From 656f10e80439ed94610058b595bcbc73dd91b10f Mon Sep 17 00:00:00 2001
From: Henry Luetcke <hluetcke@ethz.ch>
Date: Thu, 8 Jul 2021 12:05:14 +0200
Subject: [PATCH] clear notebook output
---
pybis_example.ipynb | 332 ++++----------------------------------------
1 file changed, 25 insertions(+), 307 deletions(-)
diff --git a/pybis_example.ipynb b/pybis_example.ipynb
index 3989c63ebae..40fc3dd32df 100644
--- a/pybis_example.ipynb
+++ b/pybis_example.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -19,7 +19,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -28,17 +28,9 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdin",
- "output_type": "stream",
- "text": [
- " 路路路路路路路路路路路路路\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"username = 'hluetcke'\n",
"pw = getpass.getpass()"
@@ -46,7 +38,7 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -56,96 +48,27 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "'hluetcke-210707114707411xDBE993550910BD60EE612EF16B373511'"
- ]
- },
- "execution_count": 16,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"o.token"
]
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "True"
- ]
- },
- "execution_count": 17,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"o.is_session_active()"
]
},
{
"cell_type": "code",
- "execution_count": 18,
- "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://127.0.0.1:443</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://127.0.0.1:443 http://127.0.0.1:8081"
- ]
- },
- "execution_count": 18,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"o.get_datastores()"
]
@@ -351,7 +274,7 @@
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -360,80 +283,25 @@
},
{
"cell_type": "code",
- "execution_count": 20,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "experiment successfully created.\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- " <table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
- " <th>value</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr> <td>code</td> <td>EXP123456789</td> </tr><tr> <td>permId</td> <td>20210707114742976-102</td> </tr><tr> <td>identifier</td> <td>/HLUETCKE/PLAYGROUND/EXP123456789</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>project</td> <td>/HLUETCKE/PLAYGROUND</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr> <td>registrator</td> <td>hluetcke</td> </tr><tr> <td>registrationDate</td> <td>2021-07-07 13:47:43</td> </tr><tr> <td>modifier</td> <td>hluetcke</td> </tr><tr> <td>modificationDate</td> <td>2021-07-07 13:47:43</td> </tr><tr> <td>frozen</td> <td>False</td> </tr><tr> <td>frozenForDataSets</td> <td>False</td> </tr><tr> <td>frozenForSamples</td> <td>False</td> </tr><tr><td>attachments</td><td></td></tr>\n",
- " </tbody>\n",
- " </table>\n",
- " "
- ],
- "text/plain": [
- "attribute value\n",
- "----------------- ---------------------------------\n",
- "code EXP123456789\n",
- "permId 20210707114742976-102\n",
- "identifier /HLUETCKE/PLAYGROUND/EXP123456789\n",
- "type UNKNOWN\n",
- "project /HLUETCKE/PLAYGROUND\n",
- "tags []\n",
- "registrator hluetcke\n",
- "registrationDate 2021-07-07 13:47:43\n",
- "modifier hluetcke\n",
- "modificationDate 2021-07-07 13:47:43\n",
- "frozen False\n",
- "frozenForDataSets False\n",
- "frozenForSamples False"
- ]
- },
- "execution_count": 20,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"experiment.save()"
]
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "experiment 20210707114742976-102 successfully deleted.\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"experiment.delete('bla')"
]
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -442,182 +310,32 @@
},
{
"cell_type": "code",
- "execution_count": 23,
+ "execution_count": null,
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "project successfully created.\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- " <table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
- " <th>value</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr> <td>code</td> <td>TEST_PROJECT</td> </tr><tr> <td>description</td> <td>boring project</td> </tr><tr> <td>permId</td> <td>20210707120832998-103</td> </tr><tr> <td>identifier</td> <td>/HLUETCKE/TEST_PROJECT</td> </tr><tr> <td>space</td> <td>HLUETCKE</td> </tr><tr> <td>leader</td> <td></td> </tr><tr> <td>registrator</td> <td>hluetcke</td> </tr><tr> <td>registrationDate</td> <td>2021-07-07 14:08:33</td> </tr><tr> <td>modifier</td> <td>12</td> </tr><tr> <td>modificationDate</td> <td>2021-07-07 14:08:33</td> </tr><tr> <td>frozen</td> <td>False</td> </tr><tr> <td>frozenForExperiments</td> <td>False</td> </tr><tr> <td>frozenForSamples</td> <td>False</td> </tr><tr><td>attachments</td><td></td></tr>\n",
- " </tbody>\n",
- " </table>\n",
- " "
- ],
- "text/plain": [
- "attribute value\n",
- "-------------------- ----------------------\n",
- "code TEST_PROJECT\n",
- "description boring project\n",
- "permId 20210707120832998-103\n",
- "identifier /HLUETCKE/TEST_PROJECT\n",
- "space HLUETCKE\n",
- "leader\n",
- "registrator hluetcke\n",
- "registrationDate 2021-07-07 14:08:33\n",
- "modifier 12\n",
- "modificationDate 2021-07-07 14:08:33\n",
- "frozen False\n",
- "frozenForExperiments False\n",
- "frozenForSamples False"
- ]
- },
- "execution_count": 23,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"project.save()"
]
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"experiment = o.new_experiment(type='UNKNOWN', code='EXP333', project='/HLUETCKE/TEST_PROJECT')"
]
},
- {
- "cell_type": "code",
