I'm trying to read millions of rows from a database and write to a text file.
This is a continuation of my question database dump to text file with side effects
My problem now seems to be that the logging doesn't happen until the program completes. Another indicator that i'm not processing lazily is that the text file isn't written at all until the program finishes.
Based on an IRC tip it seems my issue is likely having to do with :result-set-fnand defaulting to doall in the clojure.java.jdbc/query area of the code.
I have tried to replace this with a for function but still discover that memory consumption is high as it pulls the entire result set into memory.
How can i have a :result-set-fn that doesn't pull everything in like doall? How can I progressively write the log file as the program is running, rather then dump everything once the -main execution is finished?
(let [
db-spec local-postgres
sql "select * from public.f_5500_sf "
log-report-interval 1000
fetch-size 100
field-delim "\t"
row-delim "\n"
db-connection (doto ( j/get-connection db-spec) (.setAutoCommit false))
statement (j/prepare-statement db-connection sql :fetch-size fetch-size )
joiner (fn [v] (str (join field-delim v ) row-delim ) )
start (System/currentTimeMillis)
rate-calc (fn [r] (float (/ r (/ ( - (System/currentTimeMillis) start) 100))))
row-count (atom 0)
result-set-fn (fn [rs] (lazy-seq rs))
lazy-results (rest (j/query db-connection [statement] :as-arrays? true :row-fn joiner :result-set-fn result-set-fn))
]; }}}
(.setAutoCommit db-connection false)
(info "Started dbdump session...")
(with-open [^java.io.Writer wrtr (io/writer "output.txt")]
(info "Running query...")
(doseq [row lazy-results]
(.write wrtr row)
))
(info (format "Completed write with %d rows" #row-count))
)
I took the recent fixes for clojure.java.jdbc by putting [org.clojure/java.jdbc "0.3.0-beta1"] in my project.clj dependencies listing. This one enhances/corrects the :as-arrays? true functionality of clojure.java.jdbc/query described here.
I think this helped somewhat however I may still have been able to override the :result-set-fn to vec.
The core issue was resolved by tucking all row logic into :row-fn. The initial OutOfMemory problems had to do with iterating through j/query result sets rather than defining the specific :row-fn.
New (working) code is below:
(defn -main []
(let [; {{{
db-spec local-postgres
source-sql "select * from public.f_5500 "
log-report-interval 1000
fetch-size 1000
row-count (atom 0)
field-delim "\u0001" ; unlikely to be in source feed,
; although i should still check in
; replace-newline below (for when "\t"
; is used especially)
row-delim "\n" ; unless fixed-width, target doesn't
; support non-printable chars for recDelim like
db-connection (doto ( j/get-connection db-spec) (.setAutoCommit false))
statement (j/prepare-statement db-connection source-sql :fetch-size fetch-size :concurrency :read-only)
start (System/currentTimeMillis)
rate-calc (fn [r] (float (/ r (/ ( - (System/currentTimeMillis) start) 100))))
replace-newline (fn [s] (if (string? s) (clojure.string/replace s #"\n" " ") s))
row-fn (fn [v]
(swap! row-count inc)
(when (zero? (mod #row-count log-report-interval))
(info (format "wrote %d rows" #row-count))
(info (format "\trows/s %.2f" (rate-calc #row-count)))
(info (format "\tPercent Mem used %s " (memory-percent-used))))
(str (join field-delim (doall (map #(replace-newline %) v))) row-delim ))
]; }}}
(info "Started database table dump session...")
(with-open [^java.io.Writer wrtr (io/writer "./sql/output.txt")]
(j/query db-connection [statement] :as-arrays? true :row-fn
#(.write wrtr (row-fn %))))
(info (format "\t\t\tCompleted with %d rows" #row-count))
(info (format "\t\t\tCompleted in %s seconds" (float (/ (- (System/currentTimeMillis) start) 1000))))
(info (format "\t\t\tAverage rows/s %.2f" (rate-calc #row-count)))
nil)
)
Other things i experimented (with limited success) involved the timbre logging and turning off stardard out; i wondered if with using a REPL it might cache the results before displaying back to my editor (vim fireplace) and i wasn't sure if that was utilizing a lot of the memory.
Also, I added the logging parts around memory free with (.freeMemory (java.lang.Runtime/getRuntime)). I wasn't as familiar with VisualVM and pinpointing exactly where my issue was.
I am happy with how it works now, thanks everyone for your help.
