askomics package

Submodules

askomics.ask_view module

class askomics.ask_view.AskView(request)

Bases: object

This class contains method calling the libaskomics functions using parameters from the js web interface (body variable)

add_endpoint()
api_key()
checkAdminSession()
checkAuthSession()
checkuser()
cleantmpdirectory()
connect_galaxy()
deletCsv()
deleteShortcut()

Delete a shortcut definition into the triplestore

delete_endpoints()
delete_graph()
delete_uploaded_files()
delete_user()

Delete a user from the user graphs, and remove all his data

deljob()

Remove job from database

empty_database()

Delete all named graphs and their metadatas

enable_endpoints()
getSparqlQueryInTextFormat()

Build a request from a json whith the following contents :variates,constraintesRelations

getUserAbstraction()

Get the user asbtraction to manage relation inside javascript

get_data_from_galaxy()
get_galaxy_file_content()
get_my_infos()

Get all infos about a user

get_uploaded_files()
get_users_infos()

For each users store in the triplesore, get their username, email, and admin status

get_value()

Build a request from a json whith the following contents :variates,constraintesRelations

guess_csv_header_type()

Guess the headers type of a csv file

Used for the asko-cli scripts

Returns:list of guessed types
Return type:dict
importShortcut()

Import a shortcut definition into the triplestore

list_endpoints()

Return a list with all endpoint using by a askomics session.

list_user_graph()

Return a list with all the named graphs of a user.

listjob()

Get all jobs recorded in database

load_bed_into_graph()

Load a BED file into the triplestore

load_data_into_graph()

Load tabulated files to triple store according to the type of the columns set by the user

load_gff_into_graph()

Load GFF file into the triplestore

load_remote_data_into_graph()

Load tabulated files to triple store according to the type of the columns set by the user

load_ttl_into_graph()

Load TTL file into the triplestore

lock_user()

Change a user lock status

login()
login_api()
login_api_gie()
logout()

Log out the user, reset the session

nbUsers()
prefix_uri()

get prefix uri for each entities finded in he header file

preview_ttl()

Convert tabulated files to turtle according to the type of the columns set by the user

renew_apikey()
send2galaxy()
serverinformations()
set_admin()

Change a user admin status

signup()
source_files_overview()

Get preview data for all the available files

start_points()

Get the nodes being query starters

statistics()

Get stats

update_mail()

Chage email of a user

update_passwd()

Change password of a user

uploadCsv()
uploadTtl()
upload_galaxy_file()

askomics.upload module

class askomics.upload.FileUpload(request)

Bases: object

delete()
fileinfo(name)
filepath(name)
get()
get_file_size(new_file)
options()
post()
upload()
validate(new_file)

askomics.views module

askomics.views.my_view(request)

Module contents

askomics.main(global_config, **settings)

This function returns a Pyramid WSGI application.