New upstream version 2.8.2-5+dfsg (f9830f55) · Commits · Debian Med / sra-sdk

test/sra-sort/md-created.sh

0 → 100755

+52 −0

Original line number	Diff line number	Diff line
		#!/bin/bash

		TMP=/export/home/TMP
		if [ ! -d "$TMP" ] ; then
		echo $TMP is not found: skipping the test
		exit 0
		fi

		if [ "$PANFS_PAN1" == "" ] ; then
		echo PANFS_PAN1 is not set: exiting
		exit 1
		fi

		I=`whoami`
		DSTDIR=$TMP/$I/sra-sort-md
		DST=$DSTDIR/sorted

		rm -fr $DSTDIR

		SORT=sra-sort
		which $SORT > /dev/null 2>&1
		if [ "$?" != "0" ] ; then
		echo "sra-sort not found: add it to your PATH"
		exit 10
		fi

		OPT="--tempdir $DSTDIR --mmapdir $DSTDIR --map-file-bsize 80000000000 --max-ref-idx-ids 4000000000 --max-idx-ids 4000000000 --max-large-idx-ids 800000000"
		SRC=$PANFS_PAN1/sra-test/TEST-DATA/SRR5318091-sra-sort-md
		CMD="$SORT -f -v -L6 $OPT $SRC $DST"
		echo $ $CMD

		$CMD
		EXIT=$?
		if [ $EXIT -ne 0 ] ; then
		echo "sra-sort failed with $EXIT"
		rm -r $DSTDIR
		exit $EXIT
		fi

		if [ ! -d "$DST/md" ] ; then
		echo Failure: md was not created in $DST:
		echo $ ls $DST
		ls $DST
		rm -r $DSTDIR
		exit 20
		else
		echo Success: md was created in $DST:
		echo $ ls $DST
		ls $DST
		fi

		rm -r $DSTDIR

+6 −2

Original line number	Diff line number	Diff line
		@@ -446,6 +446,10 @@ void cSRATblPairPostCopyAlign ( cSRATblPair self, const ctx_t ctx )

		cSRAPair *csra = self -> csra;

		struct KThread ** pt = NULL;
		assert ( self );
		pt = & self -> dad . thread;

		RowSetIteratorRelease ( self -> rsi, ctx );
		self -> rsi = NULL;

		@@ -458,10 +462,10 @@ void cSRATblPairPostCopyAlign ( cSRATblPair self, const ctx_t ctx )
		switch ( self -> align_idx )
		{
		case 1:
		CrossCheckRefAlignTbl ( ctx, csra -> reference -> dtbl, csra -> prim_align -> dtbl, "PRIMARY_ALIGNMENT" );
		CrossCheckRefAlignTbl ( ctx, csra -> reference -> dtbl, csra -> prim_align -> dtbl, "PRIMARY_ALIGNMENT", pt );
		break;
		case 2:
		CrossCheckRefAlignTbl ( ctx, csra -> reference -> dtbl, csra -> sec_align -> dtbl, "SECONDARY_ALIGNMENT" );
		CrossCheckRefAlignTbl ( ctx, csra -> reference -> dtbl, csra -> sec_align -> dtbl, "SECONDARY_ALIGNMENT", pt );

		#if SEQUENCE_BEFORE_SECONDARY
		cSRATblPairWhackMappingIdx ( self, ctx );

+38 −0

Original line number	Diff line number	Diff line
		@@ -47,6 +47,7 @@ typedef struct TablePair StdTblPair;
		#include <klib/text.h>
		#include <klib/namelist.h>
		#include <klib/rc.h>
		#include <kproc/thread.h> /* KThreadWait */

		#include <string.h>

		@@ -1051,5 +1052,42 @@ void TablePairDestroy ( TablePair self, const ctx_t ctx )

		MemFree ( ctx, ( void* ) self -> full_spec, self -> full_spec_size + 1 );

		if ( self -> thread != NULL ) {
		rc_t rc = 0;
		rc_t status = 0;
		STATUS ( 2, "waiting for background thread 0x%p to finish...",
		self -> thread );

		rc = KThreadWait ( self -> thread, & status );
		if ( rc != 0 )
		ERROR ( rc, "failed to wait for background thread 0x%p",
		self -> thread );
		else if ( status == 0 )
		STATUS ( 2, "...background thread 0x%p succeed", self -> thread );
		else {
		ERROR ( status, "background thread 0x%p failed", self -> thread );
		rc = status;
		}

		{
		rc_t r2 = KThreadRelease ( self -> thread );
		if ( r2 != 0 ) {
		ERROR ( r2, "failed to release background thread 0x%p",
		self -> thread );
		if ( rc == 0 )
		rc = r2;
		}
		}

		if ( rc != 0 && ctx != NULL ) {
		ctx_t * mctx = NULL;
		for ( mctx = ( ctx_t * ) ctx; mctx != NULL && mctx -> rc == 0;
		mctx = ( ctx_t* ) mctx -> caller )
		{
		mctx -> rc = rc;
		}
		}
		}

		memset ( self, 0, sizeof * self );
		}

+4 −0

Original line number	Diff line number	Diff line
		@@ -45,6 +45,7 @@
		*/
		struct VTable;
		struct DbPair;
		struct KThread;
		struct ColumnReader;
		struct ColumnWriter;
		struct ColumnPair;
		@@ -109,6 +110,9 @@ struct TablePair
		/* true if already exploded */
		bool exploded;

		/* Thread launched by TablePairPostCopy [ to do consistency-check ] */
		struct KThread * thread;

		uint8_t align [ 2 ];
		};

+9 −3

Original line number	Diff line number	Diff line
		@@ -341,11 +341,12 @@ rc_t CC CrossCheckRefAlignTblRun ( const KThread self, void data )
		ctx_t thread_ctx = { & pb -> caps, NULL, & ctx_info };
		const ctx_t *ctx = & thread_ctx;

		STATUS ( 2, "running consistency-check on background thread" );
		STATUS ( 2, "running consistency-check on background thread 0x%p", self );

		CrossCheckRefAlignTblInt ( ctx, pb -> ref_tbl, pb -> align_tbl, pb -> align_name );

		STATUS ( 2, "finished consistency-check on background thread" );
		STATUS ( 2, "finished consistency-check on background thread 0x%p: %s",
		self, ctx -> rc ? "failure" : "success ");

		VTableRelease ( pb -> align_tbl );
		VTableRelease ( pb -> ref_tbl );
		@@ -357,7 +358,8 @@ rc_t CC CrossCheckRefAlignTblRun ( const KThread self, void data )
		#endif

		void CrossCheckRefAlignTbl ( const ctx_t *ctx,
		const VTable ref_tbl, const VTable align_tbl, const char *align_name )
		const VTable ref_tbl, const VTable align_tbl, const char *align_name,
		KThread ** pt )
		{
		FUNC_ENTRY ( ctx );

		@@ -368,6 +370,9 @@ void CrossCheckRefAlignTbl ( const ctx_t *ctx,

		STATUS ( 2, "consistency-check on join indices between REFERENCE and %s tables", align_name );

		assert ( pt );
		* pt = NULL;

		#if USE_BGTHREAD
		name_len = strlen ( align_name );
		TRY ( pb = MemAlloc ( ctx, sizeof * pb + name_len, false ) )
		@@ -391,6 +396,7 @@ void CrossCheckRefAlignTbl ( const ctx_t *ctx,
		rc = KThreadMake ( & t, CrossCheckRefAlignTblRun, pb );
		if ( rc == 0 )
		{
		* pt = t;
		return;
		}