pybis demo.ipynb

       "   'storageFormat': None},\n",
       "  'properties': {'@id': 8,\n",
       "   '@type': 'as.dto.property.fetchoptions.PropertyFetchOptions',\n",
       "   'cacheMode': 'NO_CACHE',\n",
       "   'count': None,\n",
       "   'from': None,\n",
       "   'sortBy': None},\n",
       "  'registrator': None,\n",
       "  'sample': {'@id': 7,\n",
       "   '@type': 'as.dto.sample.fetchoptions.SampleFetchOptions',\n",
       "   'attachments': None,\n",
       "   'cacheMode': 'NO_CACHE',\n",
       "   'children': None,\n",
       "   'components': None,\n",
       "   'container': None,\n",
       "   'count': None,\n",
       "   'dataSets': None,\n",
       "   'experiment': None,\n",
       "   'from': None,\n",
       "   'history': None,\n",
       "   'materialProperties': None,\n",
       "   'modifier': None,\n",
       "   'parents': None,\n",
       "   'properties': None,\n",
       "   'registrator': None,\n",
       "   'sort': None,\n",
       "   'sortBy': None,\n",
       "   'space': None,\n",
       "   'tags': None,\n",
       "   'type': None},\n",
       "  'sort': None,\n",
       "  'sortBy': None,\n",
       "  'tags': {'@id': 12,\n",
       "   '@type': 'as.dto.tag.fetchoptions.TagFetchOptions',\n",
       "   'cacheMode': 'NO_CACHE',\n",
       "   'count': None,\n",
       "   'dataSets': None,\n",
       "   'experiments': None,\n",
       "   'from': None,\n",
       "   'materials': None,\n",
       "   'owner': None,\n",
       "   'samples': None,\n",
       "   'sort': None,\n",
       "   'sortBy': None},\n",
       "  'type': None},\n",
       " 'history': None,\n",
       " 'linkedData': None,\n",
       " 'materialProperties': None,\n",
       " 'measured': True,\n",
       " 'modificationDate': 1478469560726,\n",
       " 'modifier': None,\n",
       " 'parents': [],\n",
       " 'permId': {'@id': 13,\n",
       "  '@type': 'as.dto.dataset.id.DataSetPermId',\n",
       "  'permId': '20160929145446460-367'},\n",
       " 'physicalData': None,\n",
       " 'postRegistered': True,\n",
       " 'properties': {'DESCRIPTION': 'should be aa4da9f7', 'NAME': 'crc32 check'},\n",
       " 'registrationDate': 1475153686645,\n",
       " 'registrator': None,\n",
       " 'sample': {'@id': 20,\n",
       "  '@type': 'as.dto.sample.Sample',\n",
       "  'attachments': None,\n",
       "  'children': None,\n",
       "  'code': 'HOW_WONDERFUL',\n",
       "  'components': None,\n",
       "  'container': None,\n",
       "  'dataSets': None,\n",
       "  'experiment': None,\n",
       "  'fetchOptions': {'@id': 21,\n",
       "   '@type': 'as.dto.sample.fetchoptions.SampleFetchOptions',\n",
       "   'attachments': None,\n",
       "   'cacheMode': 'NO_CACHE',\n",
       "   'children': None,\n",
       "   'components': None,\n",
       "   'container': None,\n",
       "   'count': None,\n",
       "   'dataSets': None,\n",
       "   'experiment': None,\n",
       "   'from': None,\n",
       "   'history': None,\n",
       "   'materialProperties': None,\n",
       "   'modifier': None,\n",
       "   'parents': None,\n",
       "   'properties': None,\n",
       "   'registrator': None,\n",
       "   'sort': None,\n",
       "   'sortBy': None,\n",
       "   'space': None,\n",
       "   'tags': None,\n",
       "   'type': None},\n",
       "  'history': None,\n",
       "  'identifier': {'@id': 23,\n",
       "   '@type': 'as.dto.sample.id.SampleIdentifier',\n",
       "   'identifier': '/VERMEUL/HOW_WONDERFUL'},\n",
       "  'materialProperties': None,\n",
       "  'modificationDate': 1479686038994,\n",
       "  'modifier': None,\n",
       "  'parents': None,\n",
       "  'permId': {'@id': 22,\n",
       "   '@type': 'as.dto.sample.id.SamplePermId',\n",
       "   'permId': '20160630105304285-81'},\n",
       "  'properties': None,\n",
       "  'registrationDate': 1467298384285,\n",
       "  'registrator': None,\n",
       "  'space': None,\n",
       "  'tags': None,\n",
       "  'type': None},\n",
       " 'tags': [],\n",
       " 'type': None}"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dss[2].data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>isDirectory</th>\n",
       "      <th>pathInDataSet</th>\n",
       "      <th>fileSize</th>\n",
       "      <th>crc32Checksum</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>True</td>\n",
       "      <td>original</td>\n",
       "      <td>-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>True</td>\n",
       "      <td>original/JUPYTER_NOTEBOOk</td>\n",
       "      <td>-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>False</td>\n",
       "      <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
       "      <td>77667</td>\n",
       "      <td>1fae7b5a</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>True</td>\n",
       "      <td>original/JUPYTER_RESULT</td>\n",
       "      <td>-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>False</td>\n",
       "      <td>original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg</td>\n",
       "      <td>426229</td>\n",
       "      <td>aa4da9f7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  isDirectory                                  pathInDataSet fileSize  \\\n",
       "0        True                                       original       -1   \n",
       "1        True                      original/JUPYTER_NOTEBOOk       -1   \n",
       "2       False     original/JUPYTER_NOTEBOOk/pybis demo.ipynb    77667   \n",
       "3        True                        original/JUPYTER_RESULT       -1   \n",
       "4       False  original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg   426229   \n",
       "\n",
       "  crc32Checksum  \n",
       "0             0  \n",
       "1             0  \n",
       "2      1fae7b5a  \n",
       "3             0  \n",
       "4      aa4da9f7  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "files = ds.get_files()\n",
    "files[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Files downloaded to: localhost/20160929145446460-367\n"
     ]
    }
   ],
   "source": [
    "ds.download()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "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": {
    "collapsed": false
   },
   "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": {
    "collapsed": false
   },
   "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": {
    "collapsed": false
   },
   "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": 31,
   "metadata": {
    "collapsed": false
   },
   "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> <th>permId</th> <td>20160721002157457-271</td> </tr>\n",
       "    <tr> <th>properties</th> <td>{'DESCRIPTION': 'ave, some!', 'NAME': 'my_delightful_analysis'}</td> </tr>\n",
       "    <tr> <th>tags</th> <td>[]</td> </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.DataSet at 0x7efe60802d68>"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds = o.get_dataset('20160721002157457-271')\n",
    "ds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Dataset registration successful'"
      ]
     },
     "execution_count": 4,
     "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": "markdown",
   "metadata": {},
   "source": [
    "*TODO*: attach analysis to an experiment, not to a sample (usually there are a lot of datasets and samples, but only a few analyses per experiment)"
   ]
  }
 ],
 "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": "3.5.1"
  }
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