defines inclussion of network level information in the output. include_degree_info: Boolean. Defines inclussion of node degree information in the output. inlcude_tags_info: Boolean. Defines inclussion of node tags information in the output. include_tags_linkage_degree_info: #! output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute output_format: format for the output. Either "tabulated" or "xml" include_command_in_rows: Include the command to output individual user entity information at each row

Outputs given user entity set. ------ user_entity_set_id: Identifier of the user entity set, user entities of which will be outputted out_method: method to which output information will be directed attributes: list of attribute names corresponding to the attributes to be outputed include_level_info: Boolean. Defines inclussion of network level information in the output. include_degree_info: Boolean. Defines inclussion of node degree information in the output. inlcude_tags_info: Boolean. Defines inclussion of node tags information in the output. include_tags_linkage_degree_info: #! output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute output_format: format for the output. Either "tabulated" or "xml" only_selected: Boolean to decide whether to output only selected nodes or all nodes. "level" parameter is used only it is False include_command_in_rows: Include the command to output individual user entity information at each row output_only_native_values: If true, for each attribute, shows only values coming from the database providing that attribute by default

Outputs a summary of the external entities given as a list ------ user_entity_id_list: list of user entities out_method: method to which output information will be directed attributes: list of attribute names corresponding to the attributes to be outputed

Called by BianaGUI/showTableDialog.java via output_user_entity_details method

Outputs given user entity (for each attribute, shows only values coming from the database providing that attribute by default). Called by output_user_entity_set_details. ------ user_entity_set: Instace of the user entity set, user entities of which will be outputted user_entity_id_list: list of user entities out_method: method to which output information will be directed attributes: list of attribute names corresponding to the attributes to be outputed include_level_info: Boolean. Defines inclussion of network level information in the output. include_degree_info: Boolean. Defines inclussion of node degree information in the output. inlcude_tags_info: Boolean. Defines inclussion of node tags information in the output. include_tags_linkage_degree_info: #! output_1_value_per_attribute: Boolean. Defines wether 1 or multiple values are outputed per each attribute output_format: format for the output. Either "tabulated" or "xml" include_command_in_rows: Include the command to output individual user entity information at each row

str(x)

Overrides: object.__str__

(inherited documentation)

Outputs sequences associated with given user entity set in fasta format. ------ user_entity_set_id: Id of user entity set containing user entities whose sequence will be outputted only_selected: Includes all user entites if False, otherwise only selected ones out_method: method to which output information will be directed type: either "proteinsequence" or "nucleotidesequence" attributes: list of attribute names corresponding to the attributes to be outputed as sequence header inlcude_tags_info: Boolean. Defines inclussion of node tags information in the output.

Called by BianaGUI/ViewUserEntityDetails.java

Inits the Biana report where a description of the experiment and results will be written

"reportTitle" is the title that will be written on top of the report (default is 'BIANA report')

"reportOutputMethod" is the write method where the report will be written (e.g. file_object.write)
      --> if no streamOutputMethod is given, report is written to stdout

"reportFormat" is the formatting that will be applied to the report
     - 'html': report in html
     - 'txt': report in raw text

"url" is the URL where the interface to BIANA is placed

Closes the Biana report. This method is in charge of writing the closing HTML tags of the report

"reportOutputMethod" is the write method where the report will be written (e.g. file_object.write)
      --> if no streamOutputMethod is given, report is written to stdout

"reportFormat" is the formatting that will be applied to the report
     - 'html': report in html
     - 'txt': report in raw text

Attention!!! This method does not close the file object associated to the report. The user is responsible
             for closing the file (if needed).

This method adds text to the report.

Depending on the 'type' of text, it will be written one way or another

• 'regular' prints standard text
• 'title' prints a section title

This method adds information to the resport about a result file.

'resultFileName' is the name you want to give to this result file

'resultFilePath' is the path (or URL) of the result file (e.g. http://localhost/this_file.html

'associatedText' is the text shown next to the results file name (i.e description of the file)

'bulletedList' is a list of strings that will be shown under the results name as a bulleted list

Creates a new user entity set from given user entities. ------ user_entity_id_list: user entities to be included new user entity set user_entity_set_id: identifier of user entity set to be created external_entity_attribute_restriction_list: Restrictions to not to include user entities with external entities having those restriction values. List of tuples provided by the user containing external entity attribute restrictons to be applied. They will be used always in the set (network creation, etc)

#! Not called by any other method

Selects user entities in a given user entity set by given attributes ------ user_entity_set_id: identifier of user entity set identifier_description_list: list of identifiers (or (identifier, id_type) tuples in case id_type is "embedded") id_type: type of the identifiers in the file, if "embedded" then file contains (attribute_name, identifier) tuples instead of just identifiers external_entity_attribute_restriction_list: Restrictions to not to include user entities with external entities having those restriction values. List of tuples provided by the user containing external entity attribute restrictons to be applied. clear_previous_selection: Boolean to clear or not previous selection

Selects relations in a given user entity set by given attributes ------ user_entity_set_id: identifier of user entity set identifier_description_list: list of identifiers (or (identifier, id_type) tuples in case id_type is "embedded") id_type: type of the identifiers in the file, if "embedded" then file contains (attribute_name, identifier) tuples instead of just identifiers realation_attribute_restrictions: Restrictions to not to include relations with external entity relations having those restriction values. List of tuples provided by the user containing external entity attribute restrictons to be applied. relation_type_list: types of relations to be included in selection

#! Not called by any method

Clusters the user Entities according to an attribute

#! Not called by any other method