{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Working with pybis"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-190613105017193x7338CBACCD9B0721D96EA8D19C3C3965'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://openbis-tst.ethz.ch', verify_certificates=False)\n",
"import getpass\n",
"password = getpass.getpass()\n",
"\n",
"o.login('vermeul',password, save_token=True)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"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>code</th>\n",
" <th>downloadUrl</th>\n",
" <th>remoteUrl</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DSS1</td>\n",
" <td>https://openbis-tst.ethz.ch:443</td>\n",
" <td>http://127.0.0.1:8081</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code downloadUrl remoteUrl\n",
"0 DSS1 https://openbis-tst.ethz.ch:443 http://127.0.0.1:8081"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datastores()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## connect to openBIS\n",
"(using stored session token ~/.pybis/localhost.token)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"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"
]
},
{
"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",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 2,
"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",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'admin-190318124026896x8877AAC2A7790C251D8AE8A34D40FF1E'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis('https://localhost:8443', verify_certificates=False)\n",
"\n",
"import getpass\n",
"password = getpass.getpass()\n",
"\n",
"o.login('admin',password, save_token=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"you can connect to another openBIS instance if you like to:"
]
},
{
"cell_type": "code",
"execution_count": 82,
"metadata": {},
"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",
"execution_count": 29,
"metadata": {},
"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,
"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>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": {},
"source": [
"list all available spaces:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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>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,
"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_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",
"sp"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"list all the projects within that space"
]
},
{
"cell_type": "code",
"execution_count": 10,
"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>/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>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sp.get_projects()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"get details of the first project in this list"
]
},
{
"cell_type": "code",
"execution_count": 4,
"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>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>"
]
},
"execution_count": 4,
"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",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# try it: put the cursor after the dot and press TAB\n",
"pr."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Fetch the experiments that belong to a project"
]
},
{
"cell_type": "code",
"execution_count": 87,
"metadata": {},
"outputs": [],
"source": [
"pr = o.get_project('/MY_NEW_SPACE/VERMEUL_PROJECT')"
]
},
{
"cell_type": "code",
"execution_count": 88,
"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>/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",
" <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>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,
"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>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>/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",
" <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>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": 90,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiments(project='/MY_NEW_SPACE/VERMEUL_PROJECT')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**get vocabulary terms**"
]
},
{
"cell_type": "code",
"execution_count": 24,
"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>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",
"execution_count": 12,
"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>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 0x7f7ff3996a20>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiment_types()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"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>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>CHEMICAL</td>\n",
" <td></td>\n",
" <td>CHE</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ENZYME</td>\n",
" <td></td>\n",
" <td>ENZ</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MEDIA</td>\n",
" <td></td>\n",
" <td>MED</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>SOLUTION_BUFFER</td>\n",
" <td></td>\n",
" <td>SOL</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>OLIGO</td>\n",
" <td></td>\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",
" <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": [
"<pybis.pybis.Things at 0x7f7ff399dbe0>"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_sample_types()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"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>code</th>\n",
" <th>description</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>MY_VERY_EXCITING_MATERIAL</td>\n",
" <td>looks like dirt and probably is dirt</td>\n",
" <td>2016-09-24 00:46:19</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7f7ff399d518>"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_material_types()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"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>code</th>\n",
" <th>description</th>\n",
" <th>kind</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ELN_PREVIEW</td>\n",
" <td>ELN Preview image</td>\n",
" <td>PHYSICAL</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>SEQ_FILE</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>RAW_DATA</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" <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": "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": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Experiment successfully updated.\n"
]
}
],
"source": [
"e0.save()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"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>properties</th>\n",
" <th>type</th>\n",
" <th>experiment</th>\n",
" <th>sample</th>\n",
" <th>registrationDate</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>20170106004736870-407</td>\n",
" <td>{'NAME': 'dunno'}</td>\n",
" <td>ANALYZED_DATA</td>\n",
" <td>/MATERIALS/YEASTS/MY_FIRST_EXPERIMENT_WITH_PRO...</td>\n",
" <td>None</td>\n",
" <td>2017-01-06 00:47:37</td>\n",
" <td>2017-01-06 00:47:37</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fbb3966a4e0>"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e0.get_datasets()"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"scrolled": true
},
"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 0x7fbb39647eb8>"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e0"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'End Date': 'TIMESTAMP', 'syntax': 'YYYY-MM-DD HH:MIN:SS'}"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e0.p.end_date_"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"e_new = o.new_experiment('DEFAULT_EXPERIMENT')"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"e_new.project ='VERMEUL_PROJECT'"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"e_new.tags = 'too_late'"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"e_new.code = 'exp_new'"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Experiment successfully created.\n"
]
}
],
"source": [
"e_new.save()"
]
},
{
"cell_type": "code",
"execution_count": 45,
"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_EXPERIMENT007</td> </tr><tr> <td>permId</td> <td>20161004220718730-373</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td> </tr><tr> <td>type</td> <td>DEFAULT_EXPERIMENT</td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>project</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-12-20 um 10.47.26.png<br/>Ein Saurier.txt</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Experiment at 0x7f3140f55400>"
]
},
"execution_count": 45,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e = o.get_experiment('/MATERIALS/YEASTS/MY_EXPERIMENT007')\n",
"e"
]
},
{
"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>MY_EXPERIMENT007</td> </tr><tr> <td>permId</td> <td>20161004220718730-373</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td> </tr><tr> <td>type</td> <td>DEFAULT_EXPERIMENT</td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>project</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-12-20 um 10.47.26.png<br/>Ein Saurier.txt</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Experiment at 0x7fd2241efc18>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiment('20161004220718730-373')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"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>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",
" <tr>\n",
" <th>0</th>\n",
" <td>/MATERIALS/FLY43</td>\n",
" <td>20170104000802333-404</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:02</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/MATERIALS/FLY45</td>\n",
" <td>20170104000847172-405</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:36:09</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fd223f3f208>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e.get_samples()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"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>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",
" <tr>\n",
" <th>0</th>\n",
" <td>/MATERIALS/FLY43</td>\n",
" <td>20170104000802333-404</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:02</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/MATERIALS/FLY45</td>\n",
" <td>20170104000847172-405</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:36:09</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fd223f3f8d0>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_samples(experiment='20161004220718730-373')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"get all experiment with a given property"
]
},
{
"cell_type": "code",
"execution_count": 15,
"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>code</th>\n",
" <th>identifier</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>MY_EXPERIMENT013</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT013</td>\n",
" <td>YEASTS</td>\n",
" <td>DEFAULT_EXPERIMENT</td>\n",
" <td></td>\n",
" <td>2016-10-04 22:09:15</td>\n",
" <td></td>\n",
" <td>2016-12-23 16:58:43</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fd223f4c860>"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiments(is_finished=False, name='blast')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### updating an experiment."