You can use prepare-statement with the :fetch-size option. Otherwise, the query itself is eager despite the results being delivered in a lazy sequence.
prepare-statement requires a connection object, so you'll need to explicitly create one. Here's an example of how your usage might look:
(let [db-spec local-postgres
sql "select * from big_table limit 500000 "
fetch-size 10000 ;; or whatever's appropriate
cnxn (doto (j/get-connection db-spec)
(.setAutoCommit false))
stmt (j/prepare-statement cnxn sql :fetch-size fetch-size)
results (rest (j/query cnxn [stmt]))]
;; ...
)
Another option
Since the problem seems to be with query, try with-query-results. It's considered deprecated but is still there and works. Here's an example usage:
(let [db-spec local-postgres
sql "select * from big_table limit 500000 "
fetch-size 100 ;; or whatever's appropriate
cnxn (doto (j/get-connection db-spec)
(.setAutoCommit false))
stmt (j/prepare-statement cnxn sql :fetch-size fetch-size)]
(j/with-query-results results [stmt] ;; binds the results to `results`
(doseq [row results]
;;
)))
I've have found a better solution: you need to declare a cursor and fetch chunks of data from it in a transaction. Example:
(db/with-tx
(db/execute! "declare cur cursor for select * from huge_table")
(loop []
(when-let [rows (-> "fetch 10 from cur" db/query not-empty)]
(doseq [row rows]
(process-a-row row))
(recur))))
Here, db/with-tx, db/execute! and db/query are my own shortcuts declared in db namespace:
(def ^:dynamic
*db* {:dbtype "postgresql"
:connection-uri <some db url>)})
(defn query [& args]
(apply jdbc/query *db* args))
(defn execute! [& args]
(apply jdbc/execute! *db* args))
(defmacro with-tx
"Runs a series of queries into transaction."
[& body]
`(jdbc/with-db-transaction [tx# *db*]
(binding [*db* tx#]
~#body)))
Related
All,
I must suck at eLisp. Banged this first function out in no time.
(defun sort-lines-reverse (beg end)
"sort lines in reverse order"
(interactive
(if (use-region-p)
(list (region-beginning) (region-end))
(list (point-min) (point-max))))
(if (and beg end)
(sort-lines 1 beg end))
)
works perfectly. Hosed this next one
(defun sort-numeric-fields-reverse (field beg end)
"sort numeric fields in reverse order"
(interactive
(if (use-region-p)
(list (read-number "Field number: " 1) (region-beginning) (region-end))
(list (read-number "Field number: " 1) (point-min) (point-max)))
(message "calling if")
(if (and beg end)
((message "inside if")
(sort-numeric-fields field beg end)
(reverse-region beg end))
)
))
No runs no hits no errors. Don't see a single message displayed in messages. I do get my field number prompt.
A snippet of randomly generated test data if one so wishes.
8 412086510
8 744308263
8 1482781895
8 995992436
1 1021762533
1 897682569
1 963686690
1 166565707
1 2096612583
1 829723388
1 587753131
1 264251710
32 139885828
32 781244288
Adding insult to injury in my KDE Neon environment the C-M-x to bring up the lisp debugger doesn't do squat.
The only real difference between these two functions is in this one I have to prompt for a field number. Inside the if I run 2 functions instead of one. After getting the first one to work the second should have been a cakewalk.
Help would be appreciated.
Two issues:
missing ) at the end of interactive, after (if (use-region-p) ...
missing progn in (if (and beg end)...
(progn is superfluous because if has been replaced by when.)
Corrected version:
(defun sort-numeric-fields-reverse (field beg end)
"sort numeric fields in reverse order"
(interactive
(if (use-region-p)
(list (read-number "Field number: " 1) (region-beginning) (region-end))
(list (read-number "Field number: " 1) (point-min) (point-max))))
(message "calling if")
(when (and beg end)
(message "inside if")
(sort-numeric-fields field beg end)
(reverse-region beg end)))
EDIT: Code changed: if-progn replaced with when according to hint from #phils.
Hint: using an adequate editor makes the typing easy and gives you control over parentheses.
This code works, printing the rows in the given table:
(defn count-extreferences-subset [config]
(let [emr-dbs (:emr-databases config)]
(println "Counting external references: " emr-dbs)
(jdbc/with-db-connection [dbconn (:db-spec (first emr-dbs))]
(let [q "SELECT * FROM LOCREG"
rs (jdbc/query dbconn [q])]
(dorun (map println rs))))))
According to the documentation in clojure.jdbc, this should also work, but should print the rows as the result set is realized (preventing memory overflow for large result sets):
(defn count-extreferences-subset [config]
(let [emr-dbs (:emr-databases config)]
(println "Counting external references: " emr-dbs)
(jdbc/with-db-connection [dbconn (:db-spec (first emr-dbs))]
(let [q "SELECT * FROM LOCREG"
_ (jdbc/query dbconn [q] {:row-fn println})]))))
However this fails at run-time with the following exception:
java.lang.IllegalArgumentException: No value supplied for key: {:row-fn #object[clojure.core$println 0x46ed7a0e "clojure.core$println#46ed7a0e"]}
Any idea why the use of the :row-fn option is failing?
