<< Masa.20110121-setup-ramaze | 2011 | Masa.20110119-update-rpdf2txt >>
suspend
The last failure
masa@masa ~/ywesee/rpdf2txt $ ruby1.9 -I lib test/test_pdf_parser.rb 1) Failure: test_join_snippets__hex_chars(TestParser) [test/test_pdf_parser.rb:337]: <"Paroxetin besitzt eine selektive Wirkung; in-vitro Studien haben gezeigt, dass es, im Gegensatz zu\ntrizyklischen Antidepressiva, eine geringe Affinit\xE4t f\xFCr a1-, a2- und b-Adrenozeptoren sowie f\xFCr\nDopamin (D2)-, 5-HT1-artige, 5-HT2 und Histamin (H1)-Rezeptoren aufweist. Das Fehlen einer\n"> expected but was <"Paroxetin besitzt eine selektive Wirkung; in-vitro Studien haben gezeigt, dass es, im Gegensatz zu\ntrizyklischen Antidepressiva, eine geringe Affinit\xE4t f\xFCr a1-, a2- und b-Adrenozeptoren sowie f\xFCr\nDopamin (D2)-, 5-HT1-artige, 5-HT2 und Histamin (H1)-Rezeptoren aufweist. Das Fehlen einer\n">
Note
Change a test code (delete one space) test/test_pdf_parser.rb#est_join_snippets__hex_chars
Paroxetin besitzt eine selektive Wirkung; in-vitro Studien haben gezeigt, dass es, im Gegensatz zu trizyklischen Antidepressiva, eine geringe Affinit\344t f\374r a1-, a2- und b-Adrenozeptoren sowie f\374r Dopamin (D2)-, 5-HT1-artige, 5-HT2 und Histamin (H1)-Rezeptoren aufweist. Das Fehlen einer
Result
Ruby 1.8 with the latest libraries
masa@masa ~/ywesee/rpdf2txt $ ruby18 -I ~/work/rpdf2txt/lib test/suite.rb Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ...................................................................unknown encoding 370 0 R ........F.............. Finished in 8.873084 seconds. 1) Failure: test_join_snippets__hex_chars(TestParser) [/home/masa/ywesee/rpdf2txt/test/test_pdf_parser.rb:337]: <"Paroxetin besitzt eine selektive Wirkung; in-vitro Studien haben gezeigt, dass es, im Gegensatz zu\ntrizyklischen Antidepressiva, eine geringe Affinit� f� a1-, a2- und b-Adrenozeptoren sowie f� Dopamin (D2)-, 5-HT1-artige, 5-HT2 und Histamin (H1)-Rezeptoren aufweist. Das Fehlen einer\n"> expected but was <"Paroxetin besitzt eine selektive Wirkung; in-vitro Studien haben gezeigt, dass es, im Gegensatz zu\ntrizyklischen Antidepressiva, eine geringe Affinit� f� a1-, a2- und b-Adrenozeptoren sowie f� Dopamin (D2)-, 5-HT1-artige, 5-HT2 und Histamin (H1)-Rezeptoren aufweist. Das Fehlen einer\n">. 112 tests, 227 assertions, 1 failures, 0 errors
Ruby 1.8 with the updated libraries
masa@masa ~/ywesee/rpdf2txt $ ruby18 -I lib test/suite.rb Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ...................................................................unknown encoding 370 0 R ....................... Finished in 8.914007 seconds. 112 tests, 227 assertions, 0 failures, 0 errors
Ruby 1.9 with the updated libraries
masa@masa ~/ywesee/rpdf2txt $ ruby1.9 -I lib test/suite.rb test/suite.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/ywesee/rpdf2txt/test/test_pdf_object.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/ywesee/rpdf2txt/test/test_pdf_parser.rb:28: warning: variable $KCODE is no longer effective; ignored Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ......................................................... ..........unknown encoding 370 0 R ....................... Finished in 7.409007228 seconds. 112 tests, 227 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications 100% passed
