From e21aa6799de7ec53def4a2c28654f0d4199b7af9 Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Fri, 27 Jan 2017 09:49:39 +0100
Subject: [PATCH] new pybis demo notebook to show the new features
---
src/python/pybis/notebooks/pybis demo.ipynb | 6780 ++++++++++++-------
1 file changed, 4433 insertions(+), 2347 deletions(-)
diff --git a/src/python/pybis/notebooks/pybis demo.ipynb b/src/python/pybis/notebooks/pybis demo.ipynb
index 2fce041b236..1fa84df24be 100644
--- a/src/python/pybis/notebooks/pybis demo.ipynb
+++ b/src/python/pybis/notebooks/pybis demo.ipynb
@@ -17,7 +17,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 5,
"metadata": {
"collapsed": false
},
@@ -25,10 +25,10 @@
{
"data": {
"text/plain": [
- "'vermeul-170105170439098x34CD40C052CDA7A12E34AFFDB14FB134'"
+ "'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
- "execution_count": 3,
+ "execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
@@ -39,9 +39,16 @@
"o.token"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "check if session is still active:"
+ ]
+ },
{
"cell_type": "code",
- "execution_count": 26,
+ "execution_count": 5,
"metadata": {
"collapsed": false
},
@@ -52,7 +59,7 @@
"True"
]
},
- "execution_count": 26,
+ "execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
@@ -65,12 +72,12 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Manually connect to an instance using your username/password and storing the token for later use"
+ "login with a password if the token is no longer valid - and store the token"
]
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 4,
"metadata": {
"collapsed": false
},
@@ -85,10 +92,10 @@
{
"data": {
"text/plain": [
- "'vermeul-170105170439098x34CD40C052CDA7A12E34AFFDB14FB134'"
+ "'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
]
},
- "execution_count": 2,
+ "execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
@@ -112,7 +119,7 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 3,
"metadata": {
"collapsed": false
},
@@ -125,14 +132,16 @@
]
},
{
- "data": {
- "text/plain": [
- "'vermeul-161213095820805x4BD32D0691A016963A62966F872D0D65'"
- ]
- },
- "execution_count": 27,
- "metadata": {},
- "output_type": "execute_result"
+ "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": [
@@ -148,29 +157,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Check wether our session is still valid"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 28,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "True"
- ]
- },
- "execution_count": 28,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "o2.is_session_active()"
+ "disconnnect (or rather: make the session key invalid):"
]
},
{
@@ -191,9 +178,16 @@
"## get general information about openBIS"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Data Store Servers (DSS)"
+ ]
+ },
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {
"collapsed": false
},
@@ -227,7 +221,7 @@
"0 DSS1 https://localhost:8444/datastore_server https://localhost:8444"
]
},
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@@ -237,41 +231,15 @@
]
},
{
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "sp = o.get_space('VERMEUL')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'@id': 3, '@type': 'as.dto.space.id.SpacePermId', 'permId': 'VERMEUL'}"
- ]
- },
- "execution_count": 6,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
- "sp.permId"
+ "list all available spaces:"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {
"collapsed": false
},
@@ -331,22 +299,69 @@
"</div>"
],
"text/plain": [
- "<pybis.pybis.Things at 0x7f75484a1320>"
+ "<pybis.pybis.Things at 0x7f7ff39e4fd0>"
]
},
- "execution_count": 7,
+ "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_spaces()\n",
+ "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": 15,
+ "execution_count": 10,
"metadata": {
"collapsed": false
},
@@ -359,121 +374,53 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>code</th>\n",
- " <th>space</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",
- " <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",
+ " <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 0x7f7548264470>"
+ "<pybis.pybis.Things at 0x7f7ff39e8940>"
]
},
- "execution_count": 15,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_projects(space='MATERIALS')"
+ "sp.get_projects()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "**get vocabulary terms**"
+ "get details of the first project in this list"
]
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 4,
"metadata": {
"collapsed": false
},
@@ -485,49 +432,49 @@
" <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",
+ " <th>attribute</th>\n",
+ " <th>value</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",
+ " <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.Vocabulary at 0x7f75482525c0>"
+ "<pybis.pybis.Project at 0x7f6a2776dbe0>"
]
},
- "execution_count": 17,
+ "execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "x = o.get_terms('BACKBONE')\n",
- "x"
+ "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": [
- "## get information about general types"
+ "list all possible attributes and methods by using TAB completition"
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 5,
"metadata": {
- "collapsed": false
+ "collapsed": true
},
"outputs": [],
"source": [
- "from pybis import Openbis\n",
- "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
+ "# try it: put the cursor after the dot and press TAB\n",
+ "pr."
