pybis demo.ipynb

  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "localhost/20160929145446460-367\r\n",
      "localhost/20160929145446460-367/original\r\n",
      "localhost/20160929145446460-367/original/JUPYTER_RESULT\r\n",
      "localhost/20160929145446460-367/original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg\r\n",
      "localhost/20160929145446460-367/original/JUPYTER_NOTEBOOk\r\n",
      "localhost/20160929145446460-367/original/JUPYTER_NOTEBOOk/pybis demo.ipynb\r\n"
     ]
    }
   ],
   "source": [
    "!find localhost/20160929145446460-367"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'@id': 1,\n",
       "  '@type': 'FileInfoDssDTO',\n",
       "  'crc32Checksum': 1397688417,\n",
       "  'fileSize': '209715200',\n",
       "  'isDirectory': False,\n",
       "  'pathInDataSet': 'original/JUPYTER_RESULT/large_testfile',\n",
       "  'pathInListing': 'large_testfile'}]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds2 = o.get_dataset('20160721002157457-271')\n",
    "ds2.get_file_list(start_folder='original/JUPYTER_RESULT/large_testfile')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Files downloaded to: localhost/20160721002157457-271\n"
     ]
    }
   ],
   "source": [
    "ds2.download('original/JUPYTER_RESULT/large_testfile')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Files downloaded to: localhost/20160721002157457-271\n"
     ]
    }
   ],
   "source": [
    "ds2.download()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## upload data to openBIS\n",
    "The pybis data ingestion service «jupyter-uploader-api» in the openBIS instance is needed in order to work. Files are first uploaded to session workspace, then the ingestion service is activated which in turn registers 3 datasets:\n",
    "- a JUPYTER_CONTAINER containing:\n",
    "- JUPYTER_NOTEBOOK (containing the notebook files)\n",
    "- JUPYTER_RESULTS (containing any result files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "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>20160721002157457-271</td> </tr><tr> <td>permId</td> <td>20160721002157457-271</td> </tr><tr> <td>type</td> <td>JUPYTER_CONTAINER</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>sample</td> <td>/MY_NEW_SPACE/HOW_WONDERFUL</td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>['20160817175233002-331', '20161121005146338-398']</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.DataSet at 0x7f3140f3dd30>"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds = o.get_dataset('20160721002157457-271')\n",
    "ds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "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>YEA34</td> </tr><tr> <td>permId</td> <td>20161108230958839-384</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/YEA34</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-12-20 um 10.47.26.png</td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Sample at 0x7f89bae33d30>"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "s"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "o.new_analysis(\n",
    "    name='minimal', \n",
    "    sample = s\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Dataset registration successful'"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.new_analysis(\n",
    "    name='my new data analysis', \n",
    "    description='some meaningful description',\n",
    "    sample = s,\n",
    "    notebook_files=['pybis demo.ipynb'],\n",
    "    result_files=['PLATE1_A01_06_GFP.jpg'],\n",
    "    parents = [ds]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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