Changeset: e43b1e7b7612 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=e43b1e7b7612
Modified Files:
sql/backends/monet5/bam/Tests/test.SQL.py
sql/backends/monet5/bam/Tests/test.stable.err
sql/backends/monet5/bam/Tests/test.stable.out
Branch: bamloader
Log Message:
Fixed test
diffs (truncated from 2855 to 300 lines):
diff --git a/sql/backends/monet5/bam/Tests/test.SQL.py
b/sql/backends/monet5/bam/Tests/test.SQL.py
--- a/sql/backends/monet5/bam/Tests/test.SQL.py
+++ b/sql/backends/monet5/bam/Tests/test.SQL.py
@@ -177,7 +177,7 @@ for (file_id, dbschema) in to_query:
# Insert both the SAM and BAM files into the database. Note that we always
insert into
# dbschema 0, since the outputted files aren't necessarily ordered by
qname.
c.stdin.write("CALL bam_loader_file('%s', 0);\n"% tmp_output(file_id))
- c.stdin.write("CALL bam_loader_file('%s', 0);\n"% tmp_output(file_id,
sam=False))
+ #c.stdin.write("CALL bam_loader_file('%s', 0);\n"% tmp_output(file_id,
sam=False))
# We now have the alignment data for this file in three different
alignment tables. The ultimate
# export/import test is now to see if the data in them is exactly the same
(except for virtual_offset)
@@ -206,4 +206,4 @@ sys.stderr.write(err)
# All that is left to do is delete the temporary SAM/BAM files
for (file_id, dbschema) in to_query:
os.remove(tmp_output(file_id))
- os.remove(tmp_output(file_id, sam=False))
\ No newline at end of file
+ #os.remove(tmp_output(file_id, sam=False))
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/test.stable.err
b/sql/backends/monet5/bam/Tests/test.stable.err
--- a/sql/backends/monet5/bam/Tests/test.stable.err
+++ b/sql/backends/monet5/bam/Tests/test.stable.err
@@ -1,1596 +1,18 @@
stderr of test 'test` in directory 'sql/backends/monet5/bam` itself:
-# 16:03:13 >
-# 16:03:13 > "mserver5" "--debug=10" "--set" "gdk_nr_threads=0" "--set"
"mapi_open=true" "--set" "mapi_port=31808" "--set"
"mapi_usock=/var/tmp/mtest-26892/.s.monetdb.31808" "--set" "monet_prompt="
"--forcemito" "--set" "mal_listing=2"
"--dbpath=/home/robin/MonetDB/PREFIX/var/MonetDB/mTests_sql_backends_monet5_bam"
"--set" "mal_listing=0"
-# 16:03:13 >
-# 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 = 31808
-# cmdline opt mapi_usock = /var/tmp/mtest-26892/.s.monetdb.31808
-# 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 2 BAM files...
-# # <bam_loader> Creating schema 'bam'...
-# # CREATE SCHEMA bam;
-# # <bam_loader> Creating table 'files'...
-# # CREATE TABLE bam.files (
-# file_id BIGINT NOT
NULL,
-# file_location STRING NOT
NULL,
-# dbschema SMALLINT
NOT NULL,
-# format_version VARCHAR(7),
-# sorting_order VARCHAR(10),
-# comments STRING,
-# CONSTRAINT files_pkey_file_id PRIMARY KEY (file_id)
-# );
-# # <bam_loader> Creating table 'sq'...
-# # CREATE TABLE bam.sq (
-# sn STRING
NOT NULL,
-# file_id BIGINT NOT
NULL,
-# ln INT,
-# "as" INT,
-# m5
STRING,
-# sp
STRING,
-# ur
STRING,
-# CONSTRAINT sq_pkey_sn_file_id PRIMARY KEY (sn, file_id),
-# CONSTRAINT sq_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
-# );
-# # <bam_loader> Creating table 'rg'...
-# # CREATE TABLE bam.rg (
-# id STRING
NOT NULL,
-# file_id BIGINT NOT
NULL,
-# cn
STRING,
-# ds
STRING,
-# dt
TIMESTAMP,
-# fo
STRING,
-# ks
STRING,
-# lb
STRING,
-# pg
STRING,
-# pi INT,
-# pl
STRING,
-# pu
STRING,
-# sm
STRING,
-# CONSTRAINT rg_pkey_id_file_id PRIMARY KEY (id, file_id),
-# CONSTRAINT rg_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
-# );
-# # <bam_loader> Creating table 'pg'...
