{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Working with pybis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## connect to openBIS\n",
"(using stored session token ~/.pybis/localhost.token)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
"o.token"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"check if session is still active:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 5,
"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"login with a password if the token is no longer valid - and store the token"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": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
"execution_count": 4,
"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": "markdown",
"metadata": {},
"source": [
"you can connect to another openBIS instance if you have to:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"ename": "ValueError",
"evalue": "login to openBIS failed",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mValueError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-3-1d417cc1b72e>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mo2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mOpenbis\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'https://sprint-openbis.ethz.ch:8443'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mverify_certificates\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mFalse\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0mpassword\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mgetpass\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetpass\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0mo2\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mlogin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'vermeul'\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mpassword\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 6\u001b[0m \u001b[0mo2\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtoken\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/vagrant_python/PyBis/pybis/pybis.py\u001b[0m in \u001b[0;36mlogin\u001b[1;34m(self, username, password, save_token)\u001b[0m\n\u001b[0;32m 636\u001b[0m \u001b[0mresult\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_post_request\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mas_v3\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlogin_request\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 637\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 638\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"login to openBIS failed\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 639\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 640\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtoken\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mresult\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mValueError\u001b[0m: login to openBIS failed"
]
}
],
"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": {
"collapsed": false
},
"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": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>downloadUrl</th>\n",
" <th>hostUrl</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DSS1</td>\n",
" <td>https://localhost:8444/datastore_server</td>\n",
" <td>https://localhost:8444</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code downloadUrl hostUrl\n",
"0 DSS1 https://localhost:8444/datastore_server https://localhost:8444"
]
},
"execution_count": 6,
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>registrationDate</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANOTHER_SPACE_NAME</td>\n",
" <td>another space description</td>\n",
" <td>2016-07-15 02:54:45</td>\n",
" <td>2016-07-15 02:54:45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>MATERIALS</td>\n",
" <td>None</td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>METHODS</td>\n",
" <td>None</td>\n",
" <td>2016-06-24 11:47:53</td>\n",
" <td>2016-06-24 11:47:53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MY_NEW_SPACE</td>\n",
" <td>this is yet another space</td>\n",
" <td>2016-07-15 03:02:14</td>\n",
" <td>2016-07-15 03:02:14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>VERMEUL</td>\n",
" <td>Space for user vermeul</td>\n",
" <td>2016-06-24 11:50:48</td>\n",
" <td>2016-06-24 11:50:48</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7f7ff39e4fd0>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_spaces()"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"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": [
"list all possible attributes and methods by using TAB completition"
]
},
{
"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": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170124150556968xD89B56E418C00C50087A3B6D282B996F'"
]
},
"execution_count": 12,
"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": 13,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"pr = o.get_project('/MY_NEW_SPACE/VERMEUL_PROJECT')"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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/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>1</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": [
"<pybis.pybis.Things at 0x7fe9324b8e10>"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pr.get_experiments()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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>/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>vermeul</td>\n",
" <td>2016-07-05 23:45:04</td>\n",
" <td>vermeul</td>\n",
" <td>2016-10-07 01:05:46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</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>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</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>3</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>2017-01-20 23:41:42</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fe9324b8668>"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pr.get_samples()"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"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>20160929145446460-367</td> </tr><tr> <td>permId</td> <td>20160929145446460-367</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>[]</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 0x7fe9329712e8>"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pr.get_datasets()[13]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"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</td> </tr><tr> <td>description</td> <td>Space for user vermeul</td> </tr><tr> <td>registrator</td> <td>admin</td> </tr><tr> <td>registrationDate</td> <td>2016-06-24 11:50:48</td> </tr><tr> <td>modificationDate</td> <td>2016-06-24 11:50:48</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Space at 0x7fdf746a6080>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_space('vermeul')"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"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>FLIES</td> </tr><tr> <td>description</td> <td></td> </tr><tr> <td>permId</td> <td>20160624054751885-35</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/FLIES</td> </tr><tr> <td>space</td> <td>MATERIALS</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Project at 0x7f3140f7ac50>"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_project('/Materials/FLIES')"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>space</th>\n",
