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indigo-depict sometimes fails for mysterious reasons outputting an empty SVG
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Description

Start request POST /api.php
HTTP HEADERS:
HOST: mol.wmflabs.org
X-FORWARDED-PROTO: http
CONNECTION: close
X-FORWARDED-FOR: XXX.XXX.XXX.XXX
CONTENT-LENGTH: 2215
ORIGIN: http://mol.wmflabs.org
USER-AGENT: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.49 Safari/537.36 OPR/23.0.1522.24 (Edition Next)
CONTENT-TYPE: multipart/form-data; boundary=----WebKitFormBoundarySumuN63W0EdsSCsG
ACCEPT: */*
REFERER: http://mol.wmflabs.org/index.php/File:DA.rxn
ACCEPT-ENCODING: gzip,deflate,lzma,sdch
ACCEPT-LANGUAGE: en-GB,en-US;q=0.8,en;q=0.6
COOKIE: molwikiLoggedOut=1403685337; molwikiUserID=2; molwikiUserName=Silly+Bang; molwikiToken=16d2c3b3b217b946e12992c2add2fb03; molwiki_session=n0f93tc7n9leido5sof475uoh1
[caches] main: MemcachedPhpBagOStuff, message: MemcachedPhpBagOStuff, parser: MemcachedPhpBagOStuff
[caches] LocalisationCache: using store LCStoreDB
Fully initialised
User: got user 2 from cache
Connected to database 0 at localhost
User: loading options for user 2 from override cache.
User: logged in from session
WebRequestUpload::getName: DA.rxn normalized to 'DA.rxn'
ApiUpload::execute about to verify
FSFile::getProps: Getting file info for /tmp/php0RC5kZ
MimeMagic::construct: loading mime types from /var/www/html/mw/includes/mime.types
MimeMagic::
construct: loading mime info from /var/www/html/mw/includes/mime.info
MimeMagic::doGuessMimeType: analyzing head and tail of /tmp/php0RC5kZ for magic numbers.
DjVuImage::getInfo: not a DjVu file
MolHandlerMime::doGuessChemicalMime: magic header in /tmp/php0RC5kZ recognized as chemical/x-mdl-rxnfile
MimeMagic::guessMimeType: guessed mime type of /tmp/php0RC5kZ: chemical/x-mdl-rxnfile
MimeMagic::improveTypeFromExtension: improved mime type for .rxn: chemical/x-mdl-rxnfile
MolHandler::execMolConverter: '/usr/bin/'indigo-depict '/tmp/php0RC5kZ.rxn' '/tmp/php0RC5kZ.svg' -thickness 1.8 -bond 20 -margins 7 5
wfShellExec: /bin/bash '/var/www/html/mw/includes/limit.sh' ''\''/usr/bin/'\''indigo-depict '\''/tmp/php0RC5kZ.rxn'\'' '\''/tmp/php0RC5kZ.svg'\'' -thickness 1.8 -bond 20 -margins 7 5' 'MW_INCLUDE_STDERR=1;MW_CPU_LIMIT=180; MW_CGROUP='\'''\''; MW_MEM_LIMIT=102400; MW_FILE_SIZE_LIMIT=102400; MW_WALL_CLOCK_LIMIT=180; MW_USE_LOG_PIPE=yes'
SvgHandler::getMetadata: Expected <svg> tag, got in NS
FSFile::getProps: /tmp/php0RC5kZ loaded, 1399 bytes, chemical/x-mdl-rxnfile.

mime: <chemical/x-mdl-rxnfile> extension: <rxn>

UploadBase::detectScript: checking for embedded scripts and HTML stuff
UploadBase::detectScript: no scripts found
ZipDirectoryReader: Fatal error: zip file lacks EOCDR signature. It probably isn't a zip file.
UploadBase::detectVirus: virus scanner disabled
FSFile::getProps: Getting file info for /tmp/php0RC5kZ
MimeMagic::doGuessMimeType: analyzing head and tail of /tmp/php0RC5kZ for magic numbers.
DjVuImage::getInfo: not a DjVu file
MolHandlerMime::doGuessChemicalMime: magic header in /tmp/php0RC5kZ recognized as chemical/x-mdl-rxnfile
MimeMagic::guessMimeType: guessed mime type of /tmp/php0RC5kZ: chemical/x-mdl-rxnfile
MimeMagic::improveTypeFromExtension: improved mime type for .rxn: chemical/x-mdl-rxnfile
MolHandler::execMolConverter: '/usr/bin/'indigo-depict '/tmp/php0RC5kZ.rxn' '/tmp/php0RC5kZ.svg' -thickness 1.8 -bond 20 -margins 7 5
wfShellExec: /bin/bash '/var/www/html/mw/includes/limit.sh' ''\''/usr/bin/'\''indigo-depict '\''/tmp/php0RC5kZ.rxn'\'' '\''/tmp/php0RC5kZ.svg'\'' -thickness 1.8 -bond 20 -margins 7 5' 'MW_INCLUDE_STDERR=1;MW_CPU_LIMIT=180; MW_CGROUP='\'''\''; MW_MEM_LIMIT=102400; MW_FILE_SIZE_LIMIT=102400; MW_WALL_CLOCK_LIMIT=180; MW_USE_LOG_PIPE=yes'
SvgHandler::getMetadata: Expected <svg> tag, got in NS
FSFile::getProps: /tmp/php0RC5kZ loaded, 1399 bytes, chemical/x-mdl-rxnfile.
UploadBase::verifyExtension: mime type chemical/x-mdl-rxnfile matches extension rxn, passing file
UploadBase::verifyFile: all clear; passing.
Title::getRestrictionTypes: applicable restrictions to [[File:DA.rxn]] are {edit,move,upload}
User::getBlockedStatus: checking...


Version: unspecified
Severity: normal

Details

Reference
bz67074

Event Timeline

bzimport raised the priority of this task from to Needs Triage.Nov 22 2014, 3:38 AM
bzimport set Reference to bz67074.
bzimport added a subscriber: Unknown Object (MLST).
Rillke created this task.Jun 25 2014, 10:42 AM

Maybe hits the limits set by limit.sh ...

rillke@mediahandler-tests-mol:/var/www/html/mw/images/b/b9$ ulimit -v 70000
rillke@mediahandler-tests-mol:/var/www/html/mw/images/b/b9$ ulimit -t 140

rillke@mediahandler-tests-mol:/var/www/html/mw/images/b/b9$ sudo indigo-depict DA.rxn DA.svg -thickness 1.8 -bond 20 -margins 7 5
sudo: error in /etc/sudo.conf, line 0 while loading plugin `sudoers_policy'
sudo: unable to load /usr/lib/sudo/sudoers.so: (null)
sudo: fatal error, unable to load plugins

after increasing memory to 204800 and restarting apache, it no more failed thumbnails for that reason -- still needs investigation

Gilles triaged this task as Medium priority.Nov 24 2014, 2:46 PM
Jdforrester-WMF moved this task from Untriaged to Backlog on the Multimedia board.Sep 4 2015, 6:35 PM
Restricted Application added subscribers: Matanya, Aklapper. · View Herald TranscriptSep 4 2015, 6:35 PM

after increasing memory to 204800 and restarting apache, it no more failed thumbnails for that reason -- still needs investigation

I got the same problem, please explain what value was increased.

I got the same problem, please explain what value was increased.

I suspect it was $wgMaxShellMemory which increases MW_MEM_LIMIT while MW is shelling out to indigo-depict. If this does not help, I can look up values on mol.wmflabs.org