CHANGES.md

 # NCBI External Developer Release:
 
+
+## SRA Toolkit 2.9.3
+**October 17, 2018**
+  **kns**: added possibility to skip server's certificate validation
+  **kns**: expect to receive HTTP status 200 when sending range-request that includes the whole file
+  **vdb, vdb-copy**: fixed a bug in accessing pagemap process request for cursors which do not have pagemap thread running
+
+
+## SRA Toolkit 2.9.2-2
+**September 26, 2018**
+  **read-filter-redact**: Fixed to update HISTORY metadata
+
+
 ## SRA Toolkit 2.9.2
 **July 23, 2018**
   **kfg, vfs**: Introduced enhanced handling of download-only NGC files that lack read/decrypt permissions

build/Makefile.vers

@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # SRA-TOOLS and library version
-VERSION = 2.9.2
+VERSION = 2.9.3

debian/changelog

+sra-sdk (2.9.3+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller@debian.org>  Tue, 23 Oct 2018 15:12:22 +0200
+
 sra-sdk (2.9.2+dfsg-2) unstable; urgency=medium
 
   * Architecture: amd64

debian/patches/drop_tests.patch

@@ -2,8 +2,10 @@ Description: Drop test that should not run as root
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 19 Oct 2017 23:58:30 +0200
 
---- a/test/vdb-config/Makefile
-+++ b/test/vdb-config/Makefile
+Index: sra-sdk/test/vdb-config/Makefile
+===================================================================
+--- sra-sdk.orig/test/vdb-config/Makefile
++++ sra-sdk/test/vdb-config/Makefile
 @@ -31,5 +31,4 @@ runtests: test-vdb-config
  
  test-vdb-config:
@@ -11,11 +13,13 @@ Last-Update: Thu, 19 Oct 2017 23:58:30 +0200
 -	@ PATH=$(BINDIR):$(PATH) ; ./test-vdb-config.pl
 -	@ echo OK
 +	@ echo "This test is droped since the executable should not be run as root"
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -36,7 +36,6 @@ include $(TOP)/build/Makefile.config
- #
+Index: sra-sdk/test/Makefile
+===================================================================
+--- sra-sdk.orig/test/Makefile
++++ sra-sdk/test/Makefile
+@@ -37,7 +37,6 @@ include $(TOP)/build/Makefile.config
  SUBDIRS =    \
+ 	read-filter-redact \
  	prefetch        \
 -	dump-test       \
  	vdb-config      \

debian/patches/ignore_failing_test_for_the_moment_FIXME.patch

@@ -13,12 +13,14 @@ Description: It needs to be investigated why this test is failing with:
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Sat, 24 Mar 2018 07:41:44 +0100
 
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -35,23 +35,16 @@ include $(TOP)/build/Makefile.config
- # default
+Index: sra-sdk/test/Makefile
+===================================================================
+--- sra-sdk.orig/test/Makefile
++++ sra-sdk/test/Makefile
+@@ -36,23 +36,16 @@ include $(TOP)/build/Makefile.config
  #
  SUBDIRS =    \
+ 	read-filter-redact \
 -	prefetch        \
  	vdb-config      \
  	align-info      \
@@ -39,7 +41,7 @@ Last-Update: Sat, 24 Mar 2018 07:41:44 +0100
  
  # under construction
  #    ngs-pileup      \
-@@ -61,6 +54,8 @@ include $(TOP)/build/Makefile.targets
+@@ -62,6 +55,8 @@ include $(TOP)/build/Makefile.targets
  
  $(SUBDIRS):
  	@ $(MAKE) -C $@

shared/toolkit.vers

-2.9.2
+2.9.3

shared/toolkit.vers.h

-#define TOOLKIT_VERS 0x02090002
+#define TOOLKIT_VERS 0x02090003

test/Makefile

@@ -35,6 +35,7 @@ include $(TOP)/build/Makefile.config
 # default
 #
 SUBDIRS =    \
+	read-filter-redact \
 	prefetch        \
 	dump-test       \
 	vdb-config      \

