(in medreg branch)
---
Import of medreg doctors failed twice in the last few days. The first time because of a non responding medregom service
2014-11-22 20:19:02 +0100: MedregDoctorPlugin Start saving @app.doctors.odba_store 2014-11-22 20:19:04 +0100: MedregDoctorPlugin Finished @app.doctors.odba_store 2014-11-22 20:19:15 +0100: MedregDoctorPlugin Saved 15707 doctors in /var/www/oddb.org/data/txt/doctors_2014.11.20-1225.yaml
The second time with an error whil saving the doctors info
2014-11-22 21:46:36 +0100: MedregDoctorPlugin Searching for doctor with GLN 7601000361080. Skipped 17555, created 1 updated 6 of 33139). RuntimeError: can't modify frozen String when updating index 'doctor_index' with a ODDB::Doctor ["/var/www/oddb.org/src/util/searchterms.rb:91:in `force_encoding'", "/var/www/oddb.org/src/util/searchterms.rb:91:in `block in search_terms'", "/var/www/oddb.org/src/util/searchterms.rb:87:in `each'", "/var/www/oddb.org/src/util/searchterms.rb:87:in `inject'"] [...] RuntimeError: can't modify frozen String when updating index 'doctor_index' with a ODDB::Doctor ["/var/www/oddb.org/src/util/searchterms.rb:91:in `force_encoding'", "/var/www/oddb.org/src/util/searchterms.rb:91:in `block in search_terms'", "/var/www/oddb.org/src/util/searchterms.rb:87:in `each'", "/var/www/oddb.org/src/util/searchterms.rb:87:in `inject'"] [...] 2014-11-22 21:46:44 +0100: MedregDoctorPlugin Searching for doctor with GLN 7601000361103. Skipped 17555, created 2 updated 6 of 33139). failsafe rescued DBI::ProgrammingError < StandardError message contents do not agree with length in message type "n" lost synchronization with server: got message type "I", length 1314080082 /usr/local/lib/ruby/gems/1.9.1/gems/dbd-pg-0.3.9/lib/dbd/pg/statement.rb:62:in `rescue in execute' /usr/local/lib/ruby/gems/1.9.1/gems/dbd-pg-0.3.9/lib/dbd/pg/statement.rb:37:in `execute' /usr/local/lib/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/statement.rb:116:in `execute' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/storage.rb:263:in `block in ensure_object_connections' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/storage.rb:262:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/storage.rb:262:in `ensure_object_connections' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:553:in `store_object_connections' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:512:in `store' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:274:in `odba_isolated_store' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:395:in `block in odba_store_unsaved' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `odba_store_unsaved' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:380:in `odba_store' /var/www/oddb.org/src/util/persistence.rb:226:in `issue_create' /var/www/oddb.org/src/util/oddbapp.rb:111:in `block in create' /var/www/oddb.org/src/util/failsafe.rb:10:in `call' /var/www/oddb.org/src/util/failsafe.rb:10:in `failsafe' /var/www/oddb.org/src/util/oddbapp.rb:110:in `create' /var/www/oddb.org/src/util/persistence.rb:288:in `block in resolve' /var/www/oddb.org/src/util/persistence.rb:278:in `each' /var/www/oddb.org/src/util/persistence.rb:278:in `resolve' /var/www/oddb.org/src/util/persistence.rb:256:in `issue_update' /var/www/oddb.org/src/util/oddbapp.rb:132:in `block in update' /var/www/oddb.org/src/util/failsafe.rb:10:in `call' /var/www/oddb.org/src/util/failsafe.rb:10:in `failsafe' /var/www/oddb.org/src/util/oddbapp.rb:130:in `update' /var/www/oddb.org/src/util/oddbapp.rb:1566:in `update' /var/www/oddb.org/src/plugin/medreg_doctor.rb:391:in `store_doctor' /var/www/oddb.org/src/plugin/medreg_doctor.rb:207:in `block in get_one_doctor' /var/www/oddb.org/src/util/resilient_loop.rb:63:in `call' /var/www/oddb.org/src/util/resilient_loop.rb:63:in `block in try_run' /usr/local/lib/ruby/1.9.1/timeout.rb:68:in `timeout' /usr/local/lib/ruby/1.9.1/timeout.rb:99:in `timeout' /var/www/oddb.org/src/util/resilient_loop.rb:62:in `try_run' /var/www/oddb.org/src/plugin/medreg_doctor.rb:154:in `get_one_doctor' /var/www/oddb.org/src/plugin/medreg_doctor.rb:228:in `block in get_detail_to_glns' /var/www/oddb.org/src/plugin/medreg_doctor.rb:217:in `each' /var/www/oddb.org/src/plugin/medreg_doctor.rb:217:in `get_detail_to_glns' /var/www/oddb.org/src/plugin/medreg_doctor.rb:92:in `update' /var/www/oddb.org/src/util/updater.rb:237:in `block in update_medreg_doctors' /var/www/oddb.org/src/util/updater.rb:526:in `call' /var/www/oddb.org/src/util/updater.rb:526:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:235:in `update_medreg_doctors' jobs/import_regmed_doctors:14:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' jobs/import_regmed_doctors:12:in `<module:Util>' jobs/import_regmed_doctors:11:in `<module:ODDB>' jobs/import_regmed_doctors:10:in `<main>'
I am having the problem, that I the setup on oddb-ci2 is broken and I get only a Internal Server Error and Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request. and no entry in the apache error_log/access_log. What is going on here?