" <th>registrator</th>\n",
" <th>registrationDate</th>\n",
" <th>modifier</th>\n",
" <th>modificationDate</th>\n",
" <th>permid</th>\n",
" <th>identifier</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>BACTERIA</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-33</td>\n",
" <td>/MATERIALS/BACTERIA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CELL_LINES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-34</td>\n",
" <td>/MATERIALS/CELL_LINES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>FLIES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-35</td>\n",
" <td>/MATERIALS/FLIES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>PLASMIDS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-37</td>\n",
" <td>/MATERIALS/PLASMIDS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>POLYNUCLEOTIDES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-38</td>\n",
" <td>/MATERIALS/POLYNUCLEOTIDES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>REAGENTS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-32</td>\n",
" <td>/MATERIALS/REAGENTS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</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 0x7f3140faf710>"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ps = o.get_projects(space='materials')\n",
"ps"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"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>YEASTS</td> </tr><tr> <td>description</td> <td></td> </tr><tr> <td>permId</td> <td>20160624054751885-36</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>space</td> <td>MATERIALS</td> </tr><tr><td>attachments</td><td></td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Project at 0x7f81504f8630>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ps[6]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**get vocabulary terms**"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>PBLUESCRIPT_II_KS_PLUS</td> <td>pBluescript II KS +</td> <td>Commercial vector for cloning in bacteria (Stratagene)</td> <td>BACKBONE</td> </tr><tr> <td>PSPPOLY_A</td> <td>pSPpoly(A)</td> <td>Standard cloning vector. It can be used for in vitro trascription from SP6 promoter. It contains a poly(A) to generate poly(A)+ transcripts in vitro (Promega)</td> <td>BACKBONE</td> </tr><tr> <td>PRS30Y</td> <td>pRS30y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS31Y</td> <td>pRS31y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS40Y</td> <td>pRS40y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS41Y</td> <td>pRS41y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS42Y</td> <td>pRS42y</td> <td>2-micron-based yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>UNKNOWN</td> <td>unknown</td> <td>unknown vector</td> <td>BACKBONE</td> </tr><tr> <td>PGEX4T1</td> <td>pGEX4T1</td> <td>Vector for bacterial expression</td> <td>BACKBONE</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.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": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>generatedCodePrefix</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANTIBODY</td>\n",
" <td></td>\n",
" <td>ANT</td>\n",
" <td>2016-06-24 10:48:02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>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": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"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": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": [
"almost all entities in openBIS can be tagged:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false,
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>permId</th>\n",
" <th>reason</th>\n",
" <th>type</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>20160629183649792-77</td>\n",
" <td>no jolly good reason</td>\n",
" <td>as.dto.sample.id.SamplePermId</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>20160629185740101-79</td>\n",
" <td>no jolly good reason</td>\n",
" <td>as.dto.sample.id.SamplePermId</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>20160705234127476-205</td>\n",
" <td>jjj</td>\n",
" <td>as.dto.sample.id.SamplePermId</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>20160630111810821-87</td>\n",
" <td>no specific reason</td>\n",
" <td>as.dto.sample.id.SamplePermId</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>20160926234807546-364</td>\n",
" <td>no longer needed</td>\n",
" <td>as.dto.experiment.id.ExperimentPermId</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>20161004215320704-370</td>\n",
" <td>it was just an experiment</td>\n",
" <td>as.dto.experiment.id.ExperimentPermId</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" permId reason \\\n",
"0 20160629183649792-77 no jolly good reason \n",
"1 20160629185740101-79 no jolly good reason \n",
"2 20160705234127476-205 jjj \n",
"3 20160630111810821-87 no specific reason \n",
"4 20160926234807546-364 no longer needed \n",
"5 20161004215320704-370 it was just an experiment \n",
"\n",
" type \n",
"0 as.dto.sample.id.SamplePermId \n",
"1 as.dto.sample.id.SamplePermId \n",
"2 as.dto.sample.id.SamplePermId \n",
"3 as.dto.sample.id.SamplePermId \n",
"4 as.dto.experiment.id.ExperimentPermId \n",
"5 as.dto.experiment.id.ExperimentPermId "
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_deletions()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## working with projects"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
"o.token"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"list all projects in a given space."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"sp = o.get_space('VERMEUL')"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"p.add_attachment(fileName='testfile', description= 'another file', title= 'one more attachment')"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false,
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"e0.project = p"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"e0.add_tags('uno')"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Experiment successfully updated.\n"
