pybis demo.ipynb

       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ANALYZED_DATA</td>\n",
       "      <td></td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ATTACHMENT</td>\n",
       "      <td></td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>DRAWING_BOARD</td>\n",
       "      <td></td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>JUPYTER_CONTAINER</td>\n",
       "      <td>Jupyter Analysis Results</td>\n",
       "      <td>CONTAINER</td>\n",
       "      <td>2016-06-29 15:29:06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>JUPYTER_NOTEBOOK</td>\n",
       "      <td>Analysis Notebook Files</td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-29 15:29:07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>UNKNOWN</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-24 10:47:01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>JUPYTER_RESULT</td>\n",
       "      <td>Analysis Results Files</td>\n",
       "      <td>PHYSICAL</td>\n",
       "      <td>2016-06-29 15:29:06</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f7ff399d588>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_dataset_types()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "to get a more detailed view of an item from the list above, just provide the index number like so:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<p>DataSetType: <b>ELN_PREVIEW</b>\n",
       "<p>description: ELN Preview image</p>\n",
       "        \n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>property</th>\n",
       "      <th>label</th>\n",
       "      <th>description</th>\n",
       "      <th>dataType</th>\n",
       "      <th>mandatory</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "        <tr> <th>name</th> <td>Name</td> <td>Name</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>notes</th> <td>Notes</td> <td>Notes regarding the dataset</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>xmlcomments</th> <td>Comments List</td> <td>Several comments can be added by different users</td> <td>XML</td> <td>False</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.property.PropertyAssignments at 0x7f7ff39e41d0>"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_dataset_types()[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "you can as well use an identifier to get the details:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<p>DataSetType: <b>ELN_PREVIEW</b>\n",
       "<p>description: ELN Preview image</p>\n",
       "        \n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>property</th>\n",
       "      <th>label</th>\n",
       "      <th>description</th>\n",
       "      <th>dataType</th>\n",
       "      <th>mandatory</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "        <tr> <th>name</th> <td>Name</td> <td>Name</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>notes</th> <td>Notes</td> <td>Notes regarding the dataset</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>xmlcomments</th> <td>Comments List</td> <td>Several comments can be added by different users</td> <td>XML</td> <td>False</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.property.PropertyAssignments at 0x7f7ff39e4898>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_dataset_type('ELN_PREVIEW')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<p>SampleType: <b>YEAST</b>\n",
       "<p>description: </p>\n",
       "        <p>Code autogenerated: True</p>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>property</th>\n",
       "      <th>label</th>\n",
       "      <th>description</th>\n",
       "      <th>dataType</th>\n",
       "      <th>mandatory</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "        <tr> <th>name</th> <td>Name</td> <td>Name</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>show_in_project_overview</th> <td>Show in project overview</td> <td>Show in project overview</td> <td>BOOLEAN</td> <td>False</td> </tr><tr> <th>owner</th> <td>Owner</td> <td>Who produced/owned the sample</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>owner_number</th> <td>Owner number</td> <td>Owner number</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>genetic_modification</th> <td>Genetic modifications</td> <td>Genetic modifications composed by the Plasmid ancestors</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>genetic_background</th> <td>Genetic Background</td> <td>Genetic background of the yeast strain</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>mating_type</th> <td>Mating Type</td> <td>Mating type or ploidy of the yeast strain</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>background-specific_markers</th> <td>Background-specific markers</td> <td>Background-specific markers available in the strain for further genetic modifications</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>common_markers</th> <td>Common markers</td> <td>Common markers available in the strain for further genetic modifications</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>endogenous_plasmid</th> <td>Endogenous 2micron plasmid in yeast</td> <td>Presence of an endogenous cir 2micron plasmid</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>origin</th> <td>Origin</td> <td>How