Got the following epha-import message on oddb-ci2 and thinpower
EphaInteractionPlugin.update latest /var/www/oddb.org/data/csv/interactions_de_utf8-latest.csv true via /var/www/oddb.org/data/csv/interactions_de_utf8.csv from https://download.epha.ch/data/matrix/matrix.csv Added 20002 interactions from /var/www/oddb.org/data/csv/interactions_de_utf8-latest.csv
Does the epha-interaction import report a wrong size or does it really reimport everything twice? On thinpower bin/admin reports
bin/admin ch.oddb> epha_interactions.size -> 0 ch.oddb> epha_interactions_hash.size -> 10001 ch.oddb> ch.oddb> epha_interactions_hash.first -> [#<ODBA::Stub:138337120#33357824 @odba_class=Array @odba_container=133393900#33345444>, #<ODBA::Stub:138336780#33347814 @odba_class=ODDB::EphaInteraction @odba_container=133393900#33345444>] ch.oddb> epha_interactions_hash.first[0] -> ["J05AE03", "P01BB51"] ch.oddb> epha_interactions_hash.first[1] -> J05AE03;Ritonavir;P01BB51;Proguanil, Kombinationen;Reduzierte Atovaquon/Proguanil-Konzentrationen;Ritonavir induziert CYP2C19 und kann damit zu einem verstärkten Abbau von Proguanil zu Cycloguanil (e ch.oddb>
Therefore it looks as if the import left a correct database.
On oddb-ci2 I found the following runtime error
Defaulting to UTF-8, set your own if this is incorrect. D, [2015-03-11T10:34:40.073913 #27628] DEBUG -- : HTTPI executes HTTP GET using the httpclient adapter /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:589: [BUG] Segmentation fault ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux] -- Control frame information ----------------------------------------------- c:0024 p:0055 s:0083 b:0081 l:000067 d:000080 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:589 c:0023 p:---- s:0077 b:0077 l:000076 d:000076 FINISH c:0022 p:---- s:0075 b:0075 l:000070 d:000074 IFUNC c:0021 p:---- s:0073 b:0073 l:000072 d:000072 CFUNC :each c:0020 p:---- s:0071 b:0071 l:000070 d:000070 CFUNC :any? c:0019 p:0040 s:0068 b:0068 l:000067 d:000067 METHOD /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:587 c:0018 p:0051 s:0064 b:0064 l:000063 d:000063 METHOD /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:37 c:0017 p:0051 s:0057 b:0057 l:000046 d:000056 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:99 c:0016 p:---- s:0052 b:0052 l:000051 d:000051 FINISH c:0015 p:---- s:0050 b:0050 l:000049 d:000049 CFUNC :delete_if c:0014 p:0073 s:0047 b:0047 l:000046 d:000046 METHOD /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:96 c:0013 p:0049 s:0042 b:0042 l:000028 d:000041 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:105 c:0012 p:---- s:0039 b:0039 l:000038 d:000038 FINISH c:0011 p:---- s:0037 b:0037 l:000036 d:000036 CFUNC :each_value c:0010 p:0011 s:0034 b:0034 l:000028 d:000033 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:102 c:0009 p:0019 s:0032 b:0032 l:000031 d:000031 METHOD <internal:prelude>:10 c:0008 p:0050 s:0029 b:0029 l:000028 d:000028 METHOD /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:101 c:0007 p:0139 s:0021 b:0021 l:000020 d:000020 METHOD /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:81 c:0006 p:0030 s:0014 b:0014 l:000b38 d:000013 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:490 c:0005 p:---- s:0011 b:0011 l:000010 d:000010 FINISH c:0004 p:---- s:0009 b:0009 l:000008 d:000008 CFUNC :loop c:0003 p:0040 s:0006 b:0006 l:000b38 d:000005 BLOCK /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:487 c:0002 p:---- s:0004 b:0004 l:000003 d:000003 FINISH c:0001 p:---- s:0002 b:0002 l:000001 d:000001 TOP -- Ruby level backtrace information ---------------------------------------- /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:487:in `block in start_cleaner' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:487:in `loop' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:490:in `block (2 levels) in start_cleaner' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:81:in `clean' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:101:in `_clean' <internal:prelude>:10:in `synchronize' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:102:in `block in _clean' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:102:in `each_value' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:105:in `block (2 levels) in _clean' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:96:in `odba_retire' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:96:in `delete_if' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:99:in `block in odba_retire' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache_entry.rb:37:in `object_id2ref' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:587:in `odba_unsaved?' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:587:in `any?' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:587:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:589:in `block in odba_unsaved?' -- C level backtrace information ------------------------------------------- Oddb (OddbApp)() [0x5216d8] Oddb (OddbApp)() [0x5694c9] Oddb (OddbApp)(rb_bug+0xb4) [0x56a6e4] Oddb (OddbApp)() [0x4b4e12] /lib64/libpthread.so.0(+0x113d0) [0x7f4fb15193d0] Oddb (OddbApp)(st_lookup+0xe) [0x4bce7e] Oddb (OddbApp)() [0x50f12f] Oddb (OddbApp)() [0x517a90] Oddb (OddbApp)() [0x518333] Oddb (OddbApp)(rb_yield_values2+0x34) [0x51e754] Oddb (OddbApp)() [0x562dde] Oddb (OddbApp)() [0x51061e] Oddb (OddbApp)(rb_yield+0x47) [0x51e7a7] Oddb (OddbApp)() [0x426577] Oddb (OddbApp)() [0x426022] Oddb (OddbApp)(st_foreach+0xbc) [0x4bdfec] Oddb (OddbApp)() [0x426968] Oddb (OddbApp)(rb_ensure+0xab) [0x41b14b] Oddb (OddbApp)() [0x428c77] Oddb (OddbApp)() [0x519637] Oddb (OddbApp)() [0x51cb40] Oddb (OddbApp)(rb_block_call+0x24) [0x51cce4] Oddb (OddbApp)() [0x56241d] Oddb (OddbApp)() [0x51dd51] Oddb (OddbApp)() [0x511f3b] Oddb (OddbApp)() [0x518333] Oddb (OddbApp)(rb_yield_values+0xda) [0x51e8ba] Oddb (OddbApp)() [0x4265ac] Oddb (OddbApp)() [0x426022] Oddb (OddbApp)(st_foreach+0xbc) [0x4bdfec] Oddb (OddbApp)() [0x426968] Oddb (OddbApp)(rb_ensure+0xab) [0x41b14b] Oddb (OddbApp)(rb_hash_delete_if+0x4b) [0x428f8b] Oddb (OddbApp)() [0x51dd51] Oddb (OddbApp)() [0x511f3b] Oddb (OddbApp)() [0x518333] Oddb (OddbApp)(rb_yield+0x47) [0x51e7a7] Oddb (OddbApp)() [0x425d02] Oddb (OddbApp)() [0x426022] Oddb (OddbApp)(st_foreach+0xbc) [0x4bdfec] Oddb (OddbApp)() [0x426968] Oddb (OddbApp)(rb_ensure+0xab) [0x41b14b] Oddb (OddbApp)() [0x428d77] Oddb (OddbApp)() [0x51dd51] Oddb (OddbApp)() [0x511f3b] Oddb (OddbApp)() [0x518333] Oddb (OddbApp)() [0x51e5e4] Oddb (OddbApp)(rb_rescue2+0x163) [0x41ae03] Oddb (OddbApp)() [0x50da29] Oddb (OddbApp)() [0x51dd51] Oddb (OddbApp)() [0x511f3b] Oddb (OddbApp)() [0x518333] Oddb (OddbApp)() [0x5192c1] Oddb (OddbApp)() [0x52777e] Oddb (OddbApp)() [0x5278c9] /lib64/libpthread.so.0(+0x91a7) [0x7f4fb15111a7] /lib64/libc.so.6(clone+0x6d) [0x7f4fb090920d] -- Other runtime information ----------------------------------------------- <..>
In oddbapp.rb replaced in method delete_all_epha_interactions odba_isolated_store by odba_store and added some more debug info in the import. Still the same problem!
Zeno also remarked that we should fulfill the following requirements
We decided to implement (for epha_interactions) a utility procedure get_latest_file (there are already 5 procedure with the same name), namely
This utility prodedure should be used later on for all occurences, see above. Found nr of occurrences of latest in the following files
src/plugin/analysis.rb:9 src/plugin/atc_less.rb:2 src/plugin/bsv_xml.rb:11 src/plugin/epha_interactions.rb:7 src/plugin/medreg_doctor.rb:12 src/plugin/medreg_pharmacy.rb:15 src/plugin/ouwerkerk.rb:2 src/plugin/swissmedic.rb:33 src/plugin/swissmedicjournal.rb:3 src/plugin/swissreg.rb:1 src/plugin/text_info.rb:8 src/plugin/vaccines.rb:10
Running the import skips now sending a message, when nothing is todo. Forcing an import by removing all concerned csv files (data/csv/interactions_de_utf8-2015.03.13.csv and data/csv/interactions_de_utf8-latest.csv).
Pushed commit Fix latest in epha_interactions.rb. Fix Reporting.
Must resolve the problem on how to avoid adding the the last part, eg. aqua ad 100 ml or Excipiens Ad Emulsionem Pro as a separate component. Also my local version mangles names like Globulina Equina (immunisé Avec Coeur, Tissu Pulmonaire, Reins De Porcins) to Reins De Porcins). Handling colors like "E 127" or conserv.: E 216, E 218 is also wrong. Current diff is Attach:oddb_xml_components.txt.
Pushed the commits