]
},
{
@@ -539,54 +486,8 @@
"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 0x7f7548252438>"
+ "'vermeul-170124150556968xD89B56E418C00C50087A3B6D282B996F'"
]
},
"execution_count": 12,
@@ -595,7 +496,9 @@
}
],
"source": [
- "o.get_experiment_types()"
+ "from pybis import Openbis\n",
+ "o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
+ "o.token"
]
},
{
@@ -604,6 +507,17 @@
"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": {
@@ -613,159 +527,59 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>code</th>\n",
- " <th>description</th>\n",
- " <th>generatedCodePrefix</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>ANTIBODY</td>\n",
- " <td></td>\n",
- " <td>ANT</td>\n",
- " <td>2016-06-24 10:48:02</td>\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>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",
+ " <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 0x7f7548261ef0>"
+ "<pybis.pybis.Things at 0x7fe9324b8e10>"
]
},
- "execution_count": 13,
+ "execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_sample_types()"
+ "pr.get_experiments()"
]
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 15,
"metadata": {
"collapsed": false
},
@@ -778,42 +592,118 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>code</th>\n",
- " <th>description</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_VERY_EXCITING_MATERIAL</td>\n",
- " <td>looks like dirt and probably is dirt</td>\n",
- " <td>2016-09-24 00:46:19</td>\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": [
- " code description \\\n",
- "0 MY_VERY_EXCITING_MATERIAL looks like dirt and probably is dirt \n",
+ "<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",
- " modificationDate \n",
- "0 2016-09-24 00:46:19 "
+ " <table border=\"1\" class=\"dataframe\">\n",
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+ " <th>attribute</th>\n",
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+ " </tbody>\n",
+ " </table>\n",
+ " "
+ ],
+ "text/plain": [
+ "<pybis.pybis.DataSet at 0x7fe9329712e8>"
]
},
- "execution_count": 5,
+ "execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_material_types()"
+ "pr.get_datasets()[13]"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {
"collapsed": false
},
@@ -821,118 +711,194 @@
{
"data": {
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+ " </tbody>\n",
+ " </table>\n",
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+ ],
+ "text/plain": [
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+ "execution_count": 6,
+ "metadata": {},
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+ }
+ ],
+ "source": [
+ "o.get_space('vermeul')"
+ ]
+ },
+ {
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+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
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+ "text/html": [
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+ " </tbody>\n",
+ " </table>\n",
+ " "
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+ "text/plain": [
+ "<pybis.pybis.Project at 0x7f3140f7ac50>"
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+ "execution_count": 16,
+ "metadata": {},
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+ ],
+ "source": [
+ "o.get_project('/Materials/FLIES')"
+ ]
+ },
+ {
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+ "execution_count": 21,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
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+ "<table border=\"1\" class=\"dataframe\">\n",
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" <th>code</th>\n",
- " <th>description</th>\n",
- " <th>kind</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",
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" <tbody>\n",
" <tr>\n",
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- " <td>ELN Preview image</td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</td>\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>SEQ_FILE</td>\n",
+ " <td>CELL_LINES</td>\n",
+ " <td>MATERIALS</td>\n",
" <td></td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</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>RAW_DATA</td>\n",
+ " <td>FLIES</td>\n",
+ " <td>MATERIALS</td>\n",
" <td></td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</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>ANALYZED_DATA</td>\n",
+ " <td>PLASMIDS</td>\n",
+ " <td>MATERIALS</td>\n",
" <td></td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</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>ATTACHMENT</td>\n",
+ " <td>POLYNUCLEOTIDES</td>\n",
+ " <td>MATERIALS</td>\n",
" <td></td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</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>DRAWING_BOARD</td>\n",
+ " <td>REAGENTS</td>\n",
+ " <td>MATERIALS</td>\n",
" <td></td>\n",
- " <td>PHYSICAL</td>\n",
- " <td>2016-06-24 10:48:02</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>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",
+ " <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": [
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- "3 ANALYZED_DATA PHYSICAL 2016-06-24 10:48:02\n",
- "4 ATTACHMENT PHYSICAL 2016-06-24 10:48:02\n",
- "5 DRAWING_BOARD PHYSICAL 2016-06-24 10:48:02\n",
- "6 JUPYTER_CONTAINER Jupyter Analysis Results CONTAINER 2016-06-29 15:29:06\n",
- "7 JUPYTER_NOTEBOOK Analysis Notebook Files PHYSICAL 2016-06-29 15:29:07\n",
- "8 UNKNOWN Unknown PHYSICAL 2016-06-24 10:47:01\n",
- "9 JUPYTER_RESULT Analysis Results Files PHYSICAL 2016-06-29 15:29:06"
+ "<pybis.pybis.Things at 0x7f3140faf710>"
]
},
- "execution_count": 4,
+ "execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_dataset_types()"
+ "ps = o.get_projects(space='materials')\n",
+ "ps"
]
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 10,
"metadata": {
"collapsed": false
},
@@ -941,41 +907,42 @@
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- " <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",
+ " <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.PropertyAssignments at 0x7eff71169b38>"
+ "<pybis.pybis.Project at 0x7f81504f8630>"
]
},
- "execution_count": 8,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_dataset_types()[0]"
+ "ps[6]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "**get vocabulary terms**"
]
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 24,
"metadata": {
"collapsed": false
},
@@ -984,94 +951,127 @@
"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",
+ " <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.pybis.PropertyAssignments at 0x7f908e8c9ba8>"
+ "<pybis.masterdata.Vocabulary at 0x7f3140fafeb8>"
]
},
- "execution_count": 6,
+ "execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_dataset_type('ELN_PREVIEW')"
+ "x = o.get_terms('Backbone')\n",
+ "x"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## get information about general types"
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 11,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "<p>SampleType: <b>YEAST</b>\n",
- "<p>description: </p>\n",
- " <p>Code autogenerated: True</p>\n",
+ "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>property</th>\n",
- " <th>label</th>\n",
+ " <th></th>\n",
+ " <th>code</th>\n",
" <th>description</th>\n",
- " <th>dataType</th>\n",
- " <th>mandatory</th>\n",
+ " <th>modificationDate</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",
- " "
+ " <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.PropertyAssignments at 0x7fdc8120d828>"
+ "<pybis.pybis.Things at 0x7f7ff3996a20>"
]
},
- "execution_count": 3,
+ "execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_sample_type('YEAST')"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "almost all entities in openBIS can be tagged:"
+ "o.get_experiment_types()"
]
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 13,
"metadata": {
- "collapsed": false,
- "scrolled": false
+ "collapsed": false
},
"outputs": [
{
@@ -1083,201 +1083,158 @@
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
- " <th>registrationDate</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>A_tag</td>\n",
- " <td>2016-07-05 23:45:04</td>\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>CREATE_JSON_TAG</td>\n",
- " <td>2016-06-30 00:36:50</td>\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>CREATE_JSON_TAG_2</td>\n",
- " <td>2016-07-06 00:07:07</td>\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>CREATE_JSON_TAG_3</td>\n",
- " <td>2016-07-06 00:07:07</td>\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>CREATE_JSON_TAG_blalbal</td>\n",
- " <td>2016-11-08 10:24:18</td>\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>another_nice_tag</td>\n",
- " <td>2016-10-06 14:43:21</td>\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>another_tag</td>\n",
- " <td>2016-10-04 11:29:02</td>\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>blblblblblb</td>\n",
- " <td>2016-10-06 14:47:45</td>\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>clue</td>\n",
- " <td>2016-09-26 23:48:08</td>\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>do</td>\n",
- " <td>2016-09-12 23:57:14</td>\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>due</td>\n",
- " <td>2016-06-30 17:18:11</td>\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>fa</td>\n",
- " <td>2016-09-12 23:57:29</td>\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>gimme_a_tag</td>\n",
- " <td>2016-11-18 15:20:10</td>\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>gimme_one_more</td>\n",
- " <td>2016-10-27 02:03:25</td>\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>la</td>\n",
- " <td>2016-09-12 23:57:29</td>\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>mi</td>\n",
- " <td>2016-09-12 23:57:29</td>\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>new_tag</td>\n",
- " <td>2016-10-06 10:49:15</td>\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>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",
+ " <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": [
- " 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"
+ "<pybis.pybis.Things at 0x7f7ff399dbe0>"
]
},
- "execution_count": 9,
+ "execution_count": 13,
"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."
