Changeset: 1c284ed4b00d for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=1c284ed4b00d
Modified Files:
sql/backends/monet5/bamloader/bam_db_interface.c
sql/backends/monet5/bamloader/bam_db_interface.h
sql/backends/monet5/bamloader/bam_globals.h
sql/backends/monet5/bamloader/bam_lib.c
sql/backends/monet5/bamloader/bam_lib.h
sql/backends/monet5/bamloader/bam_loader.c
sql/backends/monet5/bamloader/bam_loader.h
sql/backends/monet5/bamloader/bam_wrapper.c
sql/backends/monet5/bamloader/bam_wrapper.h
Branch: bamloader
Log Message:
Layout.
diffs (truncated from 5460 to 300 lines):
diff --git a/sql/backends/monet5/bamloader/bam_db_interface.c
b/sql/backends/monet5/bamloader/bam_db_interface.c
--- a/sql/backends/monet5/bamloader/bam_db_interface.c
+++ b/sql/backends/monet5/bamloader/bam_db_interface.c
@@ -19,13 +19,14 @@
/*
* (author) R Cijvat
- * The code in this file handles all communication that is done with the
running database.
+ * The code in this file handles all communication that is done with
+ * the running database.
*/
#include "monetdb_config.h"
#include "bam_globals.h"
#include "bam_db_interface.h"
-
+
#define SQL_CREATE_STORAGE_0 \
"CREATE TABLE bam.alignments_"LLFMT" ( \n\
virtual_offset BIGINT NOT NULL, \n\
@@ -52,7 +53,7 @@
CONSTRAINT alignments_extra_"LLFMT"_fkey_virtual_offset FOREIGN KEY
(virtual_offset) \n\
REFERENCES bam.alignments_"LLFMT" (virtual_offset) \n\
);"
-
+
#define SQL_CREATE_STORAGE_1 \
"CREATE TABLE bam.paired_primary_alignments_"LLFMT" ( \n\
l_virtual_offset BIGINT NOT NULL, \n\
@@ -161,13 +162,13 @@
UNION ALL \n\
SELECT * \n\
FROM bam.unpaired_alignments_"LLFMT";"
-
+
#define SQL_DROP_HEADER \
"DELETE FROM bam.pg WHERE file_id = "LLFMT";\n" \
"DELETE FROM bam.rg WHERE file_id = "LLFMT";\n" \
"DELETE FROM bam.sq WHERE file_id = "LLFMT";\n" \
"DELETE FROM bam.files WHERE file_id = "LLFMT";\n"
-
+
#define SQL_DROP_STORAGE_0 \
"DROP TABLE bam.alignments_extra_"LLFMT";\n" \
"DROP TABLE bam.alignments_"LLFMT";\n"
@@ -180,8 +181,8 @@
"DROP TABLE bam.paired_primary_alignments_"LLFMT";\n" \
"DROP TABLE bam.paired_secondary_alignments_"LLFMT";\n" \
"DROP TABLE bam.unpaired_alignments_"LLFMT";\n"
-
-
+
+
#define SQL_COPY_INTO_FILES "COPY BINARY INTO bam.files FROM ('%s', '%s',
'%s', '%s', '%s', '%s');\n"
#define SQL_COPY_INTO_SQ "COPY BINARY INTO bam.sq FROM ('%s', '%s',
'%s', '%s', '%s', '%s', '%s');\n"
@@ -193,9 +194,9 @@
#define SQL_COPY_INTO_PAIRED_ALIGNMENTS "COPY BINARY INTO
bam.paired_%s_alignments_"LLFMT" FROM \
('%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', \
'%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s');\n"
-
+
#define SQL_COPY_INTO_ALIGNMENTS_EXTRA "COPY BINARY INTO
bam.alignments_extra_"LLFMT" FROM ('%s', '%s', '%s', '%s');\n"
-
+
#define BUF_SIZE_CREATE_STORAGE_0 2048
#define BUF_SIZE_CREATE_STORAGE_1 8192
#define BUF_SIZE_DROP_FILE 1024
@@ -205,137 +206,172 @@
/* Some buffers */
-char buf_sql_create_storage_0[BUF_SIZE_CREATE_STORAGE_0];
-char buf_sql_create_storage_1[BUF_SIZE_CREATE_STORAGE_1];
-char buf_sql_drop_file[BUF_SIZE_DROP_FILE];
-char buf_sql_copy_into[BUF_SIZE_COPY_INTO];
+static char buf_sql_create_storage_0[BUF_SIZE_CREATE_STORAGE_0];
+static char buf_sql_create_storage_1[BUF_SIZE_CREATE_STORAGE_1];
+static char buf_sql_drop_file[BUF_SIZE_DROP_FILE];
+static char buf_sql_copy_into[BUF_SIZE_COPY_INTO];
-str
-create_schema_if_not_exists(Client cntxt, mvc *m, str schemaname, str descr,
sql_schema **ret) {
- sql_schema *result;
- if((result = mvc_bind_schema(m, schemaname)) == NULL) {
- char buf_sql_create_schema[64];
- str sql_create_schema = buf_sql_create_schema;
- str msg;
-
- snprintf(sql_create_schema, 64, "CREATE SCHEMA %s;", schemaname);
-
- TO_LOG("#<bam_loader> Creating schema '%s'...\n", schemaname);
- RUN_SQL(cntxt, &sql_create_schema, descr, msg);