- "execution_count": 25,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "experiment successfully created.\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- " <table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
- " <th>value</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr> <td>code</td> <td>EXP333</td> </tr><tr> <td>permId</td> <td>20210707121043770-104</td> </tr><tr> <td>identifier</td> <td>/HLUETCKE/TEST_PROJECT/EXP333</td> </tr><tr> <td>type</td> <td>UNKNOWN</td> </tr><tr> <td>project</td> <td>/HLUETCKE/TEST_PROJECT</td> </tr><tr> <td>tags</td> <td>[]</td> </tr><tr> <td>registrator</td> <td>hluetcke</td> </tr><tr> <td>registrationDate</td> <td>2021-07-07 14:10:44</td> </tr><tr> <td>modifier</td> <td>hluetcke</td> </tr><tr> <td>modificationDate</td> <td>2021-07-07 14:10:44</td> </tr><tr> <td>frozen</td> <td>False</td> </tr><tr> <td>frozenForDataSets</td> <td>False</td> </tr><tr> <td>frozenForSamples</td> <td>False</td> </tr><tr><td>attachments</td><td></td></tr>\n",
- " </tbody>\n",
- " </table>\n",
- " "
- ],
- "text/plain": [
- "attribute value\n",
- "----------------- -----------------------------\n",
- "code EXP333\n",
- "permId 20210707121043770-104\n",
- "identifier /HLUETCKE/TEST_PROJECT/EXP333\n",
- "type UNKNOWN\n",
- "project /HLUETCKE/TEST_PROJECT\n",
- "tags []\n",
- "registrator hluetcke\n",
- "registrationDate 2021-07-07 14:10:44\n",
- "modifier hluetcke\n",
- "modificationDate 2021-07-07 14:10:44\n",
- "frozen False\n",
- "frozenForDataSets False\n",
- "frozenForSamples False"
- ]
- },
- "execution_count": 25,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "experiment.save()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 26,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "experiment 20210707121043770-104 successfully deleted.\n"
- ]
- }
- ],
- "source": [
- "experiment.delete('bla')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 27,
- "metadata": {},
- "outputs": [
- {
- "ename": "ValueError",
- "evalue": "Project 'TEST_PROJECT' can not be deleted because the following experiments are in the trash can: [EXP333] (Context: [])",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-27-9412c08c33df>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mproject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdelete\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'bla'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pybis/openbis_object.py\u001b[0m in \u001b[0;36mdelete\u001b[0;34m(self, reason)\u001b[0m\n\u001b[1;32m 149\u001b[0m \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 150\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 151\u001b[0;31m self.openbis.delete_openbis_entity(\n\u001b[0m\u001b[1;32m 152\u001b[0m \u001b[0mentity\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_entity\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 153\u001b[0m \u001b[0mobjectId\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'permId'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pybis/pybis.py\u001b[0m in \u001b[0;36mdelete_openbis_entity\u001b[0;34m(self, entity, objectId, reason)\u001b[0m\n\u001b[1;32m 2559\u001b[0m ]\n\u001b[1;32m 2560\u001b[0m }\n\u001b[0;32m-> 2561\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_post_request\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mas_v3\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrequest\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2562\u001b[0m \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2563\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pybis/pybis.py\u001b[0m in \u001b[0;36m_post_request\u001b[0;34m(self, resource, request)\u001b[0m\n\u001b[1;32m 1064\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1065\u001b[0m \"\"\"\n\u001b[0;32m-> 1066\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_post_request_full_url\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murljoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mresource\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrequest\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1067\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1068\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_post_request_full_url\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfull_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrequest\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;32m~/miniconda3/lib/python3.9/site-packages/pybis/pybis.py\u001b[0m in \u001b[0;36m_post_request_full_url\u001b[0;34m(self, full_url, request)\u001b[0m\n\u001b[1;32m 1090\u001b[0m \u001b[0;31m#print(full_url)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1091\u001b[0m \u001b[0;31m#print(json.dumps(request))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1092\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresp\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'error'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'message'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1093\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0;34m'result'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mresp\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1094\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresp\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'result'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;31mValueError\u001b[0m: Project 'TEST_PROJECT' can not be deleted because the following experiments are in the trash can: [EXP333] (Context: [])"
- ]
- }
- ],
- "source": [
- "project.delete('bla')"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
+ "source": [
+ "experiment.save()"
+ ]
},
{
"cell_type": "code",
--
GitLab