+ "o.get_sample_types()"
]
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": 14,
"metadata": {
"collapsed": false
},
@@ -1285,47 +1242,43 @@
{
"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",
- " "
+ "<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.Vocabulary at 0x7f75480e2f98>"
+ "<pybis.pybis.Things at 0x7f7ff399d518>"
]
},
- "execution_count": 19,
+ "execution_count": 14,
"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"
+ "o.get_material_types()"
]
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 15,
"metadata": {
"collapsed": false
},
@@ -1338,170 +1291,146 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>permId</th>\n",
- " <th>reason</th>\n",
- " <th>type</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>20160629183649792-77</td>\n",
- " <td>no jolly good reason</td>\n",
- " <td>as.dto.sample.id.SamplePermId</td>\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>20160629185740101-79</td>\n",
- " <td>no jolly good reason</td>\n",
- " <td>as.dto.sample.id.SamplePermId</td>\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>20160705234127476-205</td>\n",
- " <td>jjj</td>\n",
- " <td>as.dto.sample.id.SamplePermId</td>\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>20160630111810821-87</td>\n",
- " <td>no specific reason</td>\n",
- " <td>as.dto.sample.id.SamplePermId</td>\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>20160926234807546-364</td>\n",
- " <td>no longer needed</td>\n",
- " <td>as.dto.experiment.id.ExperimentPermId</td>\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>20161004215320704-370</td>\n",
- " <td>it was just an experiment</td>\n",
- " <td>as.dto.experiment.id.ExperimentPermId</td>\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": [
- " 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 "
+ "<pybis.pybis.Things at 0x7f7ff399d588>"
]
},
- "execution_count": 20,
+ "execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_deletions()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## working with experiments"
+ "o.get_dataset_types()"
]
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 16,
"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",
+ "\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></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",
+ " <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>\n",
- " <th>0</th>\n",
- " <td>MY_FIRST_EXPERIMENT_WITH_PROPERTY</td>\n",
- " <td>/MATERIALS/YEASTS/MY_FIRST_EXPERIMENT_WITH_PRO...</td>\n",
- " <td>YEASTS</td>\n",
- " <td>DEFAULT_EXPERIMENT</td>\n",
- " <td></td>\n",
- " <td>2016-09-24 01:51:55</td>\n",
- " <td></td>\n",
- " <td>2017-01-06 00:36:54</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
+ " <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.pybis.Things at 0x7ff35ecfbe80>"
+ "<pybis.property.PropertyAssignments at 0x7f7ff39e41d0>"
]
},
- "execution_count": 2,
+ "execution_count": 16,
"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"
+ "o.get_dataset_types()[0]"
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 17,
"metadata": {
"collapsed": false
},
@@ -1510,153 +1439,41 @@
"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>space</td> <td></td> </tr><tr> <td>project</td> <td>/MATERIALS/YEASTS</td> </tr><tr> <td>tags</td> <td>['too_late']</td> </tr><tr><td>attachments</td><td></td></tr>\n",
- " </tbody>\n",
- " </table>\n",
- " "
- ],
- "text/plain": [
- "<pybis.pybis.Experiment at 0x7ff35ed18f60>"
- ]
- },
- "execution_count": 3,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "e0 = exps[0]\n",
- "e0"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/html": [
- "<div>\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></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",
+ " <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>\n",
- " <th>0</th>\n",
- " <td>20170106004736870-407</td>\n",
- " <td>{'NAME': 'dunno'}</td>\n",
- " <td>ANALYZED_DATA</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 0x7ff35e93a828>"
- ]
- },
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "e0.get_datasets()"
- ]
- },
- {
- "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>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>True</td> </tr><tr> <td>finished_flag</td> <td>True</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",
+ " <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.pybis.PropertyHolder at 0x7ff35ed18cc0>"
+ "<pybis.property.PropertyAssignments at 0x7f7ff39e4898>"
]
},
- "execution_count": 6,
+ "execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "e0.p"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "e0.p.show_in_project_overview = False"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Experiment successfully updated\n"
- ]
- }
- ],
- "source": [
- "e0.save()"
+ "o.get_dataset_type('ELN_PREVIEW')"
]
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 17,
"metadata": {
"collapsed": false
},
@@ -1665,75 +1482,51 @@
"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",
+ "<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.pybis.Experiment at 0x7fd2241efcf8>"
