Looking whether _search_exact_classified_result works for chapter interaction. Testing via bin/admin
$seqs = [registration('60106').sequence('01')]; $res = _search_exact_classified_result($seqs, :substance); $res.atc_classes
-> [Clopidogrel]
# Testing index of substance
ch.oddb> retrieve_from_index('substance_index_sequence', 'Clopidogrel').first
-> Clopidogrel Medis 75 mg, Filmtabletten, Filmtabletten
ch.oddb> retrieve_from_index('substance_index_sequence', 'Clopidogrel').first.iksnr
-> 60108
ch.oddb> retrieve_from_index('substance_index_sequence', 'Clopidogrel').first.seqnr
-> 01
We expect the following behaviour.
Currently it returns the old search result (e.g. keppra). I suspect that yesterday commit "Replace in all URL swissmedicnr by reg" broke it. Added a watir test to catch this situation. Reverted oddb-ci2 to commit before the suspected and running watir-test again.
Watir-test still fails, but with a weird result. It went to http://oddb-ci2.dyndns.org/de/gcc/search/zone/drugs/search_query/Xadago/search_type/st_oddb?#best_result and displayed the help text for the category. But when entering a second time Xadago the URL switched to http://oddb-ci2.dyndns.org/de/gcc/search/zone/drugs/search_query/Xadago/search_type/st_oddb?#best_result but displayed still the Keppra result. Therefore it was not yesterdays commit which broke the expected behaviour. Therefore I will try to fix the problem with the current code base.
However the interaction search seems to be broken, eg. trying viagra, aspirin all emit in the log of ch.oddb
KeyError key not found: "interactions_index_de" /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:457:in `fetch' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:457:in `retrieve_from_index' /var/www/oddb.org/src/util/oddbapp.rb:109:in `retrieve_from_index' /var/www/oddb.org/src/util/oddbapp.rb:1055:in `search_by_interaction' /var/www/oddb.org/src/state/global.rb:882:in `_search_drugs'
Calling in bin/admin ch.oddb> search_by_interaction('Warfarin', 'de') returns key not found: "interactions_index_de", which is not handled by the caller.
Calling jobs/rebuild_indices interactions_index_de interactions_index_fr to see whether this fixes the problem. After restarting bin/oddbd I got a valid result for earch_by_interaction('Warfarin', 'de') namelx #<ODDB::SearchResult:0x00000001e7a788>.
I always get an empty result for search_by_interaction('Viagra', 'de').empty? on oddb_ci2 when searching for 'Asiprin', 'Warfarin' or 'Herzinsuffizienz'. But the oddb log shows HINWEIS: Textsucheanfrage enthält nur Stoppwörter oder enthält keine Lexeme, ignoriert. This is an old problem, that somehow the postgreSQL is not correctly configured on oddb-ci2. See also blog of April 3, 2014, looking at hint. Copied 3 files for each language, like this sudo cp /var/www/oddb.org/ext/fulltext/data/dicts/french/fulltext.stop /usr/share/postgresql/tsearch_data/french_fulltext.stop and ran generate_dictionaries in bin/admin. Now the problem went away.
I propose to rebuild the interactions_index_de, restart ch.oddb (to be sure that we don't have tomorrow at 2 AM the same problem as today) and see whether the indices work correctly or not.
As the index returns now correctly a (emtpy) ODDB::SearchResult when calling search_by_interaction('Xadago', 'de'), it will also again show a correct empty result and the new watir tests passes, too. Pushed commits Return an empty result, if index is not present and Test for return an empty result, if index is not present. Waiting for import_daily to finish before pulling to thinpower.
I still have the problem, that the interaction index does not return valid items. What is the expected result. I think when selecting "Interaktion" as searchtype and entering Herzinfarkt we should get results, as this is a common problem. Are there other terms we should verify? Herzinfarkt should show Clopidogrel (IKSNR 60106).
Tried looking for Herzinfarkt via Anwendung and found only few products, eg. 48313, where there Herzinfarkt is in the chapter Kontraindikationen!
Found 2416 occurrences of Warfarin via grep -ci warfarin AipsDownload_20151201.xml. Therefore it does not surprise me, that the number of interaction could be higher than the limit of 250. Searchin for drugs is not limited to this limit.
Trying to create a bin/admin expression on thinpower to override this limit.
ch.oddb> $r= search_by_interaction('Aspirin', 'de')
-> #<ODDB::SearchResult:0x0000000e763230>
ch.oddb> $r.empty?
