diff --git a/MatlabOpenbis_wrapper.m b/MatlabOpenbis_wrapper.m
new file mode 100644
index 0000000000000000000000000000000000000000..143d63130d1aca90663cda6824bfc9d307929794
--- /dev/null
+++ b/MatlabOpenbis_wrapper.m
@@ -0,0 +1,33 @@
+% 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
diff --git a/MatlabPybis_example.m b/MatlabPybis_example.m
index 7059eda238d9def21b644defd9a2e3912eae0e3b..22a3ec175213aea3a63a8076114416ff127108ed 100644
--- a/MatlabPybis_example.m
+++ b/MatlabPybis_example.m
@@ -7,16 +7,25 @@
%% first check the Python version
pyversion
% a different Python version can be selected by specifying the Python
-% executable
+% executable
% on OS X: pyversion /Users/Henry/miniconda3/bin/python
% on Windows: pyversion 3.6
-%% enter username and password for openBIS
-username = 'XYZ'; % enter user name
+%% 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
-url = 'https://XYZ.ethz.ch/openbis:8443'; % replace with correct URL
obi = py.pybis.Openbis(url, pyargs('verify_certificates', 0));
obi.login(username, pw, pyargs('save_token', 1));
clear pw
diff --git a/download_ds_files.m b/download_ds_files.m
index 9a8497a35a27017f2d7b9c2ae7ba56b6ae19de8f..d4fc355ca0c6db5a369c465c2aa9c06ce12b3a32 100644
--- a/download_ds_files.m
+++ b/download_ds_files.m
@@ -10,4 +10,3 @@ ds.download(pyargs('destination', data_dir, 'wait_until_finished', false));
file_list = cell(ds.get_file_list);
end
-
diff --git a/get_experiment_types.m b/get_experiment_types.m
new file mode 100644
index 0000000000000000000000000000000000000000..befeaeccbe9a8f7bf106016f5e918052106ab62d
--- /dev/null
+++ b/get_experiment_types.m
@@ -0,0 +1,15 @@
+function experiment_types = get_experiment_types
+%UNTITLED2 Summary of this function goes here
+% Detailed explanation goes here
+
+global obi
+
+% test connection
+test_connection(obi)
+
+experiment_types = obi.get_experiment_types();
+experiment_types = df_to_cell(experiment_types.df);
+
+
+end
+
diff --git a/pybis_example.ipynb b/pybis_example.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..4008e1d7517dc8108a1930f7aa4e1336c133cbda
--- /dev/null
+++ b/pybis_example.ipynb
@@ -0,0 +1,449 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from pybis import Openbis\n",
+ "import getpass\n",
+ "import matplotlib.pyplot as plt\n",
+ "%matplotlib inline"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Connecting to openBIS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o = Openbis('https://limb.ethz.ch/openbis:8443', verify_certificates=False)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdin",
+ "output_type": "stream",
+ "text": [
+ " 路路路路路路路路路路路路路路路路路路路路路\n"
+ ]
+ }
+ ],
+ "source": [
+ "username = 'hluetcke'\n",
+ "pw = getpass.getpass()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.login(username, pw, save_token=True) # saves the session token in ~/.pybis/example.com.token\n",
+ "del pw"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'hluetcke-181024130359554x90E8C39FF84921ECC3D5436AE2ECFD05'"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.token"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.is_session_active()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>code</th>\n",
+ " <th>downloadUrl</th>\n",
+ " <th>hostUrl</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>DSS1</td>\n",
+ " <td>https://limb.ethz.ch:443/datastore_server</td>\n",
+ " <td>https://limb.ethz.ch:443</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " code downloadUrl hostUrl\n",
+ "0 DSS1 https://limb.ethz.ch:443/datastore_server https://limb.ethz.ch:443"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.get_datastores()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Masterdata"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>code</th>\n",
+ " <th>description</th>\n",
+ " <th>modificationDate</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>IHC</td>\n",
+ " <td>Immunohistochemistry</td>\n",
+ " <td>2010-10-01 15:27:15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>LACZ</td>\n",
+ " <td>Experiments with lacZ staining.</td>\n",
+ " <td>2010-10-06 16:24:22</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>CULTURE</td>\n",
+ " <td>Culture</td>\n",
+ " <td>2010-08-19 08:49:11</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>ISH</td>\n",
+ " <td>in situ hybridization</td>\n",
+ " <td>2010-08-19 08:49:25</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>SKELETAL</td>\n",
+ " <td>Skeletal</td>\n",
+ " <td>2010-08-19 08:49:34</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>5</th>\n",
+ " <td>METHODS</td>\n",
+ " <td>Folder to store protocols</td>\n",
+ " <td>2016-05-24 16:36:12</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>6</th>\n",
+ " <td>PAPER</td>\n",
+ " <td>Experiments from a paper.</td>\n",
+ " <td>2010-11-12 12:08:37</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>7</th>\n",
+ " <td>LIGHTSHEET</td>\n",
+ " <td>Lightsheet imaging</td>\n",
+ " <td>2018-05-31 13:29:04</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>8</th>\n",
