removes mongodb store.. I never used it and won't be supporting it
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Ben Mabey
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commit
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4 changed files with 0 additions and 160 deletions
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@ -6,7 +6,6 @@
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:warn-on-reflection true
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:dependencies [[org.clojure/clojure "1.2.0"]
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[org.clojure/clojure-contrib "1.2.0"]
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[org.mongodb/mongo-java-driver "1.0"]
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[incanter/incanter-core "1.2.3"]
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[incanter/incanter-charts "1.2.3"]
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[lt/weka "3.6.3"]
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@ -1,141 +0,0 @@
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;;
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;; Distance functions
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;; @author Antonio Garrote
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;;
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(ns #^{:author "Antonio Garrote <antoniogarrote@gmail.com>"}
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clj-ml.data-store
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"Functions for storing and retrieving data sets from a persistence store, like a data
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base system.
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Currently MongoDB is the only store supported."
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(:use [clj-ml utils data])
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(:import (com.mongodb Mongo DB BasicDBObject DBCollection DBCursor)))
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(defn keywords-to-strings [format]
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"Recursively transforms all keywords into strings"
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(if (keyword? format)
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(name format)
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(if (map? format)
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(loop [acum {}
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ks (keys format)]
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(if (empty? ks)
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acum
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(recur (conj {(name (first ks))
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(keywords-to-strings (get format (first ks)))}
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acum)
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(rest ks))))
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(if (sequential? format)
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(map #(keywords-to-strings %1) format)
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format))))
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(defmulti make-data-store-connection
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"Connects to a data store.
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- The first parameter is the kind of data store to connect to.
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- The second parameter is a map with options for the connection
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to that kind of data store.
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"
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(fn [kind params] kind))
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(defmethod make-data-store-connection :mongodb
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([kind params]
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(let [_foo1 (println (:host params))
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_foo2 (println (:port params))]
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(new Mongo (:host params) (:port params)))
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))
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(defmulti data-store-connection-db
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"Returns a DB from the stablished connection"
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(fn [kind connection name & params] kind))
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(defmethod data-store-connection-db :mongodb
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([kind connection name & params]
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(.getDB connection name)))
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;; High level API
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(def *clj-ml-datasets* "-clj-ml-datasets")
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(def *clj-ml-format-suffix* "-clj-ml-schema")
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(def *clj-ml-instances-suffix* "-clj-ml-instances")
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(defmulti data-store-save-dataset
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"Persists a whole dataset in the data store"
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(fn [kind database dataset & options] kind))
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(defmethod data-store-save-dataset :mongodb
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([kind database dataset & options]
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(let [format (dataset-format dataset)
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name (md5-sum (dataset-name dataset))
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datasets-collection (.getCollection database *clj-ml-datasets*)
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schema-collection (.getCollection database (str name *clj-ml-format-suffix*))
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data-collection-tmp (.getCollection database (str name *clj-ml-instances-suffix*))
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format-to-insert (new BasicDBObject {"format" (keywords-to-strings format)})]
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(.remove datasets-collection (new BasicDBObject {"id" name}))
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(.insert datasets-collection (new BasicDBObject {"id" name}))
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(.remove schema-collection format-to-insert)
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(.insert schema-collection format-to-insert)
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(when (not (nil? data-collection-tmp))
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(.drop data-collection-tmp))
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(let [data-collection (.getCollection database (str name *clj-ml-instances-suffix*))]
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(for [i (dataset-seq dataset)]
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(.insert data-collection (new BasicDBObject (keywords-to-strings {"instance" (instance-to-vector i)}))))))))
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(declare mongo-persisted-instance-to-map)
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(defn- mongo-persisted-instance-to-vector
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"Transforms an instance persisted in a mongodb database back to a vector"
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([inst] (mongo-persisted-instance-to-vector inst false))
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([inst use-keys?]
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(loop [vals (.toMap inst)
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acum []]
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(if (empty? vals)
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acum
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(recur (rest vals)
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(conj acum (let [tmp-val (.getValue (first vals))]
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(if (= (class tmp-val) com.mongodb.BasicDBObject)
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(mongo-persisted-instance-to-map tmp-val use-keys?)
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(if (string? tmp-val)
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(if use-keys? (keyword tmp-val) tmp-val)
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tmp-val)))))))))
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(defn- mongo-persisted-instance-to-map
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"Transforms an instance persisted in a mongodb database back to a vector"
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([inst] (mongo-persisted-instance-to-map inst false))
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([inst use-keys?]
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(loop [mp (.toMap inst)
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vals (keys mp)
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acum {}]
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(if (empty? vals)
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acum
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(recur mp
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(rest vals)
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(conj acum {(keyword (first vals)) (let [tmp-val (get mp (first vals))]
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(if (= (class tmp-val) com.mongodb.BasicDBObject)
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(mongo-persisted-instance-to-map tmp-val use-keys?)
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(if (= (class tmp-val) com.mongodb.BasicDBList)
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(mongo-persisted-instance-to-vector tmp-val use-keys?)
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tmp-val)))}))))))
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(defmulti data-store-load-dataset
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"Load a whole dataset from a data store"
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(fn [kind database database-name & options] kind))
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(defmethod data-store-load-dataset :mongodb
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([kind database database-name & options]
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(let [dsf (str (md5-sum database-name) *clj-ml-format-suffix*)
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col (.getCollection database dsf)
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format (mongo-persisted-instance-to-vector (get (.next (.find col)) "format") true)
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dsi (str (md5-sum database-name) *clj-ml-instances-suffix*)
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coli (.getCollection database dsi)
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cursor (.find coli)
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insts (loop [cont (.hasNext cursor)
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acum []]
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(if cont
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(let [exp (get (. (.next cursor) toMap) "instance")]
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(recur (.hasNext cursor)
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(conj acum (mongo-persisted-instance-to-vector exp))))
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acum))]
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(make-dataset database-name format insts))))
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@ -45,12 +45,6 @@
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(let [loader (new CSVLoader)]
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(m-load-instances loader source))))
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(defmethod load-instances :mongodb
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([kind source & options]
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(let [database {:database source}
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name {:dataset-name source}]
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(clj-ml.data-store/data-store-load-dataset :mongodb database name options))))
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;; Saving of instances
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(defmulti save-instances
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@ -80,7 +74,3 @@
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([kind destiny instances & options]
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(let [saver (new CSVSaver)]
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(m-save-instances saver destiny instances))))
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(defmethod save-instances :mongodb
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([kind destiny instances & options]
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(clj-ml.data-store/data-store-save-dataset :mongodb destiny instances options)))
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@ -1,8 +0,0 @@
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(ns clj-ml.data-store-test
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(:use [clj-ml.data-store] :reload-all)
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(:use [clojure.test]))
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(deftest make-instance-num
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(is (= (keywords-to-strings
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[1 :hola {:a [:b {:d "hola"}]}])
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'(1 "hola" {"a" ("b" {"d" "hola"})}))))
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