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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Working with pybis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## connect to openBIS\n",
"(using stored session token ~/.pybis/localhost.token)"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170105170439098x34CD40C052CDA7A12E34AFFDB14FB134'"
"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": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.is_session_active()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Manually connect to an instance using your username/password and storing the token for later use"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-170105170439098x34CD40C052CDA7A12E34AFFDB14FB134'"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o = Openbis('https://localhost:8443', verify_certificates=False)\n",
"password = getpass.getpass()\n",
"o.login('vermeul',password, save_token=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"you can connect to another openBIS instance if you have to:"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-161213095820805x4BD32D0691A016963A62966F872D0D65'"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"import getpass\n",
"o2 = Openbis('https://sprint-openbis.ethz.ch:8443', verify_certificates=False)\n",
"password = getpass.getpass()\n",
"o2.login('vermeul',password)\n",
"o2.token"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Check wether our session is still valid"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o2.is_session_active()"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"o2.logout()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## get general information about openBIS"
]
},
{
"cell_type": "code",
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"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>code</th>\n",
" <th>downloadUrl</th>\n",
" <th>hostUrl</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DSS1</td>\n",
" <td>https://localhost:8444/datastore_server</td>\n",
" <td>https://localhost:8444</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code downloadUrl hostUrl\n",
"0 DSS1 https://localhost:8444/datastore_server https://localhost:8444"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datastores()"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"sp = o.get_space('VERMEUL')"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 3, '@type': 'as.dto.space.id.SpacePermId', 'permId': 'VERMEUL'}"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sp.permId"
]
},
{
"cell_type": "code",
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"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>code</th>\n",
" <th>description</th>\n",
" <th>registrationDate</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANOTHER_SPACE_NAME</td>\n",
" <td>another space description</td>\n",
" <td>2016-07-15 02:54:45</td>\n",
" <td>2016-07-15 02:54:45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>MATERIALS</td>\n",
" <td>None</td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>METHODS</td>\n",
" <td>None</td>\n",
" <td>2016-06-24 11:47:53</td>\n",
" <td>2016-06-24 11:47:53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MY_NEW_SPACE</td>\n",
" <td>this is yet another space</td>\n",
" <td>2016-07-15 03:02:14</td>\n",
" <td>2016-07-15 03:02:14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>VERMEUL</td>\n",
" <td>Space for user vermeul</td>\n",
" <td>2016-06-24 11:50:48</td>\n",
" <td>2016-06-24 11:50:48</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sp=o.get_spaces()\n",
"sp"
]
},
{
"cell_type": "code",
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"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>code</th>\n",
" <th>space</th>\n",
" <th>registrator</th>\n",
" <th>registrationDate</th>\n",
" <th>modifier</th>\n",
" <th>modificationDate</th>\n",
" <th>permid</th>\n",
" <th>identifier</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>BACTERIA</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-33</td>\n",
" <td>/MATERIALS/BACTERIA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CELL_LINES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-34</td>\n",
" <td>/MATERIALS/CELL_LINES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>FLIES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-35</td>\n",
" <td>/MATERIALS/FLIES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>PLASMIDS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-37</td>\n",
" <td>/MATERIALS/PLASMIDS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>POLYNUCLEOTIDES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-38</td>\n",
" <td>/MATERIALS/POLYNUCLEOTIDES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>REAGENTS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-32</td>\n",
" <td>/MATERIALS/REAGENTS</td>\n",
" </tr>\n",
" <tr>\n",
" <td>YEASTS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-10-04 22:04:57</td>\n",
" <td>20160624054751885-36</td>\n",
" <td>/MATERIALS/YEASTS</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_projects(space='MATERIALS')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**get vocabulary terms**"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"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>PBLUESCRIPT_II_KS_PLUS</td> <td>pBluescript II KS +</td> <td>Commercial vector for cloning in bacteria (Stratagene)</td> <td>BACKBONE</td> </tr><tr> <td>PSPPOLY_A</td> <td>pSPpoly(A)</td> <td>Standard cloning vector. It can be used for in vitro trascription from SP6 promoter. It contains a poly(A) to generate poly(A)+ transcripts in vitro (Promega)</td> <td>BACKBONE</td> </tr><tr> <td>PRS30Y</td> <td>pRS30y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS31Y</td> <td>pRS31y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS40Y</td> <td>pRS40y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS41Y</td> <td>pRS41y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS42Y</td> <td>pRS42y</td> <td>2-micron-based yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>UNKNOWN</td> <td>unknown</td> <td>unknown vector</td> <td>BACKBONE</td> </tr><tr> <td>PGEX4T1</td> <td>pGEX4T1</td> <td>Vector for bacterial expression</td> <td>BACKBONE</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Vocabulary at 0x7f75482525c0>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## get information about general types"
]
},
{
"cell_type": "code",
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
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"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>description</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DEFAULT_EXPERIMENT</td>\n",
" <td>Default Experiment</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>MATERIALS</td>\n",
" <td>Folder used to organize samples in the Invento...</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>METHODS</td>\n",
" <td>Folder used to organize samples in the Invento...</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <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",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>UNKNOWN</td>\n",
" <td>Unknown</td>\n",
" <td>2016-06-24 10:47:01</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7f7548252438>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
]
},
{
"cell_type": "code",
"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>code</th>\n",
" <th>description</th>\n",
" <th>generatedCodePrefix</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANTIBODY</td>\n",
" <td></td>\n",
" <td>ANT</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CHE</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ENZ</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MED</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>SOL</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>OLI</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>RNA</td>\n",
" <td></td>\n",
" <td>RNA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>PLASMID</td>\n",
" <td></td>\n",
" <td>PLA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>BACTERIA</td>\n",
" <td></td>\n",
" <td>BAC</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
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" <td>YEAST</td>\n",
" <td></td>\n",
" <td>YEA</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <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",
" </tr>\n",
" <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",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>EXPERIMENTAL_STEP</td>\n",
" <td></td>\n",
" <td>EXP</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>GENERAL_PROTOCOL</td>\n",
" <td></td>\n",
" <td>GEN</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>PCR_PROTOCOL</td>\n",
" <td></td>\n",
" <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",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"metadata": {},
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