]
}
],
"source": [
"e0.save()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>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": {
"collapsed": false,
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"e_new.project ='VERMEUL_PROJECT'"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"e_new.tags = 'too_late'"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"e_new.code = 'exp_new'"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Experiment successfully created.\n"
]
}
],
"source": [
"e_new.save()"
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"ex.set_properties({'FINISHED_FLAG': False})"
]
},
{
"cell_type": "raw",
"metadata": {
"collapsed": false
},
"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": 1,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"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>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 0x7f768c77d080>"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sa = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
"sa"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>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": {
"collapsed": false
},
"outputs": [],
"source": [
"sa.add_attachment('testfile')"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully updated\n"
]
}
],
"source": [
"sa.save()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>space</th>\n",
" <th>registrator</th>\n",
" <th>registrationDate</th>\n",
" <th>modifier</th>\n",
" <th>modificationDate</th>\n",
" <th>permid</th>\n",
" <th>identifier</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>BACTERIA</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-33</td>\n",
" <td>/MATERIALS/BACTERIA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CELL_LINES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-34</td>\n",
" <td>/MATERIALS/CELL_LINES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>FLIES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-35</td>\n",
" <td>/MATERIALS/FLIES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>PLASMIDS</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-37</td>\n",
" <td>/MATERIALS/PLASMIDS</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>POLYNUCLEOTIDES</td>\n",
" <td>MATERIALS</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td></td>\n",
" <td>2016-06-24 11:47:52</td>\n",
" <td>20160624054751885-38</td>\n",
" <td>/MATERIALS/POLYNUCLEOTIDES</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>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": {
"collapsed": false
},
"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": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"hier in setattr: project = VERMEUL_PROJECT\n"
]
},
{
"ename": "TypeError",
"evalue": "'Project' object is not subscriptable",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m<ipython-input-7-d22ee2dbc203>\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[0mproject\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'VERMEUL_PROJECT'\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 2477\u001b[0m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"These are methods which should not be overwritten\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2478\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 2479\u001b[1;33m \u001b[0msetattr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__dict__\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'a'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2480\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2481\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0m_repr_html_\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\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 2297\u001b[0m \u001b[1;31m# fetch object in openBIS, make sure it actually exists\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2298\u001b[0m \u001b[0mobj\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mgetattr\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[1;34m\"get_\"\u001b[0m\u001b[1;33m+\u001b[0m\u001b[0mname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 2299\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__dict__\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'_'\u001b[0m\u001b[1;33m+\u001b[0m\u001b[0mname\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mobj\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'identifier'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2300\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2301\u001b[0m \u001b[1;31m# mark attribute as modified, if it's an existing entity\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mTypeError\u001b[0m: 'Project' object is not subscriptable"
]
}
],
"source": [
"s.project = 'VERMEUL_PROJECT'"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sample successfully updated\n"
]
}
],
"source": [
"s.save()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/YEA21')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s.p.mating_type = 'A'"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s.props.show_in_project_overview = True"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'YEAST'"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.type"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[]"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.identifier\n",
"s.code\n",
"s.type\n",
"s.space\n",
"s.tags"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"list all the properties (p) of a given sample"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>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": {
"collapsed": false
},
"source": [
"fetch just a single property: sample.p.«property_name»"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"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": 26,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s_new = o.new_sample(type='YEAST', space='VERMEUL')"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"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></td> </tr><tr> <td>parents</td> <td></td> </tr><tr> <td>children</td> <td></td> </tr><tr> <td>space</td> <td></td> </tr><tr> <td>experiment</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>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f8177455898>"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s_new.delete('obsolete')"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>vocabulary term</th>\n",
" <th>label</th>\n",
" <th>description</th>\n",
" <th>vocabulary</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"outputs": [],
"source": [
