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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",
"outputs": [
{
"data": {
"text/plain": [
"'admin-190322224519031x6CD252246FDAD84555B20A030E8F60F8'"
]
},
"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"
]
},
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{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'admin-190322225222678x9B6C922E404DB51F1C50A1B9DDFF371B'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.login('admin', 'changeit', save_token=True)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\"@type\": \"as.dto.common.search.SearchResult\", \"@id\": 1, \"objects\": [], \"totalCount\": 4}\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\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>experiment</th>\n",
" <th>sample_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",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"identifier permId experiment sample_type registrator registrationDate modifier modificationDate\n",
"------------ -------- ------------ ------------- ------------- ------------------ ---------- ------------------"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_samples(start_with=1, count=0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"check if session is still active:"
]
},
{
"cell_type": "code",
"outputs": [
{
"data": {
"text/plain": [
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.is_session_active()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"login with a password if the token is no longer valid - and store the token"
]
},
{
"cell_type": "code",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'admin-190318124026896x8877AAC2A7790C251D8AE8A34D40FF1E'"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o = Openbis('https://localhost:8443', verify_certificates=False)\n",
"password = getpass.getpass()\n",
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"you can connect to another openBIS instance if you like to:"
]
},
{
"cell_type": "code",
"execution_count": 82,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-170213105248365xBB06092567F9EE09864C78CDBDB14CA9'"
]
},
"execution_count": 82,
"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": [
"disconnnect (or rather: make the session key invalid):"
]
},
{
"cell_type": "code",
"outputs": [],
"source": [
"o2.logout()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## get general information about openBIS"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Data Store Servers (DSS)"
]
},
{
"cell_type": "code",
"execution_count": 9,
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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>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"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datastores()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"list all available spaces:"
]
},
{
"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>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": [
"<pybis.pybis.Things at 0x7f7ff39e4fd0>"
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_spaces()"
]
},
{
"cell_type": "code",
"execution_count": 9,
"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_NEW_SPACE</td> </tr><tr> <td>permId</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>description</td> <td>this is yet another space</td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2016-07-15 03:02:14</td> </tr><tr> <td>modificationDate</td> <td>2016-07-15 03:02:14</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Space at 0x7f7ff5194898>"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sp = o.get_space('my_new_space')\n",
"# another way: get space number 3 from the list above.\n",
"# sp = o.get_spaces()[3]\n",
"# sp = o.get_spaces()['MY_NEW_SPACE']\n",
{
"cell_type": "markdown",
"metadata": {},
"source": [
"list all the projects within that space"
]
},
{
"cell_type": "code",
"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>/MY_NEW_SPACE/VERMEUL_PROJECT</td>\n",
" <td>20160926234755430-363</td>\n",
" <td>None</td>\n",
" <td>vermeul</td>\n",
" <td>2016-09-26 23:47:55</td>\n",
" <td>admin</td>\n",
" <td>2017-01-20 23:57:45</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7f7ff39e8940>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"get details of the first project in this list"
]
},
{
"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>VERMEUL_PROJECT</td> </tr><tr> <td>description</td> <td>my first project in my space...</td> </tr><tr> <td>permId</td> <td>20160926234755430-363</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>leader</td> <td></td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2016-09-26 23:47:55</td> </tr><tr> <td>modifier</td> <td>admin</td> </tr><tr> <td>modificationDate</td> <td>2017-01-20 23:57:45</td> </tr><tr><td>attachments</td><td>pybis.pdf</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Project at 0x7f6a2776dbe0>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pr = sp.get_projects()[0]\n",
"# this works too:\n",
"# pr = sp.get_projects()['/MY_NEW_SPACE/VERMEUL_PROJECT']\n",
"pr"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**TAB completion**: list all possible attributes and methods by hitting the TAB key"
]
},
{
"cell_type": "code",
},
"outputs": [],
"source": [
"# try it: put the cursor after the dot and press TAB\n",
"pr."
"cell_type": "markdown",
"metadata": {},
"Fetch the experiments that belong to a project"
]
},
{
"cell_type": "code",
"execution_count": 87,
"outputs": [],
"source": [
"pr = o.get_project('/MY_NEW_SPACE/VERMEUL_PROJECT')"
]
},
{
"cell_type": "code",
"execution_count": 88,
"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",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW</td>\n",
" <td>20170127005816666-430</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-27 00:58:17</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-27 00:58:17</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>20160924020719018-358</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>vermeul</td>\n",
" <td>2016-09-24 02:07:19</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-09 00:05:43</td>\n",
" </tr>\n",
" <tr>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
" <td>20161121013609807-402</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-21 01:36:10</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-20 23:41:42</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"0\t/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW\n",
"1\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
"2\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT"
"execution_count": 88,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exs = pr.get_experiments()\n",
"exs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"... using a different approach"
]
},
{
"cell_type": "code",
"execution_count": 90,
"outputs": [
{
"data": {
"text/html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\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",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW</td>\n",
" <td>20170127005816666-430</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>2017-01-27 00:58:17</td>\n",
" <td>2017-01-27 00:58:17</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>20160924020719018-358</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>2016-09-24 02:07:19</td>\n",
" <td>2017-01-09 00:05:43</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
" <td>20161121013609807-402</td>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>None</td>\n",
" <td>2016-11-21 01:36:10</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-20 23:41:42</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
"0\t/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW\n",
"1\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
"2\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT"
"execution_count": 90,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiments(project='/MY_NEW_SPACE/VERMEUL_PROJECT')"
"cell_type": "markdown",
"metadata": {},
"**get vocabulary terms**"
]
},
{
"cell_type": "code",
"execution_count": 24,
"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.masterdata.Vocabulary at 0x7f3140fafeb8>"
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"x = o.get_terms('Backbone')\n",
"x"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## get information about general types"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"OpenBIS categorizes some of its entities in «types»:\n",
"\n",
"* sample type\n",
"* experiment type\n",
"* material type\n",
"* dataset type\n",
"\n",
"The types define the collection of **properties** that can be later assigned to a sample, experiment or dataset."
]
},
{
"cell_type": "code",
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"outputs": [
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" </tr>\n",
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" <th>4</th>\n",
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" <th>5</th>\n",
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" <th>6</th>\n",
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" <th>7</th>\n",
" <td>PLASMID</td>\n",
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" <td>PLA</td>\n",
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" <td></td>\n",
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" </tr>\n",
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" <th>14</th>\n",
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" <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",