the strain/cell line was produced</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>strain_check</th> <td>Strain Check</td> <td>Check done to verify the modifications introduced in the strain</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>source</th> <td>Source</td> <td>Source from where the construct/strain/cell line obtained or purchased, if it was not produced in the lab</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>publication</th> <td>Publication</td> <td>Publication from where the information was first found OR technical sheet given by the manufacturer</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>notes</th> <td>Notes</td> <td>Notes regarding the dataset</td> <td>MULTILINE_VARCHAR</td> <td>False</td> </tr><tr> <th>xmlcomments</th> <td>Comments List</td> <td>Several comments can be added by different users</td> <td>XML</td> <td>False</td> </tr><tr> <th>annotations_state</th> <td>Annotations State</td> <td>Annotations State</td> <td>XML</td> <td>False</td> </tr><tr> <th>storage_names</th> <td>Storage Name</td> <td>Storage Name</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>storage_row</th> <td>Storage Row</td> <td>Storage Row</td> <td>INTEGER</td> <td>False</td> </tr><tr> <th>storage_column</th> <td>Storage Column</td> <td>Storage Column</td> <td>INTEGER</td> <td>False</td> </tr><tr> <th>storage_box_name</th> <td>Storage Box Name</td> <td>Storage Box Name</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>storage_box_size</th> <td>Storage Box Size</td> <td>Storage Box Size</td> <td>CONTROLLEDVOCABULARY</td> <td>False</td> </tr><tr> <th>storage_user</th> <td>Storage User Id</td> <td>Storage User Id</td> <td>VARCHAR</td> <td>False</td> </tr><tr> <th>storage_position</th> <td>Storage Position</td> <td>Storage Position</td> <td>VARCHAR</td> <td>False</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.property.PropertyAssignments at 0x7f72f022c9b0>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_sample_type('YEAST')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**tags**: almost all entities in openBIS can be tagged:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": 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>code</th>\n",
       "      <th>registrationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A_tag</td>\n",
       "      <td>2016-07-05 23:45:04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CREATE_JSON_TAG</td>\n",
       "      <td>2016-06-30 00:36:50</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CREATE_JSON_TAG_2</td>\n",
       "      <td>2016-07-06 00:07:07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CREATE_JSON_TAG_3</td>\n",
       "      <td>2016-07-06 00:07:07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CREATE_JSON_TAG_blalbal</td>\n",
       "      <td>2016-11-08 10:24:18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>another_nice_tag</td>\n",
       "      <td>2016-10-06 14:43:21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>another_tag</td>\n",
       "      <td>2016-10-04 11:29:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>blblblblblb</td>\n",
       "      <td>2016-10-06 14:47:45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>clue</td>\n",
       "      <td>2016-09-26 23:48:08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>do</td>\n",
       "      <td>2016-09-12 23:57:14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>due</td>\n",
       "      <td>2016-06-30 17:18:11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>fa</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>gimme_a_tag</td>\n",
       "      <td>2016-11-18 15:20:10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>gimme_one_more</td>\n",
       "      <td>2016-10-27 02:03:25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>la</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>mi</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>new_tag</td>\n",
       "      <td>2016-10-06 10:49:15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>no</td>\n",
       "      <td>2016-09-26 23:48:08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>one</td>\n",
       "      <td>2016-11-09 14:27:58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>re</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>so</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>three</td>\n",
       "      <td>2016-11-09 14:27:58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>ti</td>\n",
       "      <td>2016-09-12 23:57:29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>too_late</td>\n",
       "      <td>2016-10-06 10:56:07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>tre</td>\n",
       "      <td>2016-06-30 17:18:11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>two</td>\n",
       "      <td>2016-11-09 14:27:58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>uno</td>\n",
       "      <td>2016-06-30 17:18:11</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                       code     registrationDate\n",
       "0                     A_tag  2016-07-05 23:45:04\n",
       "1           CREATE_JSON_TAG  2016-06-30 00:36:50\n",
       "2         CREATE_JSON_TAG_2  2016-07-06 00:07:07\n",