Test import_gkv with the latest rpdf2txt
Load de.oddb.org data on 20110116
masa@masa ~/ywesee $ sudo -u postgres dropdb oddb masa@masa ~/ywesee $ sudo -u postgres createdb -E UTF8 -T template0 oddb masa@masa ~/ywesee $ zcat de.oddb.org/data/sql/oddb.20110116.sql.gz | psql -U postgres oddb
Run de.oddb.org
Run jobs/import_gkv
Result
Thu Jan 20 08:52:49 2011: de.oddb.org ODDB::Import::Gkv#import Imported 6308 Zubef-Entries on 20.01.2011: Visited 5956 existing Zubef-Entries Visited 2993 existing Companies Visited 1449 existing Substances Created 352 new Zubef-Entries Created 11 new Products Created 11 new Sequences Created 3315 new Companies Created 3490 new Substances Assigned 0 Chemical Equivalences Assigned 7 Companies Created 4 Incomplete Packages: http://de.oddb.org/de/drugs/package/pzn/6947611 http://de.oddb.org/de/drugs/package/pzn/6922692 http://de.oddb.org/de/drugs/package/pzn/6907333 http://de.oddb.org/de/drugs/package/pzn/6907327 Created 1 Product(s) without a name (missing product name): http://de.oddb.org/de/drugs/product/uid/3480899
Dump data and check size
masa@masa ~/ywesee/de.oddb.org $ pg_dump oddb > oddb_old_rpdf2txt.sql masa@masa ~/ywesee/de.oddb.org $ ls -al -rw-r--r-- 1 masa masa 1845079867 20. Jan 10:57 oddb_old_rpdf2txt.sql
Install the new rpdf2txt
masa@masa ~/ywesee/rpdf2txt $ ruby install.rb config masa@masa ~/ywesee/rpdf2txt $ ruby install.rb setup masa@masa ~/ywesee/rpdf2txt $ sudo ruby install.rb install
Check test-cases
masa@masa ~/ywesee/rpdf2txt $ ruby18 test/suite.rb Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ...................................................................unknown encoding 370 0 R ............................................. Finished in 12.362712 seconds. 134 tests, 295 assertions, 0 failures, 0 errors masa@masa ~/ywesee/rpdf2txt $ ruby1.9 -I /usr/lib64/ruby/site_ruby/1.8 test/suite.rb test/suite.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/ywesee/rpdf2txt/test/test_pdf_object.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/ywesee/rpdf2txt/test/test_pdf_parser.rb:28: warning: variable $KCODE is no longer effective; ignored Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ......................................................... ..........unknown encoding 370 0 R ............................................. Finished in 9.37691039 seconds. 134 tests, 295 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications 100% passed
Note
Load de.oddb.org data on 20110116
masa@masa ~/ywesee $ sudo -u postgres dropdb oddb masa@masa ~/ywesee $ sudo -u postgres createdb -E UTF8 -T template0 oddb masa@masa ~/ywesee $ zcat de.oddb.org/data/sql/oddb.20110116.sql.gz | psql -U postgres oddb
Run de.oddb.org
Run jobs/import_gkv
Result
Thu Jan 20 11:24:20 2011: de.oddb.org ODDB::Import::Gkv#import Imported 6308 Zubef-Entries on 20.01.2011: Visited 5956 existing Zubef-Entries Visited 2993 existing Companies Visited 1449 existing Substances Created 352 new Zubef-Entries Created 11 new Products Created 11 new Sequences Created 3315 new Companies Created 3490 new Substances Assigned 0 Chemical Equivalences Assigned 7 Companies Created 4 Incomplete Packages: http://de.oddb.org/de/drugs/package/pzn/6947611 http://de.oddb.org/de/drugs/package/pzn/6922692 http://de.oddb.org/de/drugs/package/pzn/6907333 http://de.oddb.org/de/drugs/package/pzn/6907327 Created 1 Product(s) without a name (missing product name): http://de.oddb.org/de/drugs/product/uid/3480899