+ "<pybis.property.PropertyAssignments at 0x7f72f022c9b0>"
]
},
- "execution_count": 9,
+ "execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "e = o.get_experiment('/MATERIALS/YEASTS/MY_EXPERIMENT007')\n",
- "e"
+ "o.get_sample_type('YEAST')"
]
},
{
- "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"
- }
- ],
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
- "o.get_experiment('20161004220718730-373')"
+ "almost all entities in openBIS can be tagged:"
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 2,
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "scrolled": false
},
"outputs": [
{
@@ -1744,195 +1537,204 @@
" <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>code</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",
+ " <td>A_tag</td>\n",
+ " <td>2016-07-05 23:45:04</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",
+ " <td>CREATE_JSON_TAG</td>\n",
+ " <td>2016-06-30 00:36:50</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",
+ " <th>2</th>\n",
+ " <td>CREATE_JSON_TAG_2</td>\n",
+ " <td>2016-07-06 00:07:07</td>\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",
+ " <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>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",
+ " <th>4</th>\n",
+ " <td>CREATE_JSON_TAG_blalbal</td>\n",
+ " <td>2016-11-08 10:24:18</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",
+ " <th>5</th>\n",
+ " <td>another_nice_tag</td>\n",
+ " <td>2016-10-06 14:43:21</td>\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",
+ " <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": [
- "<pybis.pybis.Things at 0x7fd223f4c860>"
+ " 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": 15,
+ "execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_experiments(is_finished=False, name='blast')"
+ "o.get_tags()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "### updating an experiment."
+ "**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": 3,
+ "execution_count": 7,
"metadata": {
- "collapsed": false,
- "scrolled": true
+ "collapsed": false
},
"outputs": [
{
@@ -1942,74 +1744,43 @@
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
- " <th>value</th>\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>code</td> <td>MY_EXPERIMENT3</td> </tr><tr> <td>permId</td> <td>20160924015723360-356</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/MY_EXPERIMENT3</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>samples</td> <td></td> </tr><tr> <td>datasets</td> <td></td> </tr><tr><td>attachments</td><td></td></tr>\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.Experiment at 0x7fdbc7570748>"
+ "<pybis.masterdata.Vocabulary at 0x7fca603910f0>"
]
},
- "execution_count": 3,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_experiments(type='DEFAULT_EXPERIMENT')[0]"
+ "o.get_terms('MATING_TYPE')"
]
},
{
- "cell_type": "code",
- "execution_count": 21,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
- "e3.set_properties({'FINISHED_FLAG': True})"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 12,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "e3.add_tags(['too_late'])"
- ]
- },
- {
- "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": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "e2 = o.new_experiment()"
+ "**list all the deleted items in openBIS.**\n",
+ "\n",
+ "*TODO*: fetch the deletion date"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 20,
"metadata": {
"collapsed": false
},
@@ -2017,78 +1788,136 @@
{
"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_EXPERIMENT04</td> </tr><tr> <td>permId</td> <td>20161006121402181-379</td> </tr><tr> <td>identifier</td> <td>/MATERIALS/YEASTS/MY_EXPERIMENT04</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>['another_nice_tag', 'too_late']</td> </tr><tr> <td>samples</td> <td></td> </tr><tr> <td>datasets</td> <td></td> </tr><tr><td>attachments</td><td></td></tr>\n",
- " </tbody>\n",
- " </table>\n",
- " "
+ "<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": [
- "<pybis.pybis.Experiment at 0x7fdbc73485f8>"
+ " 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": 4,
+ "execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "e=o.get_experiment('20161006121402181-379')\n",
- "e"
+ "o.get_deletions()"
]
},
{
- "cell_type": "code",
- "execution_count": 119,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
- "e.add_tags('blblblblblb')"
+ "## working with projects"
]
},
{
"cell_type": "code",
- "execution_count": 44,
+ "execution_count": 1,
"metadata": {
- "collapsed": true
+ "collapsed": false
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'vermeul-170126143455586x8A10E9354784B7ED77C8901A15079664'"
+ ]
+ },
+ "execution_count": 1,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "e3.delete(reason='it was just an experiment')"
+ "from pybis import Openbis\n",
+ "o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
+ "o.token"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## working with samples"
+ "list all projects in a given space."