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>property</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>name</td> <td>blast</td> </tr><tr> <td>show_in_project_overview</td> <td></td> </tr><tr> <td>finished_flag</td> <td>False</td> </tr><tr> <td>experimental_goals</td> <td></td> </tr><tr> <td>grant</td> <td></td> </tr><tr> <td>start_date</td> <td></td> </tr><tr> <td>end_date</td> <td></td> </tr><tr> <td>experimental_results</td> <td></td> </tr><tr> <td>xmlcomments</td> <td></td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.property.PropertyHolder at 0x7f768c61a748>"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ex = o.get_experiments(type='DEFAULT_EXPERIMENT')[0]\n",
"ex.p"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
"ex.set_properties({'FINISHED_FLAG': False})"
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"e = o.new_experiment('/MATERIALS/YEASTS', 'my_experiment0815', 'DEFAULT_EXPERIMENT', properties={\"Name\":\"blast\"})"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"e3.delete(reason='it was just an experiment')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## working with samples"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"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>YEA34</td> </tr><tr> <td>permId</td> <td>20161108230958839-384</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/YEA34</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>tags</td> <td>['uno']</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-12-20 um 10.47.26.png<br/>testfile</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f9c08388358>"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sa = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
"sa"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>property</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>name</td> <td></td> </tr><tr> <td>show_in_project_overview</td> <td>False</td> </tr><tr> <td>owner</td> <td></td> </tr><tr> <td>owner_number</td> <td></td> </tr><tr> <td>genetic_modification</td> <td></td> </tr><tr> <td>genetic_background</td> <td></td> </tr><tr> <td>mating_type</td> <td>DIPLOID</td> </tr><tr> <td>background-specific_markers</td> <td></td> </tr><tr> <td>common_markers</td> <td></td> </tr><tr> <td>endogenous_plasmid</td> <td></td> </tr><tr> <td>origin</td> <td></td> </tr><tr> <td>strain_check</td> <td></td> </tr><tr> <td>source</td> <td></td> </tr><tr> <td>publication</td> <td></td> </tr><tr> <td>notes</td> <td></td> </tr><tr> <td>xmlcomments</td> <td></td> </tr><tr> <td>annotations_state</td> <td></td> </tr><tr> <td>storage_names</td> <td></td> </tr><tr> <td>storage_row</td> <td></td> </tr><tr> <td>storage_column</td> <td></td> </tr><tr> <td>storage_box_name</td> <td></td> </tr><tr> <td>storage_box_size</td> <td></td> </tr><tr> <td>storage_user</td> <td></td> </tr><tr> <td>storage_position</td> <td></td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.property.PropertyHolder at 0x7f9c083883c8>"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sa.props"
]
},
{
"cell_type": "code",
"execution_count": 5,
"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>Bildschirmfoto 2016-12-20 um 10.47.26.png</td>\n",
" <td>nocheinfoto</td>\n",
" <td>None</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>testfile</td>\n",
" <td>None</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 Bildschirmfoto 2016-12-20 um 10.47.26.png nocheinfoto None 1\n",
"1 testfile None None 1"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sa.get_attachments()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"sa.add_attachment('testfile')"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully updated\n"
]
}
],
"source": [
"sa.save()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"localhost/20161108230958839-384/Bildschirmfoto 2016-12-20 um 10.47.26.png\n",
"localhost/20161108230958839-384/testfile\n"
]
}
],
"source": [
"sa.download_attachments()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"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>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",
" <tr>\n",
" <th>0</th>\n",
" <td>/VERMEUL/ANOTHER_SAMPLE1</td>\n",
" <td>20160706001644827-208</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-07-06 00:16:45</td>\n",
" <td></td>\n",
" <td>2016-11-09 10:18:18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/VERMEUL/BLAJLSD</td>\n",
" <td>20160630111949369-89</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-06-30 17:19:49</td>\n",
" <td></td>\n",
" <td>2016-06-30 17:19:49</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>/MY_NEW_SPACE/CHILD_OF_SAMPLE1</td>\n",
" <td>20160705234504004-206</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-07-05 23:45:04</td>\n",
" <td></td>\n",
" <td>2016-10-07 01:05:46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>20160630105304285-81</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-06-30 16:53:04</td>\n",
" <td></td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA</td>\n",
" <td>20160630110733527-86</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-06-30 17:07:34</td>\n",
" <td></td>\n",
" <td>2016-07-06 00:11:45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA3</td>\n",
" <td>20160630112720553-90</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-06-30 17:27:21</td>\n",
" <td></td>\n",
" <td>2016-06-30 17:27:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA5</td>\n",
" <td>20160706231053756-211</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-07-06 23:10:54</td>\n",
" <td></td>\n",
" <td>2016-07-06 23:10:54</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>/VERMEUL/YET_ANOTHER_SAMPLE1</td>\n",
" <td>20160706002555747-209</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td></td>\n",
" <td>2016-07-06 00:25:56</td>\n",
" <td></td>\n",
" <td>2016-11-09 10:18:18</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7f2e99f1a518>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_samples(space='VERMEUL', tags=['*'])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"get the first sample of the above list and just display the basic attributes"
]
},
{
"cell_type": "code",
"execution_count": 11,
"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>YEA21</td> </tr><tr> <td>permId</td> <td>20161025010638912-382</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/YEA21</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>['do', 'fa', 're']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f8ff54adb38>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/YEA21')\n",
"s"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Show all the properties assigned to this sample type:"
]
},
{
"cell_type": "code",
"execution_count": 6,
"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 0x7f8ff55c26d8>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.type"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"however, you still can check whether the sample type corresponds to a certain string:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.type == 'YEAST'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"get experiment related to that sample"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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_SPECIAL_EXPERIMENT</td> </tr><tr> <td>permId</td> <td>20161121013609807-402</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>project</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Experiment at 0x7f2e99ceee48>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.experiment"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<p>ExperimentType: <b>UNKNOWN</b>\n",
"<p>description: Unknown</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",
" \n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.property.PropertyAssignments at 0x7f2e99cf6ef0>"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.experiment.type"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.experiment.type == 'UNKNOWN'"
]
},
{
"cell_type": "code",
"execution_count": 12,
"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>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>PROJECT_ONE</td>\n",
" <td>VERMEUL</td>\n",
" <td></td>\n",
" <td>2017-01-15 22:01:58</td>\n",
" <td></td>\n",
" <td>2017-01-15 22:02:59</td>\n",
" <td>20170115220158336-410</td>\n",
" <td>/VERMEUL/PROJECT_ONE</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>PROTOCOLS</td>\n",
" <td>METHODS</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>20160624054751885-39</td>\n",
" <td>/METHODS/PROTOCOLS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</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",
" <th>8</th>\n",
" <td>VERMEUL_PROJECT</td>\n",
" <td>MY_NEW_SPACE</td>\n",
" <td></td>\n",
" <td>2016-09-26 23:47:55</td>\n",
" <td></td>\n",
" <td>2017-01-09 01:33:37</td>\n",
" <td>20160926234755430-363</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\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": [
"<pybis.pybis.Things at 0x7f2e99b5d9b0>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_projects()"
]
},
{
"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>YEA21</td> </tr><tr> <td>permId</td> <td>20161025010638912-382</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/YEA21</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>['do', 'fa', 're']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f8ff55c2e10>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"list all the properties (p) of a given sample"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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>URA3_HIS3_LEU2</td> <td>ura3- his3- leu2-</td> <td>The strain is a uracil, histidine, and leucine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>URA3_HIS3</td> <td>ura3- his3-</td> <td>The strain is a uracil and histidine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>URA3_LEU2</td> <td>ura3- leu2-</td> <td>The strain is a uracil and leucine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>URA3</td> <td>ura3-</td> <td>The strain is a uracil auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>HIS3_LEU2</td> <td>his3- leu2-</td> <td>The strain is a histidine and leucine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>HIS3</td> <td>his3-</td> <td>The strain is a histidine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>LEU2</td> <td>leu2-</td> <td>The strain is a leucine auxotroph</td> <td>COMMON_MARKERS</td> </tr><tr> <td>NONE</td> <td>none</td> <td>The strain does not have any background-specific auxotrophies</td> <td>COMMON_MARKERS</td> </tr><tr> <td>UNKNOWN</td> <td>unknown</td> <td>No information about the auxotrophy</td> <td>COMMON_MARKERS</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Vocabulary at 0x7f6b74235358>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.props.common_markers_"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"fetch just a single property: sample.p.«property_name»"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'comments: publication in my office'"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.p.publication"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"if you don't know the controlled vocabulary of a property, just add an underscore and press shift-enter:"
]
},
{
"cell_type": "code",
"execution_count": 15,
