Changeset: 91d6d8630be1 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=91d6d8630be1
Added Files:
sql/backends/monet5/bam/Tests/bam.pyc
sql/backends/monet5/bam/Tests/bam_lib.SQL.py
sql/backends/monet5/bam/Tests/bam_lib.stable.err
sql/backends/monet5/bam/Tests/bam_lib.stable.out
sql/backends/monet5/bam/Tests/sql/bam_lib.sql
Removed Files:
sql/backends/monet5/bam/Tests/sql/drop_last_files.sql
Modified Files:
sql/backends/monet5/bam/Tests/All
sql/backends/monet5/bam/Tests/bam_loader_files.SQL.py
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.out
sql/backends/monet5/bam/Tests/check_files_exact.sql
sql/backends/monet5/bam/Tests/drop_last_files.SQL.py
sql/backends/monet5/bam/Tests/sql/bam_loader_files.sql
sql/backends/monet5/bam/Tests/sql/sam_export.sql
Branch: bamloader
Log Message:
Added thorough testing of bam_lib and added test for just removed bug that
occurred when loading many files in one command
diffs (truncated from 3716 to 300 lines):
diff --git a/sql/backends/monet5/bam/Tests/All
b/sql/backends/monet5/bam/Tests/All
--- a/sql/backends/monet5/bam/Tests/All
+++ b/sql/backends/monet5/bam/Tests/All
@@ -25,3 +25,4 @@ HAVE_SAMTOOLS?query2.10
HAVE_SAMTOOLS?query2.11
HAVE_SAMTOOLS?query2.12
HAVE_SAMTOOLS?mergetable
+HAVE_SAMTOOLS?bam_lib
diff --git a/sql/backends/monet5/bam/Tests/bam.pyc
b/sql/backends/monet5/bam/Tests/bam.pyc
new file mode 100644
index
e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..920c4a9a9889e1cc40f6d04cb102a0f9b57a828a
GIT binary patch
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diff --git a/sql/backends/monet5/bam/Tests/bam_lib.SQL.py
b/sql/backends/monet5/bam/Tests/bam_lib.SQL.py
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_lib.SQL.py
@@ -0,0 +1,3 @@
+import bam
+
+bam.exec_sql_file("bam_lib.sql", {'PWD': bam.SRCDIR})
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.stable.err
b/sql/backends/monet5/bam/Tests/bam_lib.stable.err
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_lib.stable.err
@@ -0,0 +1,87 @@
+stderr of test 'bam_lib` in directory 'sql/backends/monet5/bam` itself:
+
+
+# 09:28:35 >
+# 09:28:35 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set"
"mapi_open=true" "--set" "mapi_port=33399" "--set"
"mapi_usock=/var/tmp/mtest-22883/.s.monetdb.33399" "--set" "monet_prompt="
"--forcemito" "--set" "mal_listing=2"
"--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam"
"--set" "mal_listing=0" "--set" "embedded_r=yes"
+# 09:28:35 >
+
+# builtin opt gdk_dbpath = /home/robin/MonetDB/PREFIX/var/monetdb5/dbfarm/demo
+# builtin opt gdk_debug = 0
+# builtin opt gdk_vmtrim = no
+# builtin opt monet_prompt = >
+# builtin opt monet_daemon = no
+# builtin opt mapi_port = 50000
+# builtin opt mapi_open = false
+# builtin opt mapi_autosense = false
+# builtin opt sql_optimizer = default_pipe
+# builtin opt sql_debug = 0
+# cmdline opt gdk_nr_threads = 0
+# cmdline opt mapi_open = true
+# cmdline opt mapi_port = 33399
+# cmdline opt mapi_usock = /var/tmp/mtest-22883/.s.monetdb.33399
+# 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 embedded_r = yes
+# cmdline opt gdk_debug = 536870922
+# <bam_loader>: Loader started for 1 BAM file...
+# # <bam_loader> Retrieving next file id...
+# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
+# # CREATE TABLE bam.alignments_1 (
+# virtual_offset BIGINT NOT NULL,
+# qname STRING NOT
NULL,
+# flag SMALLINT
NOT NULL,
+# rname STRING NOT
NULL,
+# pos INT
NOT NULL,
+# mapq SMALLINT
NOT NULL,
+# cigar STRING NOT
NULL,
+# rnext STRING NOT
NULL,
+# pnext INT
NOT NULL,
+# tlen INT
NOT NULL,
+# seq STRING
NOT NULL,
+# qual STRING
NOT NULL,
+# CONSTRAINT alignments_1_pkey_virtual_offset PRIMARY KEY
(virtual_offset)
+# );
+#
+# CREATE TABLE bam.alignments_extra_1 (
+# tag CHAR(2)
NOT NULL,
+# virtual_offset BIGINT NOT NULL,
+# type CHAR(1)
NOT NULL,
+# value STRING,
+# CONSTRAINT alignments_extra_1_pkey_tag_virtual_offset PRIMARY
KEY (tag, virtual_offset),
+# CONSTRAINT alignments_extra_1_fkey_virtual_offset FOREIGN KEY
(virtual_offset)
+# REFERENCES bam.alignments_1 (virtual_offset)
+# );
+# # <bam_loader> Creating reader threads...
+# # <bam_loader> Waiting for reader threads to finish...
+# # <Thread 0> Starting on next file...
+# # <Thread 0> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 1)...
+# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 1) processed!
+# # <Thread 0> Starting on next file...
+# # <Thread 0> No files left to work on; thread done
+# # <bam_loader> Copying data into DB...
+# # COPY BINARY INTO bam.files FROM ('bam_binaries/1/files_0',
'bam_binaries/1/files_1', 'bam_binaries/1/files_2', 'bam_binaries/1/files_3',
'bam_binaries/1/files_4', 'bam_binaries/1/files_5');
+# COPY BINARY INTO bam.sq FROM ('bam_binaries/1/sq_0',
'bam_binaries/1/sq_1', 'bam_binaries/1/sq_2', 'bam_binaries/1/sq_3',
'bam_binaries/1/sq_4', 'bam_binaries/1/sq_5', 'bam_binaries/1/sq_6');
+# COPY BINARY INTO bam.pg FROM ('bam_binaries/1/pg_0',
'bam_binaries/1/pg_1', 'bam_binaries/1/pg_2', 'bam_binaries/1/pg_3',
'bam_binaries/1/pg_4', 'bam_binaries/1/pg_5');
+# COPY BINARY INTO bam.alignments_1 FROM ('bam_binaries/1/alignments_0',
'bam_binaries/1/alignments_1', 'bam_binaries/1/alignments_2',
'bam_binaries/1/alignments_3', 'bam_binaries/1/alignments_4',
'bam_binaries/1/alignments_5', 'bam_binaries/1/alignments_6',
'bam_binaries/1/alignments_7', 'bam_binaries/1/alignments_8',
'bam_binaries/1/alignments_9', 'bam_binaries/1/alignments_10',
'bam_binaries/1/alignments_11');
+# COPY BINARY INTO bam.alignments_extra_1 FROM
('bam_binaries/1/alignments_extra_0', 'bam_binaries/1/alignments_extra_1',
'bam_binaries/1/alignments_extra_2', 'bam_binaries/1/alignments_extra_3');
+#
+# # <bam_loader>: Loader finished processing 1 BAM file...
+#
+# 09:28:35 >
+# 09:28:35 > "/usr/bin/python2" "bam_lib.SQL.py" "bam_lib"
+# 09:28:35 >
+
+MAPI = (monetdb) /var/tmp/mtest-22883/.s.monetdb.33399
+QUERY = SELECT bam_flag(111, 'Fail-hard');
+ERROR = !Unknown flag name given: Fail-hard
+MAPI = (monetdb) /var/tmp/mtest-22883/.s.monetdb.33399
+QUERY = SELECT reverse_seq('invalidchars');
+ERROR = !Invalid character found in sequence: 'i'
+
+# 09:28:36 >
+# 09:28:36 > "Done."
