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slarson/BAMS-To-NeuroLex

Created October 3, 2013 20:48
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BAMS-To-NeuroLex iPython Notebook example
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BAMS-To-NeuroLex
{
"metadata": {
"name": "BAMS-To-NeuroLex"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": "Working with the [BAMS-To-NeuroLex project](https://github.com/rsoscia/BAMS-to-NeuroLex) "
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git pull https://github.com/rsoscia/BAMS-to-NeuroLex.git",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "remote: Counting objects: 61, done.\u001b[K\r\nremote: Compressing objects: 2% (1/41) \u001b[K\rremote: Compressing objects: 4% (2/41) \u001b[K\rremote: Compressing objects: 7% (3/41) \u001b[K\rremote: Compressing objects: 9% (4/41) \u001b[K\rremote: Compressing objects: 12% (5/41) \u001b[K\rremote: Compressing objects: 14% (6/41) \u001b[K\rremote: Compressing objects: 17% (7/41) \u001b[K\rremote: Compressing objects: 19% (8/41) \u001b[K\rremote: Compressing objects: 21% (9/41) \u001b[K\rremote: Compressing objects: 24% (10/41) \u001b[K\rremote: Compressing objects: 26% (11/41) \u001b[K\rremote: Compressing objects: 29% (12/41) \u001b[K\rremote: Compressing objects: 31% (13/41) \u001b[K\rremote: Compressing objects: 34% (14/41) \u001b[K\rremote: Compressing objects: 36% (15/41) \u001b[K\rremote: Compressing objects: 39% (16/41) \u001b[K\rremote: Compressing objects: 41% (17/41) \u001b[K\rremote: Compressing objects: 43% (18/41) \u001b[K\rremote: Compressing objects: 46% (19/41) \u001b[K\rremote: Compressing objects: 48% (20/41) \u001b[K\rremote: Compressing objects: 51% (21/41) \u001b[K\rremote: Compressing objects: 53% (22/41) \u001b[K\rremote: Compressing objects: 56% (23/41) \u001b[K\rremote: Compressing objects: 58% (24/41) \u001b[K\rremote: Compressing objects: 60% (25/41) \u001b[K\rremote: Compressing objects: 63% (26/41) \u001b[K\rremote: Compressing objects: 65% (27/41) \u001b[K\rremote: Compressing objects: 68% (28/41) \u001b[K\rremote: Compressing objects: 70% (29/41) \u001b[K\rremote: Compressing objects: 73% (30/41) \u001b[K\rremote: Compressing objects: 75% (31/41) \u001b[K\rremote: Compressing objects: 78% (32/41) \u001b[K\rremote: Compressing objects: 80% (33/41) \u001b[K\rremote: Compressing objects: 82% (34/41) \u001b[K\rremote: Compressing objects: 85% (35/41) \u001b[K\rremote: Compressing objects: 87% (36/41) \u001b[K\rremote: Compressing objects: 90% (37/41) \u001b[K\rremote: Compressing objects: 92% (38/41) \u001b[K\rremote: Compressing objects: 95% (39/41) \u001b[K\rremote: Compressing objects: 97% (40/41) \u001b[K\rremote: Compressing objects: 100% (41/41) \u001b[K\rremote: Compressing objects: 100% (41/41), done.\u001b[K\r\nUnpacking objects: 1% (1/57) \rUnpacking objects: 3% (2/57) \rUnpacking objects: 5% (3/57) \rUnpacking objects: 7% (4/57) \rUnpacking objects: 8% (5/57) \rUnpacking objects: 10% (6/57) \rUnpacking objects: 12% (7/57) \rUnpacking objects: 14% (8/57) \rUnpacking objects: 15% (9/57) \rUnpacking objects: 17% (10/57) \rUnpacking objects: 19% (11/57) \rUnpacking objects: 21% (12/57) \rUnpacking objects: 22% (13/57) \rUnpacking objects: 24% (14/57) \rUnpacking objects: 26% (15/57) \rUnpacking objects: 28% (16/57) \rUnpacking objects: 29% (17/57) \rremote: Total 57 (delta 39), reused 34 (delta 16)\u001b[K\r\nUnpacking objects: 31% (18/57) \r"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Unpacking objects: 33% (19/57) \rUnpacking objects: 35% (20/57) \rUnpacking objects: 36% (21/57) \rUnpacking objects: 38% (22/57) \rUnpacking objects: 40% (23/57) \rUnpacking objects: 42% (24/57) \rUnpacking objects: 43% (25/57) \rUnpacking objects: 45% (26/57) \rUnpacking objects: 47% (27/57) \rUnpacking objects: 49% (28/57) \rUnpacking objects: 50% (29/57) \rUnpacking objects: 52% (30/57) \rUnpacking objects: 54% (31/57) \rUnpacking objects: 56% (32/57) \rUnpacking objects: 57% (33/57) \rUnpacking objects: 59% (34/57) \rUnpacking objects: 61% (35/57) \rUnpacking objects: 63% (36/57) \rUnpacking objects: 64% (37/57) \rUnpacking objects: 66% (38/57) \rUnpacking objects: 68% (39/57) \rUnpacking objects: 70% (40/57) \rUnpacking objects: 71% (41/57) \rUnpacking objects: 73% (42/57) \rUnpacking objects: 75% (43/57) \rUnpacking objects: 77% (44/57) \rUnpacking objects: 78% (45/57) \rUnpacking objects: 80% (46/57) \rUnpacking objects: 82% (47/57) \rUnpacking objects: 84% (48/57) \rUnpacking objects: 85% (49/57) \rUnpacking objects: 87% (50/57) \rUnpacking objects: 89% (51/57) \rUnpacking objects: 91% (52/57) \rUnpacking objects: 92% (53/57) \rUnpacking objects: 94% (54/57) \rUnpacking objects: 96% (55/57) \rUnpacking objects: 98% (56/57) \rUnpacking objects: 100% (57/57) \rUnpacking objects: 100% (57/57), done.