"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.pybis.Vocabulary at 0x7efe6097d828>"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.p.mating_type_"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"pybis will automatically check the controlled vocabulary when you assign a value to it:"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "Value must be one of these terms: A, ALPHA, DIPLOID, UNKNOWN",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mValueError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-24-d4d5f6a664c5>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0ms\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmating_type\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'invalid content'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;32m/vagrant_python/PyBis/pybis/pybis.py\u001b[0m in \u001b[0;36m__setattr__\u001b[1;34m(self, name, value)\u001b[0m\n\u001b[0;32m 2122\u001b[0m \u001b[0mvoc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_openbis\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_terms\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2123\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mvoc\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mterms\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 2124\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"Value must be one of these terms: \"\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;34m\", \"\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mvoc\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mterms\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2125\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0mdata_type\u001b[0m \u001b[1;32min\u001b[0m \u001b[1;33m(\u001b[0m\u001b[1;34m'INTEGER'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'BOOLEAN'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'VARCHAR'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2126\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mcheck_datatype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdata_type\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mValueError\u001b[0m: Value must be one of these terms: A, ALPHA, DIPLOID, UNKNOWN"
]
}
],
"source": [
"s.p.mating_type = 'invalid content'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"some properties are of a general type. Again, you can list it by adding an underscore _ :"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'Storage Column': 'INTEGER'}"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.p.storage_column_"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"### alter a sample and its properties"
]
},
{
"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": "code",
"execution_count": 6,
"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>FLY45</td> </tr><tr> <td>permId</td> <td>20170104000847172-405</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/FLY45</td> </tr><tr> <td>type</td> <td>FLY</td> </tr><tr> <td>parents</td> <td>['/MATERIALS/FLY43']</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>space</td> <td>MATERIALS</td> </tr><tr> <td>experiment</td> <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td>openBIS JSON-RPC.md</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7faa0c089828>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample = o.get_sample('/MATERIALS/FLY45')\n",
"sample"
]
},
{
"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>property</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>name</td> <td>a fly45 which is the child of fly43</td> </tr><tr> <td>show_in_project_overview</td> <td>False</td> </tr><tr> <td>owner</td> <td></td> </tr><tr> <td>owner_number</td> <td></td> </tr><tr> <td>genetic_modification</td> <td></td> </tr><tr> <td>fly_genotype</td> <td></td> </tr><tr> <td>associated_gene</td> <td></td> </tr><tr> <td>markers</td> <td></td> </tr><tr> <td>origin</td> <td></td> </tr><tr> <td>strain_check</td> <td></td> </tr><tr> <td>source</td> <td></td> </tr><tr> <td>mating_partners</td> <td></td> </tr><tr> <td>publication</td> <td></td> </tr><tr> <td>notes</td> <td></td> </tr><tr> <td>xmlcomments</td> <td><root>\n",
" <commentEntry date=\"1483484927350\" person=\"vermeul\"/>\n",
"</root>\n",
"</td> </tr><tr> <td>annotations_state</td> <td>�(undefined)</td> </tr><tr> <td>storage_names</td> <td></td> </tr><tr> <td>storage_row</td> <td></td> </tr><tr> <td>storage_column</td> <td></td> </tr><tr> <td>storage_box_name</td> <td></td> </tr><tr> <td>storage_box_size</td> <td></td> </tr><tr> <td>storage_user</td> <td></td> </tr><tr> <td>storage_position</td> <td></td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.PropertyHolder at 0x7faa0c089a20>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample.props"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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>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",
" <tr>\n",
" <th>0</th>\n",
" <td>/MATERIALS/FLY43</td>\n",
" <td>20170104000802333-404</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:02</td>\n",
" <td></td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7faa0c0de940>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample.get_parents()"
]
},
{
"cell_type": "code",
"execution_count": 65,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'sample' is not defined",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mNameError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-65-066328cddbd3>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0msample\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_datasets\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;31mNameError\u001b[0m: name 'sample' is not defined"
]
}
],
"source": [
"sample.get_datasets()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Files downloaded to: localhost/20170104003608559-406\n"
]
}
],
"source": [
"sample.get_datasets()[0].download()"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"localhost/20170104003608559-406\r\n",
"localhost/20170104003608559-406/original\r\n",
"localhost/20170104003608559-406/original/jupyter_useage_lab.zip\r\n"
]
}
],
"source": [
"!find localhost/20170104003608559-406"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"s_up = o.get_sample('/VERMEUL/MY_WONDERFUL_SAMPLE_NAME')"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"s_up.space = 'ANOTHER_SPACE_NAME'"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"s_up.tags = ['one', 'two', 'three']"
]
},
{
"cell_type": "code",
"execution_count": 22,
"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>identifier</td> <td>/VERMEUL/MY_WONDERFUL_SAMPLE_NAME</td> </tr><tr> <td>permId</td> <td>20160720225637704-262</td> </tr><tr> <td>code</td> <td>MY_WONDERFUL_SAMPLE_NAME</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>space</td> <td>ANOTHER_SPACE_NAME</td> </tr><tr> <td>project</td> <td>None</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>tags</td> <td>['one', 'two', 'three']</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7efe60915668>"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_up"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully updated\n"
]
}
],
"source": [
"s_up.save()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### create a new sample"
]
},
{
"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": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Experiment\n"
]
},
{
"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>YEAST_COLLECTION_1</td> </tr><tr> <td>permId</td> <td>20160624054739283-9</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/YEAST_COLLECTION_1</td> </tr><tr> <td>type</td> <td>MATERIALS</td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>project</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Experiment at 0x7f56f2f17b38>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_experiments()[31]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"to create a new sample, the sampletype must be specified"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"s_new = o.new_sample(type='YEAST', space='VERMEUL', parents=['/VERMEUL/BLAJLSD'])"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"s_new = o.new_sample(type='YEAST', space='VERMEUL')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"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></td> </tr><tr> <td>permId</td> <td></td> </tr><tr> <td>identifier</td> <td></td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td></td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"----------- -------\n",
"code\n",
"permId\n",
"identifier\n",
"type YEAST\n",
"project\n",
"parents\n",
"children\n",
"components\n",
"space VERMEUL\n",
"experiment\n",
"tags []"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"s_new.add_parents('/VERMEUL/BLAJLSD')"
]
},
{
"cell_type": "code",
"execution_count": 13,
"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></td> </tr><tr> <td>permId</td> <td></td> </tr><tr> <td>identifier</td> <td></td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>['/VERMEUL/BLAJLSD']</td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"----------- --------------------\n",
"code\n",
"permId\n",
"identifier\n",
"type YEAST\n",
"project\n",
"parents ['/VERMEUL/BLAJLSD']\n",
"children\n",
"components\n",
"space VERMEUL\n",
"experiment\n",
"tags []"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new"
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {},
"outputs": [],
"source": [
"s_new.get_parents()"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully created.\n"
]
},
{
"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>YEA86</td> </tr><tr> <td>permId</td> <td>20180926000051715-743</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA86</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"----------- ---------------------\n",
"code YEA86\n",
"permId 20180926000051715-743\n",
"identifier /VERMEUL/YEA86\n",
"type YEAST\n",
"project\n",
"parents []\n",
"children []\n",
"components []\n",
"space VERMEUL\n",
"experiment\n",
"tags []"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new.save()"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample 20180926000051715-743 successfully deleted.\n"
]
}
],
"source": [
"s_new.delete('dfd')"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully created.\n"
]
},
{
"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>YEA85</td> </tr><tr> <td>permId</td> <td>20180925234950217-726</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA85</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"----------- ---------------------\n",
"code YEA85\n",
"permId 20180925234950217-726\n",
"identifier /VERMEUL/YEA85\n",
"type YEAST\n",
"project\n",
"parents []\n",
"children []\n",
"components []\n",
"space VERMEUL\n",
"experiment\n",
"tags []"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new.save()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-180926010643993x968AC0C20F32D8AE95DF2E00E2291B8B'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis('https://localhost:8443', verify_certificates=False)\n",
"\n",
"import getpass\n",
"password = getpass.getpass()\n",
"\n",
"o.login('vermeul',password, save_token=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"o.get_samples(chil)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"s_new = o.get_sample('20180925234950217-726')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 18,
"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>YEA65</td> </tr><tr> <td>permId</td> <td>20170227154403209-436</td> </tr><tr> <td>identifier</td> <td>/VERMEUL/YEA65</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>parents</td> <td>['/VERMEUL/YEA67', '/VERMEUL/YEA68', '/VERMEUL/YEA64']</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>components</td> <td>[]</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"----------- ------------------------------------------------------\n",
"code YEA65\n",
"permId 20170227154403209-436\n",
"identifier /VERMEUL/YEA65\n",
"type YEAST\n",
"project\n",
"parents ['/VERMEUL/YEA67', '/VERMEUL/YEA68', '/VERMEUL/YEA64']\n",
"children []\n",
"components []\n",
"space VERMEUL\n",