Dump data and check size
masa@masa ~/ywesee/de.oddb.org $ pg_dump oddb > oddb_new_rpdf2txt.sql
masa@masa ~/work $ diff mail_old_rpdf2txt.txt mail_new_rpdf2txt.txt 1c1 < Thu Jan 20 08:52:49 2011: de.oddb.org ODDB::Import::Gkv#import --- > Thu Jan 20 11:24:20 2011: de.oddb.org ODDB::Import::Gkv#import 20d19 <
masa@masa ~/ywesee/de.oddb.org $ ls -al -rw-r--r-- 1 masa masa 1845079283 20. Jan 13:18 oddb_new_rpdf2txt.sql -rw-r--r-- 1 masa masa 1845079867 20. Jan 10:57 oddb_old_rpdf2txt.sql
Note
Commit
Update git bare repository online
~/git/rpdf2txt $ ls -al /usr/lib64/ruby/site_ruby/1.8/ lrwxrwxrwx rpdf2txt -> /home/ywesee/git/rpdf2txt/lib/rpdf2txt lrwxrwxrwx rpdf2txt-rockit -> /home/ywesee/git/rpdf2txt/lib/rpdf2txt-rockit ~/git/rpdf2txt $ git checkout -f
Big difference (Incompatible point)
Multilingualization (m17n)
s = open("input.dat","rb"){|f| f.read}
Careful points from 1.8 to 1.9 (encoding)
References
References
Copy the directory of ramaze online to my local
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ls -al insgesamt 64 drwxr-xr-x 12 masa masa 4096 20. Jan 09:38 . drwxr-xr-x 63 masa masa 20480 20. Jan 09:38 .. -rw-r--r-- 1 masa masa 854 20. Jan 09:38 app.rb -rwxr-xr-x 1 masa masa 733 20. Jan 09:38 config.ru drwxr-xr-x 2 masa masa 40 20. Jan 09:38 controller drwxr-xr-x 2 masa masa 24 20. Jan 09:38 data drwxr-xr-x 2 masa masa 8 20. Jan 09:38 etc drwxr-xr-x 2 masa masa 96 20. Jan 09:38 helper drwxr-xr-x 2 masa masa 16 20. Jan 09:38 layout drwxr-xr-x 3 masa masa 40 20. Jan 09:38 log drwxr-xr-x 2 masa masa 8 20. Jan 09:38 model drwxr-xr-x 5 masa masa 48 20. Jan 09:38 public drwxr-xr-x 2 masa masa 8 20. Jan 09:38 spec -rw-r--r-- 1 masa masa 407 20. Jan 09:38 start.rb drwxr-xr-x 4 masa masa 64 20. Jan 09:38 view
Check directory structure
masa@masa ~/ywesee/ramaze.ch.oddb.org $ tree . > ramaze.tree.20101120.txt
Run start.rb
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby18 start.rb
start.rb:6: uninitialized constant Encoding (NameError)
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 start.rb
/home/masa/ywesee/ramaze.ch.oddb.org/app.rb:7:in `require': no such file to load -- ramaze (LoadError)
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:7:in `<top (required)>'
from start.rb:7:in `require'
from start.rb:7:in `<main>'
Note
Install ramaze
masa@masa ~/ywesee/ramaze.ch.oddb.org $ sudo ruby1.9 /usr/bin/gem install ramaze ============================================================ Thank you for installing Ramaze! To create a new project: $ ramaze create yourproject ============================================================ Successfully installed innate-2010.07 Successfully installed ramaze-2010.06.18 2 gems installed Installing ri documentation for innate-2010.07... Installing ri documentation for ramaze-2010.06.18... Installing RDoc documentation for innate-2010.07... Installing RDoc documentation for ramaze-2010.06.18...
suspend
Errors come in Ruby 1.9 when we use rpdf2txt for the first time.
