{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# List Objects in Production\n",
"\n",
"**Task:** Connect to the DataONE production environment, retrieve the list of Objects, and print out the list."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First, load the `dataone` R package and connect to the production Coordinating Node:\n"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
"library(dataone)\n",
"cn <- CNode()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"`listObjects` accepts a number of optional arguments (see `?listObjects`) such as `count` which controls the number of objects that are returned:"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\t- $objectInfo
\n",
"\t\t\n",
"\t- $identifier
\n",
"\t\t- '0000120ce277dbb2e140d74b50ca23e5'
\n",
"\t- $formatId
\n",
"\t\t- 'http://www.isotc211.org/2005/gmd-pangaea'
\n",
"\t- $checksum
\n",
"\t\t\n",
"\t- $text
\n",
"\t\t- '0000120ce277dbb2e140d74b50ca23e5'
\n",
"\t- $.attrs
\n",
"\t\t- algorithm: 'MD5'
\n",
"
\n",
"- $dateSysMetadataModified
\n",
"\t\t- '2018-04-20T07:59:45.497+00:00'
\n",
"\t- $size
\n",
"\t\t- '19541'
\n",
"
\n",
"- $objectInfo
\n",
"\t\t\n",
"\t- $identifier
\n",
"\t\t- '000026213216f47287f0d3027f3c4be3'
\n",
"\t- $formatId
\n",
"\t\t- 'http://www.isotc211.org/2005/gmd-pangaea'
\n",
"\t- $checksum
\n",
"\t\t\n",
"\t- $text
\n",
"\t\t- '000026213216f47287f0d3027f3c4be3'
\n",
"\t- $.attrs
\n",
"\t\t- algorithm: 'MD5'
\n",
"
\n",
"- $dateSysMetadataModified
\n",
"\t\t- '2018-04-20T05:09:36.311+00:00'
\n",
"\t- $size
\n",
"\t\t- '26256'
\n",
"
\n",
"- $objectInfo
\n",
"\t\t\n",
"\t- $identifier
\n",
"\t\t- '0000aa6924377b6a7e5ab59bcec5d4f3'
\n",
"\t- $formatId
\n",
"\t\t- 'http://www.isotc211.org/2005/gmd-pangaea'
\n",
"\t- $checksum
\n",
"\t\t\n",
"\t- $text
\n",
"\t\t- '0000aa6924377b6a7e5ab59bcec5d4f3'
\n",
"\t- $.attrs
\n",
"\t\t- algorithm: 'MD5'
\n",
"
\n",
"- $dateSysMetadataModified
\n",
"\t\t- '2018-02-17T03:01:16.406+00:00'
\n",
"\t- $size
\n",
"\t\t- '35084'
\n",
"
\n",
"- $objectInfo
\n",
"\t\t\n",
"\t- $identifier
\n",
"\t\t- '0000d11ff42b22915fcce5cfa6027040'
\n",
"\t- $formatId
\n",
"\t\t- 'http://www.isotc211.org/2005/gmd-pangaea'
\n",
"\t- $checksum
\n",
"\t\t\n",
"\t- $text
\n",
"\t\t- '0000d11ff42b22915fcce5cfa6027040'
\n",
"\t- $.attrs
\n",
"\t\t- algorithm: 'MD5'
\n",
"
\n",
"- $dateSysMetadataModified
\n",
"\t\t- '2018-01-06T10:43:32.073+00:00'
\n",
"\t- $size
\n",
"\t\t- '35257'
\n",
"
\n",
"- $objectInfo
\n",
"\t\t\n",
"\t- $identifier
\n",
"\t\t- '0000eb4ff1fc59ae6c33a4981e00eabf'
\n",
"\t- $formatId
\n",
"\t\t- 'http://www.isotc211.org/2005/gmd-pangaea'
\n",
"\t- $checksum
\n",
"\t\t\n",
"\t- $text
\n",
"\t\t- '0000eb4ff1fc59ae6c33a4981e00eabf'
\n",
"\t- $.attrs
\n",
"\t\t- algorithm: 'MD5'
\n",
"
\n",
"- $dateSysMetadataModified
\n",
"\t\t- '2018-01-08T11:18:27.291+00:00'
\n",
"\t- $size
\n",
"\t\t- '49904'
\n",
"
\n",
"- $.attrs
\n",
"\t\t- count
- '5'
- start
- '0'
- total
- '2897219'
\n",
"
\n"
],
"text/latex": [
"\\begin{description}\n",
"\\item[\\$objectInfo] \\begin{description}\n",
