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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Working with pybis"
]
},
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{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-190613105017193x7338CBACCD9B0721D96EA8D19C3C3965'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://openbis-tst.ethz.ch', verify_certificates=False)\n",
"import getpass\n",
"password = getpass.getpass()\n",
"\n",
"o.login('vermeul',password, save_token=True)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>downloadUrl</th>\n",
" <th>remoteUrl</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DSS1</td>\n",
" <td>https://openbis-tst.ethz.ch:443</td>\n",
" <td>http://127.0.0.1:8081</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code downloadUrl remoteUrl\n",
"0 DSS1 https://openbis-tst.ethz.ch:443 http://127.0.0.1:8081"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datastores()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## connect to openBIS\n",
"(using stored session token ~/.pybis/localhost.token)"
]
},
{
"cell_type": "code",
"outputs": [
{
"data": {
"text/plain": [
"'admin-190322224519031x6CD252246FDAD84555B20A030E8F60F8'"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
"o.token"
]
},
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{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'admin-190322225222678x9B6C922E404DB51F1C50A1B9DDFF371B'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.login('admin', 'changeit', save_token=True)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\"@type\": \"as.dto.common.search.SearchResult\", \"@id\": 1, \"objects\": [], \"totalCount\": 4}\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>identifier</th>\n",
" <th>permId</th>\n",
" <th>experiment</th>\n",
" <th>sample_type</th>\n",
" <th>registrator</th>\n",
" <th>registrationDate</th>\n",
" <th>modifier</th>\n",
" <th>modificationDate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"identifier permId experiment sample_type registrator registrationDate modifier modificationDate\n",
"------------ -------- ------------ ------------- ------------- ------------------ ---------- ------------------"
]
},
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