+ " <td>SAMPLE</td>\n",
+ " <td>For Sample registration.</td>\n",
+ " <td>2010-11-22 10:28:53</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>9</th>\n",
+ " <td>MATERIALS</td>\n",
+ " <td>Folder to store biological and chemical samples</td>\n",
+ " <td>2016-05-24 16:35:51</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " code description modificationDate\n",
+ "-- ---------- ----------------------------------------------- -------------------\n",
+ " 0 IHC Immunohistochemistry 2010-10-01 15:27:15\n",
+ " 1 LACZ Experiments with lacZ staining. 2010-10-06 16:24:22\n",
+ " 2 CULTURE Culture 2010-08-19 08:49:11\n",
+ " 3 ISH in situ hybridization 2010-08-19 08:49:25\n",
+ " 4 SKELETAL Skeletal 2010-08-19 08:49:34\n",
+ " 5 METHODS Folder to store protocols 2016-05-24 16:36:12\n",
+ " 6 PAPER Experiments from a paper. 2010-11-12 12:08:37\n",
+ " 7 LIGHTSHEET Lightsheet imaging 2018-05-31 13:29:04\n",
+ " 8 SAMPLE For Sample registration. 2010-11-22 10:28:53\n",
+ " 9 MATERIALS Folder to store biological and chemical samples 2016-05-24 16:35:51"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.get_experiment_types()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_sample_types()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_sample_type('PLATE')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_material_types()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_dataset_types()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_terms()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### List and get datasets"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "datasets = o.get_datasets(type='HISTOLOGY')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "counter = 0\n",
+ "for ds in datasets:\n",
+ " print(ds)\n",
+ " counter += 1\n",
+ " if counter > 10:\n",
+ " break"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "ds = o.get_dataset('20101105142920015-6525')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "ds.get_files(start_folder='original')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Download and import files"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "ds.download(files='original/441_x40001.tif', destination='data', wait_until_finished=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plt.imshow(plt.imread('data/20101105142920015-6525/original/441_x40001.tif'))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.logout()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_experiment_types()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "o.get_dataset_types()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python [default]",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/pybis_test.ipynb b/pybis_test.ipynb
deleted file mode 100644
index d4442417ae3fc12e6d22a254aae7dcc482a12e81..0000000000000000000000000000000000000000
--- a/pybis_test.ipynb
+++ /dev/null
@@ -1,172 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "from pybis import Openbis\n",
- "import getpass\n",
- "import matplotlib.pyplot as plt\n",
- "%matplotlib inline"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Login to openBIS"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "o = Openbis('https://XYZ.ethz.ch/openbis:8443', verify_certificates=False)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "username = ''\n",
- "pw = getpass.getpass()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "o.login(username, pw, save_token=True) # saves the session token in ~/.pybis/example.com.token"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### List and get datasets"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "datasets = o.get_datasets(type='HISTOLOGY')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "counter = 0\n",
- "for ds in datasets:\n",
- " print(ds)\n",
- " counter += 1\n",
- " if counter > 10:\n",
- " break"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "ds = o.get_dataset('20101105142920015-6525')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "ds.get_files(start_folder='original')"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Download and import files"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "ds.download(files='original/441_x40001.tif', destination='data', wait_until_finished=True)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "plt.imshow(plt.imread('data/20101105142920015-6525/original/441_x40001.tif'))"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "o.logout()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "o.get_experiment_types()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "o.get_dataset_types()"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.5"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
diff --git a/test_connection.m b/test_connection.m
new file mode 100644
index 0000000000000000000000000000000000000000..a550daf5330b082aa9020f106dcdaafb568fb572
--- /dev/null
+++ b/test_connection.m
@@ -0,0 +1,11 @@
+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
+