But in /var/www/oddb.org/log/oddb/error.log I found
[Mon Nov 24 10:19:04 2014] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/apache/ruby-run.rb:53:in `handler' [Mon Nov 24 10:19:04 2014] [error] [client 172.25.1.75] File does not exist: /var/www/oddb.org/doc/var [Mon Nov 24 10:28:12 2014] [error] mod_ruby: error in ruby [Mon Nov 24 10:28:12 2014] [error] mod_ruby: /usr/lib64/ruby/1.9.1/rubygems.rb:30:in `require': cannot load such file -- rubygems/defaults (LoadError) [Mon Nov 24 10:28:12 2014] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/rubygems.rb:30:in `<top (required)>' [Mon Nov 24 10:28:12 2014] [error] mod_ruby: from /var/www/oddb.org/doc/index.rbx:6:in `require' [Mon Nov 24 10:28:12 2014] [error] mod_ruby: from /var/www/oddb.org/doc/index.rbx:6:in `<top (required)>' [Mon Nov 24 10:28:12 2014] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/apache/ruby-run.rb:53:in `load' [Mon Nov 24 10:28:12 2014] [error] mod_ruby: from /usr/lib64/ruby/1.9.1/apache/ruby-run.rb:53:in `handler' [Mon Nov 24 10:28:12 2014] [error] [client 172.25.1.70] File does not exist: /var/www/oddb.org/doc/var
Therefore removing and reinstalling the gems must have broken some stuff. Tried to recompile mod_ruby from scratch
git clone https://github.com/shugo/mod_ruby.git cd mod_ruby ./configure.rb <adde manually -I/usr/include/apr-1 to line APACHE_INCLUDES = -I/usr/include/apache2 make <..> /usr/local/lib/libruby-static.a: could not read symbols: Bad value collect2: ld gab 1 als Ende-Status zurück Makefile:182: recipe for target 'mod_ruby.so' failed
I am getting sick chasing installation problem on funtoo, because we are so much behind as we cannot use ruby 2.1. There fore decided to create a docker container for oddb.org with ruby 2.1.
Trying to solve mod-ruby problem by redoing the work done when installing with puppet/vagrant see https://github.com/ngiger/vagrant-oddb_org/blob/master/protocol.textile, running as root
eselect ruby set ruby19 emerge =apache-2.2.26 cd /opt/src/mod_ruby # where I still have copy of my source ./configure.rb --with-apxs --with-apr-includes=/usr/include/apr-1 make make install /etc/init.d/apache2 restart * apache2 has detected an error in your setup: Syntax error on line 7 of /etc/apache2/vhosts.d/oddb.conf: Invalid command 'RubyAddPath', perhaps misspelled or defined by a module not included in the server configuration * ERROR: apache2 failed to stop grep -r RUBY /etc/conf.d/ /etc/conf.d/apache2:APACHE2_OPTS="-D RUBY -D DEFAULT_VHOST -D INFO -D SSL -D SSL_DEFAULT_VHOST -D LANGUAGE"
Somehow emerge forgot to install mod_ruby even when RUYBB is specified in the APACHE2_OPTS. Why?
Emerge mod_ruby fails because it uses ruby18
emerge mod_ruby * IMPORTANT: config file '/etc/portage/package.license' needs updating. * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 1) www-apache/mod_ruby-1.3.0 * mod_ruby-1.3.0.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mod_ruby-1.3.0.tar.gz to /var/tmp/portage/www-apache/mod_ruby-1.3.0/work >>> Source unpacked in /var/tmp/portage/www-apache/mod_ruby-1.3.0/work >>> Compiling source in /var/tmp/portage/www-apache/mod_ruby-1.3.0/work/mod_ruby-1.3.0 ... ruby18: no such file to load -- auto_gem (LoadError) make -j13 make: *** No targets specified and no makefile found. Stop. emake failed * ERROR: www-apache/mod_ruby-1.3.0 failed (compile phase): * emake failed * * Call stack: * ebuild.sh, line 93: Called src_compile * environment, line 905: Called die * The specific snippet of code: * emake || die "emake failed"; * * If you need support, post the output of `emerge --info '=www-apache/mod_ruby-1.3.0'`, * the complete build log and the output of `emerge -pqv '=www-apache/mod_ruby-1.3.0'`. * The complete build log is located at '/var/tmp/portage/www-apache/mod_ruby-1.3.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/www-apache/mod_ruby-1.3.0/temp/environment'. * Working directory: '/var/tmp/portage/www-apache/mod_ruby-1.3.0/work/mod_ruby-1.3.0' * S: '/var/tmp/portage/www-apache/mod_ruby-1.3.0/work/mod_ruby-1.3.0' >>> Failed to emerge www-apache/mod_ruby-1.3.0, Log file: <..>
Funtoo drives me crazy!