From 747f28a7fc88e108f37cdb23b089f1167aa1c58b Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Fri, 8 Jul 2016 11:26:27 +0200
Subject: [PATCH] jupyter notebook added
---
.../pybis/pybis playground localhost.ipynb | 434 ++++++++++++++++++
1 file changed, 434 insertions(+)
create mode 100644 src/python/pybis/pybis playground localhost.ipynb
diff --git a/src/python/pybis/pybis playground localhost.ipynb b/src/python/pybis/pybis playground localhost.ipynb
new file mode 100644
index 00000000000..d2cf51a4176
--- /dev/null
+++ b/src/python/pybis/pybis playground localhost.ipynb
@@ -0,0 +1,434 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Using pybis"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Log into openBIS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "路路路路路路路路\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "'vermeul-160707110248298xF6BBB7B360CEB4604AAC9914FFC064A5'"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from pybis import Openbis\n",
+ "import getpass\n",
+ "o = Openbis('https://localhost:8443', verify_certificates=False)\n",
+ "\n",
+ "password = getpass.getpass()\n",
+ "o.login('vermeul',password)\n",
+ "o.token"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## create a sample"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "new_sample = o.new_sample(sample_name='oh_wie_schoen_ist_panama5', space_name='VERMEUL', tags=['uno','due','tre'])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA5'"
+ ]
+ },
+ "execution_count": 12,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "new_sample.ident"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## get a sample"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'20160630112919449-91'"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s = o.get_sample(\"/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA4\")\n",
+ "s.permid"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA4'"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s.ident"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "datasets = s.get_datasets()\n",
+ "ds1 = datasets[0]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[{'@id': 1,\n",
+ " '@type': 'FileInfoDssDTO',\n",
+ " 'crc32Checksum': None,\n",
+ " 'fileSize': '-1',\n",
+ " 'isDirectory': True,\n",
+ " 'pathInDataSet': 'original',\n",
+ " 'pathInListing': 'original'},\n",
+ " {'@id': 2,\n",
+ " '@type': 'FileInfoDssDTO',\n",
+ " 'crc32Checksum': None,\n",
+ " 'fileSize': '-1',\n",
+ " 'isDirectory': True,\n",
+ " 'pathInDataSet': 'original/results',\n",
+ " 'pathInListing': 'original/results'},\n",
+ " {'@id': 3,\n",
+ " '@type': 'FileInfoDssDTO',\n",
+ " 'crc32Checksum': -895786725,\n",
+ " 'fileSize': '16',\n",
+ " 'isDirectory': False,\n",
+ " 'pathInDataSet': 'original/results/blublu',\n",
+ " 'pathInListing': 'original/results/blublu'}]"
+ ]
+ },
+ "execution_count": 13,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "ds1.get_file_list()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "ds1.download('original/results/blublu')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "this is my data."
+ ]
+ }
+ ],
+ "source": [
+ "cat localhost/20160705171928021-202/original/results/blublu"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## create a dataset and upload data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "dataset = o.new_dataset(\n",
+ " sample=s, type='JUPYTER_NOTEBOOK', \n",
+ " datastore='DSS1', \n",
+ " files=['pybis_playground_localhost.ipynb']\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "dataset.register()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Analysis ##\n",
+ "An analysis has a name, description and parent dataset. Anytime it is saved, a new version of it is saved. On openBIS, an analysis is a container object which contains the result datafiles and the jupyter notebook. If an analysis is saved a second time, two new datasets are generated, both having parents of their previous datasets set."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "analysis = o.new_analysis(\n",
+ " parent=dataset,\n",
+ " name=\"my analysis\",\n",
+ " description= \"this time, there should be a meaningful explanation\",\n",
+ " results=[\"results/blublu_processed\"]\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "analysis.save()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## get available dataset types"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "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>code</th>\n",
+ " <th>description</th>\n",
+ " <th>kind</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",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>SEQ_FILE</td>\n",
+ " <td></td>\n",
+ " <td>PHYSICAL</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>RAW_DATA</td>\n",
+ " <td></td>\n",
+ " <td>PHYSICAL</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>ANALYZED_DATA</td>\n",
+ " <td></td>\n",
+ " <td>PHYSICAL</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>ATTACHMENT</td>\n",
+ " <td></td>\n",
+ " <td>PHYSICAL</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>5</th>\n",
+ " <td>DRAWING_BOARD</td>\n",
+ " <td></td>\n",
+ " <td>PHYSICAL</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",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>7</th>\n",
+ " <td>JUPYTER_NOTEBOOK</td>\n",
+ " <td>Analysis Notebook Files</td>\n",
+ " <td>PHYSICAL</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>8</th>\n",
+ " <td>UNKNOWN</td>\n",
+ " <td>Unknown</td>\n",
+ " <td>PHYSICAL</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",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " code description kind\n",
+ "0 ELN_PREVIEW ELN Preview image PHYSICAL\n",
+ "1 SEQ_FILE PHYSICAL\n",
+ "2 RAW_DATA PHYSICAL\n",
+ "3 ANALYZED_DATA PHYSICAL\n",
+ "4 ATTACHMENT PHYSICAL\n",
+ "5 DRAWING_BOARD PHYSICAL\n",
+ "6 JUPYTER_CONTAINER Jupyter Analysis Results CONTAINER\n",
+ "7 JUPYTER_NOTEBOOK Analysis Notebook Files PHYSICAL\n",
+ "8 UNKNOWN Unknown PHYSICAL\n",
+ "9 JUPYTER_RESULT Analysis Results Files PHYSICAL"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "o.get_dataset_types()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.5.1"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
--
GitLab