"experiment\n",
"tags []"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"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",
" <tr>\n",
" <th>0</th>\n",
" <td>/VERMEUL/ANOTHER_SAMPLE1</td>\n",
" <td>20160706001644827-208</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-07-06 00:16:45</td>\n",
" <td>vermeul</td>\n",
" <td>2017-11-02 18:27:37</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/ELN_SETTINGS/BENCH</td>\n",
" <td>20171208173222809-574</td>\n",
" <td>/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION</td>\n",
" <td>STORAGE</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>/VERMEUL/BLAJLSD</td>\n",
" <td>20160630111949369-89</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-06-30 17:19:49</td>\n",
" <td>vermeul</td>\n",
" <td>2017-06-22 02:40:01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>/MY_NEW_SPACE/CHILD_OF_SAMPLE1</td>\n",
" <td>20160705234504004-206</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-07-05 23:45:04</td>\n",
" <td>vermeul</td>\n",
" <td>2017-09-20 14:12:03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_112532</td>\n",
" <td>20171211112551150-600</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:25:51</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:25:51</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_112859</td>\n",
" <td>20171211112918769-603</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:29:19</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:29:19</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123501</td>\n",
" <td>20171211123518060-606</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:35:18</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:35:18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123653</td>\n",
" <td>20171211123710443-609</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:37:10</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:37:10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123736</td>\n",
" <td>20171211123753331-612</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:37:53</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:37:53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_123757</td>\n",
" <td>20171211123813756-615</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:38:14</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 12:38:14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171211_134640</td>\n",
" <td>20171211134641170-618</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 13:46:41</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 13:46:41</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_MON_171218_164249</td>\n",
" <td>20171218164250384-644</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-18 16:42:50</td>\n",
" <td>admin</td>\n",
" <td>2017-12-18 16:42:50</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_TUE_171219_110150</td>\n",
" <td>20171219110155327-649</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-19 11:01:55</td>\n",
" <td>admin</td>\n",
" <td>2017-12-19 11:01:55</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223411</td>\n",
" <td>20180227223408486-680</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:08</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:08</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223429</td>\n",
" <td>20180227223426765-684</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:27</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:27</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_TUE_180227_223705</td>\n",
" <td>20180227223703438-688</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:37:03</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:37:03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_WED_180228_102753</td>\n",
" <td>20180228102751116-695</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:27:51</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:27:51</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_WED_180228_102803</td>\n",
" <td>20180228102800818-697</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:28:01</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:28:01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_WED_180228_103709</td>\n",
" <td>20180228103707200-701</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:37:07</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 10:37:07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>/DEFAULT/CHILD_SAMPLE_WED_180228_171049</td>\n",
" <td>20180228171050238-715</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 17:10:50</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-28 17:10:50</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>/ELN_SETTINGS/DEFAULT_STORAGE</td>\n",
" <td>20171208173222809-575</td>\n",
" <td>/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION</td>\n",
" <td>STORAGE</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>/VERMEUL/EXP1</td>\n",
" <td>20170124170850531-422</td>\n",
" <td>/VERMEUL/PROJECT_ONE/PROJECT_ONE_EXP_1</td>\n",
" <td>EXPERIMENTAL_STEP</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-24 17:08:51</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-25 17:26:25</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>/MATERIALS/FLY43</td>\n",
" <td>20170104000802333-404</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-04 00:08:02</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 10:04:19</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>/MATERIALS/FLY45</td>\n",
" <td>20170104000847172-405</td>\n",
" <td>/MATERIALS/YEASTS/MY_EXPERIMENT007</td>\n",
" <td>FLY</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-04 00:08:47</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-04 00:36:09</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>/MY_NEW_SPACE/FLY51</td>\n",
" <td>20170120010813349-416</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>FLY</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-20 01:08:13</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-15 14:41:20</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>/VERMEUL/FLY84</td>\n",
" <td>20180831174909928-725</td>\n",
" <td>None</td>\n",
" <td>FLY</td>\n",
" <td>vermeul</td>\n",
" <td>2018-08-31 17:49:10</td>\n",
" <td>vermeul</td>\n",
" <td>2018-08-31 17:49:10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>/ELN_SETTINGS/GENERAL_ELN_SETTINGS</td>\n",
" <td>20171208173222969-576</td>\n",
" <td>None</td>\n",
" <td>GENERAL_ELN_SETTINGS</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:32:23</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>20160630105304285-81</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-06-30 16:53:04</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:22:52</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>/VERMEUL/HOW_WONDERFUL2</td>\n",
" <td>20160630105337180-82</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-06-30 16:53:37</td>\n",
" <td>vermeul</td>\n",
" <td>2016-07-22 11:20:03</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>/VERMEUL/HOW_WONDERFUL3</td>\n",
" <td>20160630105402002-83</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-06-30 16:54:02</td>\n",
" <td>vermeul</td>\n",
" <td>2016-06-30 16:54:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>63</th>\n",
" <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_000946</td>\n",
" <td>20171004000946100-531</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:09:46</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:09:46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>64</th>\n",
" <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_001010</td>\n",
" <td>20171004001010530-534</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:10:11</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:10:11</td>\n",
" </tr>\n",
" <tr>\n",
" <th>65</th>\n",
" <td>/DEFAULT/TEST_GET_BY_PERMID_WED_171004_001021</td>\n",
" <td>20171004001020929-537</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:10:21</td>\n",
" <td>admin</td>\n",
" <td>2017-10-04 00:10:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>66</th>\n",
" <td>/DEFAULT/TEST_SAMPLE_FRI_171208_174600</td>\n",
" <td>20171208174559963-591</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:46:00</td>\n",
" <td>admin</td>\n",
" <td>2017-12-08 17:46:00</td>\n",
" </tr>\n",
" <tr>\n",
" <th>67</th>\n",
" <td>/DEFAULT/TEST_SAMPLE_MON_171211_105927</td>\n",
" <td>20171211105946839-592</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 10:59:47</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 10:59:47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>68</th>\n",
" <td>/DEFAULT/TEST_SAMPLE_MON_171211_110318</td>\n",
" <td>20171211110357956-594</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:03:58</td>\n",
" <td>admin</td>\n",
" <td>2017-12-11 11:03:58</td>\n",
" </tr>\n",
" <tr>\n",
" <th>69</th>\n",
" <td>/DEFAULT/TEST_SAMPLE_TUE_180227_223409</td>\n",
" <td>20180227223406110-677</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:06</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>70</th>\n",
" <td>/DEFAULT/TEST_SAMPLE_TUE_180227_223428</td>\n",
" <td>20180227223424887-681</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:25</td>\n",
" <td>vermeul</td>\n",
" <td>2018-02-27 22:34:25</td>\n",
" </tr>\n",
" <tr>\n",
" <th>71</th>\n",
" <td>/MY_NEW_SPACE/YEA21</td>\n",
" <td>20161025010638912-382</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-10-25 01:06:39</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-19 00:02:53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>72</th>\n",
" <td>/MY_NEW_SPACE/YEA34</td>\n",
" <td>20161108230958839-384</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:09:59</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-25 23:48:14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>73</th>\n",
" <td>/VERMEUL/YEA35</td>\n",
" <td>20161108231507755-385</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:15:08</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:15:08</td>\n",
" </tr>\n",
" <tr>\n",
" <th>74</th>\n",
" <td>/VERMEUL/YEA36</td>\n",
" <td>20161108231536195-386</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:15:36</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:15:36</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75</th>\n",
" <td>/VERMEUL/YEA37</td>\n",
" <td>20161108231604599-387</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:16:05</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:16:05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>76</th>\n",
" <td>/MY_NEW_SPACE/YEA38</td>\n",
" <td>20161108232203635-388</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:22:04</td>\n",
" <td>vermeul</td>\n",
" <td>2017-01-18 17:16:50</td>\n",
" </tr>\n",
" <tr>\n",
" <th>77</th>\n",
" <td>/VERMEUL/YEA39</td>\n",
" <td>20161108232240159-389</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:22:40</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:22:40</td>\n",
" </tr>\n",
" <tr>\n",
" <th>78</th>\n",
" <td>/VERMEUL/YEA40</td>\n",
" <td>20161108233530315-390</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:35:30</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-08 23:35:30</td>\n",
" </tr>\n",
" <tr>\n",
" <th>79</th>\n",
" <td>/VERMEUL/YEA41</td>\n",
" <td>20161109142859057-391</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-09 14:28:59</td>\n",
" <td>vermeul</td>\n",
" <td>2016-11-09 14:28:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>80</th>\n",
" <td>/VERMEUL/YEA63</td>\n",
