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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using pybis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Log into openBIS"
]
},
{
"cell_type": "code",
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"········\n"
]
},
{
"data": {
"text/plain": [
"'vermeul-160721001911317xA9E71D59EE92752CE9F9992FB3760264'"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"import getpass\n",
"o = Openbis('https://localhost:8443', verify_certificates=False)\n",
"\n",
"password = getpass.getpass()\n",
"o.login('vermeul',password)\n",
"o.token"
]
},
{
"cell_type": "code",
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
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"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",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANOTHER_SPACE_NAME</td>\n",
" <td>another space description</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>MATERIALS</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>METHODS</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MY_NEW_SPACE</td>\n",
" <td>this is yet another space</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>VERMEUL</td>\n",
" <td>Space for user vermeul</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
" code description\n",
"0 ANOTHER_SPACE_NAME another space description\n",
"1 MATERIALS None\n",
"2 METHODS None\n",
"3 MY_NEW_SPACE this is yet another space\n",
"4 VERMEUL Space for user vermeul"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>description</th>\n",
" <th>kind</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ELN_PREVIEW</td>\n",
" <td>ELN Preview image</td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>SEQ_FILE</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>RAW_DATA</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ANALYZED_DATA</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>ATTACHMENT</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>DRAWING_BOARD</td>\n",
" <td></td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>JUPYTER_CONTAINER</td>\n",
" <td>Jupyter Analysis Results</td>\n",
" <td>CONTAINER</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>JUPYTER_NOTEBOOK</td>\n",
" <td>Analysis Notebook Files</td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>UNKNOWN</td>\n",
" <td>Unknown</td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>JUPYTER_RESULT</td>\n",
" <td>Analysis Results Files</td>\n",
" <td>PHYSICAL</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code description kind\n",
"0 ELN_PREVIEW ELN Preview image PHYSICAL\n",
"1 SEQ_FILE PHYSICAL\n",
"2 RAW_DATA PHYSICAL\n",
"3 ANALYZED_DATA PHYSICAL\n",
"4 ATTACHMENT PHYSICAL\n",
"5 DRAWING_BOARD PHYSICAL\n",
"6 JUPYTER_CONTAINER Jupyter Analysis Results CONTAINER\n",
"7 JUPYTER_NOTEBOOK Analysis Notebook Files PHYSICAL\n",
"8 UNKNOWN Unknown PHYSICAL\n",
"9 JUPYTER_RESULT Analysis Results Files PHYSICAL"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_dataset_types()"
]
},
{
"cell_type": "code",
"execution_count": 10,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
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"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",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ANTIBODY</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CHEMICAL</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ENZYME</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>MEDIA</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>SOLUTION_BUFFER</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>OLIGO</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>RNA</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>PLASMID</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>BACTERIA</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>YEAST</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>CELL_LINE</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>FLY</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>EXPERIMENTAL_STEP</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>GENERAL_PROTOCOL</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>PCR_PROTOCOL</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>WESTERN_BLOTTING_PROTOCOL</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>DRAWING_BOARD</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>UNKNOWN</td>\n",
" <td>Unknown</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code description\n",
"0 ANTIBODY \n",
"1 CHEMICAL \n",
"2 ENZYME \n",
"3 MEDIA \n",
"4 SOLUTION_BUFFER \n",
"5 OLIGO \n",
"6 RNA \n",
"7 PLASMID \n",
"8 BACTERIA \n",
"9 YEAST \n",
"10 CELL_LINE \n",
"11 FLY \n",
"12 EXPERIMENTAL_STEP \n",
"13 GENERAL_PROTOCOL \n",
"14 PCR_PROTOCOL \n",
"15 WESTERN_BLOTTING_PROTOCOL \n",
"16 DRAWING_BOARD \n",
"17 UNKNOWN Unknown"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_sample_types()"
]
},
{
"cell_type": "code",
"execution_count": 20,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
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"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>code</th>\n",
" <th>downloadUrl</th>\n",
" <th>hostUrl</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>DSS1</td>\n",
" <td>https://localhost:8444/datastore_server</td>\n",
" <td>https://localhost:8444</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" code downloadUrl hostUrl\n",
"0 DSS1 https://localhost:8444/datastore_server https://localhost:8444"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"o.get_datastores()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## working with samples"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"space = o.get_space('VERMEUL')"