test/prefetch/Makefile

@@ -36,8 +36,8 @@ KMER=$(SRA)/traces/nannot01/kmer/000/390/GCA_000390265.1_R
 KMERF=$(SRAF):data/sracloud/traces/nannot01/kmer/000/390/GCA_000390265.1_R
 REFSEQ=$(SRA)/traces/refseq/KC702174.1
 REFSEQF=$(SRAF):data/sracloud/traces/refseq/KC702174.1
-SRR=$(SRA)/traces/sra6/SRR/000052/SRR053325
-SRRF=$(SRAF):data/sracloud/traces/sra6/SRR/000052/SRR053325
+SRR=$(SRA)/traces/sra59/SRR/000052/SRR053325
+SRRF=$(SRAF):data/sracloud/traces/sra59/SRR/000052/SRR053325
 WGS=$(SRA)/traces/wgs03/WGS/AF/VF/AFVF01.1
 WGSF=$(SRAF):data/sracloud/traces/wgs03/WGS/AF/VF/AFVF01.1
 
@@ -205,10 +205,13 @@ urls_and_accs:
 
 	@rm `pwd`/tmp/sra/SRR053325.sra
 	@echo SRR FASP download when user repository is configured
-	@if ascp -h > /dev/null ; then \
+	if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    $(BINDIR)/prefetch $(SRRF) > /dev/null ; \
 	    ls `pwd`/tmp/sra/SRR053325.sra > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 else echo download of $(SRRF) when ascp is not found is disabled ; \
 	 fi
 #	@echo
@@ -216,9 +219,12 @@ urls_and_accs:
 	@rm `pwd`/tmp/refseq/KC702174.1
 	@echo REFSEQ download when user repository is configured
 	@if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	      $(BINDIR)/prefetch $(REFSEQF) > /dev/null ; \
 	    ls `pwd`/tmp/refseq/KC702174.1 > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 else echo download of $(REFSEQF) when ascp is not found is disabled ; \
 	 fi
 #	@echo
@@ -226,9 +232,12 @@ urls_and_accs:
 	@rm `pwd`/tmp/nannot/GCA_000390265.1_R
 	@echo NANNOT FASP download when user repository is configured
 	@if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	      $(BINDIR)/prefetch $(KMERF) > /dev/null ; \
 	      ls `pwd`/tmp/nannot/GCA_000390265.1_R > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 else echo download of $(KMERF) when ascp is not found is disabled ; \
 	 fi
 #	@echo
@@ -238,10 +247,13 @@ urls_and_accs:
 	@if ls `pwd`/tmp/wgs/AFVF01 2> /dev/null ; \
      then echo AFVF01 found ; exit 1; fi
 	@if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	      $(BINDIR)/prefetch $(WGSF) > /dev/null ; \
 	    echo INCORRECT DOWNLOAD OF WGS SHOULD BE FIXED: VDB-3537 ; \
 	    ls `pwd`/tmp/wgs/AFVF01 > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 else echo download of $(WGSF) when ascp is not found is disabled ; \
 	 fi
 	@echo
@@ -295,9 +307,12 @@ urls_and_accs:
 	@if ls `pwd`/tmp2/100MB 2> /dev/null ; \
      then echo 100MB found ; exit 1; fi
 	@if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \
 	    $(BINDIR)/prefetch $(LARGE) > /dev/null ; \
 	    ls `pwd`/100MB > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 else \
 	  if $(BINDIR)/prefetch $(LARGE) 2> /dev/null ; \
       then echo "prefetch <FASP URL> when ascp is not found should fail" ; \
@@ -310,9 +325,12 @@ urls_and_accs:
 	@if ls `pwd`/tmp2/1GB 2> /dev/null; \
      then echo 1GB found ; exit 1; fi
 	@if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	  export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \
 	    $(BINDIR)/prefetch fasp://anonftp@ftp.ncbi.nlm.nih.gov:1GB > /dev/null;\
 	    ls `pwd`/1GB > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	 fi
 #	@echo
 
