Changeset: 9cb7c7c1cf07 for MonetDB URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=9cb7c7c1cf07 Modified Files: sql/backends/monet5/bam/Tests/bam_loader_file.stable.err sql/backends/monet5/bam/Tests/bam_loader_file.stable.out sql/backends/monet5/bam/Tests/bam_loader_files.stable.err sql/backends/monet5/bam/Tests/bam_loader_files.stable.out sql/backends/monet5/bam/Tests/check_files.sql sql/backends/monet5/bam/Tests/check_files.stable.err sql/backends/monet5/bam/Tests/check_files.stable.out sql/backends/monet5/bam/Tests/check_files_exact.sql sql/backends/monet5/bam/Tests/check_files_exact.stable.err sql/backends/monet5/bam/Tests/check_files_exact.stable.out sql/backends/monet5/bam/Tests/drop_last_files.stable.err sql/backends/monet5/bam/Tests/drop_last_files.stable.out sql/backends/monet5/bam/Tests/query1.1.stable.err sql/backends/monet5/bam/Tests/query1.1.stable.out sql/backends/monet5/bam/Tests/query1.2.stable.err sql/backends/monet5/bam/Tests/query1.2.stable.out sql/backends/monet5/bam/Tests/query1.3.stable.err sql/backends/monet5/bam/Tests/query1.3.stable.out sql/backends/monet5/bam/Tests/query1.4.stable.err sql/backends/monet5/bam/Tests/query1.4.stable.out sql/backends/monet5/bam/Tests/query1.5.stable.err sql/backends/monet5/bam/Tests/query1.5.stable.out sql/backends/monet5/bam/Tests/query2.1.stable.err sql/backends/monet5/bam/Tests/query2.1.stable.out sql/backends/monet5/bam/Tests/query2.10.stable.err sql/backends/monet5/bam/Tests/query2.10.stable.out sql/backends/monet5/bam/Tests/query2.11.stable.err sql/backends/monet5/bam/Tests/query2.11.stable.out sql/backends/monet5/bam/Tests/query2.12.stable.err sql/backends/monet5/bam/Tests/query2.12.stable.out sql/backends/monet5/bam/Tests/query2.2.stable.err sql/backends/monet5/bam/Tests/query2.2.stable.out sql/backends/monet5/bam/Tests/query2.3.stable.err sql/backends/monet5/bam/Tests/query2.3.stable.out sql/backends/monet5/bam/Tests/query2.4.stable.err sql/backends/monet5/bam/Tests/query2.4.stable.out sql/backends/monet5/bam/Tests/query2.5.stable.err sql/backends/monet5/bam/Tests/query2.5.stable.out sql/backends/monet5/bam/Tests/query2.6.stable.err sql/backends/monet5/bam/Tests/query2.6.stable.out sql/backends/monet5/bam/Tests/query2.7.stable.err sql/backends/monet5/bam/Tests/query2.7.stable.out sql/backends/monet5/bam/Tests/query2.8.stable.err sql/backends/monet5/bam/Tests/query2.8.stable.out sql/backends/monet5/bam/Tests/query2.9.stable.err sql/backends/monet5/bam/Tests/query2.9.stable.out sql/backends/monet5/bam/Tests/sam_export.stable.err sql/backends/monet5/bam/Tests/sam_export.stable.out sql/backends/monet5/bam/Tests/verify_load.stable.err sql/backends/monet5/bam/Tests/verify_load.stable.out Branch: bamloader Log Message:
Fix system absolute paths in test outputs diffs (truncated from 2583 to 300 lines): diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err --- a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err +++ b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.err @@ -1,9 +1,9 @@ stderr of test 'bam_loader_file` in directory 'sql/backends/monet5/bam` itself: -# 13:29:48 > -# 13:29:48 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=37021" "--set" "mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=32986" "--set" "mapi_usock=/var/tmp/mtest-16074/.s.monetdb.32986" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" +# 10:22:37 > # builtin opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/monetdb5/dbfarm/demo # builtin opt gdk_debug = 0 @@ -17,16 +17,14 @@ stderr of test 'bam_loader_file` in dire # builtin opt sql_debug = 0 # cmdline opt gdk_nr_threads = 0 # cmdline opt mapi_open = true -# cmdline opt mapi_port = 37021 -# cmdline opt mapi_usock = /var/tmp/mtest-21062/.s.monetdb.37021 +# cmdline opt mapi_port = 32986 +# cmdline opt mapi_usock = /var/tmp/mtest-16074/.s.monetdb.32986 # cmdline opt monet_prompt = # cmdline opt mal_listing = 2 # cmdline opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam # cmdline opt mal_listing = 0 # cmdline opt gdk_debug = 536870922 # <bam_loader>: Loader started