For example,
masa@masa ~/work $ git clone git://scm.ywesee.com/rpdf2txt
masa@masa ~/work/rpdf2txt $ ruby1.9 -I lib bin/rpdf2txt test/data/test.pdf
/home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:82:in `make_element': cannot make an element from nil (ArgumentError)
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `block in make_elements'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `map'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `make_elements'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:361:in `initialize'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:484:in `new'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:484:in `prod'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:134:in `block in eval_ast'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:337:in `map'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:337:in `rescue in method_missing'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:333:in `method_missing'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:132:in `eval_ast'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:129:in `block in eval_ast'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:337:in `map'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:337:in `rescue in method_missing'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/syntax_tree.rb:333:in `method_missing'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:129:in `eval_ast'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:115:in `rockit_productions_eval'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit_grammar_ast_eval.rb:180:in `rockit_grammar_eval'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit.rb:47:in `block in generate_parser_from_file_to_file'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/base_extensions.rb:65:in `call'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/base_extensions.rb:65:in `time_and_puts'
from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/rockit.rb:46:in `generate_parser_from_file_to_file'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/attributesparser.rb:35:in `attributes_parser'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:76:in `_parse_attributes'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:83:in `parse_attributes'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:41:in `initialize'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:114:in `new'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:114:in `build_object'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:132:in `block in build_object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:131:in `scan'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:131:in `build_object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:48:in `object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:163:in `page_tree_root'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:145:in `build_page_tree'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:51:in `page_tree'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:41:in `extract_text'
from bin/rpdf2txt:61:in `<main>'
Note
After the run on Ruby 1.8, an encoding error comes. For example,
masa@masa ~/work/rpdf2txt $ ruby18 -I lib bin/rpdf2txt test/data/test.pdf
untitled text Page 1 of 1
Printed: Donnerstag, 14. November 2002 14:04:29 Uhr
testpdf
masa@masa ~/work/rpdf2txt $ ruby1.9 -I lib bin/rpdf2txt test/data/test.pdf
/home/masa/work/rpdf2txt/lib/rpdf2txt/attributesparser.rb:38:in `require': /home/masa/work/rpdf2txt/lib/rpdf2txt/data/pdfattributes.rb:9: invalid multibyte char (US-ASCII) (SyntaxError)
/home/masa/work/rpdf2txt/lib/rpdf2txt/data/pdfattributes.rb:9: syntax error, unexpected '~', expecting ')'
t1 = EofToken.new("EOF",/^(�~~��~^^~4311922476)/),
^
/home/masa/work/rpdf2txt/lib/rpdf2txt/data/pdfattributes.rb:9: invalid multibyte char (US-ASCII)
from /home/masa/work/rpdf2txt/lib/rpdf2txt/attributesparser.rb:38:in `attributes_parser'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:76:in `_parse_attributes'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:83:in `parse_attributes'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/object.rb:41:in `initialize'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:114:in `new'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:114:in `build_object'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:132:in `block in build_object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:131:in `scan'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:131:in `build_object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:48:in `object_catalogue'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:163:in `page_tree_root'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:145:in `build_page_tree'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:51:in `page_tree'
from /home/masa/work/rpdf2txt/lib/rpdf2txt/parser.rb:41:in `extract_text'
from bin/rpdf2txt:61:in `<main>'
Note
Commit
Note (IMPORTANT)
* But this becomes valid only when rpdf2txt runs on Ruby 1.8 for the first time. * rpdf2txt must run at least once on Ruby1.8 before it runs on Ruby 1.9.