"s_new.p.mating_type = 'ALPHA'"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"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>None</td> </tr><tr> <td>permId</td> <td>None</td> </tr><tr> <td>code</td> <td>None</td> </tr><tr> <td>type</td> <td>None</td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>project</td> <td>None</td> </tr><tr> <td>experiment</td> <td>None</td> </tr><tr> <td>parents</td> <td>None</td> </tr><tr> <td>children</td> <td>None</td> </tr><tr> <td>tags</td> <td>None</td> </tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f52d7cfb630>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s_new"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## working with datasets"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"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>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></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": [
"<pybis.pybis.Sample at 0x7f89bae953c8>"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_sample('/MY_NEW_SPACE/CHILD_OF_SAMPLE1')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"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 0x7f2b0cbd14e0>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.get_experiment()"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false,
"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>HOW_WONDERFUL</td> </tr><tr> <td>permId</td> <td>20160630105304285-81</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/HOW_WONDERFUL</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>['CREATE_JSON_TAG']</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-10-14 um 23.01.06.png</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7f89bae8bd30>"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/HOW_WONDERFUL')\n",
"s"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>properties</th>\n",
" <th>type</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/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/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/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:22:11</td>\n",
" <td>2016-11-21 00:51:47</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/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/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/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/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/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/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/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/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/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/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/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/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/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/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": [
"<pybis.pybis.Things at 0x7f89bae89550>"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.get_datasets()"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ds = s.get_datasets()[11]"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th>attribute</th>\n",
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" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr> <td>code</td> <td>20160929145446460-367</td> </tr><tr> <td>permId</td> <td>20160929145446460-367</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>[]</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 0x7f89bae835f8>"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>isDirectory</th>\n",
" <th>pathInDataSet</th>\n",
" <th>fileSize</th>\n",
" <th>crc32Checksum</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>True</td>\n",
" <td>original</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_NOTEBOOk</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
" <td>77667</td>\n",
" <td>1fae7b5a</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_RESULT</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg</td>\n",
" <td>426229</td>\n",
" <td>aa4da9f7</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"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": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_files()"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
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" <th>pathInDataSet</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>original</td>\n",
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" <tr>\n",
" <th>1</th>\n",
" <td>original/JUPYTER_NOTEBOOk</td>\n",
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" <tr>\n",
" <th>2</th>\n",
" <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
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" <tr>\n",
" <th>3</th>\n",
" <td>original/JUPYTER_RESULT</td>\n",
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" <tr>\n",
" <th>4</th>\n",
" <td>original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" pathInDataSet\n",
"0 original\n",
"1 original/JUPYTER_NOTEBOOk\n",
"2 original/JUPYTER_NOTEBOOk/pybis demo.ipynb\n",
"3 original/JUPYTER_RESULT\n",
"4 original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_files()[['pathInDataSet']]"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Files downloaded to: localhost/20160929145446460-367\n"
]
}
],
"source": [
"ds.download()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false,
"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": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
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" <th>code</th>\n",
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" <td>20160721002157457-271</td>\n",
" <td>{'NAME': 'my_delightful_analysis', 'DESCRIPTIO...</td>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>/MY_NEW_SPACE/HOW_WONDERFUL</td>\n",
" <td>2016-07-21 00:22:11</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
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" <td>20160817175233002-331</td>\n",
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" <td>2016-08-17 17:52:35</td>\n",
" <td>2016-10-05 12:46:43</td>\n",
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" <tr>\n",
" <th>2</th>\n",
" <td>20160929145446460-367</td>\n",
" <td>{'NAME': 'crc32 check', 'DESCRIPTION': 'should...</td>\n",
" <td>JUPYTER_CONTAINER</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",
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" <th>3</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/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7fa301974c18>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datasets(type='JUPYTER_CONTAINER')"
]
},
{
"cell_type": "code",
"execution_count": 66,
"metadata": {