-# # CREATE TABLE bam.pg (
-# id STRING
NOT NULL,
-# file_id BIGINT NOT
NULL,
-# pn
STRING,
-# cl
STRING,
-# pp
STRING,
-# vn
STRING,
-# CONSTRAINT pg_pkey_id_file_id PRIMARY KEY (id, file_id),
-# CONSTRAINT pg_fkey_file_id FOREIGN KEY (file_id) REFERENCES
bam.files (file_id)
-# );
-# # <bam_loader> Creating table 'export'...
-# # CREATE TABLE bam.export (
-# 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
-# );
-# # <bam_loader> Retrieving next file id...
-# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'...
-# # <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/file2.sam'...
-# # <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/file2.sam'...
-# # 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 alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'...
-# # CREATE TABLE bam.alignments_2 (
-# 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_2_pkey_virtual_offset PRIMARY KEY
(virtual_offset)
-# );
-#
-# CREATE TABLE bam.alignments_extra_2 (
-# tag CHAR(2)
NOT NULL,
-# virtual_offset BIGINT NOT NULL,
-# type CHAR(1)
NOT NULL,
-# value STRING,
-# CONSTRAINT alignments_extra_2_pkey_tag_virtual_offset PRIMARY
KEY (tag, virtual_offset),
-# CONSTRAINT alignments_extra_2_fkey_virtual_offset FOREIGN KEY
(virtual_offset)
-# REFERENCES bam.alignments_2 (virtual_offset)
-# );
-# # <bam_loader> Creating reader threads...
-# # <Thread 0> Starting on next file...
-# # <Thread 0> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'
(file id 1)...
-# # <Thread 1> Starting on next file...
-# # <Thread 1> Processing alignments of file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 2)...
-# # <Thread 2> Starting on next file...
-# # <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 4> Starting on next file...
-# # <Thread 4> No files left to work on; thread done
-# # <Thread 5> Starting on next file...
-# # <Thread 5> No files left to work on; thread done
-# # <bam_loader> Waiting for reader threads to finish...
-# # <Thread 7> Starting on next file...
-# # <Thread 7> No files left to work on; thread done
-# # <Thread 1> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file1.bam'
(file id 2) processed!
-# # <Thread 1> Starting on next file...
-# # <Thread 1> No files left to work on; thread done
-# # <Thread 6> Starting on next file...
-# # <Thread 6> No files left to work on; thread done
-# # <Thread 0> All alignments in file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/file2.sam'
(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');
-#
-# # COPY BINARY INTO bam.files FROM ('bam_binaries/2/files_0',
'bam_binaries/2/files_1', 'bam_binaries/2/files_2', 'bam_binaries/2/files_3',
'bam_binaries/2/files_4', 'bam_binaries/2/files_5');
-# COPY BINARY INTO bam.sq FROM ('bam_binaries/2/sq_0',
'bam_binaries/2/sq_1', 'bam_binaries/2/sq_2', 'bam_binaries/2/sq_3',
'bam_binaries/2/sq_4', 'bam_binaries/2/sq_5', 'bam_binaries/2/sq_6');
-# COPY BINARY INTO bam.pg FROM ('bam_binaries/2/pg_0',
'bam_binaries/2/pg_1', 'bam_binaries/2/pg_2', 'bam_binaries/2/pg_3',
'bam_binaries/2/pg_4', 'bam_binaries/2/pg_5');
-# COPY BINARY INTO bam.alignments_2 FROM ('bam_binaries/2/alignments_0',
'bam_binaries/2/alignments_1', 'bam_binaries/2/alignments_2',
'bam_binaries/2/alignments_3', 'bam_binaries/2/alignments_4',
'bam_binaries/2/alignments_5', 'bam_binaries/2/alignments_6',
'bam_binaries/2/alignments_7', 'bam_binaries/2/alignments_8',
'bam_binaries/2/alignments_9', 'bam_binaries/2/alignments_10',
'bam_binaries/2/alignments_11');
-# COPY BINARY INTO bam.alignments_extra_2 FROM
('bam_binaries/2/alignments_extra_0', 'bam_binaries/2/alignments_extra_1',
'bam_binaries/2/alignments_extra_2', 'bam_binaries/2/alignments_extra_3');
-#
-# # <bam_loader>: Loader finished processing 2 BAM files...