I believe the curly braces are the problem. Your code should follow the following pattern:
(jdbc/query db-spec
["select name, cost from fruit where cost = 12"]
:row-fn add-tax)
You can fine more information in The Clojure Cookbook. I highly recommend buying a copy!
I want to be able to write the following functions for jdbc:
(def db {:classname "com.mysql.jdbc.Driver"
:subprotocol "mysql"
:subname "//127.0.0.1:3306/santacsv"
:server "//127.0.0.1:3306"
:schema "santa"
:user "root"
:password "root"})
(defn has-schema? [db & [schema]])
(defn create-schema [db & [schema]])
(defn drop-schema [db & [schema]])
I'm not sure how to go about it. Any help would be appreciated
At a minimum, you could use clojure.java.jdbc and write the corresponding SQL to execute!.
Alternatively, I would consider using a dedicated migrations library/framework. flyway is java-based and has a java-api which you could call with interop.
Finally, there are a few clojure-based migrations libraries like lobos, but I can't speak to their maturity, so your mileage may very.
I implemented my own here:
https://github.com/zcaudate/manas/blob/master/src/manas/core.clj
(defmacro run-statement [env database body catch-body & [statement]]
`(do (Class/forName (:classname ~env))
(let [~'conn (atom nil)]
(try
(reset! ~'conn (DriverManager/getConnection
(str "jdbc:" (:subprotocol ~env) ":"
(:server ~env) "/" (or ~database (:database ~env)))
(:user ~env)
(:password ~env)))
~#(if statement
[(list 'let '[stmt (.createStatement #conn)]
(list '.executeUpdate 'stmt statement))])
~#body
(catch SQLException ~'e
~#catch-body)
(finally
(if-not (nil? (deref ~'conn))
(.close (deref ~'conn))))))))
(defn has-connection? [env & [url]]
(let [env (if url (assoc env :server url) env)]
(run-statement env "" (true) (false))))
(defn all-databases [env]
(run-statement env ""
((let [rs (.getCatalogs (.getMetaData #conn))]
(loop [rs rs acc []]
(if (.next rs)
(recur rs (conj acc (.getString rs "TABLE_CAT")))
acc))))
()))
(defn has-database? [env & [schema]]
(run-statement env schema (true) (false)))
(defn create-database [env & [schema]]
(run-statement env ""
(true)
(false)
(str "create database " (or schema (:database env)))))
(defn drop-database [env & [schema]]
(run-statement env ""
(true)
(false)
(str "drop database " (or schema (:database env)))))
I'm trying to have a function write a database sql dump to text file from a select statement. The volume returned can be very large, and I'm interested in doing this as fast as possible.
With a large result set I also need to log every x-interval the total number of rows written and how many rows per second have been written since last x-interval. I have a (map ) that is actually doing the write during a (with-open ) so i believe the side-effect of logging rows completed should happen there. (See comments in code).
My questions are:
How do i write "rows-per-second" during the interval and "total rows so far"?
Is there anything additional I want to keep in mind while writing large jdbc result sets to a file (or named-pipe, bulk loader, etc.) ?
Does the (doall ) around the (map ) function fetch all results... making it non-lazy and potentially memory intensive?
Would fixed width be possible as an option? I believe that would be faster for a named pipe to bulk loader. The trade-off would be on disk i/o in place of CPU utilization for downstream parsing. However this might require introspection on the result set returned (with .getMetaData?)
(ns metadata.db.table-dump
[:use
[clojure.pprint]
[metadata.db.connections]
[metadata.db.metadata]
[clojure.string :only (join)]
[taoensso.timbre :only (debug info warn error set-config!)]
]
[:require
[clojure.java.io :as io ]
[clojure.java.jdbc :as j ]
[clojure.java.jdbc.sql :as sql]
]
)
(set-config! [:appenders :spit :enabled?] true)
(set-config! [:shared-appender-config :spit-filename] "log.log")
(let [
field-delim "\t"
row-delim "\n"
report-seconds 10
sql "select * from comcast_lineup "
joiner (fn [v] (str (join field-delim v ) row-delim ) )
results (rest (j/query local-postgres [sql ] :as-arrays? true :row-fn joiner ))
]
(with-open [wrtr (io/writer "test.txt")]
(doall
(map #(.write wrtr %)
; Somehow in here i want to log with (info ) rows written so
; far, and "rows per second" every 10 seconds.
results ))
) (info "Completed write") )
Couple general tips:
At the JDBC level you may need to use setFetchSize to avoid loading the entire resultset into RAM before it even gets to Clojure. See What does Statement.setFetchSize(nSize) method really do in SQL Server JDBC driver?
