.gitignore

+bin
+build
+include
+lib
+shlib
+*-stamp

access/ent2api.c

@@ -1273,7 +1273,7 @@ NLM_EXTERN CONN EntrezOpenConnection (
     *arg = '\0';
 
   return QUERY_OpenServiceQueryEx
-    (StringHasNoText (e2_service) ? "Entrez2" : e2_service, NULL, 30, arg);
+    (StringHasNoText (e2_service) ? "Entrez2s" : e2_service, NULL, 30, arg);
 }
 
 #ifdef OS_MAC

api/sqnutil3.c

@@ -33198,7 +33198,7 @@ ClickableItemPtr LIBCALL ClickableGlobalItemCategorize (ValNodePtr list, int ite
        cip->clickable_item_type = item_type;
        cip->description 
           = (CharPtr) MemNew ( sizeof (Char) * (StringLen (fmt) + 15));
-       sprintf (cip->description, fmt);
+       strcpy (cip->description, fmt);
        return cip;
   }
   return NULL;

connect/ncbi_gnutls.c

@@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull pull, FSSLPush push)
 
     assert(!s_GnuTlsCredAnon);
 
+#if 0
     version = gnutls_check_version(0);
     if (strcasecmp(GNUTLS_VERSION, version) != 0) {
         CORE_LOGF(eLOG_Critical,
@@ -592,6 +593,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull pull, FSSLPush push)
                    GNUTLS_VERSION, version));
         assert(0);
     }
+#endif
 
     val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0);
     CORE_LOCK_READ;

connect/ncbi_http_connector.c

@@ -240,8 +240,14 @@ static int/*bool*/ x_UnsafeRedirectOK(SHttpConnector* uuu)
     if (uuu->unsafe_redir == eDefault) {
         if (!(uuu->flags & fHTTP_UnsafeRedirects)) {
             char val[32];
+            const char* dflt = NULL;
+            if (uuu->net_info->scheme == eURL_Https
+		&&  (strspn(uuu->net_info->host, "0123456789.")
+		     == strlen(uuu->net_info->host))) {
+                dflt = "TRUE";
+            }
             ConnNetInfo_GetValue(0, "HTTP_UNSAFE_REDIRECTS",
-                                 val, sizeof(val), 0);
+                                 val, sizeof(val), dflt);
             uuu->unsafe_redir = ConnNetInfo_Boolean(val) ? eOn : eOff;
         } else
             uuu->unsafe_redir = eOn;

connect/ncbi_util.c

@@ -49,7 +49,9 @@
 #  ifndef NCBI_OS_SOLARIS
 #    include <limits.h>
 #  endif /*!NCBI_OS_SOLARIS*/
-#  ifdef NCBI_OS_LINUX
+#  ifdef __MACH__
+#    include <mach/vm_param.h>
+#  elif defined(NCBI_OS_LINUX)
 #    include <sys/user.h>
 #  endif /*NCBI_OS_LINUX*/
 #  include <pwd.h>

connect/urlquery.c

@@ -128,7 +128,10 @@ NLM_EXTERN CONN QUERY_OpenUrlQuery (
   }
   if ( host_port ) {
     net_info->port = host_port;
+  } else {
+    net_info->scheme = eURL_Https;
   }
+
   StringNCpy_0 (net_info->path, host_path, sizeof (net_info->path));
   if (StringDoesHaveText (arguments)) {
     StringNCpy_0 (net_info->args, arguments, sizeof (net_info->args));

corelib/ncbimain.c

@@ -67,6 +67,7 @@
 #pragma segment NlmSegA
 #endif
 
+extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
 
 /*****************************************************************************
 *
@@ -95,7 +96,12 @@ main(int argc, char *argv[])
   /* Initialize connection library's logger, registry and lock */
   CONNECT_Init(0);
 
-  retval = Nlm_Main();
+  if (Nlm_Main) {
+    retval = Nlm_Main();
+  } else {
+    ErrPost(0, 0, "Neither main nor Nlm_Main defined by program.");
+    retval = -1;
+  }
 
   NlmThreadJoinAll();
 