+# 09:28:36 >
diff --git a/sql/backends/monet5/bam/Tests/bam_lib.stable.out
b/sql/backends/monet5/bam/Tests/bam_lib.stable.out
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/Tests/bam_lib.stable.out
@@ -0,0 +1,777 @@
+stdout of test 'bam_lib` in directory 'sql/backends/monet5/bam` itself:
+
+
+# 10:07:17 >
+# 10:07:17 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set"
"mapi_open=true" "--set" "mapi_port=35421" "--set"
"mapi_usock=/var/tmp/mtest-25140/.s.monetdb.35421" "--set" "monet_prompt="
"--forcemito" "--set" "mal_listing=2"
"--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam"
"--set" "mal_listing=0" "--set" "embedded_r=yes"
+# 10:07:17 >
+
+# MonetDB 5 server v11.20.0
+# This is an unreleased version
+# Serving database 'mTests_sql_backends_monet5_bam', using 4 threads
+# Compiled for x86_64-unknown-linux-gnu/64bit with 64bit OIDs and 128bit
integers dynamically linked
+# Found 7.333 GiB available main-memory.
+# 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-xps13:35421/
+# Listening for UNIX domain connection requests on
mapi:monetdb:///var/tmp/mtest-25140/.s.monetdb.35421
+# MonetDB/SQL module loaded
+# MonetDB/R module loaded
+
+Ready.
+# SQL catalog created, loading sql scripts once
+# loading sql script: 09_like.sql
+# loading sql script: 10_math.sql
+# loading sql script: 11_times.sql
+# loading sql script: 12_url.sql
+# loading sql script: 13_date.sql
+# loading sql script: 14_inet.sql
+# loading sql script: 15_querylog.sql
+# loading sql script: 16_tracelog.sql
+# loading sql script: 19_cluster.sql
+# loading sql script: 20_vacuum.sql
+# loading sql script: 21_dependency_functions.sql
+# loading sql script: 22_clients.sql
+# loading sql script: 23_skyserver.sql
+# loading sql script: 24_zorder.sql
+# loading sql script: 25_debug.sql
+# loading sql script: 26_sysmon.sql
+# loading sql script: 39_analytics.sql
+# loading sql script: 39_analytics_hge.sql
+# loading sql script: 40_json.sql
+# loading sql script: 40_json_hge.sql
+# loading sql script: 41_jsonstore.sql
+# loading sql script: 45_uuid.sql
+# loading sql script: 75_storagemodel.sql
+# loading sql script: 80_statistics.sql
+# loading sql script: 80_udf.sql
+# loading sql script: 80_udf_hge.sql
+# loading sql script: 85_bam.sql
+# loading sql script: 89_generator_hge.sql
+# loading sql script: 90_generator.sql
+# loading sql script: 99_system.sql
+
+# 10:07:18 >
+# 10:07:18 > "/usr/bin/python2" "bam_lib.SQL.py" "bam_lib"
+# 10:07:18 >
+
+#SET SCHEMA bam;
+#SELECT bam_flag(1, 'mult_segm');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(2, 'prop_alig');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(4, 'segm_unma');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(8, 'next_unma');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(16, 'segm_reve');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(32, 'next_reve');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(64, 'firs_segm');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(128, 'last_segm');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(256, 'seco_alig');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(512, 'qual_cont');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(1024, 'opti_dupl');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(2048, 'supp_alig');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ true ]
+#SELECT bam_flag(2, 'mult_segm');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
+#SELECT bam_flag(4, 'prop_alig');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
+#SELECT bam_flag(8, 'segm_unma');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
+#SELECT bam_flag(16, 'next_unma');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
+#SELECT bam_flag(4, 'segm_reve');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
+#SELECT bam_flag(2, 'next_reve');
+% .L # table_name
+% bam_flag_single_value # name
+% boolean # type
+% 5 # length
+[ false ]
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