]
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
- "from pybis import Openbis\n",
- "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
+ "sp = o.get_space('VERMEUL')"
]
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 6,
"metadata": {
"collapsed": false
},
@@ -2103,8 +1932,7 @@
" <th></th>\n",
" <th>identifier</th>\n",
" <th>permId</th>\n",
- " <th>experiment</th>\n",
- " <th>sample_type</th>\n",
+ " <th>leader</th>\n",
" <th>registrator</th>\n",
" <th>registrationDate</th>\n",
" <th>modifier</th>\n",
@@ -2114,141 +1942,44 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>/VERMEUL/ANOTHER_SAMPLE1</td>\n",
- " <td>20160706001644827-208</td>\n",
+ " <td>/VERMEUL/PROJECT_ONE</td>\n",
+ " <td>20170115220158336-410</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",
+ " <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/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>/VERMEUL/CHILD_OF_SAMPLE1</td>\n",
- " <td>20160705234504004-206</td>\n",
- " <td>/VERMEUL/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>/VERMEUL/HOW_WONDERFUL</td>\n",
- " <td>20160630105304285-81</td>\n",
- " <td>/VERMEUL/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/MY_WONDERFUL_SAMPLE_NAME</td>\n",
- " <td>20160720225637704-262</td>\n",
- " <td>None</td>\n",
- " <td>UNKNOWN</td>\n",
- " <td></td>\n",
- " <td>2016-07-20 22:56:38</td>\n",
- " <td></td>\n",
- " <td>2016-07-20 22:56:38</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>5</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>6</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>7</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>8</th>\n",
- " <td>/VERMEUL/YEA21</td>\n",
- " <td>20161025010638912-382</td>\n",
- " <td>/VERMEUL/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td>\n",
- " <td>YEAST</td>\n",
- " <td></td>\n",
- " <td>2016-10-25 01:06:39</td>\n",
- " <td></td>\n",
- " <td>2016-12-01 22:44:21</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>9</th>\n",
- " <td>/VERMEUL/YET_ANOTHER_SAMPLE1</td>\n",
- " <td>20160706002555747-209</td>\n",
+ " <td>/VERMEUL/READY_TO_DELETE</td>\n",
+ " <td>20170122214024061-421</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",
+ " <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 0x7efe60bb8978>"
+ "<pybis.pybis.Things at 0x7f882ed7bcf8>"
]
},
- "execution_count": 2,
+ "execution_count": 6,
"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"
+ "sp.get_projects()"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 7,
"metadata": {
"collapsed": false
},
@@ -2265,28 +1996,50 @@
" </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>/VERMEUL/YEA21</td> </tr><tr> <td>type</td> <td>YEAST</td> </tr><tr> <td>container</td> <td></td> </tr><tr> <td>components</td> <td></td> </tr><tr> <td>space</td> <td>VERMEUL</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>experiment</td> <td>/VERMEUL/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</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>['do', 'fa', 're']</td> </tr><tr><td>attachments</td><td></td></tr>\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.Sample at 0x7ff35e95d198>"
+ "<pybis.pybis.Project at 0x7f882ed87080>"
]
},
- "execution_count": 10,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s = o.get_sample('/VERMEUL/YEA21')\n",
- "s"
+ "p = sp.get_projects()[0]\n",
+ "p"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "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
},
@@ -2294,53 +2047,68 @@
{
"data": {
"text/html": [
- "\n",
+ "<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
- " <th>value</th>\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> <th>permId</th> <td>20161121013609807-402</td> </tr>\n",
- " <tr> <th>identifier</th> <td>/VERMEUL/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT</td> </tr>\n",
- " <tr> <th>project</th> <td>VERMEUL_PROJECT</td> </tr>\n",
- " <tr> <th>properties</th> <td>{}</td> </tr>\n",
- " <tr> <th>tags</th> <td>[]</td> </tr>\n",
- " <tr> <th>attachments</th> <td>[]</td> </tr>\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": [
- "{'properties': {}, 'tags': [], 'permId': '20161121013609807-402', 'identifier': '/VERMEUL/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT'}"
+ " fileName title description version\n",
+ "0 IMG_3587.JPG just a big mess None 1"
]
},
- "execution_count": 4,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "ex = s.get_experiment()\n",
- "ex"
+ "p.get_attachments()"
]
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 7,
"metadata": {
"collapsed": false
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "['localhost/20170115220158336-410/IMG_3587.JPG']"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "s.a.tags = ['fa', 'do','re']"
+ "p.download_attachments()"
]
},
{
"cell_type": "code",
- "execution_count": 88,
+ "execution_count": 8,
"metadata": {
"collapsed": false
},
@@ -2349,39 +2117,29 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Sample successfully updated\n"
+ "localhost/20170115220158336-410\r\n",
+ "localhost/20170115220158336-410/IMG_3587.JPG\r\n"
]
}
],
"source": [
- "s.save()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "s = o.get_sample('/VERMEUL/YEA21')"
+ "!find localhost/20170115220158336-410"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
- "s.p.mating_type = 'A'"
+ "p.add_attachment(fileName='testfile', description= 'another file', title= 'one more attachment')"
]
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 10,
"metadata": {
"collapsed": false
},
@@ -2390,151 +2148,142 @@
"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",
+ " <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.PropertyAssignments at 0x7efe6097a198>"
+ "<pybis.pybis.Project at 0x7fc53d9cd780>"
]
},
- "execution_count": 12,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s.get_type()"
+ "p"
]
},
{
"cell_type": "code",
- "execution_count": 33,
+ "execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
- "data": {
- "text/plain": [
- "[]"
- ]
- },
- "execution_count": 33,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Project successfully updated.\n"
+ ]
}
],
"source": [
- "s.identifier\n",
- "s.code\n",
- "s.type\n",
- "s.space\n",
- "s.tags"
+ "p.save()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "list all the properties (p) of a given sample"
+ "## working with experiments"
]
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 1,
"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 0x7efe6097feb8>"
- ]
- },
- "execution_count": 13,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
- "s.p.common_markers_"
+ "from pybis import Openbis\n",
+ "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
]
},
{
"cell_type": "markdown",
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"source": [
- "fetch just a single property: sample.p.«property_name»"
+ "**fetching experiments of a specific type containing tags**"
]
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 2,
"metadata": {
- "collapsed": false
+ "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": [
- "'comments: publication in my office'"
+ "<pybis.pybis.Things at 0x7f21b2d65898>"
]
},
- "execution_count": 14,
+ "execution_count": 2,
"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:"
+ "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": 15,
