removing legacy folder

legacy/MatlabOpenbis_wrapper.m

-% wrapper / demo script for Matlab openBIS toolbox
-% Todo: convert to ML live script
-
-%% Enter connection info for openBIS
-% connection details can be stored in the file user_data.json or entered manually
-try
-    user_data = jsondecode(fileread('user_data.json'));
-    username = user_data.User;
-    url = user_data.URL;
-catch
-    username = ''; % enter valid user name
-    url = 'https://XYZ.ethz.ch/openbis:8443'; % replace with correct URL
-end
-% specify openBIS password
-pw = passwordEntryDialog('CheckPasswordLength',0);
-
-%% Connect to openBIS
-login(url, username, pw)
-clear pw % remove password from workspace
-
-% login will create a global variable called obi
-global obi
-
-%% Check if connection is still active
-% we can check if the connection has timed-out or is still valid
-if obi.is_session_active
-    fprintf('\nConnection to host %s is still valid.\n', char(obi.url))
-else
-    disp('Connection is not active. Please re-connect.')
-end
-
-%% Logout
-obi.logout()
\ No newline at end of file

legacy/MatlabPybis_example.m

-% demo script for accessing openBIS from Matlab using Pybis
-% we use Matlab's capability to call Python libraries
-% Pybis documentation is available here:
-% https://sissource.ethz.ch/sispub/openbis/blob/master/pybis/src/python/README.md
-
-
-%% first check the Python version
-pyversion
-% a different Python version can be selected by specifying the Python
-% executable
-% on OS X: pyversion /Users/Henry/miniconda3/bin/python
-% on Windows: pyversion 3.6
-
-%% connection details for openBIS
-% connection details can be stored in the file user_data.json or entered manually
-try
-    user_data = jsondecode(fileread('user_data.json'));
-    username = user_data.User;
-    url = user_data.URL;
-catch
-    username = ''; % enter valid user name
-    url = 'https://XYZ.ethz.ch/openbis:8443'; % replace with correct URL
-end
-% specify openBIS password
-pw = passwordEntryDialog('CheckPasswordLength',0);
-
-
-%% connect to openBIS
-obi = py.pybis.Openbis(url, pyargs('verify_certificates', 0));
-obi.login(username, pw, pyargs('save_token', 1));
-clear pw
-obi
-
-%% select datasets
-datasets = obi.get_datasets(pyargs('type','HISTOLOGY'));
-datasets
-
-%% download dataset
-% get specific dataset
-ds_id = '20101105142049776-6512';
-ds = obi.get_dataset(ds_id);
-% download
-data_dir = 'data';
-ds.download(pyargs('destination', data_dir, 'wait_until_finished', false));
-
-%% list files / directories in dataset
-% get list and convert to Matlab cell array
-files = cell(ds.get_file_list);
-for iii = 1:numel(files)
-    iii_file = files{iii};
-    fprintf('%d - %s - isDir: %d\n', iii, string(iii_file{'pathInDataSet'}), iii_file{'isDirectory'})
-end
-
-%% Spaces
-% list spaces
-spaces = obi.get_spaces;
-spaces
-% create a new space
-space_id = 'MATLAB_TEST';
-space = obi.new_space(pyargs('code',  space_id, 'description', 'test space for Matlab access to openBIS'));
-space
-space.save;
-% delete created space afterwards
-% space.delete('just a test');
-
-%% Projects
-% list projects in Space
-space.get_projects
-% create new project
-project_code = 'test_project';
-project_description = 'my awsome project';
-project = space.new_project(pyargs('code', project_code, ...
-    'description' , project_description));
-project = project.save();
-space.get_projects
-
-
-%% clean up
-% logout
-obi.logout()
-
-
-

legacy/delete_space.m

-function delete_space(code, reason)
-% DELETE_SPACE
-% Delete space in the openBIS instance. A reason has to be specified.
-
-global obi
-
-% test connection
-test_connection(obi)
-
-space = obi.get_space(code);
-space.delete(reason);
-
-end
\ No newline at end of file

legacy/df_to_table.m

-function [matlab_table] = df_to_table(df)
-%df_to_table
-%   Returns a Matlab table for a Python dataframe
-
-csv_temp = sprintf('%s.csv', tempname);
-df.to_csv(csv_temp);
-matlab_table = readtable(csv_temp);
-delete(csv_temp);
-
-end
\ No newline at end of file

