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20150826-fix-active-agents

Summary

• Cleanup separation of active and inactive agents got fix wrong count of active agents
• Fix unit-tests (on travis-ci)

Commits

• https://github.com/ngiger/oddb.org/commit/6a3fba675750f69016b0b8c342feb7d8d558937f Remove some non-working unit test
• https://github.com/ngiger/oddb.org/commit/04937fa522974265bbd2cf6785e3e90a760ab084 Install nodejs before running travis-CI. Fixes javascript
• https://github.com/ngiger/oddb.org/commit/5d264b175a0081e9850cf419a27ff37741bc8834 Use container-based infrastructure of travis-ci
• https://github.com/ngiger/oddb.org/commit/3513aa9e2be3de5841a6efa652dc5e92add20215 Used odba_store instead of odba_isolated_store in cleanup_old_active
• https://github.com/ngiger/oddb.org/commit/17af82ba4d76a5838683411b260de265531f9e74 Add new class InactiveAgents. Fix plugin and unit tests
• https://github.com/ngiger/oddb.org/commit/d354ff749fa88bb43c9c72157fedf18a71e23394 Fix unit tests. Added new class InactiveAgents
• https://github.com/ngiger/oddb.org/commit/7829429b558fcb47393d2f30574121679ea8effb Fix errors displaying active/inactive agents
• https://github.com/ngiger/oddb.org/commit/e416733f67d9d73283680337c334c5b0d0f8daa5 Reorgized active/inactive-agents. Added automatic cleanup of variables
• https://github.com/ngiger/oddb.org/commit/8fb82c01732db67d31c944df043941e36805a3c3 Remove spagyric
• https://github.com/ngiger/oddb.org/commit/354fa73833c7aaa3342a2b4b9106dfbeff661b96 Fix test/test_model

Index

• Cleanup separation of active and inactive agents got fix wrong count of active agents
• Fix unit-tests (on travis-ci)

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.

Fix unit-tests (on travis-ci)

Waiting for travis-ci to go green after pushing the commits

• Remove some non-working unit test
• Install nodejs before running travis-CI. Fixes javascript
• Use container-based infrastructure of travis-ci

Cleanup separation of active and inactive agents got fix wrong count of active agents

Continuing work of yesterday. The cleanup function took 35 minutes to complete. But http://oddb-ci2.dyndns.org/de/gcc/show/reg/56091/seq/01/pack/004 still does not display inactive agents. Why? Had to add in view/admin/sequence.rb a class InactiveAgents, too. This fixed the problem.

Added visits to edit|show registration|sequence|package to spec/smoketest_spec.rb.

Reworked cleanup proc to produce more readable sorted feedback of registration worked on. Dropping and rereading thinpower db-dump.

Adapting plugin/swissmedic. Must test it, too. Running the unit test was a clever idea, as it made appear a few errors in the code. Also text_info_swissmedicinfo shows even more failures.

After running the cleanup method in oddbapp the oddbd becomes unresponsive. Adding a odba_store and retrying in fresh copy of the database. Remarked that when running the update script and accessing http://oddb-ci2.dyndns.org/de/gcc/show/reg/00278/seq/01 I got DBI::ProgrammingError connection not open

Okay. I think it is better to run cleanup_old_active_agent before accessing a composition in view/admin/sequence.rb. This take not long an will silently upgrade with the time the whole database. Fixed the unit-tests. Threw away a few tests where I don't see much value. Used stub/oddbapp for testing some plugins, because it is much easier to deal with creation of registrations, sequences, etc than mocking all these methods.

But the spec tests simply hang. It looks as if creating the inactive_agents on the fly breaks other stuff. Also accessing http://oddb-ci2.dyndns.org/de/gcc/show/reg/56091 suddenly hangs.

Dropping and reloading again thinpower's database. Did not help. Modifiying code to avoid calling odba_store via Apache and doing cleanup via bin/admin.

Moving odba_store from compositions -> oddbapp made the update finish in less than 10 minutes. During this time we already could access the newly written inactive_agents. Also the parallel running spec tests had lot of failures (why?) but did not timeout completely. Therefore I think it is safe now to push the 7 outstanding commits. (see above).