" <td>20170227104527381-434</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 10:45:27</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 10:45:27</td>\n",
" </tr>\n",
" <tr>\n",
" <th>81</th>\n",
" <td>/VERMEUL/YEA64</td>\n",
" <td>20170227104651646-435</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 10:46:52</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 15:51:34</td>\n",
" </tr>\n",
" <tr>\n",
" <th>82</th>\n",
" <td>/VERMEUL/YEA65</td>\n",
" <td>20170227154403209-436</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-02-27 15:44:03</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 12:21:05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>83</th>\n",
" <td>/VERMEUL/YEA66</td>\n",
" <td>20170323101102451-441</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-23 10:11:02</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 12:21:05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>84</th>\n",
" <td>/VERMEUL/YEA67</td>\n",
" <td>20170327113258723-442</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 11:32:59</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 12:03:46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>85</th>\n",
" <td>/VERMEUL/YEA68</td>\n",
" <td>20170327122105199-443</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 12:21:05</td>\n",
" <td>vermeul</td>\n",
" <td>2017-03-27 12:25:41</td>\n",
" </tr>\n",
" <tr>\n",
" <th>86</th>\n",
" <td>/VERMEUL/YEA71</td>\n",
" <td>20170518112158124-516</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:21:58</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:21:58</td>\n",
" </tr>\n",
" <tr>\n",
" <th>87</th>\n",
" <td>/VERMEUL/YEA72</td>\n",
" <td>20170518112248330-517</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:22:48</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:22:48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>88</th>\n",
" <td>/VERMEUL/YEA73</td>\n",
" <td>20170518112726306-519</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:27:26</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:27:26</td>\n",
" </tr>\n",
" <tr>\n",
" <th>89</th>\n",
" <td>/VERMEUL/YEA74</td>\n",
" <td>20170518112739712-520</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:27:40</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:27:40</td>\n",
" </tr>\n",
" <tr>\n",
" <th>90</th>\n",
" <td>/VERMEUL/YEA75</td>\n",
" <td>20170518112808649-521</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:28:09</td>\n",
" <td>vermeul</td>\n",
" <td>2017-05-18 11:28:12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>91</th>\n",
" <td>/VERMEUL/YEA76</td>\n",
" <td>20171215141946133-620</td>\n",
" <td>None</td>\n",
" <td>YEAST</td>\n",
" <td>admin</td>\n",
" <td>2017-12-15 14:19:46</td>\n",
" <td>admin</td>\n",
" <td>2017-12-15 14:19:46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>92</th>\n",
" <td>/VERMEUL/YET_ANOTHER_SAMPLE1</td>\n",
" <td>20160706002555747-209</td>\n",
" <td>None</td>\n",
" <td>UNKNOWN</td>\n",
" <td>vermeul</td>\n",
" <td>2016-07-06 00:25:56</td>\n",
" <td>vermeul</td>\n",
" <td>2017-06-22 10:56:33</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>93 rows × 8 columns</p>\n",
"</div>"
],
"text/plain": [
" identifier permId experiment sample_type registrator registrationDate modifier modificationDate\n",
"-- --------------------------------------------- --------------------- --------------------------------------------------- -------------------- ------------- ------------------- ---------- -------------------\n",
" 0 /VERMEUL/ANOTHER_SAMPLE1 20160706001644827-208 None UNKNOWN vermeul 2016-07-06 00:16:45 vermeul 2017-11-02 18:27:37\n",
" 1 /ELN_SETTINGS/BENCH 20171208173222809-574 /ELN_SETTINGS/STORAGES/STORAGES_COLLECTION STORAGE admin 2017-12-08 17:32:23 admin 2017-12-08 17:32:23\n",
" 2 /VERMEUL/BLAJLSD 20160630111949369-89 None UNKNOWN vermeul 2016-06-30 17:19:49 vermeul 2017-06-22 02:40:01\n",
" 3 /MY_NEW_SPACE/CHILD_OF_SAMPLE1 20160705234504004-206 None UNKNOWN vermeul 2016-07-05 23:45:04 vermeul 2017-09-20 14:12:03\n",
" 4 /DEFAULT/CHILD_SAMPLE_MON_171211_112532 20171211112551150-600 None UNKNOWN admin 2017-12-11 11:25:51 admin 2017-12-11 11:25:51\n",
" 5 /DEFAULT/CHILD_SAMPLE_MON_171211_112859 20171211112918769-603 None UNKNOWN admin 2017-12-11 11:29:19 admin 2017-12-11 11:29:19\n",
" 6 /DEFAULT/CHILD_SAMPLE_MON_171211_123501 20171211123518060-606 None UNKNOWN admin 2017-12-11 12:35:18 admin 2017-12-11 12:35:18\n",
" 7 /DEFAULT/CHILD_SAMPLE_MON_171211_123653 20171211123710443-609 None UNKNOWN admin 2017-12-11 12:37:10 admin 2017-12-11 12:37:10\n",
" 8 /DEFAULT/CHILD_SAMPLE_MON_171211_123736 20171211123753331-612 None UNKNOWN admin 2017-12-11 12:37:53 admin 2017-12-11 12:37:53\n",
" 9 /DEFAULT/CHILD_SAMPLE_MON_171211_123757 20171211123813756-615 None UNKNOWN admin 2017-12-11 12:38:14 admin 2017-12-11 12:38:14\n",
"10 /DEFAULT/CHILD_SAMPLE_MON_171211_134640 20171211134641170-618 None UNKNOWN admin 2017-12-11 13:46:41 admin 2017-12-11 13:46:41\n",
"11 /DEFAULT/CHILD_SAMPLE_MON_171218_164249 20171218164250384-644 None UNKNOWN admin 2017-12-18 16:42:50 admin 2017-12-18 16:42:50\n",
"12 /DEFAULT/CHILD_SAMPLE_TUE_171219_110150 20171219110155327-649 None UNKNOWN admin 2017-12-19 11:01:55 admin 2017-12-19 11:01:55\n",
"13 /DEFAULT/CHILD_SAMPLE_TUE_180227_223411 20180227223408486-680 None UNKNOWN vermeul 2018-02-27 22:34:08 vermeul 2018-02-27 22:34:08\n",
"14 /DEFAULT/CHILD_SAMPLE_TUE_180227_223429 20180227223426765-684 None UNKNOWN vermeul 2018-02-27 22:34:27 vermeul 2018-02-27 22:34:27\n",
"15 /DEFAULT/CHILD_SAMPLE_TUE_180227_223705 20180227223703438-688 None UNKNOWN vermeul 2018-02-27 22:37:03 vermeul 2018-02-27 22:37:03\n",
"16 /DEFAULT/CHILD_SAMPLE_WED_180228_102753 20180228102751116-695 None UNKNOWN vermeul 2018-02-28 10:27:51 vermeul 2018-02-28 10:27:51\n",
"17 /DEFAULT/CHILD_SAMPLE_WED_180228_102803 20180228102800818-697 None UNKNOWN vermeul 2018-02-28 10:28:01 vermeul 2018-02-28 10:28:01\n",
"18 /DEFAULT/CHILD_SAMPLE_WED_180228_103709 20180228103707200-701 None UNKNOWN vermeul 2018-02-28 10:37:07 vermeul 2018-02-28 10:37:07\n",
"19 /DEFAULT/CHILD_SAMPLE_WED_180228_171049 20180228171050238-715 None UNKNOWN vermeul 2018-02-28 17:10:50 vermeul 2018-02-28 17:10:50\n",
"20 /ELN_SETTINGS/DEFAULT_STORAGE 20171208173222809-575 /ELN_SETTINGS/STORAGES/STORAGES_COLLECTION STORAGE admin 2017-12-08 17:32:23 admin 2017-12-08 17:32:23\n",
"21 /VERMEUL/EXP1 20170124170850531-422 /VERMEUL/PROJECT_ONE/PROJECT_ONE_EXP_1 EXPERIMENTAL_STEP vermeul 2017-01-24 17:08:51 vermeul 2017-01-25 17:26:25\n",
"22 /MATERIALS/FLY43 20170104000802333-404 /MATERIALS/YEASTS/MY_EXPERIMENT007 FLY vermeul 2017-01-04 00:08:02 vermeul 2017-02-27 10:04:19\n",
"23 /MATERIALS/FLY45 20170104000847172-405 /MATERIALS/YEASTS/MY_EXPERIMENT007 FLY vermeul 2017-01-04 00:08:47 vermeul 2017-01-04 00:36:09\n",
"24 /MY_NEW_SPACE/FLY51 20170120010813349-416 /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 FLY vermeul 2017-01-20 01:08:13 vermeul 2017-05-15 14:41:20\n",
"25 /VERMEUL/FLY84 20180831174909928-725 None FLY vermeul 2018-08-31 17:49:10 vermeul 2018-08-31 17:49:10\n",
"26 /ELN_SETTINGS/GENERAL_ELN_SETTINGS 20171208173222969-576 None GENERAL_ELN_SETTINGS admin 2017-12-08 17:32:23 admin 2017-12-08 17:32:23\n",
"27 /MY_NEW_SPACE/HOW_WONDERFUL 20160630105304285-81 /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 UNKNOWN vermeul 2016-06-30 16:53:04 vermeul 2017-05-18 11:22:52\n",
"28 /VERMEUL/HOW_WONDERFUL2 20160630105337180-82 None UNKNOWN vermeul 2016-06-30 16:53:37 vermeul 2016-07-22 11:20:03\n",
"29 /VERMEUL/HOW_WONDERFUL3 20160630105402002-83 None UNKNOWN vermeul 2016-06-30 16:54:02 vermeul 2016-06-30 16:54:02\n",
"30 /VERMEUL/HOW_WONDERFUL4 20160630105953557-85 None UNKNOWN vermeul 2016-06-30 16:59:54 vermeul 2016-06-30 16:59:54\n",
"31 /VERMEUL/MON_160718_181552 20160718181615356-214 None UNKNOWN vermeul 2016-07-18 18:16:15 vermeul 2016-07-18 18:16:15\n",
"32 /VERMEUL/MON_160718_181654 20160718181656980-215 None UNKNOWN vermeul 2016-07-18 18:16:57 vermeul 2016-08-17 17:52:35\n",
"33 /ANOTHER_SPACE_NAME/MY_WONDERFUL_SAMPLE_NAME 20160720225637704-262 None UNKNOWN vermeul 2016-07-20 22:56:38 vermeul 2016-12-01 22:56:28\n",
"34 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA 20160630110733527-86 None UNKNOWN vermeul 2016-06-30 17:07:34 vermeul 2016-07-06 00:11:45\n",
"35 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA3 20160630112720553-90 None UNKNOWN vermeul 2016-06-30 17:27:21 vermeul 2016-06-30 17:27:21\n",
"36 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA5 20160706231053756-211 None UNKNOWN vermeul 2016-07-06 23:10:54 vermeul 2016-07-06 23:10:54\n",
"37 /DEFAULT/PARENT_SAMPLE_MON_171211_105928 20171211105947734-593 None UNKNOWN admin 2017-12-11 10:59:48 admin 2017-12-11 10:59:48\n",
"38 /DEFAULT/PARENT_SAMPLE_MON_171211_110500 20171211110519861-595 None UNKNOWN admin 2017-12-11 11:05:20 admin 2017-12-11 11:05:20\n",
"39 /DEFAULT/PARENT_SAMPLE_MON_171211_111846 20171211111905097-597 None UNKNOWN admin 2017-12-11 11:19:05 admin 2017-12-11 11:19:05\n",
"40 /DEFAULT/PARENT_SAMPLE_MON_171211_112532 20171211112550661-599 None UNKNOWN admin 2017-12-11 11:25:51 admin 2017-12-11 11:25:51\n",
"41 /DEFAULT/PARENT_SAMPLE_MON_171211_112859 20171211112918064-602 None UNKNOWN admin 2017-12-11 11:29:18 admin 2017-12-11 11:29:19\n",
"42 /DEFAULT/PARENT_SAMPLE_MON_171211_123501 20171211123517714-605 None UNKNOWN admin 2017-12-11 12:35:18 admin 2017-12-11 12:35:18\n",
"43 /DEFAULT/PARENT_SAMPLE_MON_171211_123653 20171211123710077-608 None UNKNOWN admin 2017-12-11 12:37:10 admin 2017-12-11 12:37:10\n",
"44 /DEFAULT/PARENT_SAMPLE_MON_171211_123736 20171211123753140-611 None UNKNOWN admin 2017-12-11 12:37:53 admin 2017-12-11 12:37:53\n",
"45 /DEFAULT/PARENT_SAMPLE_MON_171211_123757 20171211123813577-614 None UNKNOWN admin 2017-12-11 12:38:14 admin 2017-12-11 12:38:14\n",
"46 /DEFAULT/PARENT_SAMPLE_MON_171211_134640 20171211134641028-617 None UNKNOWN admin 2017-12-11 13:46:41 admin 2017-12-11 13:46:41\n",
"47 /DEFAULT/PARENT_SAMPLE_MON_171218_164249 20171218164249790-643 None UNKNOWN admin 2017-12-18 16:42:50 admin 2017-12-18 16:42:50\n",
"48 /DEFAULT/PARENT_SAMPLE_TUE_171219_110150 20171219110154568-648 None UNKNOWN admin 2017-12-19 11:01:55 admin 2017-12-19 11:01:55\n",
"49 /DEFAULT/PARENT_SAMPLE_TUE_180227_223411 20180227223407864-679 None UNKNOWN vermeul 2018-02-27 22:34:08 vermeul 2018-02-27 22:34:08\n",
"50 /DEFAULT/PARENT_SAMPLE_TUE_180227_223429 20180227223425882-683 None UNKNOWN vermeul 2018-02-27 22:34:26 vermeul 2018-02-27 22:34:26\n",
"51 /DEFAULT/PARENT_SAMPLE_TUE_180227_223705 20180227223702468-687 None UNKNOWN vermeul 2018-02-27 22:37:02 vermeul 2018-02-27 22:37:02\n",
"52 /DEFAULT/PARENT_SAMPLE_WED_180228_102753 20180228102750593-694 None UNKNOWN vermeul 2018-02-28 10:27:51 vermeul 2018-02-28 10:27:51\n",
"53 /DEFAULT/PARENT_SAMPLE_WED_180228_102803 20180228102800550-696 None UNKNOWN vermeul 2018-02-28 10:28:01 vermeul 2018-02-28 10:28:01\n",
"54 /DEFAULT/PARENT_SAMPLE_WED_180228_103709 20180228103706793-700 None UNKNOWN vermeul 2018-02-28 10:37:07 vermeul 2018-02-28 10:37:07\n",
"55 /DEFAULT/PARENT_SAMPLE_WED_180228_171049 20180228171049534-714 None UNKNOWN vermeul 2018-02-28 17:10:50 vermeul 2018-02-28 17:10:50\n",
"56 /VERMEUL/PROJ1_EXP2_SAMPLE_ONE 20170115220351496-413 /VERMEUL/PROJECT_ONE/PROJECT_ONE_EXP_2 EXPERIMENTAL_STEP vermeul 2017-01-15 22:03:52 vermeul 2017-01-15 22:04:54\n",
"57 /VERMEUL/RNA47 20170108022244150-408 None RNA vermeul 2017-01-08 02:22:44 vermeul 2017-01-08 02:22:44\n",