\r\nFrom https://github.com/rsoscia/BAMS-to-NeuroLex\r\n * branch HEAD -> FETCH_HEAD\r\nUpdating 82107fe..afa19ed\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Fast-forward\r\n Data/bams_thesaurus_2013-09-24_17-12-40.xml.zip | Bin 0 -> 86200 bytes\r\n src/BAMS_Data_Queries.py | 634 ++\r\n src/BAMS_Experimental_Queries.py | 284 +\r\n src/SPARQL_BAMS_Basal_Ganglia.py | 26 +\r\n src/SPARQL_BAMS_Store_Persist_Example.py | 71 +\r\n src/SPARQL_BAMS_Store_Query_Example.py | 72 +\r\n src/get-pip.py | 7271 +++++++++++++++++++++++\r\n 7 files changed, 8358 insertions(+)\r\n create mode 100644 Data/bams_thesaurus_2013-09-24_17-12-40.xml.zip\r\n create mode 100644 src/BAMS_Data_Queries.py\r\n create mode 100644 src/BAMS_Experimental_Queries.py\r\n create mode 100644 src/SPARQL_BAMS_Store_Persist_Example.py\r\n create mode 100644 src/SPARQL_BAMS_Store_Query_Example.py\r\n create mode 100755 src/get-pip.py\r\n"
}
],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd BAMS-to-NeuroLex/",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/home/ubuntu/ipython/BAMS-to-NeuroLex\n"
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd src",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/home/ubuntu/ipython/BAMS-to-NeuroLex/src\n"
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": "%load SPARQL_BAMS_Basal_Ganglia.py",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": "#SPARQL_BAMS_Basal_Ganglia\n#This program is used to parse through the BAMS data and figure out everything about \"Basal Ganglia\"\n\n#For Parsing\nimport rdflib\nfrom rdflib import plugin\n#from rdflib import Literal, XSD\n#from rdflib.namespace import XSD\n\n#for getting the length of the files\nimport os\n\n#For Unzipping\nimport zipfile\nfrom StringIO import StringIO\n\nplugin.register(\n 'sparql', rdflib.query.Processor,\n 'rdfextras.sparql.processor', 'Processor')\nplugin.register(\n 'sparql', rdflib.query.Result,\n 'rdfextras.sparql.query', 'SPARQLQueryResult')\n\nzipdata = StringIO()\n\n\n# open the file using a relative path\nr = open(\"../Data/BAMS1.zip\")\n\n# zipdata is a buffer holding the contents of the zip file in memory\nzipdata.write(r.read())\n\nprint(\"~40 seconds for zip to open...\")\n\n#myzipfile opens the contents of the zip file as an object that knows how to unzip\nmyzipfile = zipfile.ZipFile(zipdata)\n\n#grab the contents out of myzipfile by name\nfoofile = myzipfile.open('bams_ontology_2013-07-10_03-20-00.xml')\n\n#print \"printing first 10 lines of the zip file\"\n#for i, line in enumerate(foofile):\n#\tif i == len(foofile):\n#\t\tbreak\n#\telse:\n#\t\tprint line\n\n\n\n#Get a Graph object\ng = rdflib.Graph()\n\nprint(\"loading up the BAMS file in memory...\")\n\n#pull in an RDF document from NeuroLex, parse, and store.\nresult = g.parse(file=myzipfile.open('bams_ontology_2013-07-10_03-20-00.xml'), format=\"application/rdf+xml\")\n\nprint(\"going to get results...\")\n\n#qres = g.query(\n# \"\"\"SELECT DISTINCT ?definition\n# WHERE {\n# ?cells property:Name \"Basal ganglia\"^^xsd:string ?definition.\n# \t}\"\"\",)\n# #property:Definition\n \nqres = g.query(\n \"\"\"SELECT DISTINCT ?subject ?predicate ?object\n WHERE {\n ?subject ?predicate ?object.\n \t}\"\"\",)\n\n#qres = g.query(\n# \"\"\"SELECT DISTINCT ?subject ?predicate ?object\n# WHERE {\n# ?subject ?predicate ?object.\n# \t} LIMIT 10\"\"\",) \t\n\n#If above fails:\n#qres = g.query(\n# \"\"\"SELECT DISTINCT ?subject ?predicate ?object\n# WHERE {\n# ?subject ?predicate ?object.\n# \t} LIMIT 10\"\"\",) \n \n \n \n \n# \"\"\"SELECT DISTINCT ?definition\n# WHERE {\n# ?cells bams:name \"ganglia\"^^xsd:string ?definition.\n# \t} LIMIT 10\"\"\",)\n \n# \"\"\"SELECT DISTINCT ?definition\n# WHERE {\n# ?cells property:Definition \"birnlex_1489\"^^xsd:string ?definition.\n# \t}\"\"\",)\n\n#could write qres out to a pickle file -- save as a temp file to disk\n\nprint(\"printing results\")\n\n#Search through everything\n#for i in qres:\n#\tprint(\"Definition: %s\" %qres.result[i])\n\n#print(\"Name: %s\" %qres.result[0])\n#TypeError: not all arguments converted during string formatting\n\n\nprint(\"Name--not necessarily in strign format: \")\n#print(qres.result[0])\n#######RETURNS---TRIPLE#STRUCTURE######\n#(rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_11497'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/technique'), rdflib.term.Literal(u'PHAL'))\n\n\n#Hopefully will give us all of the results\nprint(qres.result[0])\nprint(qres.result[1])\nprint(qres.result[2])\n\nprint(qres.result[0][0])\nprint(qres.result[1][0])\nprint(qres.result[2][0])\n\nprint(qres.result[0][0])\nprint(qres.result[0][1])\nprint(qres.result[0][2])\n\n\n\n#Don't have the necessary libraries for these:\n#print(\"Normalizing Laterals: \")\n#print(normalize(qres.result[0]))\n#print(\"Python DataType: \")\n#print(toPython(qres.result[0]))\n\n#myzipfile.close('bams_ontology_2013-07-10_03-20-00.xml')\n\n#####################\n#######results#######\n#~40 seconds for zip to open...\n#loading up the BAMS file in memory...\n#going to get results...\n#Traceback (most recent call last):\n# File \"SPARQL_BAMS_Basal_Ganglia.py\", line 62, in <module>\n# }\"\"\",)\n# File \"/Library/Python/2.7/site-packages/rdflib/graph.py\", line 1045, in query\n# query_object, initBindings, initNs, **kwargs))\n# File \"/Library/Python/2.7/site-packages/rdfextras/sparql/processor.py\", line 49, in query\n# loadContexts=loadContexts)\n# File \"/Library/Python/2.7/site-packages/rdfextras/sparql/algebra.py\", line 406, in TopEvaluate\n# assert isinstance(expr,AlgebraExpression), repr(expr)\n#AssertionError: None\n\nfoofile.close()",