@@ -358,11 +376,14 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH SRR FASP URL TO OUT-FILE ; \
 	    rm -f `pwd`/tmp3/dir/file ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    $(BINDIR)/prefetch $(SRRF) -O / -o tmp3/dir/file > /dev/null ; \
 	    ls `pwd`/tmp3/dir/file > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo
@@ -384,11 +405,14 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH FASP URL TO OUT-FILE ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    rm -f `pwd`/tmp3/dir/file ; \
 	    $(BINDIR)/prefetch $(LARGE) -O / -o tmp3/dir/file > /dev/null ; \
 	    ls `pwd`/tmp3/dir/file > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo
@@ -424,11 +448,14 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH SRR FASP URL ; \
 	    rm `pwd`/tmp/sra/SRR053325.sra ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    $(BINDIR)/prefetch $(SRRF) > /dev/null ; \
 	    ls `pwd`/tmp/sra/SRR053325.sra > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo
@@ -449,11 +476,14 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH FASP URL ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \
 	    if ls `pwd`/100MB 2> /dev/null ; then exit 1; fi ; \
 	    $(BINDIR)/prefetch $(LARGE) > /dev/null ; \
 	    ls `pwd`/100MB > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo
@@ -473,11 +503,14 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH SRR FASP URL TO OUT-DIR ; \
 	    rm -f `pwd`/tmp3/dir/SRR053325.sra ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    $(BINDIR)/prefetch $(SRRF) -O tmp3/dir > /dev/null ; \
 	    ls `pwd`/tmp3/dir/SRR053325.sra > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo
@@ -500,12 +533,15 @@ out_dir_and_file:
 #	@ echo
 
 	@ if ascp -h > /dev/null ; then \
+	  if [ `hostname` != 'iebdev21' ] ; then \
 	    echo PREFETCH FASP URL TO OUT-DIR ; \
 	    export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \
 	    if ls `pwd`/tmp3/dir/100MB 2> /dev/null ; then \
         echo 100MB found ; exit 1 ; fi ; \
 	    $(BINDIR)/prefetch $(LARGE) -O tmp3/dir > /dev/null ; \
 	    ls `pwd`/tmp3/dir/100MB > /dev/null ; \
+	  else echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD HOST; echo BAD;\
+	  fi \
 	  else echo download of SRR FASP URL when ascp is not found is disabled ; \
 	  fi
 #	@ echo

test/read-filter-redact/Makefile

+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ==============================================================================
+
+default: runtests
+
+TOP ?= $(abspath ../..)
+
+include $(TOP)/build/Makefile.env
+
+runtests: check_version
+
+RUN=tmp-read-filter-redact-test-run
+FLT=tmp-read-filter-redact-test-in
+
+check_version: #/align-cache/CSRA_file
+	# remove old test files
+	@ if $(BINDIR)/vdb-unlock $(RUN) 2>/dev/null ; then echo ; fi
+	@ rm -fr tmp-read-filter-redact-test-*
+
+
+	# prepare sources
+	@ echo 1 > $(FLT)
+	@ $(BINDIR)/kar --extract ../align-cache/CSRA_file \
+		--directory $(RUN)
+
+	# make sure HISTORY meta does not exist
+	@ if $(BINDIR)/kdbmeta tmp-read-filter-redact-test-run \
+				-TSEQUENCE HISTORY 2>/dev/null; \
+		then echo "error: HISTORY found in source metadata"; exit 1; fi
+
+	# read-filter-redact
+	@ $(BINDIR)/read-filter-redact -F$(FLT) $(RUN)
+
+	# make sure HISTORY meta was created
+	@ $(BINDIR)/kdbmeta tmp-read-filter-redact-test-run -TSEQUENCE HISTORY | \
+		grep '^  <EVENT_1 build="' | grep '" run="' | \
+		grep '" tool="read-filter-redact" vers="'
+
+	# remove old test files
+	@ $(BINDIR)/vdb-unlock $(RUN)
+	@ rm -fr tmp-read-filter-redact-test-*