+ "execution_count": 3,
"metadata": {
"collapsed": false
},
@@ -2546,193 +2295,74 @@
" <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",
+ " <th>attribute</th>\n",
+ " <th>value</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",
+ " <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.Vocabulary at 0x7efe6097d828>"
+ "<pybis.pybis.Experiment at 0x7fbe86a64748>"
]
},
- "execution_count": 15,
+ "execution_count": 3,
"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:"
+ "e0 = exps[0]\n",
+ "e0"
]
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": 9,
"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"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "s.p.mating_type = 'invalid content'"
+ "e0.project = p"
]
},
{
- "cell_type": "markdown",
- "metadata": {},
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
"source": [
- "some properties are of a general type. Again, you can list it by adding an underscore _ :"
+ "e0.add_tags('uno')"
]
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 12,
"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": 2,
- "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>project</td> <td></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 0x7fd4d7f4b7b8>"
- ]
- },
- "execution_count": 2,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "sample = o.get_sample('/MATERIALS/FLY45')\n",
- "sample"
- ]
- },
- {
- "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>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 0x7fd4d7f4bf98>"
- ]
- },
- "execution_count": 3,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Experiment successfully updated.\n"
+ ]
}
],
"source": [
- "sample.props"
+ "e0.save()"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 13,
"metadata": {
"collapsed": false
},
@@ -2745,50 +2375,49 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>identifier</th>\n",
" <th>permId</th>\n",
+ " <th>properties</th>\n",
+ " <th>type</th>\n",
" <th>experiment</th>\n",
- " <th>sample_type</th>\n",
- " <th>registrator</th>\n",
+ " <th>sample</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",
+ " <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 0x7fd4d7f66358>"
+ "<pybis.pybis.Things at 0x7fbb3966a4e0>"
]
},
- "execution_count": 4,
+ "execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "sample.get_parents()"
+ "e0.get_datasets()"
]
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 19,
"metadata": {
- "collapsed": false
+ "collapsed": false,
+ "scrolled": true
},
"outputs": [
{
@@ -2803,148 +2432,112 @@
" </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>project</td> <td></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",
+ " <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.Sample at 0x7fd4d7f4b7b8>"
+ "<pybis.pybis.Experiment at 0x7fbb39647eb8>"
]
},
- "execution_count": 5,
+ "execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "sample"
+ "e0"
]
},
{
"cell_type": "code",
- "execution_count": 6,
+ "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>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>20170104003608559-406</td>\n",
- " <td>{'NAME': 'some analyzed data'}</td>\n",
- " <td>ANALYZED_DATA</td>\n",
- " <td>/MATERIALS/FLY45</td>\n",
- " <td>2017-01-04 00:36:09</td>\n",
- " <td>2017-01-04 00:36:09</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
- ],
"text/plain": [
- "<pybis.pybis.Things at 0x7fd4d7d04dd8>"
+ "{'End Date': 'TIMESTAMP', 'syntax': 'YYYY-MM-DD HH:MIN:SS'}"
]
},
- "execution_count": 6,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "sample.get_datasets()"
+ "e0.p.end_date_"
]
},
{
"cell_type": "code",
- "execution_count": 29,
+ "execution_count": 3,
"metadata": {
- "collapsed": false
+ "collapsed": true
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Files downloaded to: localhost/20170104003608559-406\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "sample.get_datasets()[0].download()"
+ "e_new = o.new_experiment('DEFAULT_EXPERIMENT')"
]
},
{
"cell_type": "code",
- "execution_count": 26,
+ "execution_count": 4,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "jupyter_useage_lab.zip\r\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "ls localhost/20170104003608559-406/original"
+ "e_new.project ='VERMEUL_PROJECT'"
]
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": 5,
"metadata": {
- "collapsed": true
+ "collapsed": false
},
"outputs": [],
"source": [
- "s_up = o.get_sample('/VERMEUL/MY_WONDERFUL_SAMPLE_NAME')"
+ "e_new.tags = 'too_late'"
]
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 6,
"metadata": {
- "collapsed": true
+ "collapsed": false
},
"outputs": [],
"source": [
- "s_up.space = 'ANOTHER_SPACE_NAME'"
+ "e_new.code = 'exp_new'"
]
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": 8,
"metadata": {
- "collapsed": true
+ "collapsed": false
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Experiment successfully created.\n"
+ ]
+ }
+ ],
"source": [
- "s_up.tags = ['one', 'two', 'three']"
+ "e_new.save()"
]
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 45,
"metadata": {
"collapsed": false
},
@@ -2961,90 +2554,28 @@
" </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",
+ " <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.Sample at 0x7efe60915668>"
+ "<pybis.pybis.Experiment at 0x7f3140f55400>"
]
},
- "execution_count": 22,
+ "execution_count": 45,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s_up"
+ "e = o.get_experiment('/MATERIALS/YEASTS/MY_EXPERIMENT007')\n",
+ "e"
]
},
{
"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": 7,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "from pybis import Openbis\n",
- "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "to create a new sample, the sampletype must be specified"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "s_new = o.new_sample(type='YEAST', space='VERMEUL')"
- ]
- },
- {
- "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,
+ "execution_count": 10,
"metadata": {
"collapsed": false
},
@@ -3056,20 +2587,18 @@
" <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",
+ " <th>attribute</th>\n",
+ " <th>value</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",
+ " <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.Vocabulary at 0x7fbfcacd5a58>"
+ "<pybis.pybis.Experiment at 0x7fd2241efc18>"
]
},
"execution_count": 10,
@@ -3078,14 +2607,72 @@
}
],
"source": [
- "s_new.p.origin_"
+ "o.get_experiment('20161004220718730-373')"
]
},
{
- "cell_type": "markdown",
- "metadata": {},
+ "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": [
- "assigning a wrong value to a property will lead to an error:"
+ "e.get_samples()"
]
},
{
@@ -3096,43 +2683,134 @@
},
"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"
- ]
+ "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": [
- "s_new.p.origin = 'crozz'"
+ "o.get_samples(experiment='20161004220718730-373')"
]
},
{
"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:"
+ "get all experiment with a given property"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 15,
"metadata": {
"collapsed": false
},
- "outputs": [],
+ "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": [
- "s_new.p.mating_type = 'ALPHA'"
+ "o.get_experiments(is_finished=False, name='blast')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### updating an experiment."