"language": "python",
"metadata": {},
"outputs": [
{
"ename": "KeyboardInterrupt",
"evalue": "",
"output_type": "pyerr",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m<ipython-input-7-9a29c6e236cb>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 54\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 55\u001b[0m \u001b[1;31m#pull in an RDF document from NeuroLex, parse, and store.\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 56\u001b[1;33m \u001b[0mresult\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mg\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mparse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfile\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mmyzipfile\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'bams_ontology_2013-07-10_03-20-00.xml'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"application/rdf+xml\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 57\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 58\u001b[0m \u001b[1;32mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"going to get results...\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/local/lib/python2.7/dist-packages/rdflib/graph.pyc\u001b[0m in \u001b[0;36mparse\u001b[1;34m(self, source, publicID, format, location, file, data, **args)\u001b[0m\n\u001b[0;32m 1000\u001b[0m \u001b[0mformat\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m\"application/rdf+xml\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1001\u001b[0m \u001b[0mparser\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mplugin\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mformat\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mParser\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-> 1002\u001b[1;33m \u001b[0mparser\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mparse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msource\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0margs\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1003\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1004\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/local/lib/python2.7/dist-packages/rdflib/plugins/parsers/rdfxml.pyc\u001b[0m in \u001b[0;36mparse\u001b[1;34m(self, source, sink, **args)\u001b[0m\n\u001b[0;32m 568\u001b[0m \u001b[1;31m# content_handler.reset()\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 569\u001b[0m \u001b[1;31m# self._parser.reset()\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 570\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_parser\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mparse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;32m/usr/lib/python2.7/xml/sax/expatreader.pyc\u001b[0m in \u001b[0;36mparse\u001b[1;34m(self, source)\u001b[0m\n\u001b[0;32m 105\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreset\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 106\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_cont_handler\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msetDocumentLocator\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mExpatLocator\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--> 107\u001b[1;33m \u001b[0mxmlreader\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mIncrementalParser\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mparse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 108\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 109\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mprepareParser\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/xml/sax/xmlreader.pyc\u001b[0m in \u001b[0;36mparse\u001b[1;34m(self, source)\u001b[0m\n\u001b[0;32m 121\u001b[0m \u001b[0mbuffer\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mfile\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_bufsize\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 122\u001b[0m \u001b[1;32mwhile\u001b[0m \u001b[0mbuffer\u001b[0m \u001b[1;33m!