"\\item[\\$identifier] '0000120ce277dbb2e140d74b50ca23e5'\n",
"\\item[\\$formatId] 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"\\item[\\$checksum] \\begin{description}\n",
"\\item[\\$text] '0000120ce277dbb2e140d74b50ca23e5'\n",
"\\item[\\$.attrs] \\textbf{algorithm:} 'MD5'\n",
"\\end{description}\n",
"\n",
"\\item[\\$dateSysMetadataModified] '2018-04-20T07:59:45.497+00:00'\n",
"\\item[\\$size] '19541'\n",
"\\end{description}\n",
"\n",
"\\item[\\$objectInfo] \\begin{description}\n",
"\\item[\\$identifier] '000026213216f47287f0d3027f3c4be3'\n",
"\\item[\\$formatId] 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"\\item[\\$checksum] \\begin{description}\n",
"\\item[\\$text] '000026213216f47287f0d3027f3c4be3'\n",
"\\item[\\$.attrs] \\textbf{algorithm:} 'MD5'\n",
"\\end{description}\n",
"\n",
"\\item[\\$dateSysMetadataModified] '2018-04-20T05:09:36.311+00:00'\n",
"\\item[\\$size] '26256'\n",
"\\end{description}\n",
"\n",
"\\item[\\$objectInfo] \\begin{description}\n",
"\\item[\\$identifier] '0000aa6924377b6a7e5ab59bcec5d4f3'\n",
"\\item[\\$formatId] 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"\\item[\\$checksum] \\begin{description}\n",
"\\item[\\$text] '0000aa6924377b6a7e5ab59bcec5d4f3'\n",
"\\item[\\$.attrs] \\textbf{algorithm:} 'MD5'\n",
"\\end{description}\n",
"\n",
"\\item[\\$dateSysMetadataModified] '2018-02-17T03:01:16.406+00:00'\n",
"\\item[\\$size] '35084'\n",
"\\end{description}\n",
"\n",
"\\item[\\$objectInfo] \\begin{description}\n",
"\\item[\\$identifier] '0000d11ff42b22915fcce5cfa6027040'\n",
"\\item[\\$formatId] 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"\\item[\\$checksum] \\begin{description}\n",
"\\item[\\$text] '0000d11ff42b22915fcce5cfa6027040'\n",
"\\item[\\$.attrs] \\textbf{algorithm:} 'MD5'\n",
"\\end{description}\n",
"\n",
"\\item[\\$dateSysMetadataModified] '2018-01-06T10:43:32.073+00:00'\n",
"\\item[\\$size] '35257'\n",
"\\end{description}\n",
"\n",
"\\item[\\$objectInfo] \\begin{description}\n",
"\\item[\\$identifier] '0000eb4ff1fc59ae6c33a4981e00eabf'\n",
"\\item[\\$formatId] 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"\\item[\\$checksum] \\begin{description}\n",
"\\item[\\$text] '0000eb4ff1fc59ae6c33a4981e00eabf'\n",
"\\item[\\$.attrs] \\textbf{algorithm:} 'MD5'\n",
"\\end{description}\n",
"\n",
"\\item[\\$dateSysMetadataModified] '2018-01-08T11:18:27.291+00:00'\n",
"\\item[\\$size] '49904'\n",
"\\end{description}\n",
"\n",
"\\item[\\$.attrs] \\begin{description*}\n",
"\\item[count] '5'\n",
"\\item[start] '0'\n",
"\\item[total] '2897219'\n",
"\\end{description*}\n",
"\n",
"\\end{description}\n"
],
"text/markdown": [
"$objectInfo\n",
": $identifier\n",
": '0000120ce277dbb2e140d74b50ca23e5'\n",
"$formatId\n",
": 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"$checksum\n",
": $text\n",
": '0000120ce277dbb2e140d74b50ca23e5'\n",
"$.attrs\n",
": **algorithm:** 'MD5'\n",
"\n",
"\n",
"\n",
"$dateSysMetadataModified\n",
": '2018-04-20T07:59:45.497+00:00'\n",
"$size\n",
": '19541'\n",
"\n",
"\n",
"\n",
"$objectInfo\n",
": $identifier\n",
