example_metadata.ipynb

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   "source": [
    "# Load and display metadata linking options\n",
    "\n",
    "*See:* https://so-tools.readthedocs.io/en/latest/ for more up-to-date information."
   ]
  },
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     "name": "#%%\n"
    }
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   "source": [
    "import os\n",
    "import sotools\n",
    "from pprint import pprint\n",
    "data_base = \"docsource/source/examples/data/\"\n",
    "public_base = \"https://my.server.net/data/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Example 00\n",
    "`ds_00` uses the `encoding` pattern for associating a rich external metadata document with the Dataset. "
   ]
  },
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     "name": "stdout",
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     "text": [
      "{\n",
      "   \"@id\":\"ds_m_encoding\",\n",
      "   \"@context\": {\n",
      "       \"@vocab\": \"https://schema.org/\"\n",
      "   },\n",
      "   \"@type\":\"Dataset\",\n",
      "   \"name\": \"Dataset with metadata encoding\",\n",
      "   \"description\": \"Dataset snippet using SO:Encoding pattern for associated XML metadata.\",\n",
      "   \"license\": \"https://creativecommons.org/publicdomain/zero/1.0/\",\n",
      "   \"identifier\": \"dataset-00\",\n",
      "   \"encoding\": {\n",
      "       \"@id\":\"ds_m_encoding#media-object\",\n",
      "       \"@type\":\"MediaObject\",\n",
      "       \"contentUrl\":\"https://my.server.net/datasets/00.xml\",\n",
      "       \"dateModified\":\"2019-10-10T12:43:11+00:00.000\",\n",
      "       \"description\":\"ISO TC211 XML rendering of metadata\",\n",
      "       \"encodingFormat\":\"http://www.isotc211.org/2005/gmd\"\n",
      "   }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# Display the source of ds_00\n",
    "\n",
    "fname = os.path.join(data_base, \"ds_m_encoding.json\")\n",
    "print(open(fname).read())"
   ]
  },
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   ],
   "source": [
    "# Load and visualize the graph structure\n",
    "\n",
    "g_00 = sotools.loadSOGraph(filename=fname, publicID=public_base)\n",
    "sotools.renderGraph(g_00)"
   ]
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     "text": [
      "[{'contentUrl': 'https://my.server.net/datasets/00.xml',\n",
      "  'dateModified': rdflib.term.Literal('2019-10-10T12:43:11+00:00.000'),\n",
      "  'description': 'ISO TC211 XML rendering of metadata',\n",
      "  'encodingFormat': 'http://www.isotc211.org/2005/gmd',\n",
      "  'subjectOf': 'https://my.server.net/data/ds_m_encoding'}]\n"
     ]
    }
   ],
   "source": [
    "# extract the metadata links\n",
    "\n",
    "mlinks = sotools.getDatasetMetadataLinks(g_00)\n",
    "pprint(mlinks)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
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   "source": [
    "## Example 01\n",
    "`ds_01` uses the `about` pattern to assert that an external metadata \n",
    "document (indicated by the `MediaObject`) is about the Dataset and the \n",
    "`data_part_a.csv` part of the Dataset."
   ]
  },
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   "outputs": [
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"@context\": {\n",
      "    \"@vocab\": \"https://schema.org/\"\n",
      "  },\n",
      "  \"@graph\": [\n",
      "    {\n",
      "      \"@type\": \"Dataset\",\n",
      "      \"@id\": \"./\",\n",
      "      \"identifier\": \"dataset-01\",\n",
      "      \"name\": \"Dataset with metadata about\",\n",
      "      \"description\": \"Dataset snippet with metadata and data components indicated by hasPart and the descriptive metadata through an about association.\",\n",
      "      \"license\": \"https://creativecommons.org/publicdomain/zero/1.0/\",\n",
      "      \"hasPart\": [\n",
      "        {\n",
      "          \"@id\": \"./metadata.xml\"\n",
      "        },\n",
      "        {\n",
      "          \"@id\": \"./data_part_a.csv\"\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@id\": \"./metadata.xml\",\n",
      "      \"@type\": \"MediaObject\",\n",
      "      \"contentUrl\": \"https://example.org/my/data/1/metadata.xml\",\n",
      "      \"dateModified\": \"2019-10-10T12:43:11+00:00.000\",\n",
      "      \"description\": \"A metadata document describing the Dataset and the data component\",\n",
      "      \"encodingFormat\":\"http://www.isotc211.org/2005/gmd\",\n",
      "      \"about\": [\n",
      "        {\n",
      "          \"@id\": \"./\"\n",
      "        },\n",
      "        {\n",
      "          \"@id\": \"./data_part_a.csv\"\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@id\": \"./data_part_a.csv\",\n",
      "      \"@type\": \"MediaObject\",\n",
      "      \"contentUrl\": \"https://example.org/my/data/1/data_part_a.csv\"\n",
      "    }\n",
      "  ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# Display the source of ds_01\n",
    "\n",
    "fname = os.path.join(data_base, \"ds_m_about.json\")\n",
    "print(open(fname).read())"
   ]
  },