masa@masa ~/work $ git clone git://scm.ywesee.com/rpdf2txt Initialized empty Git repository in /home/masa/work/rpdf2txt/.git/ remote: Counting objects: 1390, done. remote: Compressing objects: 100% (1368/1368), done. remote: Total 1390 (delta 890), reused 0 (delta 0) Receiving objects: 100% (1390/1390), 1.24 MiB, done. Resolving deltas: 100% (890/890), done. masa@masa ~/work $ cd rpdf2txt masa@masa ~/work/rpdf2txt $ ruby18 -I lib test/suite.rb Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ...................................................................unknown encoding 370 0 R ............................................. Finished in 12.870178 seconds. 134 tests, 295 assertions, 0 failures, 0 errors masa@masa ~/work/rpdf2txt $ unset RUBYOPT masa@masa ~/work/rpdf2txt $ ruby1.9 -I lib test/suite.rb test/suite.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/work/rpdf2txt/test/test_pdf_object.rb:26: warning: variable $KCODE is no longer effective; ignored /home/masa/work/rpdf2txt/test/test_pdf_parser.rb:28: warning: variable $KCODE is no longer effective; ignored Loaded suite test/suite Started ......................'invalid literal/lengths set' when filtering with /FlateDecode ......................................................... ..........unknown encoding 370 0 R ............................................. Finished in 9.454758079 seconds. 134 tests, 295 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications 100% passed
Error
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 start.rb
/home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `require': no such file to load -- oddb/persistence/odba (LoadError)
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `<top (required)>'
from start.rb:7:in `require'
from start.rb:7:in `<main>'
Experiment
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 -I ../oddb/lib;../odba start.rb
Note
Next
Download database (ch_oddb_org) data from online
Restore it
masa@masa ~/ywesee $ sudo -u postgres createdb -E UTF8 -T template0 ch_oddb_org masa@masa ~/ywesee $ zcat postgresql_database-ch_oddb_org-backup_20110120.gz | psql -U postgres ch_oddb_org
Update etc/oddb.yml
--- db_name: ch_oddb_org admins: - mhatakeyama@ywesee.com debug_recipients: - mhatakeyama@ywesee.com remote_databases: [] #credentials: # whocc: # username: mhatakeyama@ywesee.com # password: xxx server_url: 'druby://localhost:12000' run_updater: false run_exporter: false query_limit: 5 query_limit_phase: 300 log_level: DEBUG dojo_debug: true #paypal_server: www.paypal.com #paypal_receiver: mhatakeyama@ywesee.com mail_invoice_from: '"masa" <mhatakeyama@ywesee.com>' mail_invoice_smtp: mhatakeyama@ywesee.com http_server: http://oddb.masa.org/ smtp_server: smtp.gmail.com
Set a virtual host
/etc/apache2/vhosts.d/07_ch.oddb.org.conf
<VirtualHost *:80> ServerName ramaze.masa.ch.oddb.org ServerAdmin mhatakeyama@ywesee.com DefaultType text/html ProxyPreserveHost On # Configuration possibility 1 of 2: # The entire domainname, from the root (/), is served by Ramaze # Ramaze should be running at the defined host (192.168.1.100 in this example) # and on the specified port (8000 in this example) # Note the trailing slash after the port. ProxyPass / http://localhost:7000/ ProxyPassReverse / http://localhost:7000/ # End Configuration possibility 1 of 2. </VirtualHost>
Restart apache
masa@masa /etc/apache2/vhosts.d $ sudo /etc/init.d/apache2 restart * apache2 has detected an error in your setup: Syntax error on line 11 of /etc/apache2/vhosts.d/07_ch.oddb.org.conf: Invalid command 'ProxyPreserveHost', perhaps misspelled or defined by a module not included in the server configuration * ERROR: apache2 failed to start
Error
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 -I ../oddb/lib:../odba/lib ./start.rb
/home/masa/ywesee/odba/lib/odba/storage.rb:6:in `require': no such file to load -- dbi (LoadError)
from /home/masa/ywesee/odba/lib/odba/storage.rb:6:in `<top (required)>'
from /home/masa/ywesee/odba/lib/odba.rb:61:in `require'
from /home/masa/ywesee/odba/lib/odba.rb:61:in `<top (required)>'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:5:in `require'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:5:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `<top (required)>'
from ./start.rb:7:in `require'
from ./start.rb:7:in `<main>'
Install pg, dbd-pg, facets
masa@masa ~/ywesee/ramaze.ch.oddb.org $ sudo ruby1.9 /usr/bin/gem install pg -v=0.9.0 Building native extensions. This could take a while... Successfully installed pg-0.9.0 1 gem installed Installing ri documentation for pg-0.9.0... Installing RDoc documentation for pg-0.9.0... masa@masa ~/ywesee/ramaze.ch.oddb.org $ sudo ruby1.9 /usr/bin/gem install dbd-pg Successfully installed deprecated-2.0.1 Successfully installed dbi-0.4.5 Successfully installed dbd-pg-0.3.9 3 gems installed Installing ri documentation for deprecated-2.0.1... Installing ri documentation for dbi-0.4.5... Installing ri documentation for dbd-pg-0.3.9... Installing RDoc documentation for deprecated-2.0.1... Installing RDoc documentation for dbi-0.4.5... Installing RDoc documentation for dbd-pg-0.3.9...
