25-2.1 Neo4J graph example.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"name":"25-2.1 Neo4J graph example","provenance":[],"collapsed_sections":[],"authorship_tag":"ABX9TyPEHdrwp5dcGmkl1CJJ6rne"},"kernelspec":{"name":"python3","display_name":"Python 3"}},"cells":[{"cell_type":"code","metadata":{"id":"CtgshfD73zpI"},"source":["# Neo4J graph example\n","# author: Gressling, T\n","# license: MIT License # code: github.com/gressling/examples\n","# activity: single example # index: 25-2 "],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"xpL7odBAc_5c"},"source":["# https://gist.github.com/korakot/328aaac51d78e589b4a176228e4bb06f\n","# download 3.5.8 or neo4j-enterprise-4.0.0-alpha09mr02-unix\n","!curl https://neo4j.com/artifact.php?name=neo4j-community-3.5.8-unix.tar.gz -v -o neo4j.tar.gz\n","#!curl https://s3-eu-west-1.amazonaws.com/dist.neo4j.org/neo4j-community-3.5.8-unix.tar.gz?x-amz-security-token=IQoJb3JpZ2luX2VjEBgaCXVzLWVhc3QtMSJIMEYCIQC8JQ87qLW8MutNDC7kLf%2F8lCgTEeFw6XMHe0g6JGiLwQIhALrPjMot9j4eV1EiWsysYUamjICHutsaKG%2Fa%2B05ZJKD%2BKr0DCJD%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQABoMMTI4OTE2Njc5MzMwIgyekSOUHQOH4V1oebkqkQMSnlGj83iqgQ1X%2Bb9lDsjjfh%2FGggoIuvkn8RO9Ur3Ws24VznIHWrxQTECnTtQfsjhruOUbGJKv%2FlKBy9VU0aLu0zdrNcxeWZedOW09We0xVS4QTBipwW4i0UubWw%2FuDp1vAKPc1wLIq3vuvgflB4sXmTgvkQ%2FcT2%2BoIrvflqmSQ%2Fr9SB9Cqj9iACjxNQZrLs3qv2WgWxUNSsVjJYGXUx1yzx0ckCtxKYZ%2BzVBvqGuG1yULIodkGo4Kfbk5bh7s69gk8N4Gli7cQvYc9ajSFGg5IHXJU7%2BvRWeekX%2F2o7JlCRQogSNlW8kvv7o9ioD6Uj1mkOnR6rMsEv4Xo%2B2buKg7LqaPobmZwyjGnMBvZdndLXq37lAT7%2BP1i%2BVNCC7rak4Aqb3HtFMDZ%2F0nmdAitcKDWG1Am1mnaXiL3s6MZQ88SoU8h5RK0k01M%2FBxU9ZPwfi%2Bm8OAC%2Bgh6QyP9f7CPqSdI%2Fy8BSthxARcwWxl2ZwhHtUu7jqFf601aTu0iof%2FP2tH9oxty4kdH%2BI64qo7JCr9%2BzDx4OT9BTrqAfGlw5dReXwyh%2BSnYxW%2BB42cGs2JDcrFohn6UGdG3BtI%2FsjAFymH0vkCtXfN3irUPPzOoFzx216v%2F4GFfGebIpWqr85hT2f%2F28fck2XPbXiv%2BXSeffQdc8UkSL7dMHbquZ%2BmdOtCNlMhOWpnov5J7aICj9uY4AR60kNUSW3N4nra3CXjNEJWy%2B8ft49e6lnR9iKlVFxdwoXb1YAEx4egpctFcffoiaIEk2GinHjShAQgApOZFgOLe%2FDC9%2BnIwhxL7rSUfP7Ox%2FbEJF%2Br6VNYJddoD6D8xF2OVo%2FxZzv4M6eyw6Squ5r6i4LM7g%3D%3D&AWSAccessKeyId=ASIAR4BAINKRGKUIBRUS&Expires=1605973931&Signature=gzC025ItqNNdXpCJkGsm%2FvQt2WU%3D -o neo4j.tar.gz\n"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"ZpnuCAkidCUk"},"source":["# decompress and rename\n","!tar -xf neo4j.tar.gz  # or --strip-components=1\n","!mv neo4j-community-3.5.8 nj"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"wM4OVwGmdD_W"},"source":["# disable password, and start server\n","!sed -i '/#dbms.security.auth_enabled/s/^#//g' nj/conf/neo4j.conf\n","!nj/bin/neo4j start"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"P0Z3cAcTcXWE"},"source":["# from neo4j import GraphDatabase\n","# !pip install py2neo"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"nw3Lk_jCcZtV"},"source":["from py2neo import Graph\n","graph = Graph(\"bolt://localhost:7687\", auth=(\"neo4j\", \"password\"))\n","graph.delete_all()"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"k3ZaaqFTcc0b"},"source":["# define the entities of the graph (nodes)\n","from py2neo import Node"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"VgSr8MaocftL"},"source":["laboratory = Node(\"Laboratory\", name=\"Laboratory 1\")\n","lab1 = Node(\"Person\", name=\"Peter\", employee_ID=2)\n","lab2 = Node(\"Person\", name=\"Susan\", employee_ID=4)\n","sample1 = Node(\"Sample\", name=\"A-12213\", weight=45.7)\n","sample2 = Node(\"Sample\", name=\"B-33443\", weight=48.0)\n","\n","# shared sample between two experiments\n","sample3 = Node(\"Sample\", name=\"AB-33443\", weight=24.3)\n","experiment1 = Node(\"Experiment\", name=\"Screening-45\")\n","experiment2 = Node(\"Experiment\", name=\"Screening/w/Sol\")"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"bBm9jU-YckpL"},"source":["graph.create(laboratory | lab1 | lab2 | sample1 | sample2 | experiment1 |\n","experiment2)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"GrzYVjeNcnvk"},"source":["# Define the relationships of the graph (edges)\n","from py2neo import Relationship"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"D__cJVFOcqo6"},"source":["graph.create(Relationship(lab1, \"works in\", laboratory))\n","graph.create(Relationship(lab2, \"works in\", laboratory))\n","graph.create(Relationship(lab1, \"performs\", sample1))\n","graph.create(Relationship(lab2, \"performs\", sample2))\n","graph.create(Relationship(lab2, \"performs\", sample3))\n","graph.create(Relationship(sample1, \"partof\", experiment1))\n","graph.create(Relationship(sample2, \"partof\", experiment2))\n","graph.create(Relationship(sample3, \"partof\", experiment2))\n","graph.create(Relationship(sample3, \"partof\", experiment1))"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"mfaY9rL0c4c9"},"source":["import neo4jupyter\n","neo4jupyter.init_notebook_mode()\n","neo4jupyter.draw(graph)"],"execution_count":null,"outputs":[]}]}