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Minimal example with spark sql #3
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| "execution_count": 1, | ||
| "metadata": {}, | ||
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| "text/plain": [ | ||
| "Intitializing Scala interpreter ..." | ||
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| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
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| "Spark Web UI available at http://51d2d7955110:4040\n", | ||
| "SparkContext available as 'sc' (version = 3.0.0, master = local[*], app id = local-1599854411921)\n", | ||
| "SparkSession available as 'spark'\n" | ||
| ] | ||
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| "metadata": {}, | ||
| "output_type": "display_data" | ||
| }, | ||
| { | ||
| "name": "stdout", | ||
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| "text": [ | ||
| "root\n", | ||
| " |-- address: array (nullable = true)\n", | ||
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| " | | |-- postalCode: string (nullable = true)\n", | ||
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| " | | |-- state: string (nullable = true)\n", | ||
| " | | |-- state_aa: string (nullable = true)\n", | ||
| " |-- birthDate: string (nullable = true)\n", | ||
| " |-- birthDate_aa: struct (nullable = true)\n", | ||
| " | |-- end: string (nullable = true)\n", | ||
| " | |-- start: string (nullable = true)\n", | ||
| " |-- communication: array (nullable = true)\n", | ||
| " | |-- element: struct (containsNull = true)\n", | ||
| " | | |-- language: struct (nullable = true)\n", | ||
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| " |-- deceasedDateTime: timestamp (nullable = true)\n", | ||
| " |-- deceasedDateTime_aa: struct (nullable = true)\n", | ||
| " | |-- end: string (nullable = true)\n", | ||
| " | |-- start: string (nullable = true)\n", | ||
| " |-- extension: array (nullable = true)\n", | ||
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| " |-- gender: string (nullable = true)\n", | ||
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| " |-- maritalStatus: struct (nullable = true)\n", | ||
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| " | |-- text_aa: string (nullable = true)\n", | ||
| " |-- multipleBirthBoolean: boolean (nullable = true)\n", | ||
| " |-- multipleBirthInteger: long (nullable = true)\n", | ||
| " |-- name: array (nullable = true)\n", | ||
| " | |-- element: struct (containsNull = true)\n", | ||
| " | | |-- family: string (nullable = true)\n", | ||
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| " | | |-- use: string (nullable = true)\n", | ||
| " |-- resourceType: string (nullable = true)\n", | ||
| " |-- telecom: array (nullable = true)\n", | ||
| " | |-- element: struct (containsNull = true)\n", | ||
| " | | |-- system: string (nullable = true)\n", | ||
| " | | |-- use: string (nullable = true)\n", | ||
| " | | |-- value: string (nullable = true)\n", | ||
| " | | |-- value_aa: string (nullable = true)\n", | ||
| "\n" | ||
| ] | ||
| }, | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "import spark.implicits._\n", | ||
| "path: String = /home/jovyan/work/etl/output/annotated/Patient.ndjson\n", | ||
| "Patient: org.apache.spark.sql.DataFrame = [address: array<struct<city:string,city_aa:string,country:string,country_aa:string,extension:array<struct<parent:string,url:string,valueDecimal:double>>,line:array<string>,line_aa:array<string>,postalCode:string,postalCode_aa:string,state:string,state_aa:string>>, birthDate: string ... 15 more fields]\n" | ||
| ] | ||
| }, | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "// git clone https://github.com/sync-for-science/a3 \n", | ||
| "// docker run --rm -p 8888:8888 -v $(pwd):/home/jovyan/work jupyter/all-spark-notebook\n", | ||
| "\n", | ||
| "import spark.implicits._\n", | ||
| "val path = \"/home/jovyan/work/etl/output/annotated/Patient.ndjson\"\n", | ||
| "val Patient = spark.read.json(path)\n", | ||
| "Patient.printSchema()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "res1: org.apache.spark.sql.DataFrame = [count(1): bigint]\n" | ||
| ] | ||
| }, | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "Patient.createOrReplaceTempView(\"Patient\")\n", | ||
| "\n", | ||
| "spark.sql(\"create or replace temporary view pv as (SELECT count(*) FROM Patient)\")\n", | ||
| "spark.sql(\"SELECT * FROM pv\")" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "spylon-kernel", | ||
| "language": "scala", | ||
| "name": "spylon-kernel" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": "text/x-scala", | ||
| "file_extension": ".scala", | ||
| "help_links": [ | ||
| { | ||
| "text": "MetaKernel Magics", | ||
| "url": "https://metakernel.readthedocs.io/en/latest/source/README.html" | ||
| } | ||
| ], | ||
| "mimetype": "text/x-scala", | ||
| "name": "scala", | ||
| "pygments_lexer": "scala", | ||
| "version": "0.4.1" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } | ||
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This bit is the actual "how do I run it" instructions. Maybe worth pulling out into a README ;-)