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 +109,18 @@ NLM_EXTERN time_t LIBCALL  Nlm_GetSecs (void)
 *****************************************************************************/
 NLM_EXTERN Nlm_Boolean LIBCALL  Nlm_GetDayTime (Nlm_DayTimePtr dtp)
 {
+  /* This function honors the SOURCE_DATE_EPOCH specificatin
+     (https://reproducible-builds.org/specs/source-date-epoch/) */
+  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);
+    if (t == 0)
+      return FALSE;
+  } else {
+    t = time( NULL );
+  }
 #ifdef WIN32
   static TNlmMutex localtime_lock;
   if (NlmMutexLockEx( &localtime_lock ) != 0)
@@ -125,7 +136,13 @@ NLM_EXTERN Nlm_Boolean LIBCALL  Nlm_GetDayTime (Nlm_DayTimePtr dtp)
   time_t ltime;
   struct tm *dt;
   Nlm_MemFill ((Nlm_VoidPtr) dtp, 0, sizeof(Nlm_DayTime));
-	time(&ltime);
+  if (sde) {
+    ltime = strtoul(sde, NULL, 0);
+    if (ltime == 0)
+      return FALSE;
+  } else {
+    time(&ltime);
+  }
   if ((dt = localtime (&ltime)) != NULL)
  	{
         Nlm_MemCopy ((Nlm_VoidPtr) dtp, (Nlm_VoidPtr) dt, sizeof (struct tm));

debian/.gitignore

+*.xpm
+*.debhelper
+*.debhelper.log
+*.substvars
+files
+libncbi6
+libvibrant6b
+lib*-dbg
+lib*-dev
+ncbi-data
+ncbi-rrna-data
+ncbi-tools-bin
+ncbi-tools-x11
+tmp

debian/.ncbirc

+[LINKS]
+CHANNELS=LINKS_FROM_MEDLINE, LINKS_FROM_SEQUENCE
+
+[SEQUENCE_CD_DESC]
+MEDIA=ENTREZ_SEQ_CD
+
+[REFERENCE_FROM_NET]
+MEDIA=ENTREZ_NET
+
+[SEQUENCE_FROM_NET]
+MEDIA=ENTREZ_NET
+
+[LINKS_FROM_NET]
+MEDIA=ENTREZ_NET
+ENTR_SEQ__ENTR_SEQ=1
+ENTR_SEQ__ENTR_REF=1
+ENTR_REF__ENTR_SEQ=1
+ENTR_REF__ENTR_REF=1
+
+[NCBI]
+DATA=/usr/share/ncbi/data/
+MEDIA=ENTREZ_NET
+AsnLoad=
+
+[ENTR_LINK]
+CHANNELS=LINKS_FROM_NET
+
+[ENTR_REF]
+CHANNELS=REFERENCE_FROM_NET
+
+[ENTR_SEQ]
+CHANNELS=SEQUENCE_FROM_NET
+
+[ENTREZ]
+SERVICES=ENTR_LINK, ENTR_REF, ENTR_SEQ
+
+[ENTREZ_NET]
+TYPE=NET
+SERVICE_NAME=Entrez
+RESOURCE_NAME=Entrez
+RESOURCE_TYPE=Entrez
+SERV_VERS_MIN=1
+SERV_VERS_MAX=0
+RES_VERS_MIN=150
+RES_VERS_MAX=0
+FORMAL_NAME=Entrez Network Service
+
+[NET_SERV]
+DISPATCHER=130.14.25.211
+DISP_ALT_1=dispatch1.nlm.nih.gov
+DISP_ALT_2=130.14.25.47
+DISP_ALT_3=dispatch2.nlm.nih.gov
+DISP_ALT_4=dispatch3.nlm.nih.gov
+DISP_ALT_5=130.14.25.1
+DISPSERIALNO=6
+DISP_USERNAME=letondal
+DISP_RECONN_ACTION=CONT
+
+[FONTS]
+JOURNAL=Helvetica,12,i
+VOLUME=Helvetica,12,b
+PAGES=Helvetica,12
+TITLE=Times,18,b
+AUTHORS=Times,18
+AFFILIATION=Times,14
+ABSTRACT=Times,14
+MESH=Times,12
+HEADING=Helvetica,14,b
+REFERENCE=Helvetica,12
+SEQUENCE=Courier,12
+STANDARD=Times,12
+DISPLAY=Courier,10
+FETCHED=Times,14
+

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debian/Cn3D-3.0.desktop.in

+Name=Cn3D NCBI Database Viewer
+GenericName=Database Viewer
+Comment=View NCBI databases in 3D

debian/NOTES

+X apps should pull in -lvibrant BEFORE -lvibgif to avoid problematic
+shadowing.

debian/Psequin.desktop.in

+Name=Sequin DNA Sequence Submission Tool
+GenericName=Sequence Submission Tool
+Comment=Submit DNA sequences to the GenBank, EMBL, and DDBJ databases

debian/README.test

+Notes on how this package can be tested.
+_______________________________________
+
+This package can be tested by execution
+
+	bash run-unit-test
+
+in order to confirm its integrity.

debian/TODO

+* Document sequin's options properly.
+* Split blast.1 back up, preferably semi-automatically?

debian/compat

+11