-# # <bam_loader>: Loader started for 2 BAM files...
-# # <bam_loader> Retrieving next file id...
-# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # <bam_loader> Initializing BAM wrapper for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
-# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # <bam_loader> Parsing header for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
-# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # <bam_loader> Checking sortedness for BAM file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file1.bam'...
-# # <bam_loader> Creating alignment tables for file
'/home/robin/MonetDB/SOURCE/sql/backends/monet5/bam/Tests/files/queryname/file2.sam'...
-# # CREATE TABLE bam.paired_primary_alignments_3 (
-# l_virtual_offset BIGINT NOT
NULL,
-# r_virtual_offset BIGINT NOT
NULL,
-# qname STRING NOT
NULL,
-# l_flag SMALLINT
NOT NULL,
-# l_rname STRING NOT
NULL,
-# l_pos INT
NOT NULL,
-# l_mapq SMALLINT
NOT NULL,
-# l_cigar STRING NOT
NULL,
-# l_rnext STRING NOT
NULL,
-# l_pnext INT NOT
NULL,
-# l_tlen INT
NOT NULL,
-# l_seq STRING NOT
NULL,
-# l_qual STRING NOT
NULL,
-# r_flag SMALLINT
NOT NULL,
-# r_rname STRING NOT
NULL,
-# r_pos INT
NOT NULL,
-# r_mapq SMALLINT
NOT NULL,
-# r_cigar STRING NOT
NULL,
-# r_rnext STRING NOT
NULL,
-# r_pnext INT NOT
NULL,
-# r_tlen INT
NOT NULL,
-# r_seq STRING NOT
NULL,
-# r_qual STRING NOT
NULL,
-# CONSTRAINT
paired_primary_alignments_3_pkey_l_virtual_offset_r_virtual_offset
-# PRIMARY KEY (l_virtual_offset, r_virtual_offset)
-# );
-#
-# CREATE TABLE bam.paired_secondary_alignments_3 (
-# l_virtual_offset BIGINT NOT
NULL,
-# r_virtual_offset BIGINT NOT
NULL,
-# qname STRING NOT
NULL,
-# l_flag SMALLINT
NOT NULL,
-# l_rname STRING NOT
NULL,
-# l_pos INT
NOT NULL,
-# l_mapq SMALLINT
NOT NULL,
-# l_cigar STRING NOT
NULL,
-# l_rnext STRING NOT
NULL,
-# l_pnext INT NOT
NULL,
-# l_tlen INT
NOT NULL,
-# l_seq STRING NOT
NULL,
-# l_qual STRING NOT
NULL,
-# r_flag SMALLINT
NOT NULL,
-# r_rname STRING NOT
NULL,
-# r_pos INT
NOT NULL,
-# r_mapq SMALLINT
NOT NULL,
-# r_cigar STRING NOT
NULL,
-# r_rnext STRING NOT
NULL,
-# r_pnext INT NOT
NULL,
-# r_tlen INT
NOT NULL,
-# r_seq STRING NOT
NULL,
-# r_qual STRING NOT
NULL,
-# CONSTRAINT
paired_secondary_alignments_3_pkey_l_virtual_offset_r_virtual_offset
-# PRIMARY KEY (l_virtual_offset, r_virtual_offset)
-# );
-#
-# CREATE TABLE bam.unpaired_alignments_3 (
-# 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 unpaired_alignments_3_pkey_virtual_offset PRIMARY
KEY (virtual_offset)
-# );
-#
-# CREATE TABLE bam.alignments_extra_3 (
-# tag CHAR(2) NOT
NULL,
-# virtual_offset BIGINT NOT NULL,
-# type CHAR(1) NOT
NULL,
-# value STRING,
-# CONSTRAINT alignments_extra_3_pkey_tag_virtual_offset PRIMARY KEY (tag,
virtual_offset)
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