Error
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 -I ../oddb/lib:../odba/lib ./start.rb
ERROR: relation "object" already exists
ERROR: relation "prefetchable_index" already exists
ERROR: relation "extent_index" already exists
ERROR: relation "object_connection" already exists
ERROR: relation "target_id_index" already exists
ERROR: relation "collection" already exists
/usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/columninfo.rb:49:in `[]=': can't add a new key into hash during iteration (RuntimeError)
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/columninfo.rb:49:in `block in initialize'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/columninfo.rb:42:in `each_key'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/columninfo.rb:42:in `initialize'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:161:in `new'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:161:in `block in columns'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:161:in `collect'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:161:in `columns'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:36:in `block in method_missing'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:26:in `next_connection'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:35:in `method_missing'
from /home/masa/ywesee/odba/lib/odba/storage.rb:525:in `setup'
from /home/masa/ywesee/odba/lib/odba/cache.rb:433:in `setup'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:35:in `<module:ODDB>'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:28:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `<top (required)>'
from ./start.rb:7:in `require'
from ./start.rb:7:in `<main>'
test.rb
h = {'1' => 1, '2' => 2, '3' => 3}
p h
h.each_key do |k|
p k
if k == '3'
h['4'] = 4
end
end
p h
Result
Ruby 1.8
masa@masa ~/work $ ruby18 test.rb
{"1"=>1, "2"=>2, "3"=>3}
"1"
"2"
"3"
"4"
{"1"=>1, "2"=>2, "3"=>3, "4"=>4}
Ruby 1.9
masa@masa ~/work $ ruby1.9 -v
ruby 1.9.2dev (2010-07-11 revision 28618) [x86_64-linux]
masa@masa ~/work $ ruby1.9 test.rb
{"1"=>1, "2"=>2, "3"=>3}
"1"
"2"
"3"
test.rb:7:in `[]=': can't add a new key into hash during iteration (RuntimeError)
from test.rb:7:in `block in <main>'
from test.rb:4:in `each_key'
from test.rb:4:in `<main>'
Note (IMPORTANT)
* This is the feature of Ruby 1.9.2, not Ruby 1.9.1* Namely, we cannot change Hash in its iteration in Ruby 1.9.2 (but Array can do) * (In my opinion, it makes Ruby less flexible)
It works on Ruby 1.9.1
$ ruby1.9 -v
ruby 1.9.1p243 (2009-07-16 revision 24175) [x86_64-linux]
$ ruby1.9 test.rb
{"a"=>1, "b"=>2, "c"=>3}
"a"
"b"
"c"
"4"
{"a"=>1, "b"=>2, "c"=>3, "4"=>4}
test.rb
a = [1,2,3]
p a
a.each do |x|
p x
if x==3
a << 4
end
end
p a
Result
masa@masa ~/work $ ruby1.9 test.rb [1, 2, 3] 1 2 3 4 [1, 2, 3, 4]
Refer to
Wed Feb 17 01:16:12 2010 Yusuke Endoh <mame@tsg.ne.jp> * hash.c (hash_update): always raise an exception when adding a new key during iteration. Traditionally, an exception was raised only when rehash occurs, but it may lead to difficult bug to reproduce. [ruby-core:23614]
Experiment
/usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/columninfo.rb