": '000026213216f47287f0d3027f3c4be3'\n",
"$formatId\n",
": 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"$checksum\n",
": $text\n",
": '000026213216f47287f0d3027f3c4be3'\n",
"$.attrs\n",
": **algorithm:** 'MD5'\n",
"\n",
"\n",
"\n",
"$dateSysMetadataModified\n",
": '2018-04-20T05:09:36.311+00:00'\n",
"$size\n",
": '26256'\n",
"\n",
"\n",
"\n",
"$objectInfo\n",
": $identifier\n",
": '0000aa6924377b6a7e5ab59bcec5d4f3'\n",
"$formatId\n",
": 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"$checksum\n",
": $text\n",
": '0000aa6924377b6a7e5ab59bcec5d4f3'\n",
"$.attrs\n",
": **algorithm:** 'MD5'\n",
"\n",
"\n",
"\n",
"$dateSysMetadataModified\n",
": '2018-02-17T03:01:16.406+00:00'\n",
"$size\n",
": '35084'\n",
"\n",
"\n",
"\n",
"$objectInfo\n",
": $identifier\n",
": '0000d11ff42b22915fcce5cfa6027040'\n",
"$formatId\n",
": 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"$checksum\n",
": $text\n",
": '0000d11ff42b22915fcce5cfa6027040'\n",
"$.attrs\n",
": **algorithm:** 'MD5'\n",
"\n",
"\n",
"\n",
"$dateSysMetadataModified\n",
": '2018-01-06T10:43:32.073+00:00'\n",
"$size\n",
": '35257'\n",
"\n",
"\n",
"\n",
"$objectInfo\n",
": $identifier\n",
": '0000eb4ff1fc59ae6c33a4981e00eabf'\n",
"$formatId\n",
": 'http://www.isotc211.org/2005/gmd-pangaea'\n",
"$checksum\n",
": $text\n",
": '0000eb4ff1fc59ae6c33a4981e00eabf'\n",
"$.attrs\n",
": **algorithm:** 'MD5'\n",
"\n",
"\n",
"\n",
"$dateSysMetadataModified\n",
": '2018-01-08T11:18:27.291+00:00'\n",
"$size\n",
": '49904'\n",
"\n",
"\n",
"\n",
"$.attrs\n",
": count\n",
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": '0'total\n",
": '2897219'\n",
"\n",
"\n",
"\n",
"\n"
],
"text/plain": [
"$objectInfo\n",
"$objectInfo$identifier\n",
"[1] \"0000120ce277dbb2e140d74b50ca23e5\"\n",
"\n",
"$objectInfo$formatId\n",
"[1] \"http://www.isotc211.org/2005/gmd-pangaea\"\n",
"\n",
"$objectInfo$checksum\n",
"$objectInfo$checksum$text\n",
"[1] \"0000120ce277dbb2e140d74b50ca23e5\"\n",
"\n",
"$objectInfo$checksum$.attrs\n",
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" \"MD5\" \n",
"\n",
"\n",
"$objectInfo$dateSysMetadataModified\n",
"[1] \"2018-04-20T07:59:45.497+00:00\"\n",
"\n",
"$objectInfo$size\n",
"[1] \"19541\"\n",
"\n",
"\n",
"$objectInfo\n",
"$objectInfo$identifier\n",
"[1] \"000026213216f47287f0d3027f3c4be3\"\n",
"\n",
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"[1] \"http://www.isotc211.org/2005/gmd-pangaea\"\n",
"\n",
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"[1] \"000026213216f47287f0d3027f3c4be3\"\n",
"\n",
"$objectInfo$checksum$.attrs\n",
"algorithm \n",
" \"MD5\" \n",
"\n",
"\n",
"$objectInfo$dateSysMetadataModified\n",
"[1] \"2018-04-20T05:09:36.311+00:00\"\n",
"\n",
"$objectInfo$size\n",
"[1] \"26256\"\n",
"\n",
"\n",
"$objectInfo\n",
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"[1] \"0000aa6924377b6a7e5ab59bcec5d4f3\"\n",
"\n",
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"[1] \"http://www.isotc211.org/2005/gmd-pangaea\"\n",
"\n",
"$objectInfo$checksum\n",
