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data_sources.clj
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data_sources.clj
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(ns zero-one.geni.core.data-sources
(:refer-clojure :exclude [partition-by])
(:require
[camel-snake-kebab.core :refer [->camelCase]]
[clojure.edn :as edn]
[clojure.string :as string]
[clojure.java.io :as io]
[jsonista.core :as jsonista]
[zero-one.fxl.core :as fxl]
[zero-one.geni.defaults]
[zero-one.geni.interop :as interop]
[zero-one.geni.core.dataset-creation :as dataset-creation]
[zero-one.geni.core.dataset :as dataset]
[zero-one.geni.utils :refer [ensure-coll]])
(:import
(java.text Normalizer Normalizer$Form)
(org.apache.spark.sql SparkSession)))
(def default-spark zero-one.geni.defaults/spark)
(defn configure-reader-or-writer [unconfigured options]
(reduce
(fn [r [k v]] (.option r (->camelCase (name k)) v))
unconfigured
options))
(def default-options
{"csv" {:header "true" :infer-schema "true"}})
(defn deaccent [string]
;; Source: https://gist.github.com/maio/e5f85d69c3f6ca281ccd
(let [normalized (Normalizer/normalize string Normalizer$Form/NFD)]
(string/replace normalized #"\p{InCombiningDiacriticalMarks}+" "")))
(defn remove-punctuations [string]
(string/replace string #"[.,\/#!$%\^&\*;:{}=\`~()°]" ""))
(defn ->kebab-columns [dataset]
(let [new-columns (->> dataset
.columns
(map remove-punctuations)
(map deaccent)
(map camel-snake-kebab.core/->kebab-case))]
(.toDF dataset (interop/->scala-seq new-columns))))
(defn read-data! [format-name spark path options]
(let [reader-opts (dissoc options :kebab-columns :schema)
defaults (default-options format-name)
schema (:schema options)
reader (-> (.. spark read (format format-name))
(configure-reader-or-writer (merge defaults reader-opts))
(cond-> (not (nil? schema))
(.schema (dataset-creation/->schema schema))))]
(-> (.load reader path)
(cond-> (:kebab-columns options) ->kebab-columns))))
(defmulti read-avro! (fn [head & _] (class head)))
(defmethod read-avro! :default
([path] (read-avro! @default-spark path))
([path options] (read-avro! @default-spark path options)))
(defmethod read-avro! SparkSession
([spark path] (read-avro! spark path {}))
([spark path options] (read-data! "avro" spark path options)))
(defmulti read-parquet! (fn [head & _] (class head)))
(defmethod read-parquet! :default
([path] (read-parquet! @default-spark path))
([path options] (read-parquet! @default-spark path options)))
(defmethod read-parquet! SparkSession
([spark path] (read-parquet! spark path {}))
([spark path options] (read-data! "parquet" spark path options)))
(defmulti read-csv! (fn [head & _] (class head)))
(defmethod read-csv! :default
([path] (read-csv! @default-spark path))
([path options] (read-csv! @default-spark path options)))
(defmethod read-csv! SparkSession
([spark path] (read-csv! spark path {}))
([spark path options] (read-data! "csv" spark path options)))
(defmulti read-libsvm! (fn [head & _] (class head)))
(defmethod read-libsvm! :default
([path] (read-libsvm! @default-spark path))
([path options] (read-libsvm! @default-spark path options)))
(defmethod read-libsvm! SparkSession
([spark path] (read-libsvm! spark path {}))
([spark path options] (read-data! "libsvm" spark path options)))
(defmulti read-json! (fn [head & _] (class head)))
(defmethod read-json! :default
([path] (read-json! @default-spark path))
([path options] (read-json! @default-spark path options)))
(defmethod read-json! SparkSession
([spark path] (read-json! spark path {}))
([spark path options] (read-data! "json" spark path options)))
(defmulti read-text! (fn [head & _] (class head)))
(defmethod read-text! :default
([path] (read-text! @default-spark path))
([path options] (read-text! @default-spark path options)))
(defmethod read-text! SparkSession
([spark path] (read-text! spark path {}))
([spark path options] (read-data! "text" spark path options)))
(defn read-jdbc!