"collapsed": false
},
"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 0x7f3140f570f0>"
]
},
"execution_count": 66,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds = o.get_dataset('20160721002157457-271')\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [],
"source": [
"dss = o.get_datasets(type='JUPYTER_CONTAINER')"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 1,\n",
" '@type': 'as.dto.dataset.DataSet',\n",
" 'accessDate': 1479491589605,\n",
" 'children': [],\n",
" 'code': '20160929145446460-367',\n",
" 'components': None,\n",
" 'containers': [],\n",
" 'dataProducer': None,\n",
" 'dataProductionDate': None,\n",
" 'dataStore': {'@id': 14,\n",
" '@type': 'as.dto.datastore.DataStore',\n",
" 'code': 'DSS1',\n",
" 'downloadUrl': 'https://localhost:8444',\n",
" 'fetchOptions': {'@id': 15,\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': 1479681610594,\n",
" 'registrationDate': 1466761453065,\n",
" 'remoteUrl': 'https://127.0.0.1:8444'},\n",
" 'experiment': {'@id': 16,\n",
" '@type': 'as.dto.experiment.Experiment',\n",
" 'attachments': None,\n",
" 'code': 'MY_EXPERIMENT4',\n",
" 'dataSets': None,\n",
" 'fetchOptions': {'@id': 17,\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': None},\n",
" 'history': None,\n",
" 'identifier': {'@id': 19,\n",
" '@type': 'as.dto.experiment.id.ExperimentIdentifier',\n",
" 'identifier': '/VERMEUL/VERMEUL_PROJECT/MY_EXPERIMENT4'},\n",
" 'materialProperties': None,\n",
" 'modificationDate': 1479686038994,\n",
" 'modifier': None,\n",
" 'permId': {'@id': 18,\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': None},\n",
" 'fetchOptions': {'@id': 2,\n",
" '@type': 'as.dto.dataset.fetchoptions.DataSetFetchOptions',\n",
" 'cacheMode': 'NO_CACHE',\n",
" 'children': {'@id': 10,\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': 11,\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': 3,\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': 6,\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': None},\n",
" 'from': None,\n",
" 'history': None,\n",
" 'linkedData': {'@id': 5,\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': 9,\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': 4,\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': 8,\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': 7,\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': None},\n",
" 'sort': None,\n",
" 'sortBy': None,\n",
" 'tags': {'@id': 12,\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': None},\n",
" 'history': None,\n",
" 'linkedData': None,\n",
" 'materialProperties': None,\n",
" 'measured': True,\n",
" 'modificationDate': 1478469560726,\n",
" 'modifier': None,\n",
" 'parents': [],\n",
" 'permId': {'@id': 13,\n",
" '@type': 'as.dto.dataset.id.DataSetPermId',\n",
" 'permId': '20160929145446460-367'},\n",
" 'physicalData': None,\n",
" 'postRegistered': True,\n",
" 'properties': {'DESCRIPTION': 'should be aa4da9f7', 'NAME': 'crc32 check'},\n",
" 'registrationDate': 1475153686645,\n",
" 'registrator': None,\n",
" 'sample': {'@id': 20,\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': 21,\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': None},\n",
" 'history': None,\n",
" 'identifier': {'@id': 23,\n",
" '@type': 'as.dto.sample.id.SampleIdentifier',\n",
" 'identifier': '/VERMEUL/HOW_WONDERFUL'},\n",
" 'materialProperties': None,\n",
" 'modificationDate': 1479686038994,\n",
" 'modifier': None,\n",
" 'parents': None,\n",
" 'permId': {'@id': 22,\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': None},\n",
" 'tags': [],\n",
" 'type': None}"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dss[2].data"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>isDirectory</th>\n",
" <th>pathInDataSet</th>\n",
" <th>fileSize</th>\n",
" <th>crc32Checksum</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>True</td>\n",
" <td>original</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_NOTEBOOk</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
" <td>77667</td>\n",
" <td>1fae7b5a</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_RESULT</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg</td>\n",
" <td>426229</td>\n",
" <td>aa4da9f7</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"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": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"files = ds.get_files()\n",
"files[0]"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Files downloaded to: localhost/20160929145446460-367\n"
]
}
],
"source": [
"ds.download()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": {
"collapsed": false
},
"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": "markdown",
"metadata": {},
"source": [
"*TODO*: attach analysis to an experiment, not to a sample (usually there are a lot of datasets and samples, but only a few analyses per experiment)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"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 0x7f3140f49cf8>"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds = o.get_dataset('20160721002157457-271')\n",
"ds"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 22,\n",
" '@type': 'as.dto.experiment.id.ExperimentIdentifier',\n",
" 'identifier': '/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4'}"
]
},
"execution_count": 40,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.data['experiment']['identifier']"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ds.experiment = e"
]
},
{
"cell_type": "code",
"execution_count": 64,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'/MATERIALS/YEASTS/MY_EXPERIMENT007'"
]
},
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"e.identifier"
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 10,\n",
" '@type': 'as.dto.experiment.id.ExperimentIdentifier',\n",
" 'identifier': '/MATERIALS/YEASTS/MY_EXPERIMENT007',\n",
" 'isModified': True}"
]
},
"execution_count": 60,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.a._experiment"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>isDirectory</th>\n",
" <th>pathInDataSet</th>\n",
" <th>fileSize</th>\n",
" <th>crc32Checksum</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>True</td>\n",
" <td>original</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_NOTEBOOk</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_NOTEBOOk/pybis playground loc...</td>\n",
" <td>45250</td>\n",
" <td>5dff257f</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>True</td>\n",
" <td>original/JUPYTER_RESULT</td>\n",
" <td>-1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>False</td>\n",
" <td>original/JUPYTER_RESULT/large_testfile</td>\n",
" <td>209715200</td>\n",
