gistfile1.txt

{
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  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import json\n",
    "import requests"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "API_URL = 'http://localhost:8103/api/v1'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Authentication\n",
    "Authenticate with Girder and setup headers to be used in future calls to Girder to identify yourself"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "r = requests.get(API_URL + '/user/authentication', auth=('girder', 'girder')).json()\n",
    "token = r['authToken']['token']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "headers = {'Girder-Token': token}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Listing collections\n",
    "Passing the headers allows you to see collections you have permission to view, omitting them will show you only public collections."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"size\": 21282, \n",
      "  \"updated\": \"2016-08-05T17:32:07.609000+00:00\", \n",
      "  \"description\": \"\", \n",
      "  \"created\": \"2016-08-05T16:27:31.857000+00:00\", \n",
      "  \"public\": false, \n",
      "  \"_id\": \"57a4be73d2a7331829d87979\", \n",
      "  \"_modelType\": \"collection\", \n",
      "  \"_accessLevel\": 2, \n",
      "  \"name\": \"Main\"\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "for collection in requests.get(API_URL + '/collection', headers=headers).json():\n",
    "    print json.dumps(collection, indent=2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Listing folders in a collection\n",
    "Using the collection `_id` from the above list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"size\": 0, \n",
      "  \"updated\": \"2016-08-05T16:27:31.900000+00:00\", \n",
      "  \"description\": \"\", \n",
      "  \"created\": \"2016-08-05T16:27:31.900000+00:00\", \n",
      "  \"baseParentType\": \"collection\", \n",
      "  \"public\": false, \n",
      "  \"baseParentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"creatorId\": \"57a4aa23d2a7335b89a6882d\", \n",
      "  \"parentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"parentCollection\": \"collection\", \n",
      "  \"_id\": \"57a4be73d2a7331829d8797c\", \n",
      "  \"_modelType\": \"folder\", \n",
      "  \"_accessLevel\": 2, \n",
      "  \"name\": \"Analyses\"\n",
      "}\n",
      "{\n",
      "  \"size\": 21282, \n",
      "  \"updated\": \"2016-08-05T16:27:31.899000+00:00\", \n",
      "  \"description\": \"\", \n",
      "  \"created\": \"2016-08-05T16:27:31.899000+00:00\", \n",
      "  \"baseParentType\": \"collection\", \n",
      "  \"public\": false, \n",
      "  \"baseParentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"creatorId\": \"57a4aa23d2a7335b89a6882d\", \n",
      "  \"parentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"parentCollection\": \"collection\", \n",
      "  \"_id\": \"57a4be73d2a7331829d8797a\", \n",
      "  \"_modelType\": \"folder\", \n",
      "  \"_accessLevel\": 2, \n",
      "  \"name\": \"Data\"\n",
      "}\n",
      "{\n",
      "  \"size\": 0, \n",
      "  \"updated\": \"2016-08-05T16:27:31.898000+00:00\", \n",
      "  \"description\": \"\", \n",
      "  \"created\": \"2016-08-05T16:27:31.898000+00:00\", \n",
      "  \"baseParentType\": \"collection\", \n",
      "  \"public\": false, \n",
      "  \"baseParentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"creatorId\": \"57a4aa23d2a7335b89a6882d\", \n",
      "  \"parentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"parentCollection\": \"collection\", \n",
      "  \"_id\": \"57a4be73d2a7331829d8797b\", \n",
      "  \"_modelType\": \"folder\", \n",
      "  \"_accessLevel\": 2, \n",
      "  \"name\": \"Visualizations\"\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "collectionFolders = requests.get(API_URL + '/folder', params={\n",
    "                        'parentType': 'collection',\n",
    "                        'parentId': '57a4be73d2a7331829d87979'}, headers=headers).json()\n",
    "\n",
    "for collectionFolder in collectionFolders:\n",
    "    print json.dumps(collectionFolder, indent=2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Listing analyses\n",
    "Using the `_id` of the Analyses folder from above"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"size\": 0, \n",
      "  \"updated\": \"2016-08-15T18:35:25.820000+00:00\", \n",
      "  \"folderId\": \"57a4be73d2a7331829d8797c\", \n",
      "  \"description\": \"\", \n",
      "  \"created\": \"2016-08-15T18:35:25.797000+00:00\", \n",
      "  \"baseParentType\": \"collection\", \n",
      "  \"meta\": {\n",
      "    \"analysis\": {\n",
      "      \"inputs\": [\n",
      "        {\n",
      "          \"type\": \"table\", \n",
      "          \"id\": \"table\", \n",
      "          \"name\": \"table\", \n",
      "          \"format\": \"rows\"\n",
      "        }\n",
      "      ], \n",
      "      \"description\": \"\", \n",
      "      \"script\": \"out_table = table\\n\", \n",
      "      \"outputs\": [\n",
      "        {\n",
      "          \"type\": \"table\", \n",
      "          \"id\": \"out_table\", \n",
      "          \"name\": \"out_table\", \n",
      "          \"format\": \"rows\"\n",
      "        }\n",
      "      ], \n",
      "      \"mode\": \"python\", \n",
      "      \"name\": \"tablePassThrough\"\n",
      "    }\n",
      "  }, \n",
      "  \"baseParentId\": \"57a4be73d2a7331829d87979\", \n",
      "  \"creatorId\": \"57a4aa23d2a7335b89a6882d\", \n",
      "  \"_id\": \"57b20b6dd2a733485e91de8a\", \n",
      "  \"_modelType\": \"item\", \n",
      "  \"name\": \"tablePassThrough\"\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "for analysis in requests.get(API_URL + '/item', params={'folderId': '57a4be73d2a7331829d8797c'}, headers=headers).json():\n",
    "    print json.dumps(analysis, indent=2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Running an analysis\n",
    "Using the `_id` of the analysis in the above output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Prepare the input with data, and the output information\n",
    "task = {\n",
    "    \"inputs\": {\n",
    "        \"table\": {\n",
    "            \"type\": \"table\",\n",
    "            \"format\": \"rows\",\n",
    "            \"data\": {\n",
    "                \"fields\": [\"foo\"],\n",
    "                \"rows\": [\"bar\", \"baz\"]\n",
    "            }\n",
    "        }\n",
    "    },\n",
    "    \"outputs\": {\n",
    "        \"out_table\": {\n",
    "            \"type\": \"table\",\n",
    "            \"format\": \"rows\"\n",
    "        }\n",
    "    }\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# The analysis starts a job and returns its id\n",
    "job = requests.post(API_URL + '/item/' + '57b20b6dd2a733485e91de8a' + '/flow', \n",
    "                    data=json.dumps(task), \n",
    "                    headers=headers).json()\n",
    "jobId = job['_id']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"result\": {\n",
      "    \"out_table\": {\n",
      "      \"type\": \"table\", \n",
      "      \"data\": {\n",
      "        \"fields\": [\n",
      "          \"foo\"\n",
      "        ], \n",
      "        \"rows\": [\n",
      "          \"bar\", \n",
      "          \"baz\"\n",
      "        ]\n",
      "      }, \n",
      "      \"format\": \"rows\"\n",
      "    }\n",
      "  }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# Job results can be viewed with a combination of the analysis itemId and the jobId\n",
    "result = requests.get(API_URL + '/item/' + '57b20b6dd2a733485e91de8a' + '/flow/' + jobId + '/result', headers=headers)\n",
    "print json.dumps(result.json(), indent=2)"
   ]
  }
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