test/sra-stat/expected/SRR053325-biological

 <Run accession="SRR053325" read_length="fixed" spot_count="1" base_count="270" base_count_bio="237" spot_count_mates="0" base_count_bio_mates="0" spot_count_bad="0" base_count_bio_bad="0" spot_count_filtered="0" base_count_bio_filtered="0">
   <Member member_name="AVP24_435_36" spot_count="1" base_count="270" base_count_bio="237" spot_count_mates="0" base_count_bio_mates="0" spot_count_bad="0" base_count_bio_bad="0" spot_count_filtered="0" base_count_bio_filtered="0"/>
-  <Size value="10800" units="bytes"/>
+  <Size value="31401" units="bytes"/>
   <Bases cs_native="false" count="237">
     <Base value="A" count="42"/>
     <Base value="C" count="81"/>
@@ -8,4 +8,15 @@
     <Base value="T" count="56"/>
     <Base value="N" count="0"/>
   </Bases>
+  <QualityCount>
+    <Quality value="25" count="2"/>
+    <Quality value="29" count="4"/>
+    <Quality value="31" count="12"/>
+    <Quality value="32" count="7"/>
+    <Quality value="33" count="2"/>
+    <Quality value="36" count="5"/>
+    <Quality value="37" count="193"/>
+    <Quality value="38" count="13"/>
+    <Quality value="40" count="32"/>
+  </QualityCount>
 </Run>

tools/rd-filter-redact/read-filter-redact.c

@@ -35,15 +35,20 @@
 #include <vdb/schema.h> /* VSchemaRelease */
 
 #include <kdb/manager.h> /* KDBPathType */
+#include <kdb/meta.h> /* KMetadataRelease */
+#include <kdb/namelist.h> /* KMDataNodeListChild */
 
 #include <kfs/directory.h> /* KDirectory */
 #include <kfs/file.h> /* KFile */
 
+#include <klib/debug.h> /* DBGMSG */
 #include <klib/log.h> /* LOGERR */
 #include <klib/out.h> /* OUTMSG */
-#include <klib/status.h> /* STSMSG */
-#include <klib/debug.h> /* DBGMSG */
+#include <klib/printf.h> /* string_printf */
 #include <klib/rc.h> /* RC */
+#include <klib/status.h> /* STSMSG */
+#include <klib/time.h> /* KTimeLocal */
+
 #include <os-native.h>
 
 #include <assert.h>
@@ -57,8 +62,8 @@
 static KDirectory* __SpotIteratorDirectory = NULL;
 
 typedef struct CmdLine {
-	const char* table;
-	const char* file;
+    const char* table;
+    const char* file;
 } CmdLine;
 typedef struct SpotIterator {
     spotid_t crnSpotId;
@@ -91,6 +96,8 @@ typedef struct Db {
     VCursor *wCursor;
     uint32_t wIdx;
 
+    KMetadata *meta;
+
     bool locked;
 
     spotid_t nSpots;
@@ -505,19 +512,27 @@ static rc_t DbInit(rc_t rc, const CmdLine* args, Db* db)
         db->locked = true; /* has to be locked in production mode */
         rc = VDBManagerOpenTableUpdate (db->mgr, &db->tbl, NULL, args->table);
         if (rc != 0) {
-	    VDatabase *vdb;
-	    rc_t rc2 = VDBManagerOpenDBUpdate ( db->mgr, &vdb, NULL , args->table );
-	    if( rc2 == 0) {
-		rc2 = VDatabaseOpenTableUpdate ( vdb, &db->tbl, "SEQUENCE" );
-		if (rc2 == 0 ) rc = 0;
-		VDatabaseRelease ( vdb );
-	    }
-        }
-	if(rc != 0){
+            VDatabase *vdb;
+            rc_t rc2 = VDBManagerOpenDBUpdate ( db->mgr, &vdb, NULL,
+                                                args->table );
+            if( rc2 == 0) {
+                rc2 = VDatabaseOpenTableUpdate ( vdb, &db->tbl, "SEQUENCE" );
+                if (rc2 == 0 )
+                    rc = 0;
+                VDatabaseRelease ( vdb );
+            }
+        }
+        if(rc != 0){
             PLOGERR(klogErr, (klogErr, rc,
                 "while opening VTable '$(table)'", "table=%s", args->table));
-	}
+        }
     } 
+
+    if( rc == 0) {
+        rc = VTableOpenMetadataUpdate ( db->tbl, & db->meta );
+        DISP_RC(rc, "while Opening Metadata");
+    }
+
     if( rc == 0) {
         rc = VTableCreateCursorRead(db->tbl, &db->rCursor);
         DISP_RC(rc, "while creating read cursor");
@@ -558,6 +573,13 @@ static rc_t DbDestroy(Db* db)
 
     assert(db);
 
