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Results of nightly run
Searched for Stored 855 Fachinfos Ignored 0 Pseudo-Fachinfos Ignored 0 up-to-date Fachinfo-Texts Stored 0 Patinfos Ignored 0 up-to-date Patinfo-Texts Checked 0 companies Unknown Iks-Numbers: 8 Latanoprost Spirig HC® (63104) Montelukast Spirig HC® comprimés à mâcher (62799) Montelukast Spirig HC® comprimés pelliculés (62798) Azzalure (62780) LatanoTim-Vision® (12532) LatanoTim-Vision® (58212) Iscador® ampoules (solution injectable) (00000) Iscador® ampoules (solution injectable) (00539) Fachinfos without iksnrs: 0 Session failures: 0 Download errors: 0 Parse Errors: 1 ERROR: duplicate key value violates unique constraint "object_connection_pkey" New/Updates FI from swissmedicinfo.ch NEW : Fachinfo - DE - Midalgan® Balsam Neue Formel - 27.06.2013 - ["14095"] <...> CHANGE : Fachinfo - FR - Losartan Helvepharm 12,5 mg/50 mg/100 mg - 31.05.2013 - ["60234"] Skipped FI form swissmedicinfo.ch NEW : Fachinfo - DE - Enapril 5 / 10 / 20 mg - 29.03.2013 Invalid FI from swissmedicXML Not found FI in swissmedicXML
Job still running after 8 hours. At 0 AM got one email that 805 FI were imported correctly. Found the following problems where iksnr not found:
parse_and_update: calls parse_fachinfo, /var/www/oddb.org/data/html/fachinfo/de/Enapril 5 _ 10 _ 20 mg_swissmedicinfo.html, name Enapril 5 / 10 / 20 mg de title Enapril 5 / 10 / 20 mg, styles p{margin-top:0pt;margin-right:0pt;margin-bottom:0pt;margin-left:0pt;
get_iksnrs_from_string: Zulassungsnummer
55381 (Swissmedic).
parse_and_update: update_fachinfo name Enapril 5 / 10 / 20 mg returned []
Losartan Helvepharm (60234) display the FI correctly.
Did an strace of the still running process. Is in an eternal loop of sched_yield() = 0.
Probably busy waiting. Failed attaching via hijack (after sudo gem install hijack && sudo emerge gdb) got
sudo -u apache hijack 22486 => Hijacking.../usr/local/lib64/ruby/gems/1.9.1/gems/hijack-0.2.1/lib/hijack/gdb.rb:8: Use RbConfig instead of obsolete and deprecated Config. => WARNING: Did not detect a safe frame on which to set a breakpoint, hijack may fail.
grep ruby /var/log/messages returned
Jun 20 08:54:24 oddb kernel: [ 37.655528] ruby (3462): /proc/3462/oom_adj is deprecated, please use /proc/3462/oom_score_adj instead. Jun 26 17:08:30 oddb kernel: [ 49.981367] ruby (3649): /proc/3649/oom_adj is deprecated, please use /proc/3649/oom_score_adj instead. Jun 27 20:05:48 oddb kernel: [97088.223816] ruby (10341) used greatest stack depth: 3464 bytes left
To encrease the Ruby-Stack we could use ulimit. See this link. ulimit is already set to ulimit -v 10240000 in /var/lib/service/*/run. But when launched via the shell it is unlimited.
Reparsing only Enapril (55381) worked without a problem. The resulting FI looks reasonable.
Verified that also the italic with patinfo is resolved, eg de/gcc/patinfo/reg/32710/seq/01
I still get the error for some FI, eg. 32710, Ponstan.
NoMethodError undefined method `empty?' for nil:NilClass
I am not sure whether this affects exactly the medicaments where the title (given via the XML) matters or not.
Revert the code textinfo_hpricot.rb, but still got the same error.
Reverted to commit, reimported 32710, restarted oddb on the console and got
error in SBSM::Session#to_html: /de/gcc/fachinfo/reg/32710 NoMethodError undefined method `empty?' for nil:NilClass /var/www/oddb.org/src/model/fachinfo.rb:141:in `block (4 levels) in photos' <internal:prelude>:10:in `synchronize' /var/www/oddb.org/src/model/fachinfo.rb:138:in `block (3 levels) in photos' ODDB::View::Drugs::Fachinfo::COMPONENTS[[0, 3]] in create(content) error in SBSM::Session#http_headers: /de/gcc/fachinfo/reg/32710 NoMethodError undefined method `empty?' for nil:NilClass /var/www/oddb.org/src/model/fachinfo.rb:141:in `block (4 levels) in photos' <internal:prelude>:10:in `synchronize' /var/www/oddb.org/src/model/fachinfo.rb:138:in `block (3 levels) in photos' ODDB::View::Drugs::Fachinfo::COMPONENTS[[0, 3]] in create(content)
I will drop the database, reload from the current dump from thinpower and retry again.
/var/www/oddb.org/jobs/update_textinfo_swissmedicinfo --target=fi --no-download --reparse 58107 58106 78656 62111 62439 62223 62728 32917