Bug#834139: ncbi-tools6: please add support for SOURCE_DATE_EPOCH

[Sascha Steinbiss]

Source: ncbi-tools6
Severity: wishlist
Tags: patch
User: reproducible-bui...@lists.alioth.debian.org
Usertags: timestamps


Dear Maintainer,

while trying to make the metastudent-data package reproducible, I noticed that
the binary package contains BLAST index files which embed timestamps
representing the index build time. I have attached a patch to libncbi6 that
adds support for SOURCE_DATE_EPOCH [1]  to avoid embedding the current time
and date into generated index files.
I hope that this will make the build of packages including BLAST indexes in
their artifacts reproducible.

Thanks and kind regards
Sascha

[1] https://reproducible-builds.org/specs/source-date-epoch

Description: add support for SOURCE_DATE_EPOCH
 BLAST index files embed the date and time of their generation. This patch
 adds support for SOURCE_DATE_EPOCH (see public specification at
 https://reproducible-builds.org/specs/source-date-epoch/) to formatdb.
Author: Sascha Steinbiss <sa...@debian.org>
--- a/corelib/ncbitime.c
+++ b/corelib/ncbitime.c
@@ -77,6 +77,7 @@
 #include <ncbi.h>
 #include <ncbithr.h>
 #include <ncbiwin.h>
+#include <stdlib.h>
 
 #ifdef OS_UNIX
 #include <sys/times.h>
@@ -108,8 +109,14 @@
 *****************************************************************************/
 NLM_EXTERN Nlm_Boolean LIBCALL  Nlm_GetDayTime (Nlm_DayTimePtr dtp)
 {
+  const char *sde = getenv("SOURCE_DATE_EPOCH");
 #if (defined(SOLARIS_THREADS_AVAIL)  ||  defined(POSIX_THREADS_AVAIL)  ||  defined(WIN32)) && !defined(OS_UNIX_DARWIN)
-  time_t t = time( NULL );
+  time_t t;
+  if (sde) {
+    t = strtoul(sde, NULL, 0);
+   } else {
+    t = time( NULL );
+   }
 #ifdef WIN32
   static TNlmMutex localtime_lock;
   if (NlmMutexLockEx( &localtime_lock ) != 0)
@@ -125,7 +132,11 @@
   time_t ltime;
   struct tm *dt;
   Nlm_MemFill ((Nlm_VoidPtr) dtp, 0, sizeof(Nlm_DayTime));
-	time(&ltime);
+  if (sde) {
+    ltime = strtoul(sde, NULL, 0);
+  } else {
+    time(&ltime);
+  }
   if ((dt = localtime (&ltime)) != NULL)
  	{
         Nlm_MemCopy ((Nlm_VoidPtr) dtp, (Nlm_VoidPtr) dt, sizeof (struct tm));