]
},
{
"cell_type": "code",
"execution_count": 4,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
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"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>spaceCode</th>\n",
" <th>permId</th>\n",
" <th>identifier</th>\n",
" <th>experimentIdentifierOrNull</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160706001644827-208</td>\n",
" <td>/VERMEUL/ANOTHER_SAMPLE1</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630111949369-89</td>\n",
" <td>/VERMEUL/BLAJLSD</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160705234504004-206</td>\n",
" <td>/VERMEUL/CHILD_OF_SAMPLE1</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630105304285-81</td>\n",
" <td>/VERMEUL/HOW_WONDERFUL</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630105337180-82</td>\n",
" <td>/VERMEUL/HOW_WONDERFUL2</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630105402002-83</td>\n",
" <td>/VERMEUL/HOW_WONDERFUL3</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630105953557-85</td>\n",
" <td>/VERMEUL/HOW_WONDERFUL4</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160718181615356-214</td>\n",
" <td>/VERMEUL/MON_160718_181552</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160718181656980-215</td>\n",
" <td>/VERMEUL/MON_160718_181654</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160720225637704-262</td>\n",
" <td>/VERMEUL/MY_WONDERFUL_SAMPLE_NAME</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630110733527-86</td>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630111810821-87</td>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA2</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630112720553-90</td>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA3</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160630112919449-91</td>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA4</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160706231053756-211</td>\n",
" <td>/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA5</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>VERMEUL</td>\n",
" <td>20160706002555747-209</td>\n",
" <td>/VERMEUL/YET_ANOTHER_SAMPLE1</td>\n",
" <td>None</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" spaceCode permId identifier \\\n",
"0 VERMEUL 20160706001644827-208 /VERMEUL/ANOTHER_SAMPLE1 \n",
"1 VERMEUL 20160630111949369-89 /VERMEUL/BLAJLSD \n",
"2 VERMEUL 20160705234504004-206 /VERMEUL/CHILD_OF_SAMPLE1 \n",
"3 VERMEUL 20160630105304285-81 /VERMEUL/HOW_WONDERFUL \n",
"4 VERMEUL 20160630105337180-82 /VERMEUL/HOW_WONDERFUL2 \n",
"5 VERMEUL 20160630105402002-83 /VERMEUL/HOW_WONDERFUL3 \n",
"6 VERMEUL 20160630105953557-85 /VERMEUL/HOW_WONDERFUL4 \n",
"7 VERMEUL 20160718181615356-214 /VERMEUL/MON_160718_181552 \n",
"8 VERMEUL 20160718181656980-215 /VERMEUL/MON_160718_181654 \n",
"9 VERMEUL 20160720225637704-262 /VERMEUL/MY_WONDERFUL_SAMPLE_NAME \n",
"10 VERMEUL 20160630110733527-86 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA \n",
"11 VERMEUL 20160630111810821-87 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA2 \n",
"12 VERMEUL 20160630112720553-90 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA3 \n",
"13 VERMEUL 20160630112919449-91 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA4 \n",
"14 VERMEUL 20160706231053756-211 /VERMEUL/OH_WIE_SCHOEN_IST_PANAMA5 \n",
"15 VERMEUL 20160706002555747-209 /VERMEUL/YET_ANOTHER_SAMPLE1 \n",
"\n",
" experimentIdentifierOrNull \n",
"0 None \n",
"1 None \n",
"2 None \n",
"3 None \n",
"4 None \n",
"5 None \n",
"6 None \n",
"7 None \n",
"8 None \n",
"9 None \n",
"10 None \n",
"11 None \n",
"12 None \n",
"13 None \n",
"14 None \n",
"15 None "
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"space.get_samples()"
]
},
{
"cell_type": "code",
"execution_count": 13,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"outputs": [],
"source": [
"new_sample = o.new_sample(sample_name='my_wonderful_sample_name', space_name='VERMEUL', tags=['uno','due','tre'])"
]
},
{
"cell_type": "code",
"execution_count": 17,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'/VERMEUL/MY_WONDERFUL_SAMPLE_NAME'"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"new_sample.ident"
]
},
{
"cell_type": "code",
"execution_count": 19,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'20160720225637704-262'"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"new_sample.permid"
]
},
{
"cell_type": "code",
"execution_count": 3,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'20160630112919449-91'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample = o.get_sample(\"/VERMEUL/OH_WIE_SCHOEN_IST_PANAMA4\")\n",
"sample.permid"
]
},
{
"cell_type": "code",
"execution_count": 3,
piotr.kupczyk@id.ethz.ch
committed
"metadata": {},
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"outputs": [
{
"data": {
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" 'physicalData': None,\n",
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" 'properties': {'DESCRIPTION': 'This is a new description of my analysis',\n",
" 'NAME': 'another Analysis name'},\n",
" 'registrationDate': 1467708677283,\n",
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" {'@id': 20,\n",
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" 'linkedData': None,\n",
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" 'registrationDate': 1467734061565,\n",
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" 'accessDate': 1467670624035,\n",
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" 'registrator': None,\n",
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" 'physicalData': None,\n",
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