Make sure clojure.java.jdbc is actually returning a lazy seq (it probably is?)-- if not, consider resultset-seq
doall will indeed force the whole thing to be in RAM; try doseq instead
Consider using an atom to keep count of rows written as you go; you can use this to write rows-so-far, etc.
Sketch:
(let [ .. your stuff ..
start (System/currentTimeMillis)
row-count (atom 0)]
(with-open [^java.io.Writer wrtr (io/writer "test.txt")]
(doseq [row results]
(.write wrtr row)
(swap! row-count inc)
(when (zero? (mod #row-count 10000))
(println (format "written %d rows" #row-count))
(println (format "rows/s %.2f" (rate-calc-here)))))))
You may get some use out of my answer to Idiomatic clojure for progress reporting?
To your situation specifically
1) You could add an index to your map as the second argument to the anonymous function, then in the function you are mapping look at the index to see what row you are writing. which can be used to update an atom.
user> (def stats (atom {}))
#'user/stats
user> (let [start-time (. (java.util.Date.) getTime)]
(dorun (map (fn [line index]
(println line) ; write to log file here
(reset! stats [{:lines index
:start start-time
:end (. (java.util.Date.) getTime)}]))
["line1" "line2" "line3"]
(rest (range)))))
line1
line2
line3
nil
user> #stats
[{:lines 3, :start 1383183600216, :end 1383183600217}]
user>
The contents of stats can then be printed/logged every few seconds to update the UI
3) you most certainly want to use dorun instead of doall because as you suspect this will run out of memory on a large enough data set. dorun drops the results as they are written so you can run it on infinitely large data if you want to wait long enough.
Given a set of delimited data in the following format:
1|Star Wars: Episode IV - A New Hope|1977|Action,Sci-Fi|George Lucas
2|Titanic|1997|Drama,History,Romance|James Cameron
In elisp, how can I generate sql insert statements in this format?
insert into table
values(1,"Star Wars: Episode IV - A New Hope",1977","Action,Sci-Fi","George Lucas",0);
insert into table
values(2,"Titanic",1997,"Drama,History,Romance","James Cameron",0);
To simplify the problem, let's allow for a parameter to tell which
columns are text or numeric. (e.g. 0,1,0,1,1)
Here's how I would do it in Perl.
my #ctypes=qw/0 1 0 1 1/;
while(<>) {
chop;
#F=split('\|', $_);
print "insert into table values(";
foreach my $col (#F) {
my $type=shift(#ctypes);
print ($type == 1 ? '"'.$col.'"' : $col);
print ",";
}
print "0);\n";
}
To insert the data at the end of a buffer:
(require 'cl)
(defun* insert-statements (rows ctypes &key (table-name "table") (delimiter "|"))
(let* ((values-template
(mapconcat '(lambda (type) (if (= type 1) "\"%s\"" "%s")) ctypes ","))
(template (format "insert into %s values(%s);\n" table-name values-template)))
(mapcar '(lambda (row) (insert (apply 'format (cons template (split-string row delimiter)))))
rows)))
(let ((data "1|Star Wars: Episode IV - A New Hope|1977|Action,Sci-Fi|George Lucas
2|Titanic|1997|Drama,History,Romance|James Cameron")
(ctypes '(0 1 0 1 1)))
(save-excursion
(goto-char (point-max))
(insert-statements (split-string data "\n") ctypes)))
This solution may not scale well compared with the Perl solution.
Alternatively, we could insert the values into a database using SqlMode:
(require 'cl)
(defun* insert-statements (rows ctypes &key (table-name "table") (delimiter "|"))
(let* ((values-template
(mapconcat '(lambda (type) (if (= type 1) "\"%s\"" "%s")) ctypes ","))
(template (format "insert into %s values(%s);" table-name values-template)))
(mapcar '(lambda (row) (sql-send-string
(apply 'format (cons template (split-string row delimiter)))) )
rows)))
(sql-sqlite)
(sql-send-string "create table test (id, title, yr, genre, director);")
(let ((data "1|Star Wars: Episode IV - A New Hope|1977|Action,Sci-Fi|George Lucas
2|Titanic|1997|Drama,History,Romance|James Cameron")
(ctypes '(0 1 0 1 1)))
(insert-statements (split-string data "\n") ctypes :table-name 'test))
(sql-send-string "select title from test;")
(sql-send-string "drop table test;")
you can write a simple program to go through each line and look for delimiter | and generate insert statements. if you are familiar with using mysql you can import the data into mysql table using "load data" command. you will have to have the data in file though