Merge tag 'upstream/10.9.20190131+ds'

Upstream version 10.9.20190131(+ds).

6 files changed, 94 insertions, 25 deletions

diff --git a/debian/changelog b/debian/changelog
index b3e653f..31303aa 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-ncbi-entrez-direct (10.8.20190128+ds-1) UNRELEASED; urgency=medium
+ncbi-entrez-direct (10.9.20190131+ds-1) UNRELEASED; urgency=medium
 
   * New upstream release.  (NOT RELEASED YET.)
   * debian/man/{archive-pubmed,download-pubmed,edirect,efilter,
@@ -10,7 +10,7 @@ ncbi-entrez-direct (10.8.20190128+ds-1) UNRELEASED; urgency=medium
   * debian/rules: Stop installing retired scripts local-phrase-search and
     (implicitly) pm-{clean,current,erase,log,repack,uids,verify}.
 
- -- Aaron M. Ucko <ucko@debian.org>  Wed, 06 Feb 2019 22:36:07 -0500
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 06 Feb 2019 22:38:28 -0500
 
 ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium
 
diff --git a/edirect.pl b/edirect.pl
index d031584..69681d1 100755
--- a/edirect.pl
+++ b/edirect.pl
@@ -43,7 +43,7 @@ use File::Spec;
 
 # EDirect version number
 
-$version = "10.8";
+$version = "10.9";
 
 BEGIN
 {
diff --git a/nquire b/nquire
index b63d295..a48c3f5 100755
--- a/nquire
+++ b/nquire
@@ -43,7 +43,7 @@ use File::Spec;
 
 # nquire version number
 
-$version = "10.8";
+$version = "10.9";
 
 BEGIN
 {
@@ -571,7 +571,7 @@ sub nquire {
     }
   }
 
-  # if present, -http get or -get must be next
+  # if present, -http get or -get must be next (now also allow -http post or -post)
 
   # nquire -get -url "http://collections.mnh.si.edu/services/resolver/resolver.php" -voucher "Birds:625456"
 
@@ -586,6 +586,9 @@ sub nquire {
     } elsif ( $pat eq "-get" ) {
       $i++;
       $http = "get";
+    } elsif ( $pat eq "-post" ) {
+      $i++;
+      $http = "post";
     }
   }
 
@@ -653,6 +656,31 @@ sub nquire {
       if ( $i < $max ) {
         $url = "http://qa.ncbi.nlm.nih.gov/entrez/eutils";
       }
+
+    } elsif ( $pat eq "-hydra" ) {
+      # internal citation match request (undocumented)
+      $i++;
+      if ( $i < $max ) {
+        $url = "https://www.ncbi.nlm.nih.gov/projects/hydra/hydra_search.cgi";
+        $pat = $args[$i];
+        $pat = map_macros ($pat);
+        $enc = do_uri_escape ($pat);
+        $arg="search=pubmed_search_citation_top_20.1&query=$enc";
+        $amp = "&";
+        $i++;
+      }
+
+    } elsif ( $pat eq "-revhist" ) {
+      # internal sequence revision history request (undocumented)
+      $i++;
+      if ( $i < $max ) {
+        $url = "https://www.ncbi.nlm.nih.gov/sviewer/girevhist.cgi";
+        $pat = $args[$i];
+        $arg="cmd=seqid&txt=on&seqid=asntext&os=PUBSEQ_OS&val=$pat";
+        $amp = "&";
+        $i++;
+      }
+
     } elsif ( $pat eq "-pubchem" ) {
       # shortcut for PubChem Power User Gateway REST service base (undocumented)
       # nquire -pubchem "compound/name/creatine/property" "IUPACName,MolecularWeight,MolecularFormula" "XML"
@@ -676,28 +704,45 @@ sub nquire {
           }
         }
       }
-    } elsif ( $pat eq "-hydra" ) {
-      # internal citation match request (undocumented)
+
+    } elsif ( $pat eq "-mygene" or $pat eq "-mygene.info" ) {
+      # shortcut for mygene.info (undocumented)
       $i++;
       if ( $i < $max ) {
-        $url = "https://www.ncbi.nlm.nih.gov/projects/hydra/hydra_search.cgi";
-        $pat = $args[$i];
-        $pat = map_macros ($pat);
-        $enc = do_uri_escape ($pat);
-        $arg="search=pubmed_search_citation_top_20.1&query=$enc";
-        $amp = "&";
-        $i++;
+        $url = "http://mygene.info/v3";
+        if ( $http eq "" ) {
+          $http = "get";
+        }
       }
-    } elsif ( $pat eq "-revhist" ) {
-      # internal sequence revision history request (undocumented)
+    } elsif ( $pat eq "-myvariant" or $pat eq "-myvariant.info" ) {
+      # shortcut for myvariant.info (undocumented)
       $i++;
       if ( $i < $max ) {
-        $url = "https://www.ncbi.nlm.nih.gov/sviewer/girevhist.cgi";
-        $pat = $args[$i];
-        $arg="cmd=seqid&txt=on&seqid=asntext&os=PUBSEQ_OS&val=$pat";
-        $amp = "&";
-        $i++;
+        $url = "http://myvariant.info/v1";
+        if ( $http eq "" ) {
+          $http = "get";
+        }
+      }
+    } elsif ( $pat eq "-mychem" or $pat eq "-mychem.info" ) {
+      # shortcut for mychem.info (undocumented)
+      $i++;
+      if ( $i < $max ) {
+        $url = "http://mychem.info/v1";
+        if ( $http eq "" ) {
+          $http = "get";
+        }
       }
+
+    } elsif ( $pat eq "-wikipathways" ) {
+      # shortcut for webservice.wikipathways.org (undocumented)
+      $i++;
+      if ( $i < $max ) {
+        $url = "http://webservice.wikipathways.org";
+        if ( $http eq "" ) {
+          $http = "get";
+        }
+      }
+
     } elsif ( $pat eq "-biosample" ) {
       # internal biosample_chk request on live database (undocumented)
       $i++;
diff --git a/rchive.go b/rchive.go
index c5114e0..a49eb12 100644
--- a/rchive.go
+++ b/rchive.go
@@ -62,7 +62,7 @@ import (
 