- if(msg != MAL_SUCCEED) {
- REUSE_EXCEPTION(msg, MAL, "create_schema_if_not_exists", "Could
not create bam schema: %s", msg);
- return msg;
- }
- if((result = mvc_bind_schema(m, schemaname)) == NULL) {
- throw(MAL, "create_schema_if_not_exists", "Could not create bam
schema");
- }
- }
- if(ret) *ret = result;
- return MAL_SUCCEED;
+str
+create_schema_if_not_exists(Client cntxt, mvc * m, str schemaname, str descr,
+ sql_schema ** ret)
+{
+ sql_schema *result;
+
+ if ((result = mvc_bind_schema(m, schemaname)) == NULL) {
+ char buf_sql_create_schema[64];
+ str sql_create_schema = buf_sql_create_schema;
+ str msg;
+
+ snprintf(sql_create_schema, 64, "CREATE SCHEMA %s;",
+ schemaname);
+
+ TO_LOG("#<bam_loader> Creating schema '%s'...\n", schemaname);
+ RUN_SQL(cntxt, &sql_create_schema, descr, msg);
+ if (msg != MAL_SUCCEED) {
+ REUSE_EXCEPTION(msg, MAL,
+ "create_schema_if_not_exists",
+ "Could not create bam schema: %s",
+ msg);
+ return msg;
+ }
+ if ((result = mvc_bind_schema(m, schemaname)) == NULL) {
+ throw(MAL, "create_schema_if_not_exists",
+ "Could not create bam schema");
+ }
+ }
+ if (ret)
+ *ret = result;
+ return MAL_SUCCEED;
}
/**
- * Function tries to bind to a table with the given name. If it fails (==
NULL), it attempts to create the table.
- * The function fails if a binding to the table is impossible, even after
creation.
- * If the function succeeds, it adjusts the optionally given pointer to point
to the binded sql_table.
+ * Function tries to bind to a table with the given name. If it fails
+ * (== NULL), it attempts to create the table.
+ * The function fails if a binding to the table is impossible, even
+ * after creation. If the function succeeds, it adjusts the
+ * optionally given pointer to point to the binded sql_table.
*/
-str
-create_table_if_not_exists(Client cntxt, mvc *m, sql_schema *s, str tablename,
str sql_creation, str descr, sql_table **ret) {
- sql_table *result;
- str msg;
- if((result = mvc_bind_table(m, s, tablename)) == NULL) {
- TO_LOG("#<bam_loader> Creating table '%s'...\n", tablename);
+str
+create_table_if_not_exists(Client cntxt, mvc * m, sql_schema * s,
+ str tablename, str sql_creation, str descr,
+ sql_table ** ret)
+{
+ sql_table *result;
+ str msg;
- RUN_SQL(cntxt, &sql_creation, descr, msg);
- if(msg != MAL_SUCCEED) {
- REUSE_EXCEPTION(msg, MAL, "create_table_if_not_exists", "Could not
create table '%s': %s", tablename, msg);
- return msg;
- }
- if((result = mvc_bind_table(m, s, tablename)) == NULL) {
- throw(MAL, "create_table_if_not_exists", "Could not create table
'%s'", tablename);
- }
- }
- if(ret) *ret = result;
- return MAL_SUCCEED;
+ if ((result = mvc_bind_table(m, s, tablename)) == NULL) {
+ TO_LOG("#<bam_loader> Creating table '%s'...\n", tablename);
+
+ RUN_SQL(cntxt, &sql_creation, descr, msg);
+ if (msg != MAL_SUCCEED) {
+ REUSE_EXCEPTION(msg, MAL,
+ "create_table_if_not_exists",
+ "Could not create table '%s': %s",
+ tablename, msg);
+ return msg;
+ }
+ if ((result = mvc_bind_table(m, s, tablename)) == NULL) {
+ throw(MAL, "create_table_if_not_exists",
+ "Could not create table '%s'", tablename);
+ }
+ }
+ if (ret)
+ *ret = result;
+ return MAL_SUCCEED;
}
/**
- * Function returns the highest file id that currently exists in the bam.files
table and stores this number + 1 in the next_file_id
- * variable. Function doesn't use a mutex to guarantee that the returned value
is up to date at return time. If this is required,
+ * Function returns the highest file id that currently exists in the
+ * bam.files table and stores this number + 1 in the next_file_id
+ * variable. Function doesn't use a mutex to guarantee that the
+ * returned value is up to date at return time. If this is required,
* the calling function should activate a mutex.
