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Got the following error:
Plugin: ODDB::SwissindexPharmaPlugin Error: NoMethodError Message: undefined method `each' for nil:NilClass Backtrace: (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:396:in `check_item' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' (druby://thinpower:37072) /var/www/oddb.org/src/plugin/swissindex.rb:103:in `block (2 levels) in update_package_trade_status' (druby://thinpower:37072) /var/www/oddb.org/src/model/sequence.rb:175:in `each' (druby://thinpower:37072) /var/www/oddb.org/src/model/sequence.rb:175:in `each_package' (druby://thinpower:37072) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://thinpower:37072) /var/www/oddb.org/src/model/registration.rb:149:in `block in each_package' (druby://thinpower:37072) /var/www/oddb.org/src/model/registration.rb:148:in `each_value' (druby://thinpower:37072) /var/www/oddb.org/src/model/registration.rb:148:in `each_package' (druby://thinpower:37072) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://thinpower:37072) /var/www/oddb.org/src/util/oddbapp.rb:635:in `block in each_package' (druby://thinpower:37072) /var/www/oddb.org/src/util/oddbapp.rb:634:in `each_value' (druby://thinpower:37072) /var/www/oddb.org/src/util/oddbapp.rb:634:in `each_package' (druby://thinpower:37072) /var/www/oddb.org/src/plugin/swissindex.rb:90:in `block in update_package_trade_status' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `call' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://thinpower:37072) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/invokemethod.rb:10:in `block_yield' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/invokemethod.rb:17:in `block in perform_with_block' (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:14:in `session' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/invokemethod.rb:14:in `perform_with_block' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1506:in `perform' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:50001) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/swissindex.rb:88:in `update_package_trade_status' /var/www/oddb.org/src/util/updater.rb:512:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:423:in `update_package_trade_status_by_swissindex' jobs/update_swissindex_pharma:16:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' jobs/update_swissindex_pharma:13:in `<module:Util>' jobs/update_swissindex_pharma:11:in `<module:ODDB>' jobs/update_swissindex_pharma:10:in `<main>'
Running update_swissindex_pharma on my VM to see whether I can reproduce the behaviour here.
Got the following error while running
Plugin: ODDB::SwissindexPharmaPlugin Error: NoMethodError Message: undefined method `configure' for Savon:Module Backtrace: (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:34:in `initialize' (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:14:in `new' (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:14:in `session' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/invokemethod.rb:14:in `perform_with_block' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1506:in `perform' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/swissindex.rb:88:in `update_package_trade_status' /var/www/oddb.org/src/util/updater.rb:512:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:423:in `update_package_trade_status_by_swissindex' /var/www/oddb.org/jobs/update_swissindex_pharma:16:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' /var/www/oddb.org/jobs/update_swissindex_pharma:13:in `<module:Util>' /var/www/oddb.org/jobs/update_swissindex_pharma:11:in `<module:ODDB>' /var/www/oddb.org/jobs/update_swissindex_pharma:10:in `<main>'
On thinpower I found
On my VM I found
Replacing Savon 2.1.0 by 0.9.7 by changing the Gemfile and running "sudo bundle update". Restarted all oddb services. Then running import again. Now I get the following error
Plugin: ODDB::SwissindexPharmaPlugin Error: DRb::DRbConnError Message: druby://oddb.niklaus.org:60667 - #<Errno::ETIMEDOUT: Connection timed out - connect(2)> Backtrace: (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:736:in `rescue in block in open' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:730:in `block in open' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:729:in `each' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:729:in `open' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1191:in `initialize' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1171:in `new' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1171:in `open' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1087:in `block in method_missing' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1105:in `with_friend' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1086:in `method_missing' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/invokemethod.rb:10:in `block_yield' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/invokemethod.rb:17:in `block in perform_with_block' (druby://localhost:50001) /var/www/oddb.org/ext/swissindex/src/swissindex.rb:14:in `session' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/invokemethod.rb:14:in `perform_with_block' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1506:in `perform' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:50001) /usr/lib64/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/swissindex.rb:88:in `update_package_trade_status' /var/www/oddb.org/src/util/updater.rb:512:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:423:in `update_package_trade_status_by_swissindex' /var/www/oddb.org/jobs/update_swissindex_pharma:16:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' /var/www/oddb.org/jobs/update_swissindex_pharma:13:in `<module:Util>' /var/www/oddb.org/jobs/update_swissindex_pharma:11:in `<module:ODDB>' /var/www/oddb.org/jobs/update_swissindex_pharma:10:in `<main>'
Corrected host host/ip in /etc/hosts and rerunning import. The import did run without problems. See Attach:swissindex.txt
Will drop the PG-DB and import yesterday's import. After running the import I still don't get an error. Weird!
