SQL/XML Dumps/Wikibase dumps via cron

All about Wikibase (rdf) dumps via cron
Okay, maybe not all about them, but enough to get you adding your own scripts for new datasets.

Much of this is specific to the WMF puppet repo, but it builds on scripts in the Wikibase extension that are used to dump wikidata entities in various formats. We can just look at one of these formats to see how it works. It may be helpful for you to have a look at SQL/XML_Dumps/"Other"_dump_jobs_via_cron in combination with the current document.

All dumps except for xml/sql dumps run from cron via shell scripts which can be found in our puppet manifests. See   for these. We’ll start by looking at common functions available to all scripts.

Common functions for dump scripts
The script   provides paths to a number of directories, such as the base directory tree for all of these dumps, and the path to the dumps configuration files. It also provides a function for extracting values from the output of a little python script that gets multiple values from those config files, such as paths to useful executables, and the directory tree for temporary files. You should always source  at the top of your script.

Configuration files
We have a few dumps configuration files available; one is for xml/sql dumps and you won’t want that. One is for WMCS instances and you won’t want that either. The one you do want is  in the   dir, available to you in the   variable. This name is historical; everything other than xml/sql dumps was considered “other” and is put in a separate directory tree, and even generated by separate hosts writing to a separate filesystem.

Where to write files, what to name them
We like output files to have the wiki db name, the date in YYYYMMDD format, and the sort of dump being produced in the name, the type of output (json, txt, ttl etc) as well as the compression type as the extension. Typically files are arranged in directories by dump type and then date. For example, cirrussearch dumps are in the subdirectory cirrussearch under a further subdirectory of YYYYMMDD for the date that run was started, with files for all wikis in the same directory. Output files for mediainfo data from commons in rdf format might be in  for example.

Thus, at the beginning of the script you should save the date in the right format. The base directory tree for these dump output files is available to you in  so you can just tack on the dump name and the date as subdirs after that.

Getting config values for your script
We use absolute paths for everything including e.g. gzip and php. This makes things a bit safer and also lets us switch between versions of php on a rolling basis when we start moving to a new version. We also need to be able to get the directory where  and its ilk reside. The   script is available for retrieving these values. You will set up a single argument with the config file sections and setting names you want to retrieve, call the script once, get the output, and then use the  function (included in the   script we saw earlier) to extract each value to its own shell variable. You’ll want to check that the value isn’t empty (that something horrible hasn’t gone wrong with the config file or whatever) by using, also provided in

Example code
Enough blah blah, let’s look at code right from   and see for ourselves. This code does all of the above for you, but it’s a good idea to know what all the pieces are before you start building on top of them.

Reminder that all of this is done for you in wikibasedumps-shared.sh so you need only source that in your dumpwikibase(somenewformat).sh script.

There is more here, but we don't need to look at all of the code for it. Instead, we summarize the interesting parts below.

Shared functions for wikibase dumps
A number of convenience functions are provided for you in  so please make use of them:


 * tosses old log files, typically written to files in   or
 * runs DCAT.php on the output files if there is a config specified for it.
 * generates md5 and sha1 checksums for and output file and stashes them in files to be made available for download.
 * gets the number of batches we’ll need to run, based on the number of processes we run at once and the max page id and some other stuffs.
 * sets the first and last page id we want to retrieve in a specific batch, etc.
 * gets a properly sorted list of all the output files matching some wildcard.
 * gets the byte count of one or more files. This is used as a sanity check to make sure we don’t suddenly have much tinier output files than expected.
 * logs errors and handles retries of a batch.
 * is used in the case that we have run this script manually to continue a previously failed run. It will determine where we left off.
 * is used at the end to move the temporary files we write into their permanent name and location.

These are all pretty self-explanatory, and the calls to them in e.g.  should be good examples.

Per-project functions for wikibase rdf dumps
You’ll be setting up for some other format but these are the sort of things you’ll want to provide.

Let’s look at the example for commons rdf dumps:

Pretty simple stuff.