([options] (read-jdbc! @default-spark options))
([spark options]
(let [unconfigured-reader (.. spark sqlContext read (format "jdbc"))
configured-reader (configure-reader-or-writer unconfigured-reader options)]
(.load configured-reader))))
(defn- partition-by-arg [partition-id]
(into-array java.lang.String (map name (ensure-coll partition-id))))
(defn write-data! [format dataframe path options]
(let [mode (:mode options)
partition-id (:partition-by options)
unconfigured-writer (-> dataframe
(.write)
(.format format)
(cond-> mode (.mode mode))
(cond-> partition-id
(.partitionBy (partition-by-arg partition-id))))
configured-writer (configure-reader-or-writer
unconfigured-writer
(dissoc options :mode :partition-by))]
(.save configured-writer path)))
(defn write-parquet!
([dataframe path] (write-parquet! dataframe path {}))
([dataframe path options] (write-data! "parquet" dataframe path options)))
(defn write-csv!
([dataframe path] (write-csv! dataframe path {"header" "true"}))
([dataframe path options] (write-data! "csv" dataframe path (merge options {"header" "true"}))))
(defn write-libsvm!
([dataframe path] (write-libsvm! dataframe path {}))
([dataframe path options] (write-data! "libsvm" dataframe path options)))
(defn write-json!
([dataframe path] (write-json! dataframe path {}))
([dataframe path options] (write-data! "json" dataframe path options)))
(defn write-text!
([dataframe path] (write-text! dataframe path {}))
([dataframe path options] (write-data! "text" dataframe path options)))
(defn write-avro!
([dataframe path] (write-avro! dataframe path {}))
([dataframe path options] (write-data! "avro" dataframe path options)))
(defn write-jdbc! [dataframe options]
(let [mode (:mode options)
unconfigured-writer (-> dataframe
(.write)
(.format "jdbc")
(cond-> mode (.mode mode)))
configured-writer (configure-reader-or-writer
unconfigured-writer
(dissoc options :mode))]
(.save configured-writer)))
;; EDN
(defn file-exists? [path]
(.exists (io/file path)))
(defn read-as-keywords [json-str]
(jsonista/read-value json-str jsonista/keyword-keys-object-mapper))
(defn write-edn!
([dataframe path] (write-edn! dataframe path {}))
([dataframe path options]
(let [records (->> dataframe
.toJSON
.collect
(mapv read-as-keywords))
overwrite (if (= (:mode options) "overwrite") true false)]
(if (and overwrite (file-exists? path))
(spit path records)
(throw (Exception. (format "path file:%s already exists!" path)))))))
(defmulti read-edn! (fn [head & _] (class head)))
(defmethod read-edn! :default
([path] (read-edn! @default-spark path))
([path options] (read-edn! @default-spark path options)))
(defmethod read-edn! SparkSession
([spark path] (read-edn! spark path {}))
([spark path options]
(let [dataset (->> path
slurp
edn/read-string
(dataset-creation/records->dataset spark))]
(-> dataset
(cond-> (:kebab-columns options) ->kebab-columns)))))
;; Excel
(defn write-xlsx!
([dataframe path] (write-xlsx! dataframe path {}))
([dataframe path options]
(let [records (dataset/collect dataframe)
col-keys (dataset/columns dataframe)
overwrite (if (= (:mode options) "overwrite") true false)]
(if (and overwrite (file-exists? path))
(fxl/write-xlsx!
(fxl/concat-below
(fxl/row->cells (dataset/column-names dataframe))
(fxl/records->cells col-keys records))
path)
(throw (Exception. (format "path file:%s already exists!" path)))))))
(defmulti read-xlsx! (fn [head & _] (class head)))
(defmethod read-xlsx! :default
([path] (read-xlsx! @default-spark path))
([path options] (read-xlsx! @default-spark path options)))
(defmethod read-xlsx! SparkSession
([spark path] (read-xlsx! spark path {:header true}))
([spark path options]
(let [cells (fxl/read-xlsx! path)
table (fxl/cells->table cells (:sheet options))
col-names (if (:header options)
(first table)
(map #(str "_c" %) (-> table first count range)))
table (if (:header options) (rest table) table)
dataset (dataset-creation/table->dataset spark table col-names)]
(-> dataset
(cond-> (:kebab-columns options) ->kebab-columns)))))