Installed via rvm (as user root into /usr/local/rvm) ruby-1.9.3.p0. To run it I set (logged in as root) the PATH to include /usr/local/rvm/bin and then sudo -u apache /usr/local/rvm/rubies/ruby-1.9.3-p0/bin/ruby /var/www/oddb.org/jobs/update_swissindex_pharma. But no I get errors because my RVM installation does not have the ruby patches applies (csv, columninfo, etc). Applying the patches from /usr/local/share/*.patch manually. Now the job begins to run. Completed again without any error! Don't know how to provoke it.
Got the following error:
Error: ArgumentError Message: invalid byte sequence in US-ASCII Backtrace: (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/csv.rb:2071:in `=~' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/csv.rb:2071:in `init_separators' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/csv.rb:1603:in `initialize' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/csv.rb:1362:in `new' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/csv.rb:1362:in `open' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/csv_exporter.rb:98:in `dump' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:105:in `block (2 levels) in export_doc_csv' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:103:in `each' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:103:in `block in export_doc_csv' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:286:in `call' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:286:in `block in safe_export' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/tempfile.rb:316:in `open' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:285:in `safe_export' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:99:in `export_doc_csv' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/csv_export.rb:25:in `export_doctors' /var/www/oddb.org/src/util/exporter.rb:104:in `block in export_doc_csv' /var/www/oddb.org/src/util/exporter.rb:435:in `call' /var/www/oddb.org/src/util/exporter.rb:435:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:102:in `export_doc_csv' /var/www/oddb.org/src/util/exporter.rb:58:in `run' /var/www/oddb.org/jobs/export_daily:13:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' /var/www/oddb.org/jobs/export_daily:12:in `<module:Util>' /var/www/oddb.org/jobs/export_daily:11:in `<module:ODDB>' /var/www/oddb.org/jobs/export_daily:10:in `<main>'
Removed 'mock' in favor of 'flexmock'. See commit Removed mock in favor of flexmock
There were quite few problems because we used test-unit instead of test/unit. Also we have to exclude 5 test files as they create problems, most of them use 'util/session'. See commit Use test/unit instead of test-unit. Skip some problematic files
Now calling ruby test/suite.rb gives a result like
2699 tests, 3977 assertions, 169 failures, 336 errors, 0 pendings, 0 omissions, 17 notifications 83.8829% passed 32.87 tests/s, 48.43 assertions/s Coverage report generated for Unit Tests to /opt/src/oddb.org/coverage. 22482 / 33886 LOC (66.35%) covered.
The skipped files show up in the log as
Skipping rwv2 dependent tests. Obsolete!! Skipping bsv_xml csv_export Skipping file bsv_xml.rb Skipping file csv_export.rb skipping ipn oddbapp session updater Skipping file ipn.rb Skipping file oddbapp.rb Skipping file session.rb Skipping file updater.rb
Reworked test/suite.rb to generate correct overall coverage info and a status and the end. Manuall grepping the log shows that we still have some errors and failures.
239 tests, 593 assertions, 17 failures, 21 errors, 0 pendings, 0 omissions, 0 notifications 796 tests, 816 assertions, 54 failures, 83 errors, 0 skips 271 tests, 299 assertions, 33 failures, 23 errors, 1 skips 3 tests, 3 assertions, 0 failures, 0 errors, 0 skips 6 tests, 6 assertions, 1 failures, 0 errors, 0 skips 43 tests, 43 assertions, 10 failures, 0 errors, 0 skips 446 tests, 658 assertions, 14 failures, 72 errors, 0 skips 661 tests, 1380 assertions, 22 failures, 1 errors, 0 skips 312 tests, 457 assertions, 17 failures, 6 errors, 0 skips
But it is important, that we run each test/suite.rb independent of each other as running them all in one run induces errors, which are not present when run individually! E.g I want to be sure that "grep ^Error: suite.log | grep galenic" does not return anything.
Corrections made with these commits: