Utils

class modules.gemtractor.utils.Utils

Bases: object

some utils that may make life easier

static _Utils__cleanup(root_dir, max_age)

get rid of old stuff

will remove cached and unused file in a certain directory

Parameters:

• root_dir (str) – the directory to traverse
• max_age (int) – the max age of files that will survive

static _Utils__collect_stats(root_dir)

collect some stats about the files below root_dir

Parameters:root_dir (str) – the root directory Returns:tupel of number of files and the sum of their sizes Return type:typel of ints

_Utils__logger = <Logger modules.gemtractor.utils (INFO)>

static _create_dir(d)

create some directory (recursively) the pythonic way

Parameters:d (str) – the directories to create

static _get_bigg_model_base_path(model_id)

get the path at which we would store a BiGG model

Parameters:model_id (str) – the model’s id Returns:the path to the cached BiGG model Return type:str

static _get_biomodel_base_path(model_id)

get the path at which we would store a biomodels model

Parameters:model_id (str) – the model’s id Returns:the path to the cached model from biomodels Return type:str

static add_model_note(model, filter_species, filter_reactions, filter_enzymes, filter_enzyme_complexes, remove_reaction_enzymes_removed, remove_ghost_species, discard_fake_enzymes, remove_reaction_missing_species, removing_enzyme_removes_complex)

‘ annotate the model to indicate that is has been generated using the GEMtractor

adds a note to the model note..

Parameters:

• model (libsbml:Model) – the SBML model
• filter_species (list of str) – species identifiers to get rid of
• filter_reactions (list of str) – reaction identifiers to get rid of
• filter_enzymes (list of str) – enzyme identifiers to get rid of
• filter_enzyme_complexes (list of str) – enzyme-complex identifiers to get rid of, every list-item should be of format: ‘A + B + gene42’
• remove_reaction_enzymes_removed (bool) – should we remove a reaction if all it’s genes were removed?
• remove_ghost_species (bool) – should species be removed, that do not participate in any reaction anymore - even though they might be required in other entities?
• discard_fake_enzymes (bool) – should fake enzymes (implicitly assumes enzymes, if no enzymes are annotated to a reaction) be removed?
• remove_reaction_missing_species (bool) – remove a reaction if one of the participating genes was removed?
• removing_enzyme_removes_complex (bool) – if an enzyme is removed, should also all enzyme complexes be removed in which it participates?

static cleanup()

get rid of old stuff

will remove cached and unused file for the whole instance

static collect_stats(response_obj)

collect some health stats about this instance

will check cached and uploaded files and their sizes

Parameters:response_obj (dict) – the response object to attach the information to

static create_generated_file_web(sessionid)

get a file to generate something for the user

Parameters:sessionid (str) – the users’ session id Returns:path to a file that is safe for the user Return type:str

static del_session_key(request, context, key)

delete a certain session key as requested by the user

Parameters:

• request (django:HttpRequest) – django’s HTTP request object
• context (dict) – the context object
• key (str) – the key to delete

static get_bigg_model(model_id, force=False)

Retrieve a specific model from BiGG

uses _get_bigg_model_base_path() to determine the path to the model

Parameters:

• model_id (str) – the model’s id
• force (bool) – should the cache be renewed even if it’s not too old?

Returns:

the path to the model

Return type:

str

Raises:

• HTTPError – if there was a problem contacting BiGG
• URLError – if there was a problem contacting BiGG

static get_bigg_models(force=False)

Retrieve the list of models from BiGG

Parameters:

force (bool) – should the cache be renewed even if it’s not too old?

Returns:

the list of models at BiGG

Return type:

json object

Raises:

• HTTPError – if there was a problem contacting BiGG
• URLError – if there was a problem contacting BiGG
• JSONDecodeError – if the BiGG answer is no proper JSON

static get_biomodel(model_id, force=False)

Retrieve a specific model from biomodels

uses _get_biomodel_base_path() to determine the path to the model

Parameters:

• model_id (str) – the model’s id
• force (bool) – should the cache be renewed even if it’s not too old?

Returns:

the path to the model

Return type:

str

Raises:

• HTTPError – if there was a problem contacting biomodels
• URLError – if there was a problem contacting biomodels

static get_biomodels(force=False)

Retrieve the list of models from Biomodels

Parameters:

force (bool) – should the cache be renewed even if it’s not too old?

Returns:

the list of models for our search at Biomodels

Return type:

json object

Raises:

• HTTPError – if there was a problem contacting Biomodels
• URLError – if there was a problem contacting Biomodels
• JSONDecodeError – if the Biomodels answer is no proper JSON

static get_model_path(model_type, model_id, sessionid)

get the path to a model

depending on how the model was obtained (downloaded from BiGG/biomodels or uploaded) the path may differ

Parameters:

• model_type (str) – the obtain type (see constants.Constants)
• model_id (str) – the model’s id
• sessionid (str) – the user’s session id - only relevant if the model was uploaded

Returns:

the path to the model

Return type:

str

static get_upload_path(sessionid)

get a file to upload something for the user

Parameters:sessionid (str) – the users’ session id Returns:path to a file that is safe for the user Return type:str

static human_readable_bytes(byt)

convert a size in bytes to a human readable string

Parameters:byt (int) – the byte size Returns:the human readable size (such as 1 MB or 2.7 TB) Return type:str

static rm_cached_bigg_model(model_id)

remove a cached BiGG model

uses _get_bigg_model_base_path() to determine the path to the model

Parameters:model_id (str) – the model’s id

static rm_cached_biomodel(model_id)

remove a cached model from biomodels

uses _get_biomodel_base_path() to determine the path to the model

Parameters:model_id (str) – the model’s id

static serve_file(file_path, file_name, file_type)

deliver a file to the user

Parameters:

• file_path (str) – the path to the file to deliver
• file_name (str) – the name to suggest to the client (browser)
• file_type (str) – the mime type to suggest to the client (browser)