minor changes

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/pybis/blob/master/src/python/PyBis/README.md
-
-
-%% first check the Python version
-pyversion
-% a different Python version can be selected by specifying the Python
-% executable, e.g. pyversion /Users/Henry/miniconda3/bin/python
-
-%% enter username and password for openBIS
-username = 'hluetcke';
-pw = passwordEntryDialog('CheckPasswordLength',0);
-
-%% connect to openBIS
-obi = py.pybis.Openbis('https://limb.ethz.ch/openbis:8443', 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 = '/Users/Henry/Data/Projects/MatlabOpenbis/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()
-
-
-
+% 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/pybis/blob/master/src/python/PyBis/README.md
+
+
+%% first check the Python version
+pyversion
+% a different Python version can be selected by specifying the Python
+% executable, e.g. pyversion /Users/Henry/miniconda3/bin/python
+
+%% enter username and password for openBIS
+username = 'hluetcke';
+pw = passwordEntryDialog('CheckPasswordLength',0);
+
+%% connect to openBIS
+obi = py.pybis.Openbis('https://limb.ethz.ch/openbis:8443', 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 = '/Users/Henry/Data/Projects/MatlabOpenbis/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()
+
+
+