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{
"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",
"metadata": {},
"outputs": [
{
"name": "stdin",
"output_type": "stream",
"text": [
" ·····················\n"
]
}
],
"source": [
"username = 'hluetcke'\n",
"pw = getpass.getpass()"
]
},
{
"cell_type": "code",
"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",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'hluetcke-181024154540290xCA25DBE8ED8C9FB138503F6C3F0C8D69'"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.token"
]
},
{
"cell_type": "code",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.is_session_active()"
]
},
{
"cell_type": "code",
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"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"
]
},
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"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",
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