=\u001b[0m \u001b[1;34m\"\"\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 123\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfeed\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mbuffer\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 124\u001b[0m \u001b[0mbuffer\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mfile\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_bufsize\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 125\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/xml/sax/expatreader.pyc\u001b[0m in \u001b[0;36mfeed\u001b[1;34m(self, data, isFinal)\u001b[0m\n\u001b[0;32m 205\u001b[0m \u001b[1;31m# document. When feeding chunks, they are not normally final -\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 206\u001b[0m \u001b[1;31m# except when invoked from close.\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 207\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_parser\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mParse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0misFinal\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 208\u001b[0m \u001b[1;32mexcept\u001b[0m \u001b[0mexpat\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0merror\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0me\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 209\u001b[0m \u001b[0mexc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mSAXParseException\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mexpat\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mErrorString\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0me\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcode\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0me\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/xml/sax/expatreader.pyc\u001b[0m in \u001b[0;36mstart_element_ns\u001b[1;34m(self, name, attrs)\u001b[0m\n\u001b[0;32m 336\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 337\u001b[0m self._cont_handler.startElementNS(pair, None,\n\u001b[1;32m--> 338\u001b[1;33m AttributesNSImpl(newattrs, qnames))\n\u001b[0m\u001b[0;32m 339\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 340\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mend_element_ns\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/local/lib/python2.7/dist-packages/rdflib/plugins/parsers/rdfxml.pyc\u001b[0m in \u001b[0;36mstartElementNS\u001b[1;34m(self, name, qname, attrs)\u001b[0m\n\u001b[0;32m 150\u001b[0m \u001b[0mbase\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfrag\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0murldefrag\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msystemId\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 151\u001b[0m \u001b[0mcurrent\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbase\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbase\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 152\u001b[1;33m \u001b[0mlanguage\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mattrs\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mLANG\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mNone\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 153\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mlanguage\u001b[0m \u001b[1;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 154\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mparent\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/xml/sax/xmlreader.pyc\u001b[0m in \u001b[0;36mget\u001b[1;34m(self, name, alternative)\u001b[0m\n\u001b[0;32m 326\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 327\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0malternative\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 328\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_attrs\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0malternative\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 329\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 330\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mcopy\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;31mKeyboardInterrupt\u001b[0m: "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": "~40 seconds for zip to open...\nloading up the BAMS file in memory...\n"
}
],
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": false,