for 1 BAM file... -# # <bam_loader> Creating schema 'bam'... -# # CREATE SCHEMA bam; # # <bam_loader> Creating table 'files'... # # CREATE TABLE bam.files ( # file_id BIGINT NOT NULL, @@ -442,12 +440,12 @@ stderr of test 'bam_loader_file` in dire # # # <bam_loader>: Loader finished processing 1 BAM file... # -# 13:29:48 > -# 13:29:48 > "/usr/bin/python2" "bam_loader_file.SQL.py" "bam_loader_file" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "/usr/bin/python2" "bam_loader_file.SQL.py" "bam_loader_file" +# 10:22:37 > -# 13:29:48 > -# 13:29:48 > "Done." -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "Done." +# 10:22:37 > diff --git a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.out b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.out --- a/sql/backends/monet5/bam/Tests/bam_loader_file.stable.out +++ b/sql/backends/monet5/bam/Tests/bam_loader_file.stable.out @@ -1,9 +1,9 @@ stdout of test 'bam_loader_file` in directory 'sql/backends/monet5/bam` itself: -# 13:29:48 > -# 13:29:48 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=37021" "--set" "mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=32986" "--set" "mapi_usock=/var/tmp/mtest-16074/.s.monetdb.32986" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" +# 10:22:37 > # MonetDB 5 server v11.18.0 # This is an unreleased version @@ -13,8 +13,8 @@ stdout of test 'bam_loader_file` in dire # Copyright (c) 1993-July 2008 CWI. # Copyright (c) August 2008-2014 MonetDB B.V., all rights reserved # Visit http://www.monetdb.org/ for further information -# Listening for connection requests on mapi:monetdb://robin-xps13:37021/ -# Listening for UNIX domain connection requests on mapi:monetdb:///var/tmp/mtest-21062/.s.monetdb.37021 +# Listening for connection requests on mapi:monetdb://robin-xps13:32986/ +# Listening for UNIX domain connection requests on mapi:monetdb:///var/tmp/mtest-16074/.s.monetdb.32986 # MonetDB/SQL module loaded Ready. @@ -45,12 +45,12 @@ Ready. # loading sql script: 85_bam.sql # loading sql script: 99_system.sql -# 13:29:48 > -# 13:29:48 > "/usr/bin/python2" "bam_loader_file.SQL.py" "bam_loader_file" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "/usr/bin/python2" "bam_loader_file.SQL.py" "bam_loader_file" +# 10:22:37 > -# 13:29:48 > -# 13:29:48 > "Done." -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "Done." +# 10:22:37 > diff --git a/sql/backends/monet5/bam/Tests/bam_loader_files.stable.err b/sql/backends/monet5/bam/Tests/bam_loader_files.stable.err --- a/sql/backends/monet5/bam/Tests/bam_loader_files.stable.err +++ b/sql/backends/monet5/bam/Tests/bam_loader_files.stable.err @@ -1,9 +1,9 @@ stderr of test 'bam_loader_files` in directory 'sql/backends/monet5/bam` itself: -# 13:29:48 > -# 13:29:48 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=37021" "--set" "mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=32986" "--set" "mapi_usock=/var/tmp/mtest-16074/.s.monetdb.32986" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" +# 10:22:37 > # builtin opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/monetdb5/dbfarm/demo # builtin opt gdk_debug = 0 @@ -17,8 +17,8 @@ stderr of test 'bam_loader_files` in dir # builtin opt sql_debug = 0 # cmdline opt gdk_nr_threads = 0 # cmdline opt mapi_open = true -# cmdline opt mapi_port = 37021 -# cmdline opt mapi_usock = /var/tmp/mtest-21062/.s.monetdb.37021 +# cmdline opt mapi_port = 32986 +# cmdline opt mapi_usock = /var/tmp/mtest-16074/.s.monetdb.32986 # cmdline opt monet_prompt = # cmdline opt mal_listing = 2 # cmdline opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam @@ -84,20 +84,20 @@ stderr of test 'bam_loader_files` in dir # ); # # <bam_loader> Creating reader threads... # # <Thread 0> Starting on next file... -# # <Thread 1> Starting on next file... -# # <Thread 1> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam' (file id 6)... # # <Thread 0> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam' (file id 5)... # # <Thread 2> Starting on next file... -# # <Thread 2> No files left to work on; thread done # # <bam_loader> Waiting for reader threads to finish... +# # <Thread 1> Starting on next file... +# # <Thread 3> Starting on next file... +# # <Thread 3> No files left to work on; thread done +# # <Thread 2> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam' (file id 6)... +# # <Thread 1> No files left to work on; thread done # # <Thread 0> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam' (file id 5) processed! # # <Thread 0> Starting on next file... # # <Thread 0> No files left to work on; thread done -# # <Thread 3> Starting on next file... -# # <Thread 3> No files left to work on; thread done -# # <Thread 1> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam' (file id 6) processed! -# # <Thread 1> Starting on next file... -# # <Thread 1> No files left to work on; thread done +# # <Thread 2> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam' (file id 6) processed! +# # <Thread 2> Starting on next file... +# # <Thread 2> No files left to work on; thread done # # <bam_loader> Copying data into DB... # # COPY BINARY INTO bam.files FROM ('bam_binaries/5/files_0', 'bam_binaries/5/files_1', 'bam_binaries/5/files_2', 'bam_binaries/5/files_3', 'bam_binaries/5/files_4', 'bam_binaries/5/files_5'); # COPY BINARY INTO bam.sq FROM ('bam_binaries/5/sq_0', 'bam_binaries/5/sq_1', 'bam_binaries/5/sq_2', 'bam_binaries/5/sq_3', 'bam_binaries/5/sq_4', 'bam_binaries/5/sq_5', 'bam_binaries/5/sq_6'); @@ -337,21 +337,21 @@ stderr of test 'bam_loader_files` in dir # SELECT * # FROM bam.unpaired_alignments_8; # # <bam_loader> Creating reader threads... +# # <Thread 1> Starting on next file... +# # <Thread 1> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam' (file id 7)... # # <Thread 0> Starting on next file... -# # <Thread 0> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam' (file id 7)... +# # <Thread 0> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam' (file id 8)... +# # <Thread 2> Starting on next file... # # <bam_loader> Waiting for reader threads to finish... -# # <Thread 2> Starting on next file... -# # <Thread 2> Processing alignments of file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam' (file id 8)... +# # <Thread 2> No files left to work on; thread done +# # <Thread 3> Starting on next file... +# # <Thread 3> No files left to work on; thread done +# # <Thread 1> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam' (file id 7) processed! # # <Thread 1> Starting on next file... # # <Thread 1> No files left to work on; thread done -# # <Thread 3> Starting on next file... -# # <Thread 3> No files left to work on; thread done -# # <Thread 0> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam' (file id 7) processed! +# # <Thread 0> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam' (file id 8) processed! # # <Thread 0> Starting on next file... # # <Thread 0> No files left to work on; thread done -# # <Thread 2> All alignments in file '/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam' (file id 8) processed! -# # <Thread 2> Starting on next file... -# # <Thread 2> No files left to work on; thread done # # <bam_loader> Copying data into DB... # # COPY BINARY INTO bam.files FROM ('bam_binaries/7/files_0', 'bam_binaries/7/files_1', 'bam_binaries/7/files_2', 'bam_binaries/7/files_3', 'bam_binaries/7/files_4', 'bam_binaries/7/files_5'); # COPY BINARY INTO bam.sq FROM ('bam_binaries/7/sq_0', 'bam_binaries/7/sq_1', 'bam_binaries/7/sq_2', 'bam_binaries/7/sq_3', 'bam_binaries/7/sq_4', 'bam_binaries/7/sq_5', 'bam_binaries/7/sq_6'); @@ -371,12 +371,12 @@ stderr of test 'bam_loader_files` in dir # # # <bam_loader>: Loader finished processing 2 BAM files... # -# 13:29:49 > -# 13:29:49 > "/usr/bin/python2" "bam_loader_files.SQL.py" "bam_loader_files" -# 13:29:49 > +# 10:22:37 > +# 10:22:37 > "/usr/bin/python2" "bam_loader_files.SQL.py" "bam_loader_files" +# 10:22:37 > -# 13:29:49 > -# 13:29:49 > "Done." -# 13:29:49 > +# 10:22:38 > +# 10:22:38 > "Done." +# 10:22:38 > diff --git a/sql/backends/monet5/bam/Tests/bam_loader_files.stable.out b/sql/backends/monet5/bam/Tests/bam_loader_files.stable.out --- a/sql/backends/monet5/bam/Tests/bam_loader_files.stable.out +++ b/sql/backends/monet5/bam/Tests/bam_loader_files.stable.out @@ -1,9 +1,9 @@ stdout of test 'bam_loader_files` in directory 'sql/backends/monet5/bam` itself: -# 13:29:48 > -# 13:29:48 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=37021" "--set" "mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" -# 13:29:48 > +# 10:22:37 > +# 10:22:37 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=32986" "--set" "mapi_usock=/var/tmp/mtest-16074/.s.monetdb.32986" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" +# 10:22:37 > # MonetDB 5 server v11.18.0 # This is an unreleased version @@ -13,18 +13,18 @@ stdout of test 'bam_loader_files` in dir # Copyright (c) 1993-July 2008 CWI. # Copyright (c) August 2008-2014 MonetDB B.V., all rights reserved # Visit http://www.monetdb.org/ for further information -# Listening for connection requests on mapi:monetdb://robin-xps13:37021/ -# Listening for UNIX domain connection requests on mapi:monetdb:///var/tmp/mtest-21062/.s.monetdb.37021 +# Listening for connection requests on mapi:monetdb://robin-xps13:32986/ +# Listening for UNIX domain connection requests on mapi:monetdb:///var/tmp/mtest-16074/.s.monetdb.32986 # MonetDB/SQL module loaded Ready. -# 13:29:49 > -# 13:29:49 > "/usr/bin/python2" "bam_loader_files.SQL.py" "bam_loader_files" -# 13:29:49 > +# 10:22:37 > +# 10:22:37 > "/usr/bin/python2" "bam_loader_files.SQL.py" "bam_loader_files" +# 10:22:37 > -# 13:29:49 > -# 13:29:49 > "Done." -# 13:29:49 > +# 10:22:38 > +# 10:22:38 > "Done." +# 10:22:38 > diff --git a/sql/backends/monet5/bam/Tests/check_files.sql b/sql/backends/monet5/bam/Tests/check_files.sql --- a/sql/backends/monet5/bam/Tests/check_files.sql +++ b/sql/backends/monet5/bam/Tests/check_files.sql @@ -1,3 +1,3 @@ -SELECT file_location, dbschema, format_version, sorting_order, comments +SELECT dbschema, format_version, sorting_order, comments FROM bam.files ORDER BY file_location; \ No newline at end of file diff --git a/sql/backends/monet5/bam/Tests/check_files.stable.err b/sql/backends/monet5/bam/Tests/check_files.stable.err --- a/sql/backends/monet5/bam/Tests/check_files.stable.err +++ b/sql/backends/monet5/bam/Tests/check_files.stable.err @@ -1,9 +1,9 @@ stderr of test 'check_files` in directory 'sql/backends/monet5/bam` itself: -# 13:29:49 > -# 13:29:49 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=37021" "--set" "mapi_usock=/var/tmp/mtest-21062/.s.monetdb.37021" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" -# 13:29:49 > +# 10:22:38 > +# 10:22:38 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set" "mapi_open=true" "--set" "mapi_port=32986" "--set" "mapi_usock=/var/tmp/mtest-16074/.s.monetdb.32986" "--set" "monet_prompt=" "--forcemito" "--set" "mal_listing=2" "--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam" "--set" "mal_listing=0" +# 10:22:38 > # builtin opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/monetdb5/dbfarm/demo # builtin opt gdk_debug = 0 @@ -17,20 +17,20 @@ stderr of test 'check_files` in director # builtin opt sql_debug = 0 # cmdline opt gdk_nr_threads = 0 # cmdline opt mapi_open = true -# cmdline opt mapi_port = 37021 -# cmdline opt mapi_usock = /var/tmp/mtest-21062/.s.monetdb.37021 +# cmdline opt mapi_port = 32986 +# cmdline opt mapi_usock = /var/tmp/mtest-16074/.s.monetdb.32986 # cmdline opt monet_prompt = # cmdline opt mal_listing = 2 # cmdline opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam # cmdline opt mal_listing = 0 # cmdline opt gdk_debug = 536870922 -# 13:29:50 > -# 13:29:50 > "mclient" "-lsql" "-ftest" "-Eutf-8" "-i" "-e" "--host=/var/tmp/mtest-21062" "--port=37021" -# 13:29:50 > +# 10:22:38 > +# 10:22:38 > "mclient" "-lsql" "-ftest" "-Eutf-8" "-i" "-e" "--host=/var/tmp/mtest-16074" "--port=32986" +# 10:22:38 > -# 13:29:50 > -# 13:29:50 > "Done." -# 13:29:50 > +# 10:22:38 > _______________________________________________ checkin-list mailing list checkin-list@monetdb.org https://www.monetdb.org/mailman/listinfo/checkin-list