+    {
+        rc_t rc2 = KMetadataRelease(db->meta);
+        db->meta = NULL;
+        if (rc == 0)
+        {   rc = rc2; }
+    }
+
     {
         rc_t rc2 = VCursorRelease(db->rCursor);
         db->rCursor = NULL;
@@ -623,7 +645,7 @@ static rc_t Work(Db* db, SpotIterator* it)
             rc = VCursorReadDirect(db->rCursor, row_id, db->rFilterIdx,
                 elem_bits, bufferIn, sizeof bufferIn, &row_len);
             DISP_RC(rc, "while reading READ_FILTER");
-	    nreads = row_len;
+            nreads = row_len;
         }
         if (toRedact) {
             buffer = filter;
@@ -664,6 +686,168 @@ static rc_t Work(Db* db, SpotIterator* it)
     return rc;
 }
 
+static uint32_t get_child_count( KMDataNode *node )
+{
+    uint32_t res = 0;
+    KNamelist *names;
+    rc_t rc = KMDataNodeListChild ( node, &names );
+    DISP_RC( rc, "get_child_count:KMDataNodeListChild() failed" );
+    if ( rc == 0 )
+    {
+        rc = KNamelistCount ( names, &res );
+        DISP_RC( rc, "get_child_count:KNamelistCount() failed" );
+        KNamelistRelease ( names );
+    }
+    return res;
+}
+
+static rc_t fill_timestring( char * s, size_t size )
+{
+    KTime tr;
+    rc_t rc;
+    
+    KTimeLocal ( &tr, KTimeStamp() );
+    rc = string_printf ( s, size, NULL, "%lT", &tr );
+
+    DISP_RC( rc, "fill_timestring:string_printf( date/time ) failed" );
+    return rc;
+}
+
+static rc_t enter_time( KMDataNode *node, const char * key )
+{
+    char timestring[ 160 ];
+    rc_t rc = fill_timestring( timestring, sizeof timestring );
+    if ( rc == 0 )
+    {
+        rc = KMDataNodeWriteAttr ( node, key, timestring );
+        DISP_RC( rc, "enter_time:KMDataNodeWriteAttr( timestring ) failed" );
+    }
+    return rc;
+}
+
+static rc_t enter_version( KMDataNode *node, const char * key )
+{
+    char buff[ 32 ];
+    rc_t rc;
+
+    rc = string_printf ( buff, sizeof( buff ), NULL, "%.3V", KAppVersion() );
+    assert ( rc == 0 );
+    rc = KMDataNodeWriteAttr ( node, key, buff );
+    DISP_RC( rc, "enter_version:KMDataNodeWriteAttr() failed" );
+    return rc;
+}
+
+static rc_t enter_date_name_vers( KMDataNode *node )
+{
+    rc_t rc = enter_time( node, "run" );
+    DISP_RC( rc, "enter_date_name_vers:enter_time() failed" );
+    if ( rc == 0 )
+    {
+        rc = KMDataNodeWriteAttr ( node, "tool", "read-filter-redact" );
+        DISP_RC( rc, "enter_date_name_vers:"
+            "KMDataNodeWriteAttr(tool=read-filter-redact) failed" );
+        if ( rc == 0 )
+        {
+            rc = enter_version ( node, "vers" );
+            DISP_RC( rc, "enter_date_name_vers:enter_version() failed" );
+            if ( rc == 0 )
+            {
+                rc = KMDataNodeWriteAttr ( node, "build", __DATE__ );
+                DISP_RC( rc, "enter_date_name_vers:KMDataNodeWriteAttr"
+                    "(build=_DATE_) failed" );
+            }
+        }
+    }
+    return rc;
+}
+
+static rc_t update_history ( KMetadata *dst_meta ) {
+    rc_t rc = 0;
+    rc_t r2 = 0;
+    char event_name[ 32 ] = "";
+
+    KMDataNode *hist_node = NULL;
+    rc = KMetadataOpenNodeUpdate ( dst_meta, &hist_node, "HISTORY" );
+    DISP_RC(rc, "while Opening HISTORY Metadata");
+    if ( rc == 0 ) {
+        uint32_t index = get_child_count( hist_node );
+
+        if ( index > 0 ) { /* make sure EVENT_[i-1] exists */
+            const KMDataNode *node = NULL;
+            rc_t r = KMDataNodeOpenNodeRead ( hist_node, & node, "EVENT_%u",
+                                                                        index );
+            if ( r != 0 )
+                PLOGERR(klogErr, (klogErr, r,
