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" <tr>\n",
" <th>0</th>\n",
" <td>DEFAULT_EXPERIMENT</td>\n",
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" <th>1</th>\n",
" <td>MATERIALS</td>\n",
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" <td>2016-06-24 10:48:02</td>\n",
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" <th>2</th>\n",
" <td>METHODS</td>\n",
" <td>Folder used to organize samples in the Invento...</td>\n",
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" <th>3</th>\n",
" <td>BOARDS</td>\n",
" <td>Folder used to organize boards</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <th>4</th>\n",
" <td>UNKNOWN</td>\n",
" <td>Unknown</td>\n",
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" <th>4</th>\n",
" <td>SOLUTION_BUFFER</td>\n",
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" <td>2016-06-24 10:48:02</td>\n",
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" <th>6</th>\n",
" <td>RNA</td>\n",
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" <td>RNA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <th>7</th>\n",
" <td>PLASMID</td>\n",
" <td></td>\n",
" <td>PLA</td>\n",
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" <td></td>\n",
" <td>BAC</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <tr>\n",
" <th>9</th>\n",
" <td>YEAST</td>\n",
" <td></td>\n",
" <td>YEA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <th>10</th>\n",
" <td>CELL_LINE</td>\n",
" <td></td>\n",
" <td>CEL</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <tr>\n",
" <th>11</th>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>FLY</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
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" <tr>\n",
" <th>12</th>\n",
" <td>EXPERIMENTAL_STEP</td>\n",
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" <td>2016-06-24 10:48:02</td>\n",
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" <th>13</th>\n",
" <td>GENERAL_PROTOCOL</td>\n",
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" <th>14</th>\n",
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" <td>PCR</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>WESTERN_BLOTTING_PROTOCOL</td>\n",
" <td></td>\n",
" <td>WES</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>DRAWING_BOARD</td>\n",
" <td></td>\n",
" <td>DRA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>UNKNOWN</td>\n",
" <td>Unknown</td>\n",
" <td>S</td>\n",
" <td>2016-06-24 10:47:01</td>\n",
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" <td>ELN_PREVIEW</td>\n",
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" <td>ANALYZED_DATA</td>\n",
" <td></td>\n",
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" <td>2016-06-24 10:48:02</td>\n",
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" <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",
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" <th>5</th>\n",
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" <td>DRAWING_BOARD</td>\n",
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" <td>JUPYTER_CONTAINER</td>\n",
" <td>Jupyter Analysis Results</td>\n",
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" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>Analysis Notebook Files</td>\n",
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" <td>2016-06-29 15:29:07</td>\n",
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" <td>Unknown</td>\n",
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" <th>9</th>\n",
" <td>JUPYTER_RESULT</td>\n",
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" <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",
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" <th>6</th>\n",
" <td>another_tag</td>\n",
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" <th>7</th>\n",
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" <th>8</th>\n",
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" <th>9</th>\n",
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" <th>12</th>\n",
" <td>gimme_a_tag</td>\n",
" <td>2016-11-18 15:20:10</td>\n",
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" <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": [
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" 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"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"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."
},
"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>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_terms('MATING_TYPE')"
"cell_type": "markdown",
"metadata": {},
"**list all the deleted items in openBIS.**\n",
"\n",
"*TODO*: fetch the deletion date"
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
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"<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>"
" 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 "
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cell_type": "markdown",
"metadata": {},
"## working with projects"
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"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",
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"sp = o.get_space('VERMEUL')"
"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>identifier</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>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>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>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "code",
},
"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",