       "3         CREATE_JSON_TAG_3  2016-07-06 00:07:07\n",
       "4   CREATE_JSON_TAG_blalbal  2016-11-08 10:24:18\n",
       "5          another_nice_tag  2016-10-06 14:43:21\n",
       "6               another_tag  2016-10-04 11:29:02\n",
       "7               blblblblblb  2016-10-06 14:47:45\n",
       "8                      clue  2016-09-26 23:48:08\n",
       "9                        do  2016-09-12 23:57:14\n",
       "10                      due  2016-06-30 17:18:11\n",
       "11                       fa  2016-09-12 23:57:29\n",
       "12              gimme_a_tag  2016-11-18 15:20:10\n",
       "13           gimme_one_more  2016-10-27 02:03:25\n",
       "14                       la  2016-09-12 23:57:29\n",
       "15                       mi  2016-09-12 23:57:29\n",
       "16                  new_tag  2016-10-06 10:49:15\n",
       "17                       no  2016-09-26 23:48:08\n",
       "18                      one  2016-11-09 14:27:58\n",
       "19                       re  2016-09-12 23:57:29\n",
       "20                       so  2016-09-12 23:57:29\n",
       "21                    three  2016-11-09 14:27:58\n",
       "22                       ti  2016-09-12 23:57:29\n",
       "23                 too_late  2016-10-06 10:56:07\n",
       "24                      tre  2016-06-30 17:18:11\n",
       "25                      two  2016-11-09 14:27:58\n",
       "26                      uno  2016-06-30 17:18:11"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_tags()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**get the terms of a (controlled) vocabulary.**\n",
    "\n",
    "Some assigned properties have a controlled vocabulary, which means you can not enter anything you want."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>vocabulary term</th>\n",
       "                <th>label</th>\n",
       "                <th>description</th>\n",
       "                <th>vocabulary</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>A</td> <td>a</td> <td>None</td> <td>MATING_TYPE</td> </tr><tr> <td>ALPHA</td> <td>alpha</td> <td>None</td> <td>MATING_TYPE</td> </tr><tr> <td>DIPLOID</td> <td>diploid</td> <td>None</td> <td>MATING_TYPE</td> </tr><tr> <td>UNKNOWN</td> <td>unknown</td> <td>None</td> <td>MATING_TYPE</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.masterdata.Vocabulary at 0x7fca603910f0>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_terms('MATING_TYPE')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**list all the deleted items in openBIS.**\n",
    "\n",
    "*TODO*: fetch the deletion date"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>permId</th>\n",
       "      <th>reason</th>\n",
       "      <th>type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>20160629183649792-77</td>\n",
       "      <td>no jolly good reason</td>\n",
       "      <td>as.dto.sample.id.SamplePermId</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>20160629185740101-79</td>\n",
       "      <td>no jolly good reason</td>\n",
       "      <td>as.dto.sample.id.SamplePermId</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>20160705234127476-205</td>\n",
       "      <td>jjj</td>\n",
       "      <td>as.dto.sample.id.SamplePermId</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>20160630111810821-87</td>\n",
       "      <td>no specific reason</td>\n",
       "      <td>as.dto.sample.id.SamplePermId</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>20160926234807546-364</td>\n",
       "      <td>no longer needed</td>\n",
       "      <td>as.dto.experiment.id.ExperimentPermId</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>20161004215320704-370</td>\n",
       "      <td>it was just an experiment</td>\n",
       "      <td>as.dto.experiment.id.ExperimentPermId</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  permId                     reason  \\\n",
       "0   20160629183649792-77       no jolly good reason   \n",
       "1   20160629185740101-79       no jolly good reason   \n",
       "2  20160705234127476-205                        jjj   \n",
       "3   20160630111810821-87         no specific reason   \n",
       "4  20160926234807546-364           no longer needed   \n",
       "5  20161004215320704-370  it was just an experiment   \n",
       "\n",
       "                                    type  \n",
       "0          as.dto.sample.id.SamplePermId  \n",
       "1          as.dto.sample.id.SamplePermId  \n",
       "2          as.dto.sample.id.SamplePermId  \n",
       "3          as.dto.sample.id.SamplePermId  \n",
       "4  as.dto.experiment.id.ExperimentPermId  \n",
       "5  as.dto.experiment.id.ExperimentPermId  "
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_deletions()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## working with projects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pybis import Openbis\n",
    "o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
    "o.token"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "list all projects in a given space."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sp = o.get_space('VERMEUL')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\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>leader</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>/VERMEUL/PROJECT_ONE</td>\n",