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"[1] \"0000aa6924377b6a7e5ab59bcec5d4f3\"\n",
"\n",
"$objectInfo$checksum$.attrs\n",
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" \"MD5\" \n",
"\n",
"\n",
"$objectInfo$dateSysMetadataModified\n",
"[1] \"2018-02-17T03:01:16.406+00:00\"\n",
"\n",
"$objectInfo$size\n",
"[1] \"35084\"\n",
"\n",
"\n",
"$objectInfo\n",
"$objectInfo$identifier\n",
"[1] \"0000d11ff42b22915fcce5cfa6027040\"\n",
"\n",
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"[1] \"http://www.isotc211.org/2005/gmd-pangaea\"\n",
"\n",
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"$objectInfo$checksum$text\n",
"[1] \"0000d11ff42b22915fcce5cfa6027040\"\n",
"\n",
"$objectInfo$checksum$.attrs\n",
"algorithm \n",
" \"MD5\" \n",
"\n",
"\n",
"$objectInfo$dateSysMetadataModified\n",
"[1] \"2018-01-06T10:43:32.073+00:00\"\n",
"\n",
"$objectInfo$size\n",
"[1] \"35257\"\n",
"\n",
"\n",
"$objectInfo\n",
"$objectInfo$identifier\n",
"[1] \"0000eb4ff1fc59ae6c33a4981e00eabf\"\n",
"\n",
"$objectInfo$formatId\n",
"[1] \"http://www.isotc211.org/2005/gmd-pangaea\"\n",
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"$objectInfo$checksum\n",
"$objectInfo$checksum$text\n",
"[1] \"0000eb4ff1fc59ae6c33a4981e00eabf\"\n",
"\n",
"$objectInfo$checksum$.attrs\n",
"algorithm \n",
" \"MD5\" \n",
"\n",
"\n",
"$objectInfo$dateSysMetadataModified\n",
"[1] \"2018-01-08T11:18:27.291+00:00\"\n",
"\n",
"$objectInfo$size\n",
"[1] \"49904\"\n",
"\n",
"\n",
"$.attrs\n",
" count start total \n",
" \"5\" \"0\" \"2897219\" \n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"listObjects(cn, count = 5)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"As another example, we can filter to _just_ CSV objects created within a time frame:"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"5"
],
"text/latex": [
"5"
],
"text/markdown": [
"5"
],
"text/plain": [
"[1] 5"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"csvs <- listObjects(cn, \n",
" fromDate = \"2020-01-01T00:00:00.000Z\", \n",
" toDate = \"2021-01-01T00:00:00.000Z\", \n",
" formatId = \"text/csv\", \n",
" count = 5)\n",
"length(csvs$objectInfo)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can see we received five results like we requested but there are many more available:\n"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"total: '28191'"
],
"text/latex": [
"\\textbf{total:} '28191'"
],
"text/markdown": [
"**total:** '28191'"
],
"text/plain": [
" total \n",
"\"28191\" "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"csvs$.attrs[3]\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Knowing this, we can use the `start` argument to page through the results:\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"page_two <- listObjects(cn, \n",
" fromDate = \"2020-01-01T00:00:00.000Z\", \n",
" toDate = \"2021-01-01T00:00:00.000Z\", \n",
" formatId = \"text/csv\", \n",
" count = 5,\n",
" start = 5)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"page_two"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
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