"58 /VERMEUL/S42 20161118132053585-392 None UNKNOWN vermeul 2016-11-18 13:20:54 vermeul 2016-11-18 13:20:54\n",
"59 /VERMEUL/TEST001 20171215142200853-621 None UNKNOWN admin 2017-12-15 14:22:01 admin 2017-12-15 14:22:01\n",
"60 /DEFAULT/TEST_GET_BY_ID_WED_171004_000944 20171004000944680-530 None UNKNOWN admin 2017-10-04 00:09:45 admin 2017-10-04 00:09:45\n",
"61 /DEFAULT/TEST_GET_BY_ID_WED_171004_001010 20171004001009668-533 None UNKNOWN admin 2017-10-04 00:10:10 admin 2017-10-04 00:10:10\n",
"62 /DEFAULT/TEST_GET_BY_ID_WED_171004_001020 20171004001020119-536 None UNKNOWN admin 2017-10-04 00:10:20 admin 2017-10-04 00:10:20\n",
"63 /DEFAULT/TEST_GET_BY_PERMID_WED_171004_000946 20171004000946100-531 None UNKNOWN admin 2017-10-04 00:09:46 admin 2017-10-04 00:09:46\n",
"64 /DEFAULT/TEST_GET_BY_PERMID_WED_171004_001010 20171004001010530-534 None UNKNOWN admin 2017-10-04 00:10:11 admin 2017-10-04 00:10:11\n",
"65 /DEFAULT/TEST_GET_BY_PERMID_WED_171004_001021 20171004001020929-537 None UNKNOWN admin 2017-10-04 00:10:21 admin 2017-10-04 00:10:21\n",
"66 /DEFAULT/TEST_SAMPLE_FRI_171208_174600 20171208174559963-591 None UNKNOWN admin 2017-12-08 17:46:00 admin 2017-12-08 17:46:00\n",
"67 /DEFAULT/TEST_SAMPLE_MON_171211_105927 20171211105946839-592 None UNKNOWN admin 2017-12-11 10:59:47 admin 2017-12-11 10:59:47\n",
"68 /DEFAULT/TEST_SAMPLE_MON_171211_110318 20171211110357956-594 None UNKNOWN admin 2017-12-11 11:03:58 admin 2017-12-11 11:03:58\n",
"69 /DEFAULT/TEST_SAMPLE_TUE_180227_223409 20180227223406110-677 None UNKNOWN vermeul 2018-02-27 22:34:06 vermeul 2018-02-27 22:34:06\n",
"70 /DEFAULT/TEST_SAMPLE_TUE_180227_223428 20180227223424887-681 None UNKNOWN vermeul 2018-02-27 22:34:25 vermeul 2018-02-27 22:34:25\n",
"71 /MY_NEW_SPACE/YEA21 20161025010638912-382 /MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT YEAST vermeul 2016-10-25 01:06:39 vermeul 2017-01-19 00:02:53\n",
"72 /MY_NEW_SPACE/YEA34 20161108230958839-384 /MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT YEAST vermeul 2016-11-08 23:09:59 vermeul 2017-01-25 23:48:14\n",
"73 /VERMEUL/YEA35 20161108231507755-385 None YEAST vermeul 2016-11-08 23:15:08 vermeul 2016-11-08 23:15:08\n",
"74 /VERMEUL/YEA36 20161108231536195-386 None YEAST vermeul 2016-11-08 23:15:36 vermeul 2016-11-08 23:15:36\n",
"75 /VERMEUL/YEA37 20161108231604599-387 None YEAST vermeul 2016-11-08 23:16:05 vermeul 2016-11-08 23:16:05\n",
"76 /MY_NEW_SPACE/YEA38 20161108232203635-388 None YEAST vermeul 2016-11-08 23:22:04 vermeul 2017-01-18 17:16:50\n",
"77 /VERMEUL/YEA39 20161108232240159-389 None YEAST vermeul 2016-11-08 23:22:40 vermeul 2016-11-08 23:22:40\n",
"78 /VERMEUL/YEA40 20161108233530315-390 None YEAST vermeul 2016-11-08 23:35:30 vermeul 2016-11-08 23:35:30\n",
"79 /VERMEUL/YEA41 20161109142859057-391 None YEAST vermeul 2016-11-09 14:28:59 vermeul 2016-11-09 14:28:59\n",
"80 /VERMEUL/YEA63 20170227104527381-434 None YEAST vermeul 2017-02-27 10:45:27 vermeul 2017-02-27 10:45:27\n",
"81 /VERMEUL/YEA64 20170227104651646-435 None YEAST vermeul 2017-02-27 10:46:52 vermeul 2017-02-27 15:51:34\n",
"82 /VERMEUL/YEA65 20170227154403209-436 None YEAST vermeul 2017-02-27 15:44:03 vermeul 2017-03-27 12:21:05\n",
"83 /VERMEUL/YEA66 20170323101102451-441 None YEAST vermeul 2017-03-23 10:11:02 vermeul 2017-03-27 12:21:05\n",
"84 /VERMEUL/YEA67 20170327113258723-442 None YEAST vermeul 2017-03-27 11:32:59 vermeul 2017-03-27 12:03:46\n",
"85 /VERMEUL/YEA68 20170327122105199-443 None YEAST vermeul 2017-03-27 12:21:05 vermeul 2017-03-27 12:25:41\n",
"86 /VERMEUL/YEA71 20170518112158124-516 None YEAST vermeul 2017-05-18 11:21:58 vermeul 2017-05-18 11:21:58\n",
"87 /VERMEUL/YEA72 20170518112248330-517 None YEAST vermeul 2017-05-18 11:22:48 vermeul 2017-05-18 11:22:48\n",
"88 /VERMEUL/YEA73 20170518112726306-519 None YEAST vermeul 2017-05-18 11:27:26 vermeul 2017-05-18 11:27:26\n",
"89 /VERMEUL/YEA74 20170518112739712-520 None YEAST vermeul 2017-05-18 11:27:40 vermeul 2017-05-18 11:27:40\n",
"90 /VERMEUL/YEA75 20170518112808649-521 None YEAST vermeul 2017-05-18 11:28:09 vermeul 2017-05-18 11:28:12\n",
"91 /VERMEUL/YEA76 20171215141946133-620 None YEAST admin 2017-12-15 14:19:46 admin 2017-12-15 14:19:46\n",
"92 /VERMEUL/YET_ANOTHER_SAMPLE1 20160706002555747-209 None UNKNOWN vermeul 2016-07-06 00:25:56 vermeul 2017-06-22 10:56:33"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_samples()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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_EXPERIMENT4</td> </tr><tr> <td>permId</td> <td>20160924020719018-358</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>type</td> <td>DEFAULT_EXPERIMENT</td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>project</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td> </tr><tr> <td>tags</td> <td>['A_tag', 'another_tag', 'too_late', 'tre']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Experiment at 0x7f10ecdadd30>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e = o.get_experiment('/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4')\n",
"e"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"controlled vocabulary: find out which terms are allowed by adding an underscore to the property."
]
},
{
"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>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>CROSS</td> <td>cross</td> <td>The strain was produced by crossing two parent strains</td> <td>ORIGIN</td> </tr><tr> <td>TRANSFORMATION</td> <td>transformation</td> <td>The strain/ cell line was obtained by transformation</td> <td>ORIGIN</td> </tr><tr> <td>SPORULATION</td> <td>transformation sporulation</td> <td>The strain was obtained by sporulating a parent diploid strain</td> <td>ORIGIN</td> </tr><tr> <td>NEGATIVE_SELECTION</td> <td>negative selection</td> <td>The strain/cell line was obtained by negative selection</td> <td>ORIGIN</td> </tr><tr> <td>TRANSFECTION</td> <td>transfection</td> <td>The strain/cell line was obtained by transfection</td> <td>ORIGIN</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Vocabulary at 0x7fbfcacd5a58>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new.p.origin_"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"assigning a wrong value to a property will lead to an error:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "Value must be one of these terms: CROSS, TRANSFORMATION, SPORULATION, NEGATIVE_SELECTION, TRANSFECTION",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mValueError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-12-d9539d489991>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0ms_new\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0morigin\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'crozz'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;32m/vagrant_python/PyBis/pybis/pybis.py\u001b[0m in \u001b[0;36m__setattr__\u001b[1;34m(self, name, value)\u001b[0m\n\u001b[0;32m 2099\u001b[0m \u001b[0mvoc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_openbis\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_terms\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2100\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mvoc\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mterms\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 2101\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"Value must be one of these terms: \"\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;34m\", \"\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mvoc\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mterms\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2102\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0mdata_type\u001b[0m \u001b[1;32min\u001b[0m \u001b[1;33m(\u001b[0m\u001b[1;34m'INTEGER'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'BOOLEAN'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'VARCHAR'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2103\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mcheck_datatype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdata_type\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mValueError\u001b[0m: Value must be one of these terms: CROSS, TRANSFORMATION, SPORULATION, NEGATIVE_SELECTION, TRANSFECTION"
]
}
],
"source": [
"s_new.p.origin = 'crozz'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"s_new.p. + TAB autocompletes all available properties for that given sample type. To show the current attributes of our new sample just use this:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"s_new.p.mating_type = 'ALPHA'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## working with datasets"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170213105629815x0CF2F2467FF08E65E79A1E25E0334BC3'"
]
},
"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": "code",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ds = o.get_dataset('20160929145446460-367') # has no physical data, because it's a container"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ds = o.get_dataset('20160719143426517-259')"
]
},
{
"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>20160719143426517-259</td> </tr><tr> <td>permId</td> <td>20160719143426517-259</td> </tr><tr> <td>type</td> <td>JUPYTER_RESULT</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>sample</td> <td>/VERMEUL/MON_160718_181654</td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr> <td>accessDate</td> <td>2016-08-18 13:43:54</td> </tr><tr> <td>dataProducer</td> <td></td> </tr><tr> <td>dataProductionDate</td> <td></td> </tr><tr> <td>registrator</td> <td></td> </tr><tr> <td>registrationDate</td> <td>2016-07-19 14:34:33</td> </tr><tr> <td>modifier</td> <td></td> </tr><tr> <td>modificationDate</td> <td>2016-07-19 14:34:33</td> </tr><tr> <td>dataStore</td> <td>DSS1</td> </tr><tr> <td>measured</td> <td>True</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"property value\n",
"------------------ --------------------------\n",
"code 20160719143426517-259\n",
"permId 20160719143426517-259\n",
"type JUPYTER_RESULT\n",
"experiment\n",
"sample /VERMEUL/MON_160718_181654\n",
"parents []\n",
"children []\n",
"container\n",
"components\n",
"tags []\n",
"accessDate 2016-08-18 13:43:54\n",
"dataProducer\n",
"dataProductionDate\n",
"registrator\n",
"registrationDate 2016-07-19 14:34:33\n",
"modifier\n",
"modificationDate 2016-07-19 14:34:33\n",
"dataStore DSS1\n",
"measured True"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
"ds.status # always fetches the current status from the server, no caching"
]
},
{
"cell_type": "code",
"execution_count": 4,
"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>speedHint</td> <td>-50</td> </tr><tr> <td>complete</td> <td>UNKNOWN</td> </tr><tr> <td>shareId</td> <td>1</td> </tr><tr> <td>size</td> <td>None</td> </tr><tr> <td>fileFormatType</td> <td>None</td> </tr><tr> <td>storageFormat</td> <td>None</td> </tr><tr> <td>location</td> <td>68D4E291-7D2C-413C-B318-895E139D29D1/7c/3b/03/20160719143426517-259</td> </tr><tr> <td>presentInArchive</td> <td>False</td> </tr><tr> <td>storageConfirmation</td> <td>True</td> </tr><tr> <td>locatorType</td> <td>None</td> </tr><tr> <td>status</td> <td>AVAILABLE</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"attribute value\n",
"------------------- -------------------------------------------------------------------\n",
"speedHint -50\n",
"complete UNKNOWN\n",
"shareId 1\n",
"size\n",
"fileFormatType\n",
"storageFormat\n",
"location 68D4E291-7D2C-413C-B318-895E139D29D1/7c/3b/03/20160719143426517-259\n",
"presentInArchive False\n",
"storageConfirmation True\n",
