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20160118-price-search-without-interaction

Summary

  • price and combined search should not consider interaction section of FI
  • oddb.org did hang at 04:27 AM
  • sort order does not match expectations for evidentia
  • migel: jobs/update_migel_products_with_report no longer works
  • evidentia: Change FI chapter to "Präklinische Daten"
  • fachinfos not present in ODDB.org (e.g. 00675 "Pro-Symbioflor")

Commits

Index

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)

price and combined search should not consider interaction section of FI

Example is Gentamycin, which is found only in interaction sections of Fachinfo. Added watir tests for these two examples. Fixing the issue was easy. Tests pass. Now running the whole watir test suite before pushing commit https://github.com/ngiger/oddb.org/commit/a39698732794652b2947fe6dbadad0b90b9142c2 Don't consider interaction in price search

sort order does not match expectations for evidentia

When entering Cordarone we find first "Cordarone Amiodaroni Hydrochloridum Injektionslösung" before "Cordarone Amiodaroni Hydrochloridum Tabletten". Evidentia would like to have it differently. Adding debugging info for evidentia. Another example is Avalox. Problem occurs when we have several medicaments with the same trademark time and one is original and the other one a generics (even if they come both from the same company!). This case is not covered by any unit test at the moment. Fix was easy.

Pushed commmit Fix sort order of orginal for evidentia

oddb.org did hang at 04:27 AM

Found many entries in the error log. looks like it startet like this

log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: Mon Jan 18 04:27:02 +0100 2016 - 70092467200720 - DRb::DRbConnError - druby://localhost:10001 - #<Errno::ECONNREFUSED: Connection refused - connect(2)>
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:736:in `open'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:729:in `each'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:729:in `open'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1189:in `initialize'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1169:in `new'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1169:in `open'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1085:in `method_missing'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1103:in `with_friend'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/drb/drb.rb:1084:in `method_missing'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/site_ruby/1.8/cgi/drbsession.rb:20:in `initialize'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/cgi/session.rb:273:in `new'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/cgi/session.rb:273:in `initialize'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/site_ruby/1.8/sbsm/request.rb:88:in `new'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/site_ruby/1.8/sbsm/request.rb:88:in `drb_process'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/site_ruby/1.8/sbsm/request.rb:61:in `process'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /var/www/oddb.org/doc/index.rbx:21
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/apache/ruby-run.rb:53:in `load'
log/oddb/error_log:[Mon Jan 18 04:27:02 2016] [error] access to /de/gcc/rezept/ean/7680528970172 failed for (null), reason: /usr/lib64/ruby/1.8/apache/ruby-run.rb:53:in `handler'
log/oddb/error_log:[Mon Jan 18 04:27:05 2016] [error] access to /de/gcc/feedbacks/reg/65980/seq/01/pack/001 failed for (null), reason: Mon Jan 18 04:27:05 +0100 2016 - 70092467184460 - DRb::DRbConnError 

Looks like DRB service on port 10001 SERVER_URI_FOR_CRAWLER in the log /service/ch.oddb-crawler/log/main/current we find

