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20141001-yus-dump-yaml

Summary

• Dump yus-database to yaml to better understand YUS-affiliations
• Analysing error with Download Zulassungsinhaber Desitin

Commits

• https://github.com/ngiger/yus/commit/1dd54f305ecebe6ef80ba99e613b4000f34641a3 Added option to dump yus to yaml
• https://github.com/ngiger/yus/commit/edbed237ce0bd2e5cafa23138706d3c911d79f36 Log result of allowed?
• https://github.com/ngiger/yus/commit/3afdece89330a02dfe343472f4dd2253eebefb79 Trying to fix travis build on master branch
• https://github.com/ngiger/yus/commit/cbdb98e492b30e3a2e09bc9e1f7156c7782df6c1 Add bin/yus_dump
• https://github.com/ngiger/yus/commit/ede758744cc995f96bbf08e55873070ef755f76f Unittest less verbose
• https://github.com/ngiger/yus/commit/7607dbf5753a9c0c3c52d8ef31cb097c79876bd7 Added require 'rubygems' for all bin/*
• https://github.com/ngiger/yus/commit/13e8ffeb9d0e3daa56cf3439ea7b57faedbf223f Corrected dump of ODBA items
• https://github.com/ngiger/yus/commit/c0c02e4651cfd79565c268b39311efe6dd9a6465 Corrected .travis.yml and Gemfile to avoid errors
• https://github.com/ngiger/yus/commit/6ccf10767be77bf5c1d50a2d7b6b12f256ee9181 Add user name to debug allowed?
• https://github.com/ngiger/yus/commit/72aa0d4081204f1d49625e93619c112aa58d7f01 Removed ruby-password from gem because of problem on travis-CI
• https://github.com/ngiger/yus/commit/35f96dffa24cac50868da6466baae01e9fdad6e4 One should call rake test before pushing!
• https://github.com/ngiger/yus/commit/69f32d9ce2e6367b7f7180a688ca4660e11ae0fd Prepare for release 1.0.2

Index

• Analysing error with Download Zulassungsinhaber Desitin
• Dump yus-database to yaml to better understand YUS-affiliations

Keep in Mind

• 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!
• Fix analyses search. Eg. for Akute myeloische Leukämie

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Analysing error with Download Zulassungsinhaber Desitin

I still have the same error, that I don't get a CSV-file when trying to download the CSV export for Desiting. Using HttpFox showed me that loading http://oddb-ci2.dyndns.org/de/gcc/export_csv/zone/drugs/search_query/Desitin/search_type/st_company produced the error

00:01:07.670 0.461 1080 0 GET (Aborted) NS_BINDING_ABORTED http://oddb-ci2.dyndns.org/resources/dojo/dojo/window.js

Now I am using httpfox on oddb-ci2.

Improved debugging with adding user-name when logging Allowed?. Fixed some build-errors on travis -ci too. See commits

• Add user name to debug allowed?
• Removed ruby-password from gem because of problem on travis-CI
• One should call rake test before pushing!

Dump yus-database to yaml to better understand YUS-affiliations

I want to add a possibility to dump the yus-DB to yaml to better understand the differences between the YUS-DB on thinpower and one created following the examples found elsewhere in this wiki.

Porting the dump from the branch without_needle to the master branch and comparing the output of dumps produced by the unit-tests. Took some time to make the tests pass again on branch master. Dumping the attribute @persistance does not produce any output. Dumping works after changing the variable to be dumped form @persistence -> @needle.persistence.

The following differences between the dumps for branch master Attach::master_dump.txt and without_needle Attach::without_needle_dump.txt were found:

• Entries are ordered differently (this is known difference for hashes between ruby 1.8 and ruby >= 1.9
• Timestamps for fields valid_from are different (expected)
• Empty field passhash: not present in master (??)
• Yus affiliations look different
  • for without_needle

  entity_name: !ruby/object:Yus::Entity 
    affiliations: 
    - &id001 !ruby/object:Yus::Entity 
      affiliations: []

• for master-branch (Ruby 1.8.6 old)

  entity_name: !ruby/object:Yus::Entity 
    affiliations: 
    - *id001

• a_yus_group is defined differently
  • for without_needle

  a_yus_group: *id001

• for master-branch (Ruby 1.8.6 old)

  a_yus_group: &id001 !ruby/object:Yus::Entity 
    affiliations: []

    last_logins: {}

    name: a_yus_group
    preferences: {}

    privileges: 
      set_password: !ruby/object:Yus::Privilege 
        items: 
          a_yus_group: :never
    tokens: {}

    valid_from: 2014-10-01 09:41:59.892694 +02:00
    valid_until: entity_pass

Conclusion: My port of yus to a model without needle is not correct. Must be fixed! Nevertheless the results for the master branch could be pushed with the following commits

• Added option to dump yus to yaml
• Log result of allowed?
• Trying to fix travis build on master branch

The questions are:

• Must the implementation of without_needle be fixed if all unit-tests pass?
• How can one migrate data from the master-branch to the without_needle branch for a real database
• How the rald database dumps look like. (I will try to answer this question first)

Adding a possibility in oddb.org to dump the yus-database to yaml via bin/admin. NO! I added a new bin/yus_dump to the yus gem with commits

• Add bin/yus_dump
• Unittest less verbose

When running the new bin/yus_dump I don't get a nice representation as I see in the yaml file only

-- !ruby/object:Yus::Persistence::Odba
entities: &id001
  downloaduser: !ruby/object:ODBA::Stub
    odba_id: 13
    odba_container: *id001

Adapted the dumping to yaml to get the real entities from the DB-Cache. But this does not work with my MockPersistence. Maybe I must adapt it to more closely reflect how the Persistence works.

Pushed the following commit to fix the dump issue with the master branch under ruby 1.8.6

• Added require 'rubygems' for all bin/*
• Corrected dump of ODBA items
• Corrected .travis.yml and Gemfile to avoid errors

Okay. Importing database from thinpower and dumping it worked fine. Observered that there are non UTF-8 string in it like :city: "Z\xC3\xBCrich"