       "      <td>20170115220158336-410</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-15 22:01:58</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-26 23:36:43</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/VERMEUL/READY_TO_DELETE</td>\n",
       "      <td>20170122214024061-421</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-22 21:40:24</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-22 21:40:24</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f882ed7bcf8>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sp.get_projects()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>PROJECT_ONE</td> </tr><tr> <td>description</td> <td></td> </tr><tr> <td>permId</td> <td>20170115220158336-410</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/PROJECT_ONE</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>leader</td> <td></td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2017-01-15 22:01:58</td> </tr><tr> <td>modifier</td> <td></td> </tr><tr> <td>modificationDate</td> <td>2017-01-26 23:36:43</td> </tr><tr><td>attachments</td><td>IMG_3587.JPG</td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Project at 0x7f882ed87080>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = sp.get_projects()[0]\n",
    "p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'description': None, 'fileName': 'IMG_3587.JPG', 'title': 'just a big mess'}]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p.attachments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fileName</th>\n",
       "      <th>title</th>\n",
       "      <th>description</th>\n",
       "      <th>version</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>IMG_3587.JPG</td>\n",
       "      <td>just a big mess</td>\n",
       "      <td>None</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       fileName            title description  version\n",
       "0  IMG_3587.JPG  just a big mess        None        1"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p.get_attachments()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['localhost/20170115220158336-410/IMG_3587.JPG']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p.download_attachments()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "localhost/20170115220158336-410\r\n",
      "localhost/20170115220158336-410/IMG_3587.JPG\r\n"
     ]
    }
   ],
   "source": [
    "!find localhost/20170115220158336-410"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "p.add_attachment(fileName='testfile', description= 'another file', title= 'one more attachment')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "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>PROJECT_ONE</td> </tr><tr> <td>description</td> <td></td> </tr><tr> <td>permId</td> <td>20170115220158336-410</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/PROJECT_ONE</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>leader</td> <td></td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2017-01-15 22:01:58</td> </tr><tr> <td>modifier</td> <td></td> </tr><tr> <td>modificationDate</td> <td>2017-01-24 15:13:08</td> </tr><tr><td>attachments</td><td>IMG_3587.JPG<br/>testfile</td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Project at 0x7fc53d9cd780>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Project successfully updated.\n"
     ]
    }
   ],
   "source": [
    "p.save()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## working with experiments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pybis import Openbis\n",
    "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**fetching experiments of a specific type containing tags**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\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>/MATERIALS/YEASTS/MY_FIRST_EXPERIMENT_WITH_PRO...</td>\n",
       "      <td>20160924015154859-355</td>\n",
       "      <td>YEASTS</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-09-24 01:51:55</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-27 00:12:25</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f21b2d65898>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exps = o.get_experiments(\n",
    "        project='YEASTS',\n",
    "        space='MATERIALS', \n",
    "        type='DEFAULT_EXPERIMENT',\n",
    "        tags='*', \n",
    "        is_finished=True\n",
    ")\n",
    "exps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>MY_FIRST_EXPERIMENT_WITH_PROPERTY</td> </tr><tr> <td>permId</td> <td>20160924015154859-355</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/MY_FIRST_EXPERIMENT_WITH_PROPERTY</td> </tr><tr> <td>type</td> <td>DEFAULT_EXPERIMENT</td> </tr><tr> <td>project</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>tags</td> <td>['too_late', 'uno']</td> </tr><tr><td>attachments</td><td>testfile</td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Experiment at 0x7fbe86a64748>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "e0 = exps[0]\n",
    "e0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "e0.project = p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "e0.add_tags('uno')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},