askomics.api package

Submodules

askomics.api.admin module

Admin routes

askomics.api.admin.get_users()

Get all users

Returns:users: list of all users info error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.admin.set_admin()

change admin status of a user

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.admin.set_blocked()

Change blocked status of a user

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.admin.set_quota()

Change quota of a user

Returns:users: updated users error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.auth module

Authentication routes

askomics.api.auth.admin_required(f)

Login required function

askomics.api.auth.login()

Log a user

Returns:Information about the logged user
Return type:json
askomics.api.auth.login_api_key(key)

Log user with his API key

Parameters:key (string) – User API key
Returns:Information about the logged user
Return type:json
askomics.api.auth.login_required(f)

Login required function

askomics.api.auth.logout()

Logout the current user

Returns:no username and logged false
Return type:json
askomics.api.auth.signup()

Register a new user

Returns:Info about the user
Return type:json
askomics.api.auth.update_apikey()

Update the user apikey

Returns:The user with his new apikey
Return type:json
askomics.api.auth.update_galaxy()

Update the user apikey

Returns:The user with his new apikey
Return type:json
askomics.api.auth.update_password()

Update the user passord

Returns:The user
Return type:json
askomics.api.auth.update_profile()

Update user profile (names and email)

Returns:The updated user
Return type:json

askomics.api.catch_url module

Catch_all route

askomics.api.catch_url.catch_all(path)

Return all routes to home

Parameters:path (str) – Original path
Returns:Redirect to route /
Return type:redirect

askomics.api.datasets module

Api routes

askomics.api.datasets.delete_datasets()

Delete some datasets (db and triplestore) with a celery task

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.datasets.get_datasets()

Get datasets information

Returns:datasets: list of all datasets of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.datasets.toogle_public()

Toggle public status of a dataset

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.file module

Api routes

askomics.api.file.delete_files()

Delete files

Returns:files: list of all files of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.file.get_files()

Get files info of the logged user

Returns:files: list of all files of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.file.get_preview()

Get files preview

Returns:previewFiles: preview of selected files error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.file.integrate()

Integrate a file

Returns:task_id: celery task id error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.file.serve_file(path, user_id, username)

Serve a static ttl file of a user

Parameters:
  • path (string) – The file path to serve
  • user_id (int) – user id
  • username (string) – username
Returns:

the file

Return type:

file

askomics.api.file.upload_chunk()

Upload a file chunk

Returns:path: name of the local file. To append the next chunk into it error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.file.upload_url()

Upload a distant file with an URL

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.galaxy module

Api routes

askomics.api.galaxy.get_dataset_content()

Download a galaxy datasets into AskOmics

Returns:dataset_content: content of the requested Galaxy dataset error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.galaxy.get_datasets()

Get galaxy datasets and histories of a user

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.galaxy.get_queries()

Get galaxy queries (json datasets)

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.galaxy.upload_datasets()

Download a galaxy datasets into AskOmics

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.query module

askomics.api.query.get_abstraction()

Get abstraction

Returns:abstraction: abstraction error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.query.get_preview()

Get a preview of query

Returns:resultsPreview: Preview of the query results headerPreview: Header of the results table error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.query.query()

Get start points

Returns:startpoint: list of start points error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.query.save_result()

Save a query in filesystem and db, using a celery task

Returns:task_id: celery task id error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.results module

askomics.api.results.delete_result()

Summary

Returns:files: list of all files of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.download_result()

Download result file

askomics.api.results.get_graph_state()

Summary

Returns:preview: list of result preview header: result header error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.get_preview()

Summary

Returns:preview: list of result preview header: result header error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.get_results()

Get …

Returns:files: list of all files of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.get_sparql_query()

Get sparql query of result for the query editor

Returns:query: the sparql query error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.publish_query()

Publish a query template from a result

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.send2galaxy()

Send a result file into Galaxy

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.set_description()

Update a result description

Returns:files: all files error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json
askomics.api.results.set_public()

Change public status of a file, and return all files

Returns:files: list of all files of current user error: True if error, else False errorMessage: the error message of error, else an empty string
Return type:json

askomics.api.sparql module

askomics.api.sparql.prefix()

Get the default sparql query

Returns:default query
Return type:json
askomics.api.sparql.query()

Perform a sparql query

Returns:query results
Return type:json
askomics.api.sparql.save_query()

Perform a sparql query

Returns:query results
Return type:json

askomics.api.start module

askomics.api.start.hello()

Dummy routes

Returns:error: True if error, else False errorMessage: the error message of error, else an empty string message: a welcome message
Return type:json
askomics.api.start.start()

Starting route

Returns:Information about a eventualy logged user, and the AskOmics version and a footer message
Return type:json

askomics.api.view module

Render route

askomics.api.view.home(path)

Render the html of AskOmics

Returns:Html code of AskOmics
Return type:html

Module contents