Index>

20151223-yus-ruby-2-x

Summary

• Analyse error "method_missing called on unexpected T_NODE"
• Run yus under Ruby 2.x in docker

Commits

• https://github.com/ngiger/oddb-docker/commit/83bca08f22119472c8dba0501ecce4265486b17c Initial commit
• https://github.com/ngiger/oddb-docker/commit/135bcbb9db20bb664df3ba9b236b1641ee4b2e7d Documented some design decisions

yus (branch ruby2x)

• https://github.com/ngiger/yus/commit/2fc902ee538f96ff9f87920b63bd1a1bb7d2f9f5 Added support for running yus via docker
• https://github.com/ngiger/yus/commit/dc032c8e45eefb109fa942b9810ce0dd90c88157 Made all test scripts executable
• https://github.com/ngiger/yus/commit/26faf2b00d3ef9a4ddac16dc5a7e4412a78a9134 Replaced hoe by bundler/gem_tasks
• https://github.com/ngiger/yus/commit/20543f9804b0a4ac84fba2f599f71e18bcb472a2 First (failing) spec test with docker
• https://github.com/ngiger/yus/commit/c539f6b97a6b286c4afcf0fb1228c3b762148c95 Added forgotten yus.gempspec
• https://github.com/ngiger/yus/commit/fb3e3a3325c330ab670f43dacbf10a5af2e7273d Added cracklib-runtime for travis builds
• https://github.com/ngiger/yus/commit/cd48932d6f4ba6e6eddb42c38bb593972f41339a libcrack2-dev is needed to to build ruby-password

Index

• Analyse error "method_missing called on unexpected T_NODE"
• Run yus under Ruby 2.x in docker

Keep in Mind for work to do

• Fix dojo error http://www.sitepen.com/blog/2012/10/31/debugging-dojo-common-error-messages/#forgot-dom-ready
• I removed on May-27 tests for ix_registrationss, fix_sequences, fix_compositions, fix_packages from test/test_plugin/swissmedic.rb,as he could not find any references for them in the src code. Did I erroneously remove stuff when cleaning up the swissmedic import earlier?
• The whole test for older/newer Packages must be adapted to xlsx. One must compare the rows (e.g. by creating csv files) and do the same stuff in xlsx!
• creat gem: task: input=file with ean-codes, standard output show ean-codes + atc-code. Source is Swissmedic Packungen.xlsx or XML.
• Import via data/medreg_companies.yaml
• Fix problem with radioactivatum 99m-technetio when parsing Wirkstoffe
• Fix galenic_forms when parsing swissmedic.xlsx
• Cleanup generic_type. Replace it everywhere by sl_generic_type and adapt code accordingly.
• Get updated ATC-codes from EPha for oddb.org, too.
• Use refdatabase for oddb.org, too.
• Check whether we should revert the part which touche src/plugin/text_info.rb of commit 17af82ba4d76a5838683411b260de265531f9e74. We should improve test/stub/oddbapp.rb to work similar for update/pointer as the real oddbapp. In this case we would have a good Stub for plugins. May we need a different stub when working with plugins (which create/modify/destroy ODDB-Objects), when in most other cases a very simple stub is sufficient.
• When a logged in admin user changes an atc_code of a product, the corresponding atc_class must update its sequences, too.
• Order of entering search type and value should not matter. Both should show long URL with search
• Remove parser for minifi (but keep the minifi)

Analyse error "method_missing called on unexpected T_NODE"

Found the following error this morning

Plugin: ODDB::TextInfoPlugin
Error: NotImplementedError
Message: method `method_missing' called on unexpected T_NODE object (0x00000059a78510 flags=0x623c klass=0x0)
Backtrace:
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing'
/var/www/oddb.org/src/plugin/text_info.rb:177:in `block in store_patinfo'
/var/www/oddb.org/src/plugin/text_info.rb:177:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:177:in `collect'
/var/www/oddb.org/src/plugin/text_info.rb:177:in `store_patinfo'
/var/www/oddb.org/src/plugin/text_info.rb:317:in `block in update_patinfo'
/var/www/oddb.org/src/plugin/text_info.rb:307:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:307:in `update_patinfo'
/var/www/oddb.org/src/plugin/text_info.rb:1203:in `parse_and_update'
/var/www/oddb.org/src/plugin/text_info.rb:1213:in `block (3 levels) in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1212:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:1212:in `block (2 levels) in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1211:in `each_pair'
/var/www/oddb.org/src/plugin/text_info.rb:1211:in `block in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1208:in `each_pair'
/var/www/oddb.org/src/plugin/text_info.rb:1208:in `import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1416:in `block in import_swissmedicinfo_by_index'
/var/www/oddb.org/src/plugin/text_info.rb:1415:in `each_pair'
/var/www/oddb.org/src/plugin/text_info.rb:1415:in `import_swissmedicinfo_by_index'
/var/www/oddb.org/src/plugin/text_info.rb:1477:in `import_swissmedicinfo'
/var/www/oddb.org/src/util/updater.rb:573:in `block in update_notify_simple'
/var/www/oddb.org/src/util/updater.rb:549:in `call'
/var/www/oddb.org/src/util/updater.rb:549:in `wrap_update'
/var/www/oddb.org/src/util/updater.rb:567:in `update_notify_simple'
/var/www/oddb.org/src/util/updater.rb:344:in `update_textinfo_swissmedicinfo'
/var/www/oddb.org/src/util/updater.rb:198:in `run'
jobs/import_daily:13: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_daily:12:in `<module:Util>'
jobs/import_daily:11:in `<module:ODDB>'
jobs/import_daily:10:in `<main>