Now let’s see how all that gets used in


 * 1) !/bin/bash
 * 2) This file is maintained by puppet!
 * 3) puppet:///modules/snapshot/cron/wikibase/dumpwikibaserdf.sh
 * 4) Generate a RDF dump for wikibase datasets and remove old ones.
 * 5) This script requires a second shell script with function definitions
 * 6) in it specific to the given wikibase project and entity types;
 * 7) place it in modules/snapshot/cron/wikibase/ rdf_functions.sh
 * 8) using one of the existing files as a guide, and then add the
 * 9) project name to PROJECTS below.
 * 10) The project name should be the wiki db name without the 'wiki'
 * 11) suffix. If someday we move to run wikibase on wiktionaries
 * 12) or what have you, we'll redo the project and file name logic!
 * 1) The project name should be the wiki db name without the 'wiki'
 * 2) suffix. If someday we move to run wikibase on wiktionaries
 * 3) or what have you, we'll redo the project and file name logic!

This code works only for commons and wikidata (db names commonswiki, wikidatawiki).

PROJECTS="wikidata|commons"

if "$1" == '--help' ; then echo -e "$0 $PROJECTS --help for help" exit 1 fi

projectName=$1 if [ -z "$projectName" ]; then echo -e "Missing project name." echo -e "$0 $PROJECTS --help for help" exit 1 fi if [ "$projectName" != "wikidata" -a "$projectName" != "commons" ]; then echo -e "Unknown project name." echo -e "$0 $PROJECTS --help for help" exit 1 fi

Source all those common settings and functions.

. /usr/local/bin/wikibasedumps-shared.sh . /usr/local/bin/${projectName}rdf_functions.sh

if "$2" == '--help' ; then usage exit 1 fi

In case we are doing a manual run to finish up a run that broke partway through.

continue=0 if "$2" == '--continue' ; then shift continue=1 fi

For rdf dumps this can currently be “all”, “truthy”, or “nt”.

dumpName=$2 if [ -z "$dumpName" ]; then echo "No dump name given." usage exit 1 fi

if [ $continue -gt 0 ]; then # Remove old leftovers, as we start from scratch. rm -f $tempDir/$projectName$dumpFormat-$dumpName.*-batch*.gz fi

For rdf dumps this varies according to the dumpName, the dumpflavor variable eventually gets passed in as an arg to the maintenance script. For other formats you may want something else or to not even have this. setDumpFlavor

Yeah more special format stuff for the rdf jobs.

dumpFormat=$3 extraFormat=$4

if "$dumpFormat" != "ttl"  &&  "$dumpFormat" != "nt" ; then echo "Unknown format: $dumpFormat" usage exit 1 fi

if [ -n "$extraFormat" ]; then declare -A serdiDumpFormats serdiDumpFormats=(["ttl"]="turtle" ["nt"]="ntriples") extraIn=${serdiDumpFormats[$dumpFormat]} extraOut=${serdiDumpFormats[$extraFormat]} if [ -z "$extraIn" -o -z "$extraOut" -o "$extraIn" = "$extraOut" ]; then extraFormat="" fi fi

Set up that dump output file name though!

setFilename

failureFile="/tmp/dump${projectName}${dumpFormat}-${dumpName}-failure" logLocation="/var/log/${projectName}dump" mainLogFile="${logLocation}/dump${projectName}${dumpFormat}-${filename}-main.log"

This is hardcoded in; how many batches are we dumping at once? Increases to this are inevitable but should be coordinated with the dba and whoever is managing the host(s) generating the dumps.

shards=8

i=0 rm -f $failureFile

When is the output so small that it’s probably broken?

setDumpNameToMinSize

Set up batch info

getNumberOfBatchesNeeded ${projectName}wiki numberOfBatchesNeeded=$(($numberOfBatchesNeeded / $shards))

if $numberOfBatchesNeeded -lt 1 ; then shards=4 numberOfBatchesNeeded=1 pagesPerBatch=$(( $maxPageId / $shards )) fi
 * 1) wiki is too small for default settings, change settings to something sane
 * 2) this assumes wiki has at least four entities, which sounds plausible

What are we dumping again? This sets the entity-type arg for the rdf dumps maintenance script.

setEntityType

while [ $i -lt $shards ]; do   (

Gotta get errors from anywhere in the pipeline.

set -o pipefail errorLog=${logLocation}/dump$projectName$dumpFormat-$filename-$i.log

batch=0

if [ $continue -gt 0 ]; then getContinueBatchNumber "$tempDir/$projectName$dumpFormat-$dumpName.$i-batch*.gz" fi

retries=0 while [ $batch -lt $numberOfBatchesNeeded ] && [ ! -f $failureFile ]; do           setPerBatchVars

echo "(`date --iso-8601=minutes`) Starting batch $batch" >> $errorLog

Actually run the script, woo hoo!