"input": "!sudo pip install rdflib",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Downloading/unpacking rdflib\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Downloading rdflib-4.0.1.tar.gz (903Kb): \r Downloading rdflib-4.0.1.tar.gz (903Kb): 0% 4.1Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 0% 8.2Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 1% 12Kb \r Downloading rdflib-4.0.1.tar.gz (903Kb): 1% 16Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 2% 20Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 2% 24Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 3% 28Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 3% 32Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 4% 36Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 4% 40Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 4% 45Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 5% 49Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 5% 53Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 6% 57Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 6% 61Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 7% 65Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 7% 69Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 8% 73Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 8% 77Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 9% 81Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 9% 86Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 9% 90Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 10% 94Kb"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "\r Downloading rdflib-4.0.1.tar.gz (903Kb): 10% 98Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 11% 102Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 11% 106Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 12% 110Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 12% 114Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 13% 118Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 13% 122Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 14% 126Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 14% 131Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 14% 135Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 15% 139Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 15% 143Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 16% 147Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 16% 151Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 17% 155Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 17% 159Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 18% 163Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 18% 167Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 19% 172Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 19% 176Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 19% 180Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 20% 184Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 20% 188Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 21% 192Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 21% 196Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 22% 200Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 22% 204Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 23% 208Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 23% 212Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 24% 217Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 24% 221Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 24% 225Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 25% 229Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 25% 233Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 26% 237Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 26% 241Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 27% 245Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 27% 249Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 28% 253Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 28% 258Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 29% 262Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 29% 266Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 29% 270Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 30% 274Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 30% 278Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 31% 282Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 31% 286Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 32% 290Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 32% 294Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 33% 299Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 33% 303Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 33% 307Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 34% 311Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 34% 315Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 35% 319Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 35% 323Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 36% 327Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 36% 331Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 37% 335Kb\r Downloading rdflib-4.0.1.tar.gz (903Kb): 37% 339Kb"
},
{
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"output_type": "stream",
"stream": "stdout",