-> false
ch.oddb> $r.atc_classes.size
-> 38
ch.oddb> $r.package_count
-> 147
$drug_name = 'Aspirin'
$r = ODDB::SearchResult.new; $r.exact = true; $r.search_query = $drug_name; $r.search_type = :atc; $r.error_limit = 2500; $seqs = retrieve_from_index("interactions_index_de", $drug_name , $r)
ch.oddb> $seqs.size
-> 136
ch.oddb> $seqs.first
-> Vimovo, Filmtabletten
ch.oddb> $seqs = retrieve_from_index("interactions_index_de", 'Warfarin')
-> Array
ch.oddb> $seqs.size
-> 2567
ch.oddb> $seqs.first
-> Caduet 10/10, Filmtabletten
ch.oddb> $seqs.first.iksnr
-> 57633
Pushed commit Must add test/stub/odba, too to fix unit-tests on travis-CI.
Must fix the problem on thinpower
src/util/language.rb:53:in `method_missing': undefined method `update' for #<ODDB::LimitationText:0x000000062713b0> @40000000565e975408c6e8fc /var/www/oddb.org/src/util/language.rb:53:in `method_missing': undefined method `update' for #<ODDB::LimitationText:0x000000062713b0> (NoMethodError) @40000000565e975408caf80c from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' @40000000565e975408cafbf4 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:590:in `block in update_indices' @40000000565e975408cafbf4 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:589:in `each' @40000000565e975408caffdc from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:589:in `update_indices' @40000000565e975408caffdc from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:515:in `store' @40000000565e975408cb0b94 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:274:in `odba_isolated_store' @40000000565e975408cb0b94 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:395:in `block in odba_store_unsaved' @40000000565e975408cb9834 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `each' @40000000565e975408cb9834 from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `odba_store_unsaved' @40000000565e975408cb9c1c from /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:380:in `odba_store' @40000000565e975408cb9c1c from /var/www/oddb.org/src/util/oddbapp.rb:1532:in `initialize' @40000000565e975408cba004 from bin/oddbd:46:in `new' @40000000565e975408cba7d4 from bin/oddbd:46:in `<main>'
Added my most hackiest and ugliest patch ever with line 46 or src/util/languag return if language.eql?('update') && !self.respond_to?(:update).
Loading yesterdays dump to hope being able to reproduce the problem locally. Afterwards must look via bin/admin. The following procedures might be a starting point count_limitation_texts and multilinguify_analysis.
Could reproduce the problem here. Adding more debug output and I already catched a culprit.
Descriptions.method_missing symbol update language "update" update? false: 01.04.10.: Einfache Sedativa/Tranquillantia Gesamthaft zugelassen 120 Punkte. Iniectabilia sine limitatione
Why do we suddenly have this problem? I think I might have make a mistaken when in end of october I removed the pharmacode from bsv-import. Analysing the commit 990ef52a9187bd7b21694367f2588a3c409ee91c again.
Looking at the results for first of decembre I find the report
ch.ODDB.org Report - SL-Update (XML) - 12/2015 Created SL-Entries 39 Updated SL-Entries 9295 Deleted SL-Entries 50 Created Limitation-Texts 29 Updated Limitation-Texts 1882 Deleted Limitation-Texts 0
Looking also at the import of first of november
ch.ODDB.org Report - SL-Update (XML) - 11/2015 Created SL-Entries 127 Updated SL-Entries 9221 Deleted SL-Entries 71 Created Limitation-Texts 17 Updated Limitation-Texts 1865 Deleted Limitation-Texts 0
In both months I updated Limitation text. What changed in between or did the data change? Compared ./oddb_limitation.xml of yesterday oddb2xml with the one from november 25 and found only expected differences. Using bin/admin packages.find{|x| x.limitation && x.limitation_text && /Einfache Sedativa\/Tranquillantia/.match(x.limitation_text.to_s)} to get insight. Found 72 entries.
Did not find 'Einfache Sedativa/Tranquillantia' which causes the problem in oddb2xml/oddb_limitation.xml. The code "01.04.10" however is found many times. The first result belongs to ["48285", "01", "031"] Tranxilium Tabs 20mg.
The limitationtext with oid 34323858 causes the problem and belongs to 32497/01/012 Seresta, Tabletten. Using registration('32497').sequence('01').package('012').delete_sl_entry in bin/admin made the limitation_text disappear from the package, but the startup problem remains.
If I try to call ch.oddb> delete registration('32497').sequence('02').package('047').sl_entry.limitation_text.pointer@2 in bin/admin I get undefined method `delete' for #<ODDB::LimitationText:0x00000006a3e9f8>@@
Deleting it directly in the cache works via bin/admin ODBA.cache.delete(ODBA.cache.fetch(34323858)). This deletes the limitation_text in the database, but not the sl_entry and oddbd restarts now without problem. Doing the same on thinpower. This worked, but as expected the limitation_text is no longer present on http://ch.oddb.org/de/gcc/show/reg/32497/seq/01/pack/012