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 27,
"metadata": {
"collapsed": false
},
@@ -3144,43 +2822,75 @@
" <table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
- " <th>attribute</th>\n",
+ " <th>property</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",
+ " <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.pybis.Sample at 0x7f52d7cfb630>"
+ "<pybis.property.PropertyHolder at 0x7f768c61a748>"
]
},
- "execution_count": 11,
+ "execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s_new"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## working with datasets"
+ "ex = o.get_experiments(type='DEFAULT_EXPERIMENT')[0]\n",
+ "ex.p"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "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)"
@@ -3188,10 +2898,9 @@
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 18,
"metadata": {
- "collapsed": false,
- "scrolled": true
+ "collapsed": false
},
"outputs": [
{
@@ -3206,28 +2915,28 @@
" </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>/VERMEUL/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>VERMEUL</td> </tr><tr> <td>project</td> <td></td> </tr><tr> <td>experiment</td> <td>/VERMEUL/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",
+ " <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 0x7fd4d7b3e5f8>"
+ "<pybis.pybis.Sample at 0x7f768c77d080>"
]
},
- "execution_count": 17,
+ "execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s = o.get_sample('/VERMEUL/HOW_WONDERFUL')\n",
- "s"
+ "sa = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
+ "sa"
]
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": 5,
"metadata": {
"collapsed": false
},
@@ -3240,199 +2949,99 @@
" <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",
+ " <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>20160721002154012-269</td>\n",
- " <td>{}</td>\n",
- " <td>JUPYTER_NOTEBOOK</td>\n",
- " <td>/VERMEUL/HOW_WONDERFUL</td>\n",
- " <td>2016-07-21 00:22:11</td>\n",
- " <td>2016-11-06 22:59:21</td>\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>20160721002157457-270</td>\n",
- " <td>{}</td>\n",
- " <td>JUPYTER_RESULT</td>\n",
- " <td>/VERMEUL/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>{'DESCRIPTION': 'ave, some!', 'NAME': 'my_deli...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>{'DESCRIPTION': 'should be aa4da9f7', 'NAME': ...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>{'DESCRIPTION': 'some meaningful description',...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/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>/VERMEUL/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>/VERMEUL/HOW_WONDERFUL</td>\n",
- " <td>2016-11-21 00:53:59</td>\n",
- " <td>2016-11-21 00:53:59</td>\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": [
- "<pybis.pybis.Things at 0x7fd4d7b5e0f0>"
+ " 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": 21,
+ "execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s.get_datasets()"
+ "sa.get_attachments()"
]
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
- "ds = s.get_datasets()[11]"
+ "sa.add_attachment('testfile')"
]
},
{
"cell_type": "code",
- "execution_count": 23,
+ "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
},
@@ -3445,249 +3054,177 @@
" <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",
+ " <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>True</td>\n",
- " <td>original</td>\n",
- " <td>-1</td>\n",
- " <td>0</td>\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>True</td>\n",
- " <td>original/JUPYTER_NOTEBOOk</td>\n",
- " <td>-1</td>\n",
- " <td>0</td>\n",
- " </tr>\n",
- " <tr>\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>False</td>\n",
- " <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
- " <td>77667</td>\n",
- " <td>1fae7b5a</td>\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>True</td>\n",
- " <td>original/JUPYTER_RESULT</td>\n",
- " <td>-1</td>\n",
- " <td>0</td>\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>False</td>\n",
- " <td>original/JUPYTER_RESULT/PLATE1_A01_06_GFP.jpg</td>\n",
- " <td>426229</td>\n",
- " <td>aa4da9f7</td>\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": [
- " 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 "
+ "<pybis.pybis.Things at 0x7f2e99f1a518>"
]
},
- "execution_count": 23,
+ "execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "ds.get_files()"
+ "o.get_samples(space='VERMEUL', tags=['*'])"
]
},
{
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Files downloaded to: localhost/20160929145446460-367\n"
- ]
- }
- ],
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
- "ds.download()"
+ "get the first sample of the above list and just display the basic attributes"
]
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 11,
"metadata": {
- "collapsed": false,
- "scrolled": true
+ "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",
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- " <td>2016-11-06 22:59:21</td>\n",
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- " </tr>\n",
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- " <td>20160721002157457-271</td>\n",
- " <td>{'NAME': 'my_delightful_analysis', 'DESCRIPTIO...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/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>3</th>\n",
- " <td>20160721005440169-272</td>\n",
- " <td>{}</td>\n",
- " <td>JUPYTER_NOTEBOOK</td>\n",
- " <td>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/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>/VERMEUL/HOW_WONDERFUL</td>\n",
- " <td>2016-09-29 14:54:47</td>\n",
- " <td>2016-11-06 22:59:21</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
+ "\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.Things at 0x7fbfcab4dbe0>"
+ "<pybis.pybis.Sample at 0x7f8ff54adb38>"
]
},
- "execution_count": 17,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_datasets(withSamples='20160630105304285-81')"
+ "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": 9,
+ "execution_count": 6,
"metadata": {
"collapsed": false
},
@@ -3695,67 +3232,115 @@
{
"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",
+ "\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>\n",
- " <th>0</th>\n",
- " <td>20160721002157457-271</td>\n",
- " <td>{'DESCRIPTION': 'ave, some!', 'NAME': 'my_deli...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/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>20160817175233002-331</td>\n",
- " <td>{'DESCRIPTION': 'done!', 'NAME': 'demo_analysis'}</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>2</th>\n",
- " <td>20160929145446460-367</td>\n",