"locatorType\n",
"status AVAILABLE"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.physicalData"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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>CHILD_OF_SAMPLE1</td> </tr><tr> <td>permId</td> <td>20160705234504004-206</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/CHILD_OF_SAMPLE1</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>tags</td> <td>['A_tag', 'due']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"property value\n",
"---------- --------------------------------------------\n",
"code CHILD_OF_SAMPLE1\n",
"permId 20160705234504004-206\n",
"identifier /MY_NEW_SPACE/CHILD_OF_SAMPLE1\n",
"type UNKNOWN\n",
"space MY_NEW_SPACE\n",
"project\n",
"experiment /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
"tags ['A_tag', 'due']"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/CHILD_OF_SAMPLE1')\n",
"s"
]
},
{
"cell_type": "code",
"execution_count": 9,
"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_EXPERIMENT4</td> </tr><tr> <td>permId</td> <td>20160924020719018-358</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>type</td> <td>DEFAULT_EXPERIMENT</td> </tr><tr> <td>project</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td> </tr><tr> <td>tags</td> <td>['A_tag', 'another_tag', 'too_late', 'tre']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"property value\n",
"---------- --------------------------------------------\n",
"code MY_EXPERIMENT4\n",
"permId 20160924020719018-358\n",
"identifier /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
"type DEFAULT_EXPERIMENT\n",
"project /MY_NEW_SPACE/VERMEUL_PROJECT\n",
"tags ['A_tag', 'another_tag', 'too_late', 'tre']"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.get_experiment()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/HOW_WONDERFUL')"
]
},
{
"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>permId</th>\n",
" <th>properties</th>\n",
" <th>type</th>\n",
" <th>experiment</th>\n",
" <th>sample</th>\n",
" <th>registrationDate</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>20160721002154012-269</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:22:11</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>20160721002157457-270</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:22:11</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>20160721002157457-271</td>\n",
" <td>{'NAME': 'my_delightful_analysis', 'DESCRIPTIO...</td>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:22:11</td>\n",
" <td>2017-01-20 23:41:42</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>20160721005440169-272</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:54:51</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>20160721005441238-273</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:54:51</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>20160818092513667-332</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-08-18 09:25:15</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>20160818092513706-333</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-08-18 09:25:15</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>20160826103944978-335</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-08-26 10:39:46</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>20160826103945007-336</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-08-26 10:39:46</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>20160929145446441-365</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-09-29 14:54:47</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>20160929145446460-366</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-09-29 14:54:47</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>20160929145446460-367</td>\n",
" <td>{'NAME': 'crc32 check', 'DESCRIPTION': 'should...</td>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-09-29 14:54:47</td>\n",
" <td>2016-11-06 22:59:21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>20161121005146312-396</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>20161121005146338-397</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>20161121005146338-398</td>\n",
" <td>{'NAME': 'my new data analysis', 'DESCRIPTION'...</td>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>20161121005357966-399</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>20161121005357983-400</td>\n",
" <td>{}</td>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" permId properties type experiment sample registrationDate modificationDate\n",
"-- --------------------- ------------------------------------------------------------------------------ ----------------- -------------------------------------------- --------------------------- ------------------- -------------------\n",
" 0 20160721002154012-269 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-07-21 00:22:11 2016-11-06 22:59:21\n",
" 1 20160721002157457-270 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-07-21 00:22:11 2016-11-06 22:59:21\n",
" 2 20160721002157457-271 {'NAME': 'my_delightful_analysis', 'DESCRIPTION': 'ave, some!'} JUPYTER_CONTAINER /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-07-21 00:22:11 2017-01-20 23:41:42\n",
" 3 20160721005440169-272 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-07-21 00:54:51 2016-11-06 22:59:21\n",
" 4 20160721005441238-273 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-07-21 00:54:51 2016-11-06 22:59:21\n",
" 5 20160818092513667-332 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-08-18 09:25:15 2016-11-06 22:59:21\n",
" 6 20160818092513706-333 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-08-18 09:25:15 2016-11-06 22:59:21\n",
" 7 20160826103944978-335 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-08-26 10:39:46 2016-11-06 22:59:21\n",
" 8 20160826103945007-336 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-08-26 10:39:46 2016-11-06 22:59:21\n",
" 9 20160929145446441-365 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-09-29 14:54:47 2016-11-06 22:59:21\n",
"10 20160929145446460-366 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-09-29 14:54:47 2016-11-06 22:59:21\n",
"11 20160929145446460-367 {'NAME': 'crc32 check', 'DESCRIPTION': 'should be aa4da9f7'} JUPYTER_CONTAINER /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-09-29 14:54:47 2016-11-06 22:59:21\n",
"12 20161121005146312-396 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-11-21 00:51:47 2016-11-21 00:53:59\n",
"13 20161121005146338-397 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-11-21 00:51:47 2016-11-21 00:53:59\n",
"14 20161121005146338-398 {'NAME': 'my new data analysis', 'DESCRIPTION': 'some meaningful description'} JUPYTER_CONTAINER /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-11-21 00:51:47 2016-11-21 00:53:59\n",
"15 20161121005357966-399 {} JUPYTER_NOTEBOOK /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-11-21 00:53:59 2016-11-21 00:53:59\n",
"16 20161121005357983-400 {} JUPYTER_RESULT /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4 /MY_NEW_SPACE/HOW_WONDERFUL 2016-11-21 00:53:59 2016-11-21 00:53:59"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.get_datasets()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"ds = s.get_datasets()[11]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
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},
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{
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" <th>isDirectory</th>\n",
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" <th>crc32Checksum</th>\n",
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"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": 6,
"metadata": {},
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}
],
"source": [
"ds.get_files()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
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"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
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" pathInDataSet\n",
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"3 original/JUPYTER_RESULT\n",
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],
"source": [
"ds.get_files()[['pathInDataSet']]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"DataSet 20160929145446460-367 archived\n"
]
}
],
"source": [
"ds.archive(remove_from_data_store=False)"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Files downloaded to: localhost/20160929145446460-367\n"
]
}
],
"source": [
"ds.download('/tmp')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"scrolled": true
},
"outputs": [
{
"ename": "TypeError",
"evalue": "get_datasets() got an unexpected keyword argument 'withSamples'",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mTypeError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-3-1a1f42c5c6c5>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mo\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_datasets\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mwithSamples\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m'20160630105304285-81'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;31mTypeError\u001b[0m: get_datasets() got an unexpected keyword argument 'withSamples'"
]
}
],
"source": [
"o.get_datasets(withSamples='20160630105304285-81')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
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" <thead>\n",
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"</div>"
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"text/plain": [
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"source": [
"o.get_datasets(type='JUPYTER_CONTAINER')"
]
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{
"cell_type": "code",
"execution_count": 14,
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{
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" <th>attribute</th>\n",
" <th>value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>code</td> <td>20160721002157457-271</td> </tr><tr> <td>permId</td> <td>20160721002157457-271</td> </tr><tr> <td>type</td> <td>JUPYTER_CONTAINER</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>sample</td> <td>/MY_NEW_SPACE/HOW_WONDERFUL</td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>['20160817175233002-331', '20161121005146338-398', '20170120234141588-419']</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"property value\n",
"---------- ---------------------------------------------------------------------------\n",
"code 20160721002157457-271\n",
"permId 20160721002157457-271\n",
"type JUPYTER_CONTAINER\n",
"experiment /MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
"sample /MY_NEW_SPACE/HOW_WONDERFUL\n",
"parents []\n",
"children ['20160817175233002-331', '20161121005146338-398', '20170120234141588-419']\n",
"container\n",
"components\n",
"tags []"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds = o.get_dataset('20160721002157457-271')\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"ename": "KeyError",
"evalue": "'_physicalData'",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mKeyError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-24-86a39a42256d>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mds\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0ma\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__dict__\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'_physicalData'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;31mKeyError\u001b[0m: '_physicalData'"
]
}
],
"source": [
