20150831-sort-active-agents
Summary
- fix cleanup active agent
- Sort active agents
- Missing space after "Entspricht"
- Correct alignment
- Spaces between "Wirkstoff" and "Stärke"
Commits
- https://github.com/ngiger/oddb.org/commit/a6dcc7ac6f18a7b01ea25d203775c55e3f81e3dc Added jobs/update_active_agents
- https://github.com/ngiger/oddb.org/commit/c91d326feae4d3211c549b4410dc021becbb23fe Sort active and inactive agents
- https://github.com/ngiger/oddb.org/commit/af5b79d19879b4ff070432f1b3d1e755d9c493da Added space for new labels
- https://github.com/ngiger/oddb.org/commit/a825bd487670669ffd61109cafd17af298264a33 Don't display compositions without an active_agent
- https://github.com/ngiger/oddb.org/commit/4998c455ba73174fa4dfb7e9adfd92986b17048b Add some additional space before composition
Index
- Sort active agents
- fix cleanup active agent
- Missing space after "Entspricht"
- Correct alignment
- Correct vertical spaces for Moviprep
- 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 looking at moviprep, there is an erronous empty line after Excipiens ad Pulverem pro Charta (the corresp field is empty).
Also Zeno would like to have a bigger vertical space to separate the different compositions (e.g before "Beichnung B"). This was fixed by adding 6px with commit
Will continue tomorrow to have a look why htmlgrid does emit empty rows instead of nothing when a component is deleted.
Correct alignment
When looking at Numeta, we see that are 4 empty lines below "Zusammensetzung". See 
.
This must be corrected. Also Zeno would like to align everything on top. The easiest way to do this is by adding vertical-align : top; to the element td.list in all oddb.css. But is this okay for all lists we have in oddb.org? Waiting for Zeno's answer before pushing change. Currently the same search is now 
.
If we only omit the empty lines, but leave the css, it looks like this: 
Zeno wants this variant. Pushed commit Don't display compositions without an active_agent
Missing space after "Entspricht"
In Nutriflex there is not a separating space between "Entspricht" and "I)". Fixed with commit Added space for new labels
Sort active agents
Fixed with commit Sort active and inactive agents
fix cleanup active agent
What did I achieve yesterday? Running cleanup_active_agents_in_compositions does no more block access via oddbd/apache2. Results survive correctly a restart of oddbd. For me it looks as if the error stems either from a wrecked database or an err in odba/or dbd-pg gem. Tomorrow will add a parameter to cleanup_active_agents_in_compositions to be able to restart from a given IKSNR and finish the update of the database in smaller steps.
To avoid the threading issue I will move the code to a separate job, remove all the threading and mutex stuff and try again.
Things look better, error and success mail arrive. Dropping and reloading thinpowers database to verify proper operation. Job did sent mail less than 60 minutes after being started. log/job.pid is deleted but system.unpeer_cache ODBA.cache is still running 50 minutes later. The jobs is consume almost 100% of one cpu.
Writing backtrace via bin/admin File.open('threads.list', 'w+') { |f| Thread.list.each {|t| f.puts "Thread #{t}"; f.puts t.backtrace} }
Calling strace for the process in question via sudo strace -f -p 5910 yields ony
Process 5910 attached with 3 threads [pid 5963] restart_syscall(<... resuming interrupted call ...> <unfinished ...> [pid 5932] select(4, [3], NULL, NULL, NULL <unfinished ...> [pid 5910] sched_yield() = 0 [pid 5910] sched_yield() = 0 [pid 5910] sched_yield() = 0 [pid 5910] sched_yield() = 0 [pid 5910] sched_yield() = 0
Why does it not finish? Stuff like http://oddb-ci2.dyndns.org/de/gcc/show/reg/65826/seq/01 show correct active and inactive agents. Killed the process (-9 required) and restarted oddbd. Watir smoketest is okay.
Pushed commit Added jobs/update_active_agents