- " <td>{'DESCRIPTION': 'should be aa4da9f7', 'NAME': ...</td>\n",
- " <td>JUPYTER_CONTAINER</td>\n",
- " <td>/VERMEUL/HOW_WONDERFUL</td>\n",
- " <td>2016-09-29 14:54:47</td>\n",
- " <td>2016-11-06 22:59:21</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
+ " <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.pybis.Things at 0x7f7cfb9d8860>"
+ "<pybis.property.PropertyAssignments at 0x7f8ff55c26d8>"
]
},
- "execution_count": 9,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "o.get_datasets(type='JUPYTER_CONTAINER')"
+ "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": 29,
+ "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
},
@@ -3764,45 +3349,58 @@
"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>attribute</th>\n",
- " <th>value</th>\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>permId</th> <td>20160721002157457-271</td> </tr>\n",
- " <tr> <th>properties</th> <td>{'DESCRIPTION': 'ave, some!', 'NAME': 'my_delightful_analysis'}</td> </tr>\n",
- " <tr> <th>tags</th> <td>[]</td> </tr>\n",
- " </tbody>\n",
- "</table>\n",
+ " \n",
+ " </tbody>\n",
+ " </table>\n",
" "
],
"text/plain": [
- "<pybis.pybis.DataSet at 0x7fd4d7b65588>"
+ "<pybis.property.PropertyAssignments at 0x7f2e99cf6ef0>"
]
},
- "execution_count": 29,
+ "execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "ds = o.get_dataset('20160721002157457-271')\n",
- "ds"
+ "s.experiment.type"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
- "collapsed": false,
- "scrolled": true
+ "collapsed": false
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "dss = o.get_datasets(type='JUPYTER_CONTAINER')"
+ "s.experiment.type == 'UNKNOWN'"
]
},
{
@@ -3814,110 +3412,1910 @@
"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",
+ "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",
+ " <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 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",
+ " <th></th>\n",
+ " <th>pathInDataSet</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>original</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>original/JUPYTER_NOTEBOOk</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>original/JUPYTER_NOTEBOOk/pybis demo.ipynb</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>original/JUPYTER_RESULT</td>\n",
+ " </tr>\n",
+ " <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",
+ " <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>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>1</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>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",
+ " </tr>\n",
+ " <tr>\n",
+ " <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",
@@ -4110,18 +5508,483 @@
" 'type': None}"
]
},
- "execution_count": 12,
+ "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": [
- "dss[2].data"
+ "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": 5,
+ "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
},
@@ -4158,9 +6021,9 @@
" <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",
+ " <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",
@@ -4170,30 +6033,163 @@
" <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",
+ " <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": [
- " 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 "
+ "<pybis.pybis.Things at 0x7feeb68907b8>"
]
},
"execution_count": 5,
@@ -4202,134 +6198,170 @@
}
],
"source": [
- "files = ds.get_files()\n",
- "files[0]"
+ "ds.get_children()"
]
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Files downloaded to: localhost/20160929145446460-367\n"
- ]
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 24,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
- "ds.download()"
+ "from pybis import Openbis\n",
+ "o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
+ "o.is_token_valid()"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 25,
"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"
- ]
- }
- ],
+ "outputs": [],
"source": [
- "!find localhost/20160929145446460-367"
+ "ds = o.get_dataset('20160721002157457-271')"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "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": [
- "[{'@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'}]"
+ "<pybis.pybis.DataSet at 0x7f89bae27e10>"
]
},
- "execution_count": 10,
+ "execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "ds2 = o.get_dataset('20160721002157457-271')\n",
- "ds2.get_file_list(start_folder='original/JUPYTER_RESULT/large_testfile')"
+ "ds"
]
},
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Files downloaded to: localhost/20160721002157457-271\n"
- ]
+ "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": [
- "ds2.download('original/JUPYTER_RESULT/large_testfile')"
+ "ds.a.__dict__['_sample']"
]
},
{
"cell_type": "code",
- "execution_count": 28,
+ "execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Files downloaded to: localhost/20160721002157457-271\n"
- ]
+ "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": [
- "ds2.download()"
+ "ds.a.__dict__['_experiment']"
]
},
{
- "cell_type": "markdown",
- "metadata": {},
+ "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": [
- "## 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)"
+ "s = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
+ "s"
]
},
{
"cell_type": "code",
- "execution_count": 31,
+ "execution_count": 28,
"metadata": {
"collapsed": false
},
@@ -4338,70 +6370,124 @@
"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> <th>permId</th> <td>20160721002157457-271</td> </tr>\n",
- " <tr> <th>properties</th> <td>{'DESCRIPTION': 'ave, some!', 'NAME': 'my_delightful_analysis'}</td> </tr>\n",
- " <tr> <th>tags</th> <td>[]</td> </tr>\n",
- " </tbody>\n",
- "</table>\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.pybis.DataSet at 0x7efe60802d68>"
+ "<pybis.property.PropertyHolder at 0x7f89bae33fd0>"
]
},
- "execution_count": 31,
+ "execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "ds = o.get_dataset('20160721002157457-271')\n",
- "ds"
+ "s.props"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "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": [
- "'Dataset registration successful'"
+ "<pybis.pybis.DataSet at 0x7f3140fb58d0>"
]
},
- "execution_count": 4,
+ "execution_count": 29,
"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",
- ")"
+ "ds_new"
]
},
{
- "cell_type": "markdown",
- "metadata": {},
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
"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)"
+ "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": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
}
],
"metadata": {
--
GitLab