Found the following entries in the log to see where it comes from

015-12-23 07:19:44 +0100: /var/www/oddb.org/src/plugin/text_info.rb:1197:in `block in parse_and_update': _infos de  NilClass
2015-12-23 07:19:44 +0100: /var/www/oddb.org/src/plugin/text_info.rb:1197:in `block in parse_and_update': _infos fr ellaOne 30 mg comprimé
Qu’est-ce que ellaOne et quand est-il utilisé?
ellaOne est pris sur prescription du médecin.
ellaOne est un contraceptif d'urgen ODDB::PatinfoDocument
2015-12-23 07:19:44 +0100: /var/www/oddb.org/src/plugin/text_info.rb:1202:in `parse_and_update': calling update_patinfo ellaOne 30 mg comprimé, ["62531"]
2015-12-23 07:19:44 CETlog notify Error: Fach- und Patienteninfo Updates (swissmedicinfo.ch): start outgoing process ["log"]. Must attach 0 files and 0 parts. 
2015-12-23 07:19:44 CETUtil.send_mail list_and_recipients ["log"]

On oddb-ci2 the FI and PI was added/updated without any problem this night. On thinpower the FI got updated, but we have no PI. Loading thinpowers database on oddb-ci2 and running update_textinfo_swissmedicinfo --target=pi on oddb-ci2. Could not reproduce the error here. Waiting whether tomorrow we will have the same problem or not.

Run yus under Ruby 2.x in docker

I will start a new github repository oddb-docker where I want to setup an infrastructure which can be easily duplicated to run test (unit-tests and Watir). As some of the tests take many hours to complete, eg. check the whole import_daily it is desirable that the developer has the possibility to run several of these test in parallel. This will allow working on a feature branch and fixing some (hopefully small) problem in the production branch.

Added a readme and documented there some reflections with commits

• Initial commit
• Documented some design decisions

Looking around for a gem/tool to add spec tests for my dockerfiles/docker-compose.yml. Found Testing Dockerfiles with Serverspec

Installing docker and docker-compose via

• sudo emerge --sync
• sudo emerge --oneshot portage
• sudo emerge docker docker-compose

This seems to work out fine. Got docker 1.9.1 and docker-compose 1.5.2. Change yus like this

• add docker-compose.yml
• Dockerfile
• test/yus_demo.yml (to specify db_host, db_name, etc)
• modified bin/yusd
  • allow specifying a database host, as the database is running in another container

As I need to create /etc/yus/data/yus.{key,crt} I looked how I did it via a puppet manifest https://github.com/ngiger/vagrant-oddb_org/blob/master/static-modules/oddb_org/templates/yus_create_yml.rb.erb

Now I am asking myself.

• Should I reuse/adapt all the puppet stuff. It would probably be necessary to port it to a more or less recent version of puppet and correct/add the needed spec test
• Shall I split it into various part? E.g. yus, migel, oddb.org as other stuff like the currency daemon will probable not need a sophisticated setup.
• Shall just create some isolated puppet files and call them. What about templates? Inlining them? Installing Puppet?
• What about the Apache vhosts?
• If I split it up, how can I access the same hiera configuration?

As shown in https://docs.travis-ci.com/user/docker/ it should be easy to run a docker command when running on travis-ci. Creating a new branch ruby2x. Replaced using hoe by bundler/gem_tasks. Pushed commits

• Added support for running yus via docker
• Made all test scripts executable
• Replaced hoe by bundler/gem_tasks
• First (failing) spec test with docker
• Added forgotten yus.gempspec
• Added cracklib-runtime for travis builds
• libcrack2-dev is needed to to build ruby-password

Now docker-compose up begins to start bin/yusd, but has some error because the id_rsa.key and yus.yml are not yet correct. Eg. Output was Failed creating certificate using: openssl req -key /etc/yus_demo/data/yus.key -out /etc/yus_demo/data/yus.crt -new -x509 -batch -passin pass:''

rake test works fine and runs all unit tests. Will work on making rake rspec to run spec tests against a docker instance which has the code installed. Eg. docker-compose build/up must work, yus_add, yus_show, etc will be exercised.

Will fix this next year!