@40000000569c88410e9f7a14 Attention: monkey-patching CSV::Cell
@40000000569c88410e9f7dfc could not find htmlgrid.so, falling back to pure-ruby class
@40000000569c88410e9f81e4 process: Oddb (OddbApp:Crawler)
@40000000569c88410e9f81e4 init system
@40000000569c88410e9f85cc init system: 10.118303521
@40000000569c88410e9f85cc setup drb-delegation
@40000000569c88410e9f85cc reset
@40000000569c88410e9f85cc reset: 10.118456945
@40000000569c88410e9f85cc system initialized
@40000000569c88410e9f89b4 initialized: 10.118519694
@40000000569c88410e9fb0c4 explain_colors {[0, 0]=>:explain_original, [0, 1]=>:explain_generic, [0, 2]=>"explain_unknown"}
@40000000569c9f9a1b46b82c explain_colors {[0, 0]=>:explain_original, [0, 1]=>:explain_generic, [0, 2]=>"explain_unknown"}
@40000000569c9f9a1b46c3e4 explain_colors {[0, 0]=>:explain_original, [0, 1]=>:explain_generic, [0, 2]=>"explain_unknown"}
@40000000569c9f9a1b46c3e4 explain_colors {[0, 0]=>:explain_original, [0, 1]=>:explain_generic, [0, 2]=>"explain_unknown"}
@40000000569c9f9a1b46c7cc error in SBSM::Session#process: /en/oekk/print/fachinfo/25144
@40000000569c9f9a1b46c7cc NoMethodError
@40000000569c9f9a1b46cbb4 undefined method `package' for #<OddbPrevalence:0x00000005c0bbd8>
@40000000569c9f9a1b4719d4 /var/www/oddb.org/src/util/oddbapp.rb:952:in `search_oddb'
@40000000569c9f9a1b4719d4 /var/www/oddb.org/src/util/session.rb:198:in `search_oddb'
@40000000569c9f9a1b4719d4 /var/www/oddb.org/src/state/global.rb:890:in `_search_drugs'
@40000000569c9f9a1b471dbc /var/www/oddb.org/src/state/global.rb:909:in `_search_drugs_state'
@40000000569c9f9a1b471dbc /var/www/oddb.org/src/state/global.rb:862:in `search'
@40000000569ca02a265dd894 error in SBSM::Session#process: /de/gcc/search/zone/drugs/search_query/2588492/search_type/st_oddb
@40000000569ca02a265de064 NoMethodError
@40000000569ca02a265de44c undefined method `package' for #<OddbPrevalence:0x00000005c0bbd8>
@40000000569ca02a265de44c /var/www/oddb.org/src/util/oddbapp.rb:952:in `search_oddb'
@40000000569ca02a265de834 /var/www/oddb.org/src/util/session.rb:198:in `search_oddb'
@40000000569ca02a265de834 /var/www/oddb.org/src/state/global.rb:890:in `_search_drugs'
@40000000569ca02a265e326c /var/www/oddb.org/src/state/global.rb:909:in `_search_drugs_state'
@40000000569ca02a265e326c /var/www/oddb.org/src/state/global.rb:862:in `search'
@40000000569ca0471f09f9ec error in SBSM::Session#process: /de/gcc/search/zone/drugs/search_query/2588492
@40000000569ca0471f0a05a4 NoMethodError
@40000000569ca0471f0a05a4 undefined method `package' for #<OddbPrevalence:0x00000005c0bbd8>
@40000000569ca0471f0a098c /var/www/oddb.org/src/util/oddbapp.rb:952:in `search_oddb'
@40000000569ca0471f0a098c /var/www/oddb.org/src/util/session.rb:198:in `search_oddb'
@40000000569ca0471f0a0d74 /var/www/oddb.org/src/state/global.rb:890:in `_search_drugs'
@40000000569ca0471f0a0d74 /var/www/oddb.org/src/state/global.rb:909:in `_search_drugs_state'
@40000000569ca0471f0a57ac /var/www/oddb.org/src/state/global.rb:862:in `search'

We should probably have a look at all the errors in the log and fix these problems. In this case we try to search by pharmacode, which in any case is no longer supported.

Looks like in my commit Remove pharmacode from bsv-import form 21 Oct 2015 I removed the method package in src/util/oddbapp.rb without removing its use search_oddb. Should we still offer the search pharmacode?

Yes. We should. Adapting the test

Just stumbled over the case that IKSNR 00675 Pro-Symbioflor® has a fachinfo in swissmedicinfo.ch but not on ch.oddb.org.

 
ch.oddb> registration('00675').fachinfo.class
-> NilClass
ch.oddb> registration('00675').name_base
-> Pro-Symbioflor

Also found that the definition of the method active_sequences in src/util/oddbapp.rb is not returning the expected result. There are cases like IKSNR 60811 Keragraf, which have an active registration, but no package attached. Modifying the method and calling jobs/rebuild_indices unwanted_effects_index_de to see whether this fixes the problem with Fortex, which should not return any drugs.

The index about unwanted_effects seems to be wrong, as I could not find any occurrence of Fortex in the sequences given back. I think this might be related to an error in the used dictionary.

Pushed commit Reactivate search by pharmacode

migel: jobs/update_migel_products_with_report no longer works

Looking for minimal invasive way to make it work after rename Migel -> SwissIndex in oddb.org. This should be fixed withRenamed SwissindexNonPharma -> SwissindexMigel. Looking whether it works on thinpower. Had to restart the swissindex servicies.

"evidentia: Change FI chapter to "Präklinische Daten"

Fixed with commit Fix Präklinische Daten for evidentia

fachinfos not present in ODDB.org (e.g. 00675 "Pro-Symbioflor")

Why is this FI not present? Looking in my logs I find

ywesee@thinpower /var/www/oddb.org $ grep 00675 log/oddb/debug/2016/01.log 
7680006750012: http://ch.oddb.org/de/gcc/drug/reg/00675/seq/01/pack/001
2016-01-12 11:19:09 +0100: deactivate_not_found_package check "00675". 0 @deletes_packages
7680006750012: http://ch.oddb.org/de/gcc/drug/reg/00675/seq/01/pack/001
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