$php $multiversionscript extensions/Wikibase/repo/maintenance/dumpRdf.php \ --wiki ${projectName}wiki \ --shard $i \ --sharding-factor $shards \ --batch-size $(($shards * 250)) \ --format $dumpFormat ${dumpFlavor:+--flavor} ${dumpFlavor:+"$dumpFlavor"} \ $entityTypes \ --dbgroupdefault dump \ --part-id $i-$batch \ $firstPageIdParam \ $lastPageIdParam 2>> $errorLog | gzip -9 > $tempDir/$projectName$dumpFormat-$dumpName.$i-batch$batch.gz

exitCode=$? if [ $exitCode -gt 0 ]; then handleBatchFailure continue fi

retries=0 let batch++ done ) &   let i++ done

wait

This  thing is literally “did something fail”

if [ -f $failureFile ]; then echo -e "\n\n(`date --iso-8601=minutes`) Giving up after a shard failed." >> $mainLogFile rm -f $failureFile

exit 1 fi

i=0

Everything got written to temp files in the temp dir, do size sanity check, then concat them all together

while [ $i -lt $shards ]; do   getTempFiles "$tempDir/$projectName$dumpFormat-$dumpName.$i-batch*.gz" if [ -z "$tempFiles" ]; then echo "No files for shard $i!" >> $mainLogFile exit 1 fi   getFileSize "$tempFiles" if [ $fileSize -lt ${dumpNameToMinSize[$dumpName]} ]; then echo "File size of $tempFile is only $fileSize. Aborting." >> $mainLogFile exit 1 fi   cat $tempFiles >> $tempDir/$projectName$dumpFormat-$dumpName.gz    let i++ done

This is rdf specific stuff.

if [ -n "$extraFormat" ]; then # Convert primary format to extra format i=0 while [ $i -lt $shards ]; do       getTempFiles "$tempDir/$projectName$dumpFormat-$dumpName.$i-batch*.gz" (           set -o pipefail            for tempFile in $tempFiles; do                extraFile=${tempFile/$projectName$dumpFormat/$projectName$extraFormat}                gzip -dc $tempFile | serdi -i $extraIn -o $extraOut -b -q - | gzip -9 > $extraFile                exitCode=$?                if [ $exitCode -gt 0 ]; then                    echo -e "\n\n(`date --iso-8601=minutes`) Converting $tempFile failed with exit code $exitCode" >> $errorLog                fi            done        ) & let i++ done wait fi

i=0 while [ $i -lt $shards ]; do   getTempFiles "$tempDir/$projectName$dumpFormat-$dumpName.$i-batch*.gz" rm -f $tempFiles if [ -n "$extraFormat" ]; then getTempFiles "$tempDir/$projectName$extraFormat-$dumpName.$i-batch*.gz" cat $tempFiles >> $tempDir/$projectName$extraFormat-$dumpName.gz       rm -f $tempFiles fi   let i++ done

They recompress the gzip output to bzip2 here, ymmv

nthreads=$(( $shards / 2)) if [ $nthreads -lt 1 ]; then nthreads=1 fi

But first they move the concatted temp file into place.

moveLinkFile $projectName$dumpFormat-$dumpName.gz $filename.$dumpFormat.gz latest-$dumpName.$dumpFormat.gz $projectName

gzip -dc "$targetDir/$filename.$dumpFormat.gz" | "$lbzip2" -n $nthreads -c > $tempDir/$projectName$dumpFormat-$dumpName.bz2 moveLinkFile $projectName$dumpFormat-$dumpName.bz2 $filename.$dumpFormat.bz2 latest-$dumpName.$dumpFormat.bz2 $projectName

The rdf specific extra format stuff, more of it

if [ -n "$extraFormat" ]; then moveLinkFile $projectName$extraFormat-$dumpName.gz $filename.$extraFormat.gz latest-$dumpName.$extraFormat.gz $projectName gzip -dc "$targetDir/$filename.$extraFormat.gz" | "$lbzip2" -n $nthreads -c > $tempDir/$projectName$extraFormat-$dumpName.bz2 moveLinkFile $projectName$extraFormat-$dumpName.bz2 $filename.$extraFormat.bz2 latest-$dumpName.$extraFormat.bz2 $projectName fi

Clean up old logs, run dcat if there’s a config, and we’re done at last!

pruneOldLogs setDcatConfig runDcat