 // RCHIVE VERSION AND HELP MESSAGE TEXT
 
-const rchiveVersion = "10.8"
+const rchiveVersion = "10.9"
 
 const rchiveHelp = `
 Processing Flags
diff --git a/transmute b/transmute
index 36dba33..d142738 100755
--- a/transmute
+++ b/transmute
@@ -43,7 +43,7 @@ use File::Spec;
 
 # transmute version number
 
-$version = "10.8";
+$version = "10.9";
 
 BEGIN
 {
diff --git a/xtract.go b/xtract.go
index dfd540a..7813d24 100644
--- a/xtract.go
+++ b/xtract.go
@@ -53,7 +53,7 @@ import (
 
 // XTRACT VERSION AND HELP MESSAGE TEXT
 
-const xtractVersion = "10.8"
+const xtractVersion = "10.9"
 
 const xtractHelp = `
 Overview
@@ -5764,7 +5764,7 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {
 			acc = append(acc, "-element", "INSDSeq_accession-version", "-clr", "-rst", "-tab", "\\n")
 		}
 	} else {
-		acc = append(acc, "-pattern", "INSDSeq", "-ACCN", "INSDSeq_accession-version")
+		acc = append(acc, "-pattern", "INSDSeq", "-ACCN", "INSDSeq_accession-version", "-SEQ", "INSDSeq_sequence")
 	}
 
 	if doIndex {
@@ -5935,6 +5935,30 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {
 			// report capitalization or vocabulary failure
 			checkAgainstVocabulary(str, "element", insdtags)
 
+		} else if str == "sub_sequence" {
+
+			// special sub_sequence qualifier shows sequence under feature intervals
+			acc = append(acc, "-block", "INSDFeature_intervals")
+			if isPipe {
+				acc = append(acc, "-lbl", "")
+			} else {
+				acc = append(acc, "-lbl", "\"\"")
+			}
+
+			acc = append(acc, "-subset", "INSDInterval", "-FR", "INSDInterval_from", "-TO", "INSDInterval_to")
+			if isPipe {
+				acc = append(acc, "-pfx", "", "-tab", "", "-nucleic", "&SEQ[&FR:&TO]")
+			} else {
+				acc = append(acc, "-pfx", "\"\"", "-tab", "\"\"", "-nucleic", "\"&SEQ[&FR:&TO]\"")
+			}
+
+			acc = append(acc, "-subset", "INSDFeature_intervals")
+			if isPipe {
+				acc = append(acc, "-lbl", "\\t")
+			} else {
+				acc = append(acc, "-lbl", "\"\\t\"")
+			}
+
 		} else {
 
 			acc = append(acc, "-block", "INSDQualifier")