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kb_ObjectUtilities.spec
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kb_ObjectUtilities.spec
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/*
** A KBase module: kb_ObjectUtilities
**
** This module contains basic utility Apps for manipulating objects (other than Reads and Sets, which are found in kb_ReadsUtilities and kb_SetUtilities)
*/
module kb_ObjectUtilities {
/*
** The workspace object refs are of form:
**
** objects = ws.get_objects([{'ref': params['workspace_id']+'/'+params['obj_name']}])
**
** "ref" means the entire name combining the workspace id and the object name
** "id" is a numerical identifier of the workspace or object, and should just be used for workspace
** "name" is a string identifier of a workspace or object. This is received from Narrative.
*/
typedef string workspace_name;
typedef string file_path;
typedef string sequence;
typedef string data_obj_name;
typedef string data_obj_ref;
typedef int bool;
/* KButil_copy_object()
**
** Method for copying an object of a limited number of common types
*/
typedef structure {
workspace_name workspace_name;
data_obj_ref input_ref;
string output_name;
} KButil_copy_object_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
} KButil_copy_object_Output;
funcdef KButil_copy_object (KButil_copy_object_Params params) returns (KButil_copy_object_Output) authentication required;
/* KButil_Concat_MSAs()
**
** Method for Concatenating MSAs into a combined MSA
*/
typedef structure {
workspace_name workspace_name;
data_obj_ref input_refs;
data_obj_name output_name;
string desc;
bool blanks_flag;
} KButil_Concat_MSAs_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
} KButil_Concat_MSAs_Output;
funcdef KButil_Concat_MSAs (KButil_Concat_MSAs_Params params) returns (KButil_Concat_MSAs_Output) authentication required;
/* KButil_count_ws_objects()
**
** Method for counting number of workspace objects when data panel fails
*/
typedef structure {
workspace_name workspace_name;
list<string> object_types;
bool verbose;
} KButil_count_ws_objects_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
mapping<string,list<data_obj_ref>> ws_obj_refs;
} KButil_count_ws_objects_Output;
funcdef KButil_count_ws_objects (KButil_count_ws_objects_Params params) returns (KButil_count_ws_objects_Output) authentication required;
/* KButil_hide_ws_objects()
**
** Method for hiding workspace objects in bulk
*/
typedef structure {
workspace_name workspace_name;
list<string> object_types;
bool verbose;
bool hide_all;
} KButil_hide_ws_objects_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
} KButil_hide_ws_objects_Output;
funcdef KButil_hide_ws_objects (KButil_hide_ws_objects_Params params) returns (KButil_hide_ws_objects_Output) authentication required;
/* KButil_unhide_ws_objects()
**
** Method for unhiding workspace objects in bulk
*/
typedef structure {
workspace_name workspace_name;
list<string> object_types;
bool verbose;
bool unhide_all;
} KButil_unhide_ws_objects_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
} KButil_unhide_ws_objects_Output;
funcdef KButil_unhide_ws_objects (KButil_unhide_ws_objects_Params params) returns (KButil_unhide_ws_objects_Output) authentication required;
/* KButil_update_genome_species_name()
**
** Method for adding/changing Genome objects species names
*/
typedef structure {
workspace_name workspace_name;
list<data_obj_ref> input_refs;
string species_names;
} KButil_update_genome_species_name_Params;
typedef structure {
data_obj_name report_name;
data_obj_ref report_ref;
list<data_obj_ref> updated_object_refs;
} KButil_update_genome_species_name_Output;
funcdef KButil_update_genome_species_name (KButil_update_genome_species_name_Params params) returns (KButil_update_genome_species_name_Output) authentication required;
/* KButil_update_genome_fields_from_files()
**
** Method for adding/changing values in Genome object fields, from files
*/
typedef structure {
workspace_name workspace_name;
/*list<data_obj_ref> input_refs;*/
file_path target_list_file;
file_path object_newname_file;
file_path species_name_file;
file_path source_file;
file_path domain_file;
file_path genome_type_file;
file_path release_file;
file_path taxonomy_hierarchy_file;
file_path taxonomy_ncbi_id_file;
file_path genome_qual_scores_file;
file_path gene_functions_file;
bool keep_spoofed_mRNAs;
} KButil_update_genome_fields_from_files_Params;
typedef structure {
list<data_obj_ref> updated_object_refs;
} KButil_update_genome_fields_from_files_Output;
funcdef KButil_update_genome_fields_from_files (KButil_update_genome_fields_from_files_Params params) returns (KButil_update_genome_fields_from_files_Output) authentication required;
/* KButil_update_genome_lineage_from_files()
**
** Method for adding/changing values in Genome object tax and lineage fields, from files
*/
typedef structure {
workspace_name workspace_name;
/*list<data_obj_ref> input_refs;*/
file_path target_list_file;
file_path release_file;
file_path taxonomy_hierarchy_file;
bool delete_old_taxon_assignments;
} KButil_update_genome_lineage_from_files_Params;
typedef structure {
list<data_obj_ref> updated_object_refs;
} KButil_update_genome_lineage_from_files_Output;
funcdef KButil_update_genome_lineage_from_files (KButil_update_genome_lineage_from_files_Params params) returns (KButil_update_genome_lineage_from_files_Output) authentication required;
/* KButil_update_genome_features_from_file()
**
** Method for adding values to Genome object features, from file
*/
typedef structure {
/*workspace_name workspace_name;*/ /* taken from genome or ama */
file_path feature_update_file;
file_path genome_ref_map;
} KButil_update_genome_features_from_file_Params;
typedef structure {
list<data_obj_ref> updated_object_refs;
} KButil_update_genome_features_from_file_Output;
funcdef KButil_update_genome_features_from_file (KButil_update_genome_features_from_file_Params params) returns (KButil_update_genome_features_from_file_Output) authentication required;
};