*/
str
-next_file_id(mvc *m, sql_table *files, lng *next_file_id)
+next_file_id(mvc * m, sql_table * files, lng * next_file_id)
{
- sql_column *c;
- BAT *b = NULL;
- BATiter li;
- sht i;
- BUN p = 0, q = 0;
- lng max_file_id = 0;
-
- assert(m != NULL);
- assert(files != NULL);
-
- /* Try to bind the file_id column of the bam.files table */
- if((c = mvc_bind_column(m, files, "file_id")) == NULL) {
- throw(MAL, "next_file_id", "Could not retrieve the next file id: Error
binding file_id column of 'files' table");
- }
-
- /* Loop through all BATs for this column, i.e. the real BAT and the delta
BATs and find the maximum file_id */
- for(i=0; i<3; ++i) {
- b = store_funcs.bind_col(m->session->tr, c, i);
- if(b != NULL) {
- li = bat_iterator(b);
- BATloop(b, p, q) {
- lng t = *(lng *)BUNtail(li, p);
- max_file_id = MAX(max_file_id, t);
- }
- BBPreleaseref(b->batCacheid);
- }
- }
- *next_file_id = max_file_id+1;
- return MAL_SUCCEED;
+ sql_column *c;
+ BAT *b = NULL;
+ BATiter li;
+ sht i;
+ BUN p = 0, q = 0;
+ lng max_file_id = 0;
+
+ assert(m != NULL);
+ assert(files != NULL);
+
+ /* Try to bind the file_id column of the bam.files table */
+ if ((c = mvc_bind_column(m, files, "file_id")) == NULL) {
+ throw(MAL, "next_file_id",
+ "Could not retrieve the next file id: Error binding
file_id column of 'files' table");
+ }
+
+ /* Loop through all BATs for this column, i.e. the real BAT
+ * and the delta BATs and find the maximum file_id */
+ for (i = 0; i < 3; ++i) {
+ b = store_funcs.bind_col(m->session->tr, c, i);
+ if (b != NULL) {
+ li = bat_iterator(b);
+ BATloop(b, p, q) {
+ lng t = *(lng *) BUNtail(li, p);
+
+ max_file_id = MAX(max_file_id, t);
+ }
+ BBPreleaseref(b->batCacheid);
+ }
+ }
+ *next_file_id = max_file_id + 1;
+ return MAL_SUCCEED;
}
str
-create_alignment_storage_0(Client cntxt, str descr, bam_wrapper *bw) {
- str sql_create_storage = buf_sql_create_storage_0;
- str msg;
- snprintf(sql_create_storage, BUF_SIZE_CREATE_STORAGE_0,
SQL_CREATE_STORAGE_0,
- bw->file_id, bw->file_id, bw->file_id, bw->file_id, bw->file_id,
bw->file_id);
- RUN_SQL(cntxt, &sql_create_storage, descr, msg);
- if(msg != MAL_SUCCEED) {
- REUSE_EXCEPTION(msg, MAL, "create_alignment_storage_0",
- "Could not create alignment storage for file '%s'
(file id '"LLFMT"'): %s",
- bw->file_location, bw->file_id, msg);
- }
- return msg;
+create_alignment_storage_0(Client cntxt, str descr, bam_wrapper * bw)
+{
+ str sql_create_storage = buf_sql_create_storage_0;
+ str msg;
+
+ snprintf(sql_create_storage, BUF_SIZE_CREATE_STORAGE_0,
+ SQL_CREATE_STORAGE_0, bw->file_id, bw->file_id, bw->file_id,
+ bw->file_id, bw->file_id, bw->file_id);
+ RUN_SQL(cntxt, &sql_create_storage, descr, msg);
+ if (msg != MAL_SUCCEED) {
+ REUSE_EXCEPTION(msg, MAL, "create_alignment_storage_0",
+ "Could not create alignment storage for file
'%s' (file id '"
+ LLFMT "'): %s", bw->file_location,
+ bw->file_id, msg);
+ }
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