catmaid_2_vfb_pubs.ipynb

gistfile1.txt

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 "cells": [
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   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Zwart et al. 2016', 'Berck, Khandelwal et al. 2016', 'Eichler, Li, Litwin-Kumar et al. 2017', 'Larderet, Fritsch et al. 2017', 'Ohyama, Schneider-Mizell et al. 2015', 'Jovanic, Schneider-Mizell et al. 2016', 'Schlegel et al. 2016', 'Fushiki et al. 2016', 'Takagi et al. 2017', 'Heckscher et al. 2015', 'Gerhard et al. 2017', 'Burgos et al 2018', 'Miroschnikow et al. 2018', 'Jovanic et al. 2019', 'Carreira-Rosario, Arzan Zarin, Clark et al. 2018', 'Zarin, Mark et al. 2019', 'Mark et al. 2019']\n"
     ]
    }
   ],
   "source": [
    "import requests\n",
    "import json\n",
    "\n",
    "URL=\"https://l1em.catmaid.virtualflybrain.org\"\n",
    "PROJECT_ID = 1 \n",
    "\n",
    "client = requests.session()\n",
    "client.get(\"%s\" % (URL))\n",
    "for key in client.cookies.keys():\n",
    "    if key[:4] == 'csrf':\n",
    "        csrf_key = key\n",
    "csrftoken = client.cookies[csrf_key]\n",
    "\n",
    "call_papers = {\"annotated_with\":\"papers\",\"with_annotations\":False,\"annotation_reference\":\"name\"}\n",
    "papers = client.post(\"%s/%d/annotations/query-targets\" % (URL,PROJECT_ID), data=call_papers, headers={\"Referer\": URL, \"X-CSRFToken\":csrftoken}).json()[\"entities\"]\n",
    "print([p['name'] for p in papers])\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'p.short_form': 'FBrf0238464', 'ds.short_form': 'Burgos2018', 'ds.label': 'Nociceptive system neurons - EM (Burgos2017)'}, {'p.short_form': 'FBrf0237618', 'ds.short_form': 'Takagi2017', 'ds.label': 'Larval wave neurons and circuit partners - EM  (Takagi2017)'}, {'p.short_form': 'FBrf0233076', 'ds.short_form': 'Zwart2016', 'ds.label': 'Larval motor circuit neurons (Zwart2016)'}, {'p.short_form': 'FBrf0232785', 'ds.short_form': 'Berck2016', 'ds.label': 'Larval olfactory system neurons - EM (Berk2016)'}, {'p.short_form': 'FBrf0237760', 'ds.short_form': 'Larderet2017', 'ds.label': 'larval visual circuit neurons (Larderet2017)'}, {'p.short_form': 'FBrf0234450', 'ds.short_form': 'Schlegel2016', 'ds.label': 'larval hugin neurons - EM (Schlegel2016)'}, {'p.short_form': 'FBrf0236359', 'ds.short_form': 'Eichler2017', 'ds.label': 'Larval MB neurons - EM (Eichler2017)'}, {'p.short_form': 'FBrf0231611', 'ds.short_form': 'Fushiki2016', 'ds.label': 'Larval peristalitic lcomotor system neurons - EM (Fushiki2016)'}, {'p.short_form': 'FBrf0237057', 'ds.short_form': 'Gerhard2017', 'ds.label': 'Nociceptive circuit neurons - EM (Gerhard2017)'}, {'p.short_form': 'FBrf0229965', 'ds.short_form': 'Heckscher2015', 'ds.label': 'Eve+ neurons, sensorimotor circuit - EM (Heckscher2015)'}, {'p.short_form': 'FBrf0228257', 'ds.short_form': 'Ohyama2015', 'ds.label': 'Neurons involved in larval fast escape response - EM (Ohyama2016)'}, {'p.short_form': 'FBrf0233796', 'ds.short_form': 'Jovanic2016', 'ds.label': 'larval sensorimotor decision pathways (Jovanic2016)'}]\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('/repos/VFB_neo4j/src/')\n",
    "from uk.ac.ebi.vfb.neo4j.neo4j_tools import neo4j_connect, results_2_dict_list\n",
    "\n",
    "nc  =  neo4j_connect('http://kb.virtualflybrain.org', 'neo4j', 'neo4j')\n",
    "query  = \"MATCH (n:Site { label: 'VFB CATMAID L1 CNS'})<-[r:hasDbXref]\" \\\n",
    "         \"-(x:Individual)-[:has_source]->(ds:DataSet)-[]->(p:pub) \" \\\n",
    "         \"return distinct p.short_form, ds.short_form, ds.label\"\n",
    "q = nc.commit_list([query])\n",
    "r  =  results_2_dict_list(q)\n",
    "print(r)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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