"text": "\r Downloading html5lib-1.0b3.tar.gz (884Kb): 96% 856Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 97% 860Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 97% 864Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 98% 868Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 98% 872Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 99% 876Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 99% 880Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 99% 884Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): 100% 884Kb\r Downloading html5lib-1.0b3.tar.gz (884Kb): \r Downloading html5lib-1.0b3.tar.gz (884Kb): 884Kb downloaded\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py egg_info for package html5lib\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\nDownloading/unpacking six (from html5lib->rdflib)\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Downloading six-1.4.1.tar.gz\r\n Running setup.py egg_info for package six\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\nInstalling collected packages: rdflib, isodate, pyparsing, SPARQLWrapper, html5lib, six\r\n Running setup.py install for rdflib\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " no previously-included directories found matching 'docs/_build'\r\n warning: no previously-included files matching '*.pyc' found anywhere in distribution\r\n warning: no previously-included files matching '*$py.class' found anywhere in distribution\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Installing rdf2dot script to /usr/local/bin\r\n Installing csv2rdf script to /usr/local/bin\r\n Installing rdfgraphisomorpishm script to /usr/local/bin\r\n Installing rdfs2dot script to /usr/local/bin\r\n Installing rdfpipe script to /usr/local/bin\r\n Running setup.py install for isodate\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py install for pyparsing\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py install for SPARQLWrapper\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n warning: no previously-included files found matching 'Makefile'\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py install for html5lib\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py install for six\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\nSuccessfully installed rdflib isodate pyparsing SPARQLWrapper html5lib six\r\nCleaning up...\r\n"
}
],
"prompt_number": 14
},
{
"cell_type": "code",
"collapsed": false,
"input": "!sudo pip install rdfextras",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Requirement already satisfied (use --upgrade to upgrade): rdfextras in /usr/local/lib/python2.7/dist-packages\r\nRequirement already satisfied (use --upgrade to upgrade): rdflib>=3.2.1 in /usr/local/lib/python2.7/dist-packages (from rdfextras)\r\nRequirement already satisfied (use --upgrade to upgrade): pyparsing<=1.5.7 in /usr/local/lib/python2.7/dist-packages (from rdfextras)\r\nRequirement already satisfied (use --upgrade to upgrade): isodate in /usr/local/lib/python2.7/dist-packages (from rdflib>=3.2.1->rdfextras)\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Requirement already satisfied (use --upgrade to upgrade): SPARQLWrapper in /usr/local/lib/python2.7/dist-packages (from rdflib>=3.2.1->rdfextras)\r\nRequirement already satisfied (use --upgrade to upgrade): html5lib in /usr/local/lib/python2.7/dist-packages (from rdflib>=3.2.1->rdfextras)\r\nRequirement already satisfied (use --upgrade to upgrade): six in /usr/local/lib/python2.7/dist-packages (from html5lib->rdflib>=3.2.1->rdfextras)\r\nCleaning up...\r\n"
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": "#SPARQL_BAMS_Basal_Ganglia\n#This program is used to parse through the BAMS data and figure out everything about \"Basal Ganglia\"\n\n#For Parsing\nimport rdflib\nfrom rdflib import plugin\n\n#for getting the length of the files\nimport os\n\n#for working with tempfiles\nimport os.path as op\nimport tempfile\n\n#For Unzipping\nimport zipfile\nfrom StringIO import StringIO\n\nplugin.register(\n 'sparql', rdflib.query.Processor,\n 'rdfextras.sparql.processor', 'Processor')\nplugin.register(\n 'sparql', rdflib.query.Result,\n 'rdfextras.sparql.query', 'SPARQLQueryResult')\n\nzipdata = StringIO()\n\n# open the file using a relative path\nr = open(\"../Data/BAMS1.zip\")\n\n# zipdata is a buffer holding the contents of the zip file in memory\nzipdata.write(r.read())\n\nprint(\"~40 seconds for zip to open...\")\n\n#myzipfile opens the contents of the zip file as an object that knows how to unzip\nmyzipfile = zipfile.ZipFile(zipdata)\n\n#grab the contents out of myzipfile by name\nfoofile = myzipfile.open('bams_ontology_2013-07-10_03-20-00.xml')\n\nprint(\"loading up the BAMS file in memory...\")\n\n#Get a Graph object using a Sleepycat persistent store\ng = rdflib.Graph('Sleepycat',identifier='BAMS')\n\n# first time create the store\n# put the store in a temp directory so it doesn't get confused with stuff we should commit\ntempStore = op.join( tempfile.gettempdir(), 'myRDF_BAMS_Store')\ng.open(tempStore, create = True)\n\n#pull in the BAMS RDF document, parse, and store.\nresult = g.parse(file=myzipfile.open('bams_ontology_2013-07-10_03-20-00.xml'), format=\"application/rdf+xml\")\n\nfoofile.close()\n\n# when done!\ng.close()\n\nprint(\"Graph stored to disk\")",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": "*"