+                    "while opening metanode HISTORY/EVENT_'$(n)'",
+                    "n=%u", index));
+            else
+                KMDataNodeRelease ( node );
+        }
+
+        ++ index;
+
+        { /* make sure EVENT_[i] does not exist */
+            const KMDataNode *node = NULL;
+            rc_t r = KMDataNodeOpenNodeRead ( hist_node, & node, "EVENT_%u",
+                                                                        index );
+            if ( r == 0 ) {
+                uint32_t mx = index * 2;
+                KMDataNodeRelease ( node );
+                r = RC ( rcExe, rcMetadata, rcReading, rcNode, rcExists );
+                PLOGERR(klogErr, (klogErr, r,
+                    "while opening metanode HISTORY/EVENT_'$(n)'",
+                    "n=%u", index));
+                r = 0;
+                for ( ; index < mx; ++ index ) {
+                    r = KMDataNodeOpenNodeRead ( hist_node, & node, "EVENT_%u",
+                                                                        index);
+                    if ( r == 0 ) {
+                        KMDataNodeRelease ( node );
+                        r = RC ( rcExe, rcMetadata, rcReading,
+                                        rcNode, rcExists );
+                        PLOGERR(klogErr, (klogErr, r,
+                            "while opening metanode HISTORY/EVENT_'$(n)'",
+                            "n=%u", index));
+                        r = 0;
+                    }
+                    else
+                        break;
+                }
+                if ( r == 0 ) {
+                    rc = RC ( rcExe, rcMetadata, rcReading, rcNode, rcExists );
+                    LOGERR( klogErr, rc,
+                        "cannot find next event metanode in HISTORY" );
+                }
+            }
+            else
+                KMDataNodeRelease ( node );
+        }
+
+        rc = string_printf ( event_name, sizeof( event_name ), NULL, "EVENT_%u",
+                                                                     index );
+        DISP_RC( rc, "update_history:string_printf(EVENT_NR) failed" );
+
+        if ( rc == 0 )
+        {
+            KMDataNode *event_node;
+            rc = KMDataNodeOpenNodeUpdate ( hist_node, &event_node,
+                                            event_name );
+            DISP_RC( rc,
+                "update_history:KMDataNodeOpenNodeUpdate('EVENT_NR') failed" );
+            if ( rc == 0 )
+            {
+                rc = enter_date_name_vers( event_node );
+                KMDataNodeRelease ( event_node );
+            }
+        }
+    }
+
+    r2 = KMDataNodeRelease ( hist_node );
+    if ( r2 != 0 && rc == 0 )
+        rc = r2;
+    return rc;
+}
+
 static rc_t Run(const CmdLine* args)
 {
     rc_t rc = 0;
@@ -698,6 +882,9 @@ static rc_t Run(const CmdLine* args)
         rc = Work(&db, &it);
     }
 
+    if (rc == 0)
+        rc = update_history(db.meta);
+
     if (rc == 0) {
         PLOGMSG(klogInfo, (klogInfo,
             "Success: redacted $(redacted) spots out of $(all)",
@@ -745,7 +932,7 @@ rc_t CC Usage(const Args* args)
     rc_t rc;
 
     if (args == NULL)
-        rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
+        rc = RC (rcExe, rcArgv, rcAccessing, rcSelf, rcNull);
     else
         rc = ArgsProgram (args, &fullpath, &progname);
     if (rc)
@@ -852,7 +1039,7 @@ rc_t CC KMain(int argc, char* argv[])
 
     ArgsWhack(args);
 
-    if (rc == RC(rcVDB, rcTable, rcOpening, rcSchema, rcNotFound))
+    if (rc == SILENT_RC(rcVDB, rcTable, rcOpening, rcSchema, rcNotFound))
     {   exit(10); }
 
     return rc;