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" <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 playground loc...</td>\n",
" <td>45250</td>\n",
" <td>5dff257f</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",
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" <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": [
"<pybis.pybis.Things at 0x7feeb68907b8>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pybis import Openbis\n",
"o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
"o.is_token_valid()"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"ds = o.get_dataset('20160721002157457-271')"
]
},
{
"cell_type": "code",
"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",
" "
],
"<pybis.pybis.DataSet at 0x7f89bae27e10>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"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": [
"ds.a.__dict__['_sample']"
]
},
{
"cell_type": "code",
"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": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.a.__dict__['_experiment']"
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"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"
}
],
"s = o.get_sample('/MY_NEW_SPACE/YEA34')\n",
"s"
]
},
{
"cell_type": "code",
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
" <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",
"<pybis.property.PropertyHolder at 0x7f89bae33fd0>"
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ds_new = o.new_dataset(type='Attachment')"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"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",
" "
],
"<pybis.pybis.DataSet at 0x7f3140fb58d0>"
"metadata": {},
"output_type": "execute_result"
}
],
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [],
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"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": []
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}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
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