"ds.a.__dict__['_physicalData']"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
"ds.data['physicalData']"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": true
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 1,\n",
" '@type': 'as.dto.dataset.DataSet',\n",
" 'accessDate': 1477299522237,\n",
" 'children': [{'@id': 33,\n",
" '@type': 'as.dto.dataset.DataSet',\n",
" 'accessDate': 1477522476771,\n",
" 'children': None,\n",
" 'code': '20160817175233002-331',\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'dataProducer': None,\n",
" 'dataProductionDate': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'fetchOptions': {'@id': 34,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'measured': True,\n",
" 'modificationDate': 1475664402592,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'permId': {'@id': 35,\n",
" '@type': 'as.dto.dataset.id.DataSetPermId',\n",
" 'permId': '20160817175233002-331'},\n",
" 'physicalData': None,\n",
" 'postRegistered': True,\n",
" 'properties': None,\n",
" 'registrationDate': 1471449154550,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" {'@id': 36,\n",
" '@type': 'as.dto.dataset.DataSet',\n",
" 'accessDate': 1479685906571,\n",
" 'children': None,\n",
" 'code': '20161121005146338-398',\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'dataProducer': None,\n",
" 'dataProductionDate': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'fetchOptions': {'@id': 37,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'measured': True,\n",
" 'modificationDate': 1479686038994,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'permId': {'@id': 38,\n",
" '@type': 'as.dto.dataset.id.DataSetPermId',\n",
" 'permId': '20161121005146338-398'},\n",
" 'physicalData': None,\n",
" 'postRegistered': True,\n",
" 'properties': None,\n",
" 'registrationDate': 1479685906571,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" {'@id': 39,\n",
" '@type': 'as.dto.dataset.DataSet',\n",
" 'accessDate': 1484952101835,\n",
" 'children': None,\n",
" 'code': '20170120234141588-419',\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'dataProducer': None,\n",
" 'dataProductionDate': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'fetchOptions': {'@id': 40,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'measured': True,\n",
" 'modificationDate': 1484952101835,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'permId': {'@id': 41,\n",
" '@type': 'as.dto.dataset.id.DataSetPermId',\n",
" 'permId': '20170120234141588-419'},\n",
" 'physicalData': None,\n",
" 'postRegistered': True,\n",
" 'properties': None,\n",
" 'registrationDate': 1484952101835,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'tags': None,\n",
" 'type': None}],\n",
" 'code': '20160721002157457-271',\n",
" 'components': None,\n",
" 'containers': [],\n",
" 'dataProducer': None,\n",
" 'dataProductionDate': None,\n",
" 'dataStore': {'@id': 19,\n",
" '@type': 'as.dto.datastore.DataStore',\n",
" 'code': 'DSS1',\n",
" 'downloadUrl': 'https://localhost:8444',\n",
" 'fetchOptions': {'@id': 20,\n",
" '@type': 'as.dto.datastore.fetchoptions.DataStoreFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'from': None,\n",
" 'sort': None,\n",
" 'sortBy': None},\n",
" 'modificationDate': 1486921080093,\n",
" 'registrationDate': 1466761453065,\n",
" 'remoteUrl': 'https://127.0.0.1:8444'},\n",
" 'experiment': {'@id': 21,\n",
" '@type': 'as.dto.experiment.Experiment',\n",
" 'attachments': None,\n",
" 'code': 'MY_EXPERIMENT4',\n",
" 'dataSets': None,\n",
" 'fetchOptions': {'@id': 22,\n",
" '@type': 'as.dto.experiment.fetchoptions.ExperimentFetchOptions',\n",
" 'attachments': None,\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'dataSets': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'project': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'samples': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': 8},\n",
" 'history': None,\n",
" 'identifier': {'@id': 24,\n",
" '@type': 'as.dto.experiment.id.ExperimentIdentifier',\n",
" 'identifier': '/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4'},\n",
" 'materialProperties': None,\n",
" 'modificationDate': 1483916743101,\n",
" 'modifier': None,\n",
" 'permId': {'@id': 23,\n",
" '@type': 'as.dto.experiment.id.ExperimentPermId',\n",
" 'permId': '20160924020719018-358'},\n",
" 'project': None,\n",
" 'properties': None,\n",
" 'registrationDate': 1474675639018,\n",
" 'registrator': None,\n",
" 'samples': None,\n",
" 'tags': None,\n",
" 'type': {'@id': 25,\n",
" '@type': 'as.dto.experiment.ExperimentType',\n",
" 'code': 'DEFAULT_EXPERIMENT',\n",
" 'description': 'Default Experiment',\n",
" 'fetchOptions': 8,\n",
" 'modificationDate': 1466758081586,\n",
" 'permId': {'@id': 26,\n",
" '@type': 'as.dto.entitytype.id.EntityTypePermId',\n",
" 'permId': 'DEFAULT_EXPERIMENT'},\n",
" 'propertyAssignments': None}},\n",
" 'fetchOptions': {'@id': 2,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': {'@id': 13,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'components': None,\n",
" 'containers': {'@id': 14,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'count': None,\n",
" 'dataStore': {'@id': 4,\n",
" '@type': 'as.dto.datastore.fetchoptions.DataStoreFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'from': None,\n",
" 'sort': None,\n",
" 'sortBy': None},\n",
" 'experiment': {'@id': 7,\n",
" '@type': 'as.dto.experiment.fetchoptions.ExperimentFetchOptions',\n",
" 'attachments': None,\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'dataSets': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'project': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'samples': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': {'@id': 8,\n",
" '@type': 'as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'from': None,\n",
" 'propertyAssignments': None,\n",
" 'sort': None,\n",
" 'sortBy': None}},\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': {'@id': 6,\n",
" '@type': 'as.dto.dataset.fetchoptions.LinkedDataFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'externalDms': None,\n",
" 'from': None,\n",
" 'sort': None,\n",
" 'sortBy': None},\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': {'@id': 12,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': None,\n",
" 'components': None,\n",
" 'containers': None,\n",
" 'count': None,\n",
" 'dataStore': None,\n",
" 'experiment': None,\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'physicalData': None,\n",
" 'properties': None,\n",
" 'registrator': None,\n",
" 'sample': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': None,\n",
" 'type': None},\n",
" 'physicalData': {'@id': 5,\n",
" '@type': 'as.dto.dataset.fetchoptions.PhysicalDataFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'fileFormatType': None,\n",
" 'from': None,\n",
" 'locatorType': None,\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'storageFormat': None},\n",
" 'properties': {'@id': 11,\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': 9,\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': {'@id': 10,\n",
" '@type': 'as.dto.sample.fetchoptions.SampleTypeFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'from': None,\n",
" 'propertyAssignments': None,\n",
" 'sort': None,\n",
" 'sortBy': None}},\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': {'@id': 15,\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': {'@id': 3,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetTypeFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'count': None,\n",
" 'from': None,\n",
" 'propertyAssignments': None,\n",
" 'sort': None,\n",
" 'sortBy': None}},\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'measured': True,\n",
" 'modificationDate': 1484952101835,\n",
" 'modifier': None,\n",
" 'parents': [],\n",
" 'permId': {'@id': 16,\n",
" '@type': 'as.dto.dataset.id.DataSetPermId',\n",
" 'permId': '20160721002157457-271'},\n",
" 'physicalData': None,\n",
" 'postRegistered': True,\n",
" 'properties': {'DESCRIPTION': 'ave, some!', 'NAME': 'my_delightful_analysis'},\n",
" 'registrationDate': 1469053331423,\n",
" 'registrator': None,\n",
" 'sample': {'@id': 27,\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': 28,\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': 10},\n",
" 'history': None,\n",
" 'identifier': {'@id': 30,\n",
" '@type': 'as.dto.sample.id.SampleIdentifier',\n",
" 'identifier': '/MY_NEW_SPACE/HOW_WONDERFUL'},\n",
" 'materialProperties': None,\n",
" 'modificationDate': 1479686038994,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'permId': {'@id': 29,\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': {'@id': 31,\n",
" '@type': 'as.dto.sample.SampleType',\n",
" 'autoGeneratedCode': False,\n",
" 'code': 'UNKNOWN',\n",
" 'description': 'Unknown',\n",
" 'fetchOptions': 10,\n",
" 'generatedCodePrefix': 'S',\n",
" 'listable': True,\n",
" 'modificationDate': 1466758020978,\n",
" 'permId': {'@id': 32,\n",
" '@type': 'as.dto.entitytype.id.EntityTypePermId',\n",
" 'permId': 'UNKNOWN'},\n",
" 'propertyAssignments': None,\n",
" 'showParentMetadata': False,\n",
" 'subcodeUnique': False}},\n",
" 'tags': [],\n",
" 'type': {'@id': 17,\n",
" '@type': 'as.dto.dataset.DataSetType',\n",
" 'code': 'JUPYTER_CONTAINER',\n",
" 'description': 'Jupyter Analysis Results',\n",
" 'fetchOptions': 3,\n",
" 'kind': 'CONTAINER',\n",
" 'modificationDate': 1467206946405,\n",
" 'permId': {'@id': 18,\n",
" '@type': 'as.dto.entitytype.id.EntityTypePermId',\n",
" 'permId': 'JUPYTER_CONTAINER'},\n",
" 'propertyAssignments': None}}"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.data"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"dss = o.get_datasets(type='JUPYTER_CONTAINER')"
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"files = ds.get_files()\n",
"files[0]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Files downloaded to: localhost/20160929145446460-367\n"
]
}
],
"source": [
"ds.download()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"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": {},
"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": {},
"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": {},
"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": 32,
"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>20160721002157457-271</td> </tr><tr> <td>permId</td> <td>20160721002157457-271</td> </tr><tr> <td>type</td> <td>JUPYTER_CONTAINER</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>sample</td> <td>/MY_NEW_SPACE/HOW_WONDERFUL</td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>['20160817175233002-331', '20161121005146338-398']</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.DataSet at 0x7f3140f3dd30>"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds = o.get_dataset('20160721002157457-271')\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 29,
"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>YEA34</td> </tr><tr> <td>permId</td> <td>20161108230958839-384</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/YEA34</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-12-20 um 10.47.26.png</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f89bae33d30>"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"o.new_analysis(\n",
" name='minimal', \n",
" sample = s\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'Dataset registration successful'"
]
},
"execution_count": 30,
"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": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"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": "3.6.0"
}
},
"nbformat": 4,
"nbformat_minor": 1
}