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     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "# Load and visualize the graph structure\n",
    "\n",
    "g_01 = sotools.loadSOGraph(filename=fname, publicID=public_base)\n",
    "sotools.renderGraph(g_01)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    },
    "pycharm": {
     "is_executing": false,
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'contentUrl': 'https://example.org/my/data/1/metadata.xml',\n",
      "  'dateModified': rdflib.term.Literal('2019-10-10T12:43:11+00:00.000'),\n",
      "  'description': 'A metadata document describing the Dataset and the data '\n",
      "                 'component',\n",
      "  'encodingFormat': 'http://www.isotc211.org/2005/gmd',\n",
      "  'subjectOf': 'https://my.server.net/data/'}]\n"
     ]
    }
   ],
   "source": [
    "# extract the metadata links\n",
    "\n",
    "mlinks = sotools.getDatasetMetadataLinks(g_01)\n",
    "pprint(mlinks)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Example 02\n",
    "`ds_02` uses the `subjectOf` pattern (i.e. inverse of `about`) to indicate that the\n",
    "Dataset is the subjectOf the external metadata document referenced in the CreativeWork \n",
    "at `ds-02/metadata.xml`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false,
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     "outputs_hidden": false
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    "pycharm": {
     "is_executing": false,
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    \"@context\": {\n",
      "        \"@vocab\": \"https://schema.org/\",\n",
      "        \"datacite\": \"http://purl.org/spar/datacite/\"\n",
      "    },\n",
      "    \"@id\": \"ds-02\",\n",
      "    \"url\": \"https://my.server.org/data/ds-02\",\n",
      "    \"@type\": \"Dataset\",\n",
      "    \"identifier\": \"dataset-02\",\n",
      "    \"name\": \"Dataset subjectOf metadata\",\n",
      "    \"description\": \"Dataset snippet with descriptive metadata indicated through subjectOf relation.\",\n",
      "    \"license\": \"https://creativecommons.org/publicdomain/zero/1.0/\",\n",
      "    \"subjectOf\": {\n",
      "        \"@id\": \"ds-02/metadata.xml\",\n",
      "        \"@type\": \"CreativeWork\",\n",
      "        \"name\": \"Dublin Core Metadata Document Describing the Dataset\",\n",
      "        \"url\": \"https://my.server.org/data/ds-02/metadata.xml\",\n",
      "        \"encodingFormat\": [\"application/rdf+xml\", \"http://ns.dataone.org/metadata/schema/onedcx/v1.0\"]\n",
      "    }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# Display the source of ds_02\n",
    "\n",
    "fname = os.path.join(data_base, \"ds_m_subjectof.json\")\n",
    "print(open(fname).read())"
   ]
  },
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     "name": "#%%\n"
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   },
   "outputs": [
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     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "# Load and visualize the graph structure\n",
    "\n",
    "g_02 = sotools.loadSOGraph(filename=fname, publicID=public_base)\n",
    "sotools.renderGraph(g_02)"
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   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    },
    "pycharm": {
     "is_executing": false,
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'contentUrl': 'https://my.server.org/data/ds-02/metadata.xml',\n",
      "  'dateModified': None,\n",
      "  'description': 'None',\n",
      "  'encodingFormat': 'http://ns.dataone.org/metadata/schema/onedcx/v1.0',\n",
      "  'subjectOf': 'https://my.server.net/data/ds-02'},\n",
      " {'contentUrl': 'https://my.server.org/data/ds-02/metadata.xml',\n",
      "  'dateModified': None,\n",
      "  'description': 'None',\n",
      "  'encodingFormat': 'application/rdf+xml',\n",
      "  'subjectOf': 'https://my.server.net/data/ds-02'}]\n"
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   "source": [
    "# extract the metadata links\n",
    "# Multiple entries are responsive to the query because there are two\n",
    "# encodingFormat values\n",
    "\n",
    "mlinks = sotools.getDatasetMetadataLinks(g_02)\n",
    "pprint(mlinks)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example 03\n",
    "\n",
    "Load content from an ARM landing page."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
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   "source": [
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    "\n",
    "g_03 = sotools.loadSOGraphFromUrl(url)\n",
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   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
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     "text": [
      "[{'contentUrl': 'https://www.archive.arm.gov/metadata/adc/xml/kasacrspeccmaskcopol.xml',\n",
      "  'dateModified': rdflib.term.Literal('2019-11-25T15:58:13.142132', datatype=rdflib.term.URIRef('http://schema.org/Date')),\n",
      "  'description': 'ISO TC211 XML rendering of metadata.',\n",
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      "[{'propertyId': 'DOI',\n",
      "  'url': 'http://dx.doi.org/10.5439/1095597',\n",
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