},
{
"cell_type": "code",
"collapsed": false,
"input": "#SPARQL_BAMS_Basal_Ganglia\n#This program is used to parse through the BAMS data and figure out everything about \"Basal Ganglia\"\n\n#For Parsing\nimport rdflib\nfrom rdflib import plugin\n\n#for getting the length of the files\nimport os\n\n#for working with tempfiles\nimport os.path as op\nimport tempfile\n\nplugin.register(\n 'sparql', rdflib.query.Processor,\n 'rdfextras.sparql.processor', 'Processor')\nplugin.register(\n 'sparql', rdflib.query.Result,\n 'rdfextras.sparql.query', 'SPARQLQueryResult')\n\n#Get a Graph object\ng = rdflib.Graph('Sleepycat',identifier='BAMS')\n\nprint(\"loading up the BAMS file in memory...\")\n\n# assumes myRDF_BAMS_Store has been created\ntempStore = op.join( tempfile.gettempdir(), 'myRDF_BAMS_Store')\ng.open(tempStore)\n\nprint(\"going to get results...\")\n\nqres = g.query(\n \"\"\"SELECT ?subject ?predicate ?object\n WHERE {\n ?subject ?predicate ?object.\n \t} LIMIT 5\"\"\")\n\nprint(\"printing results\")\n\n\nprint(\"The graph has \" + str(len(g)) + \" items in it\")\n\nprint(\"Name--not necessarily in strign format: \")\nprint(qres.result[0])\n\n# when done!\ng.close()",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "loading up the BAMS file in memory...\ngoing to get results...\nprinting results"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "\nThe graph has 670161 items in it"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "\nName--not necessarily in strign format: \n<rdfextras.sparql.query.SPARQLQueryResult object at 0xbcb42c10>\n[(rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/description'), rdflib.term.Literal(u'Collator note: NIc does not receive projections from this region, because all of the atlas levels were inspected and no label was found.')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/reference'), rdflib.term.BNode('Nf3802d7fa0f149fd8bbdf766b11d949b')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/connection')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/receiver'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/brain_parts/Nucleus-incertus-compact-part/')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/sender'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/brain_parts/Nucleus-reuniens-rostral-division-anterior-part/')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/strength_label'), rdflib.term.Literal(u'does not exist')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/technique'), rdflib.term.Literal(u'CTB')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/collator'), rdflib.term.Literal(u'510')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_63097'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/description'), rdflib.term.Literal(u'Collator note: this connection is considered to be absent, because all of the atlas levels were inspected by authors.')), (rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_63097'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/reference'), rdflib.term.BNode('N23f34f3238ac412ebd08db48fc88a0f4'))]\n(rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/description'), rdflib.term.Literal(u'Collator note: NIc does not receive projections from this region, because all of the atlas levels were inspected and no label was found.'))\n"
}
],
"prompt_number": 41
},
{
"cell_type": "code",
"collapsed": false,
"input": "qres = g.query(\n \"\"\"SELECT ?subject ?predicate ?object\n WHERE {\n ?subject ?predicate ?object.\n \t} LIMIT 5\"\"\")",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 42
},
{
"cell_type": "code",
"collapsed": false,
"input": "print(qres.result[0])",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "(rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/conn_42771'), rdflib.term.URIRef(u'http://brancusi1.usc.edu/RDF/description'), rdflib.term.Literal(u'Collator note: NIc does not receive projections from this region, because all of the atlas levels were inspected and no label was found.'))\n"
}
],
"prompt_number": 43
},
{
"cell_type": "code",
"collapsed": false,
"input": "!rm -rf myRDFLibStore/",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 36
},
{
"cell_type": "code",
"collapsed": false,
"input": "!sudo ls -l /tmp",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "total 4\r\ndrwxr-xr-x 2 root root 4096 Sep 24 22:37 myRDF_BAMS_Store\r\n"
}
],
"prompt_number": 40
},
{
"cell_type": "code",
"collapsed": false,
"input": "",
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
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