" <td>534f0861</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" isDirectory pathInDataSet fileSize \\\n",
"0 True original -1 \n",
"1 True original/JUPYTER_NOTEBOOk -1 \n",
"2 False original/JUPYTER_NOTEBOOk/pybis playground loc... 45250 \n",
"3 True original/JUPYTER_RESULT -1 \n",
"4 False original/JUPYTER_RESULT/large_testfile 209715200 \n",
"\n",
" crc32Checksum \n",
"0 0 \n",
"1 0 \n",
"2 5dff257f \n",
"3 0 \n",
"4 534f0861 "
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_files()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"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>HOW_WONDERFUL</td> </tr><tr> <td>permId</td> <td>20160630105304285-81</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/HOW_WONDERFUL</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>parents</td> <td>[]</td> </tr><tr> <td>children</td> <td>[]</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>experiment</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>tags</td> <td>['CREATE_JSON_TAG']</td> </tr><tr><td>attachments</td><td>Bildschirmfoto 2016-10-14 um 23.01.06.png</td></tr>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.Sample at 0x7feecae980f0>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_sample()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"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 0x7feeb6890cf8>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_experiment()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>properties</th>\n",
" <th>type</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>20160817175233002-331</td>\n",
" <td>{'NAME': 'demo_analysis', 'DESCRIPTION': 'done!'}</td>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>/VERMEUL/MON_160718_181654</td>\n",
" <td>2016-08-17 17:52:35</td>\n",
" <td>2016-10-05 12:46:43</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</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/HOW_WONDERFUL</td>\n",
" <td>2016-11-21 00:51:47</td>\n",
" <td>2016-11-21 00:53:59</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<pybis.pybis.Things at 0x7feeb68907b8>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.get_children()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
"o.is_token_valid()"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ds = o.get_dataset('20160721002157457-271')"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"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 0x7f89bae27e10>"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 26,\n",
" '@type': 'as.dto.sample.id.SampleIdentifier',\n",
" 'identifier': '/MY_NEW_SPACE/HOW_WONDERFUL'}"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.a.__dict__['_sample']"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{'@id': 22,\n",
" '@type': 'as.dto.experiment.id.ExperimentIdentifier',\n",
" 'identifier': '/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4'}"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.a.__dict__['_experiment']"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"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": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
"s"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"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 0x7f89bae33fd0>"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s.props"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ds_new = o.new_dataset(type='Attachment')"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"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>type</td> <td>ATTACHMENT</td> </tr><tr> <td>experiment</td> <td></td> </tr><tr> <td>sample</td> <td>/MY_NEW_SPACE/YEA34</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>\n",
" </tbody>\n",
" </table>\n",
" "
],
"text/plain": [
"<pybis.pybis.DataSet at 0x7f3140fb58d0>"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds_new"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ds_new.sample = s"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "TypeError",
"evalue": "'NoneType' object is not subscriptable",
"output_type": "error",
"traceback": [
"\u001b[1;31m\u001b[0m",
"\u001b[1;31mTypeError\u001b[0mTraceback (most recent call last)",
"\u001b[1;32m<ipython-input-31-16e14e3283ca>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mds_new\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfile_list\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\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;36mfile_list\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m 1977\u001b[0m \"\"\"\n\u001b[0;32m 1978\u001b[0m \u001b[0mfiles\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m[\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1979\u001b[1;33m \u001b[1;32mfor\u001b[0m \u001b[0mfile\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_file_list\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecursive\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mTrue\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 1980\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mfile\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'isDirectory'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1981\u001b[0m \u001b[1;32mpass\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/vagrant_python/PyBis/pybis/pybis.py\u001b[0m in \u001b[0;36mget_file_list\u001b[1;34m(self, recursive, start_folder)\u001b[0m\n\u001b[0;32m 2028\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2029\u001b[0m resp = requests.post(\n\u001b[1;32m-> 2030\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m\"dataStore\"\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m\"downloadUrl\"\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;34m'/datastore_server/rmi-dss-api-v1.json'\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2031\u001b[0m \u001b[0mjson\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdumps\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrequest\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 2032\u001b[0m \u001b[0mverify\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopenbis\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mverify_certificates\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mTypeError\u001b[0m: 'NoneType' object is not subscriptable"
]
}
],
"source": [
"ds_new.file_list()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
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},
"outputs": [],
"source": []
}
],
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"language": "python",
"name": "python3"
},
"language_info": {
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"name": "ipython",
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
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