pybis_example.ipynb

{
 "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": [
      " ·····················\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-181108105858142x7C2F61FBD12303B58F25E1786983C2BA'"
      ]
     },
     "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": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "o.get_datastores()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Masterdata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "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": [
    "### Samples / objects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "o.get_sample_types()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "obj = o.new_object(type='UNKNOWN', space='MATLAB_TEST', code='12345')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "obj.save()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sample = o.get_sample('/MATLAB_TEST/911922')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sample.delete('just a test')"
   ]
  },
  {
   "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('20101105142049776-6512')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds.get_files(start_folder='original')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Experiments / collections"
   ]
  },
  {
   "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>identifier</th>\n",
       "      <th>permId</th>\n",
       "      <th>project</th>\n",
       "      <th>type</th>\n",
       "      <th>registrator</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modifier</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/MATLAB_TEST/TEST_PROJECT/E1300</td>\n",
       "      <td>20181106172403609-9285</td>\n",
       "      <td>TEST_PROJECT</td>\n",
       "      <td>ISH</td>\n",
       "      <td>hluetcke</td>\n",
       "      <td>2018-11-06 17:24:04</td>\n",
       "      <td>hluetcke</td>\n",
       "      <td>2018-11-06 17:24:04</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    identifier                       permId                  project       type    registrator    registrationDate     modifier    modificationDate\n",
       "--  -------------------------------  ----------------------  ------------  ------  -------------  -------------------  ----------  -------------------\n",
       " 0  /MATLAB_TEST/TEST_PROJECT/E1300  20181106172403609-9285  TEST_PROJECT  ISH     hluetcke       2018-11-06 17:24:04  hluetcke    2018-11-06 17:24:04"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_experiments(\n",
    "    project='TEST_PROJECT',\n",
    "    space='MATLAB_TEST'\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>attribute</th>\n",
       "                <th>value</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>code</td> <td>E1300</td> </tr><tr> <td>permId</td> <td>20181106172403609-9285</td> </tr><tr> <td>identifier</td> <td>/MATLAB_TEST/TEST_PROJECT/E1300</td> </tr><tr> <td>type</td> <td>ISH</td> </tr><tr> <td>project</td> <td>/MATLAB_TEST/TEST_PROJECT</td> </tr><tr> <td>tags</td> <td>['henry', 'test']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "attribute    value\n",
       "-----------  -------------------------------\n",
       "code         E1300\n",
       "permId       20181106172403609-9285\n",
       "identifier   /MATLAB_TEST/TEST_PROJECT/E1300\n",
       "type         ISH\n",
       "project      /MATLAB_TEST/TEST_PROJECT\n",
       "tags         ['henry', 'test']"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "experiment = o.get_experiment('/MATLAB_TEST/TEST_PROJECT/E1300')\n",
    "experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "property    value\n",
       "----------  ----------\n",
       "age         3S\n",
       "probe       VENTROPTIN\n",
       "probe_2\n",
       "probe_3\n",
       "date"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "experiment.props"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "experiment = o.new_experiment(type='METHODS', code='METH123456', project='/MATLAB_TEST/TEST_PROJECT')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Experiment successfully created.\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>attribute</th>\n",
       "                <th>value</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>code</td> <td>METH123456</td> </tr><tr> <td>permId</td> <td>20181108105941662-9286</td> </tr><tr> <td>identifier</td> <td>/MATLAB_TEST/TEST_PROJECT/METH123456</td> </tr><tr> <td>type</td> <td>METHODS</td> </tr><tr> <td>project</td> <td>/MATLAB_TEST/TEST_PROJECT</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "attribute    value\n",
       "-----------  ------------------------------------\n",
       "code         METH123456\n",
       "permId       20181108105941662-9286\n",
       "identifier   /MATLAB_TEST/TEST_PROJECT/METH123456\n",
       "type         METHODS\n",
       "project      /MATLAB_TEST/TEST_PROJECT\n",
       "tags         []"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "experiment.save()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download and import files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds.download(files='', 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.get_experiment_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_projects(space='MATLAB_TEST', code=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "project = o.new_project(space='MATLAB_TEST', code='ANOTHER_TEST', description='TGIF')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "project.save()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "project.delete('just a test')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Logout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "o.logout()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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