legacy/download_ds_files.m

-function [file_list] = download_ds_files(obi, ds_id, data_dir)
-%UNTITLED Summary of this function goes here
-%   Detailed explanation goes here
-
-ds = obi.get_dataset(ds_id);
-% download
-ds.download(pyargs('destination', data_dir, 'wait_until_finished', false));
-
-% get list and convert to Matlab cell array
-file_list = cell(ds.get_file_list);
-
-end

legacy/get_dataset_types.m

-function dataset_types = get_dataset_types
-%get_dataset_types
-%   Returns a table of all available dataset types
-
-global obi
-
-% test connection
-test_connection(obi)
-
-dataset_types = obi.get_dataset_types();
-
-dataset_types = df_to_table(dataset_types.df);
-
-end

legacy/get_datasets.m

-function [datasets] = get_datasets(ds_type)
-%UNTITLED2 Summary of this function goes here
-%   Detailed explanation goes here
-
-global obi
-
-datasets = obi.get_datasets(pyargs('type',ds_type));
-datasets = df_to_table(datasets.df);
-end

legacy/get_experiment_types.m

-function experiment_types = get_experiment_types
-%get_experiment_types
-%   Returns a table of all available experiment types
-
-global obi
-
-% test connection
-test_connection(obi)
-
-experiment_types = obi.get_experiment_types();
-
-experiment_types = df_to_table(experiment_types.df);
-
-end

legacy/get_material_types.m

-function material_types = get_material_types
-%get_material_types
-%   Returns a table of all available material types
-
-global obi
-
-% test connection
-test_connection(obi)
-
-material_types = obi.get_material_types();
-
-material_types = df_to_table(material_types.df);
-
-end

legacy/get_sample_types.m

-function sample_types = get_sample_types
-%get_sample_types
-%   Returns a table of all available sample types
-
-global obi
-
-% test connection
-test_connection(obi)
-
-sample_types = obi.get_sample_types();
-
-sample_types = df_to_table(sample_types.df);
-
-end

legacy/get_spaces.m

-function spaces = get_spaces
-% GET_SPACES
-% Get a list of all available spaces (DataFrame object). To create a sample or a 
-% dataset, you need to specify in which space it should live.
-
-global obi
-
-% test connection
-test_connection(obi)
-
-spaces = obi.get_spaces();
-
-spaces = df_to_table(spaces.df);
-
-end

legacy/get_terms.m

-function terms = get_terms
-%get_sample_types
-%Returns information about existing vocabulary terms. 
-%If a vocabulary code is provided, it only returns the terms of that vocabulary
-
-global obi
-
-% test connection
-test_connection(obi)
-
-terms = obi.get_terms();
-
-terms = df_to_table(terms.df);
-
-end

legacy/login.m

-function login(varargin)
-%UNTITLED Summary of this function goes here
-%   Detailed explanation goes here
-
-global obi
-
-if nargin
-    url = varargin{1};
-    user = varargin{2};
-    pw = varargin{3};
-else
-    [url, user, pw] = user_url_pw_inputdlg;
-end
-
-obi = py.pybis.Openbis(url, pyargs('verify_certificates', 0));
-obi.login(user, pw, pyargs('save_token', 1));
-
-end
-
-function [url, user, pw] = user_url_pw_inputdlg
-
-prompt = {'openBIS URL:', 'openBIS user:'};
-title = 'openBIS connection details';
-definput = {'https://XYZ.ethz.ch/openbis:8443', ''};
-answer = inputdlg(prompt, title, 1, definput);
-
-url = answer{1};
-user = answer{2};
-
-pw = passwordEntryDialog('CheckPasswordLength',0);
-
-end
\ No newline at end of file

legacy/logout.m

-function logout
-%LOGOUT
-%   Log out of openBIS. After logout, the session token is no longer valid.
-
-global obi
-
-% test connection
-test_connection(obi)
-
-obi.logout;
-
-end
-

legacy/new_space.m

-function new_space(code, description)
-% NEW_SPACE
-% Creates a new space in the openBIS instance.
-
-global obi
-
-% test connection
-test_connection(obi)
-
-space = obi.new_space(pyargs('code',  code, 'description', description));
-space.save;
-
-end
\ No newline at end of file

legacy/test_connection.m

-function test_connection(obi)
-
-if ~ismethod(obi, 'is_session_active')
-    error('No connection to openBIS. Did you log in?') 
-end
-if ~obi.is_session_active
-   error('No active connection found. Try to re-connect.') 
-end
-
-end
-