def initialize(hash=nil)
@hash = hash.dup rescue nil
@hash ||= Hash.new
# coerce all strings to symbols
hash_tmp = {}
@hash.each_key do |x|
if x.kind_of? String
sym = x.to_sym
if @hash.has_key? sym
raise ::TypeError,
"#{self.class.name} may construct from a hash keyed with strings or symbols, but not both"
end
#@hash[sym] = @hash[x]
hash_tmp[sym] = @hash[x]
@hash.delete(x)
end
end
hash_tmp.each do |k,v|
@hash[k] = v
end
Result
masa@masa ~/ywesee/ramaze.ch.oddb.org $ ruby1.9 -I ../oddb/lib:../odba/lib ./start.rb
ERROR: relation "object" already exists
ERROR: relation "prefetchable_index" already exists
ERROR: relation "extent_index" already exists
ERROR: relation "object_connection" already exists
ERROR: relation "target_id_index" already exists
ERROR: relation "collection" already exists
ERROR: relation "target_id_oddb_drugs_sequence_fachinfo_indications_de" already exists
ERROR: relation "oddb_business_company_name" already exists
/usr/lib64/ruby/gems/1.9.1/gems/dbd-pg-0.3.9/lib/dbd/pg/statement.rb:62:in `rescue in execute': ERROR: relation "oddb_business_company_name" already exists (DBI::ProgrammingError)
from /usr/lib64/ruby/gems/1.9.1/gems/dbd-pg-0.3.9/lib/dbd/pg/statement.rb:37:in `execute'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/base_classes/database.rb:96:in `execute'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/base_classes/database.rb:114:in `do'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:106:in `do'
from /home/masa/ywesee/odba/lib/odba/storage.rb:176:in `create_index'
from /home/masa/ywesee/odba/lib/odba/index.rb:226:in `initialize'
from /home/masa/ywesee/odba/lib/odba/cache.rb:148:in `new'
from /home/masa/ywesee/odba/lib/odba/cache.rb:148:in `block in create_index'
from /home/masa/ywesee/odba/lib/odba/storage.rb:558:in `call'
from /home/masa/ywesee/odba/lib/odba/storage.rb:558:in `block in transaction'
from /usr/lib64/ruby/gems/1.9.1/gems/dbi-0.4.5/lib/dbi/handles/database.rb:209:in `transaction'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:36:in `block in method_missing'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:26:in `next_connection'
from /home/masa/ywesee/odba/lib/odba/connection_pool.rb:35:in `method_missing'
from /home/masa/ywesee/odba/lib/odba/storage.rb:554:in `transaction'
from /home/masa/ywesee/odba/lib/odba/cache.rb:520:in `transaction'
from /home/masa/ywesee/odba/lib/odba/cache.rb:140:in `create_index'
from /home/masa/ywesee/odba/lib/odba/cache.rb:131:in `block in create_deferred_indices'
from /home/masa/ywesee/odba/lib/odba/cache.rb:125:in `each'
from /home/masa/ywesee/odba/lib/odba/cache.rb:125:in `create_deferred_indices'
from /home/masa/ywesee/odba/lib/odba/cache.rb:437:in `setup'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:35:in `<module:ODDB>'
from /home/masa/ywesee/oddb/lib/oddb/persistence/odba.rb:28:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/model/init.rb:3:in `<top (required)>'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `require'
from /home/masa/ywesee/ramaze.ch.oddb.org/app.rb:32:in `<top (required)>'
from ./start.rb:7:in `require'
from ./start.rb:7:in `<main>'
Note