Merge tag 'upstream/10.9.20190205+ds'

Upstream version 10.9.20190205(+ds).

3 files changed, 149 insertions, 33 deletions

diff --git a/debian/changelog b/debian/changelog
index 31303aa..0e16441 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-ncbi-entrez-direct (10.9.20190131+ds-1) UNRELEASED; urgency=medium
+ncbi-entrez-direct (10.9.20190205+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 (10.9.20190131+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 22:38:28 -0500
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 06 Feb 2019 22:39:48 -0500
 
 ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium
 
diff --git a/nquire b/nquire
index a48c3f5..717996d 100755
--- a/nquire
+++ b/nquire
@@ -63,10 +63,12 @@ BEGIN
 }
 use lib $LibDir;
 
+use JSON::PP;
 use LWP::UserAgent;
 use POSIX;
 use URI::Escape;
 use Net::FTP;
+use XML::Simple;
 
 # definitions
 
@@ -81,6 +83,7 @@ sub clearflags {
   $alias = "";
   $debug = false;
   $http = "";
+  $j2x = false;
   $output = "";
 }
 
@@ -229,6 +232,33 @@ sub do_uri_escape {
   return $rslt;
 }
 
+sub convert_bools {
+  my %unrecognized;
+
+  local *_convert_bools = sub {
+    my $ref_type = ref($_[0]);
+    if (!$ref_type) {
+      # Nothing.
+    }
+    elsif ($ref_type eq 'HASH') {
+      _convert_bools($_) for values(%{ $_[0] });
+    }
+    elsif ($ref_type eq 'ARRAY') {
+      _convert_bools($_) for @{ $_[0] };
+    }
+    elsif (
+       $ref_type eq 'JSON::PP::Boolean' || $ref_type eq 'Types::Serialiser::Boolean'
+    ) {
+      $_[0] = $_[0] ? 1 : 0;
+    }
+    else {
+      ++$unrecognized{$ref_type};
+    }
+  };
+
+  &_convert_bools;
+}
+
 # nquire executes an external URL query from command line arguments
 
 my $nquire_help = qq{
@@ -439,6 +469,58 @@ Federated Query
       }" |
   xtract -pattern result -block binding -element "binding\@name" literal
 
+BioThings Queries
+
+  nquire -variant variant "chr6:g.26093141G>A" -fields dbsnp.gene |
+  xtract -pattern gene -element \@geneid
+
+  nquire -gene query -q "symbol:OPN1MW" -species 9606 |
+  xtract -pattern hits -element "\@_id"
+
+  nquire -gene query -q "symbol:OPN1MW AND taxid:9606" |
+  xtract -pattern hits -element "\@_id"
+
+  nquire -gene gene 2652 -fields pathway.wikipathways |
+  xtract -pattern pathway -element "\@id"
+
+  nquire -gene query -q "pathway.wikipathways.id:WP455" -size 300 |
+  xtract -pattern hits -element "\@_id"
+
+  nquire -chem query -q "drugbank.targets.uniprot:P05231 AND drugbank.targets.actions:inhibitor" -fields hgvs |
+  xtract -pattern hits -element "\@_id"
+
+EDirect Expansion
+
+  ExtractIDs() {
+    xtract -pattern BIO_THINGS -block Id -tab "\\n" -element "Id"
+  }
+
+  WrapIDs() {
+    xtract -wrp BIO_THINGS -pattern opt -wrp "Type" -lbl "\$1" \\
+      -wrp "Count" -num "\$2" -block "\$2" -wrp "Id" -element "\$3" |
+    xtract -format
+  }
+
+  nquire -gene query -q "symbol:OPN1MW AND taxid:9606" |
+  WrapIDs entrezgene hits "\@entrezgene" |
+
+  ExtractIDs |
+  while read geneid
+  do
+    nquire -gene gene "\$geneid" -fields pathway.wikipathways
+  done |
+  WrapIDs pathway.wikipathways.id pathway "\@id" |
+
+  ExtractIDs |
+  while read pathid
+  do
+    nquire -gene query -q "pathway.wikipathways.id:\$pathid" -size 300
+  done |
+  WrapIDs entrezgene hits "\@entrezgene" |
+
+  ExtractIDs |
+  sort -n
+
 };
 
 my @pubchem_properties = qw(
@@ -498,6 +580,14 @@ sub nquire {
   @args = @ARGV;
   $max = scalar @args;
 
+  %biothingsHash = (
+    '-gene'     =>  'http://mygene.info/v3',
+    '-variant'  =>  'http://myvariant.info/v1',
+    '-chem'     =>  'http://mychem.info/v1',
+    '-drug'     =>  'http://c.biothings.io/v1',
+    '-taxon'    =>  'http://t.biothings.io/v1',
+  );
+
   if ( $max < 1 ) {
     return;
   }
@@ -705,42 +795,20 @@ sub nquire {
         }
       }
 
-    } elsif ( $pat eq "-mygene" or $pat eq "-mygene.info" ) {
-      # shortcut for mygene.info (undocumented)
-      $i++;
-      if ( $i < $max ) {
-        $url = "http://mygene.info/v3";
-        if ( $http eq "" ) {
-          $http = "get";
-        }
-      }
-    } elsif ( $pat eq "-myvariant" or $pat eq "-myvariant.info" ) {
-      # shortcut for myvariant.info (undocumented)
+    } elsif ( defined $biothingsHash{$pat} ) {
+      # shortcuts for biothings services (undocumented)
       $i++;
-      if ( $i < $max ) {
-        $url = "http://myvariant.info/v1";
-        if ( $http eq "" ) {
+      $url = $biothingsHash{$pat};
+      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";
-        }
       }
+      $j2x = true;
 
     } 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" ) {
@@ -825,6 +893,33 @@ sub nquire {
   # perform query
   $output = do_post ($url, $arg);
 
+  if ( $j2x ) {
+    my $jc = JSON::PP->new->ascii->pretty->allow_nonref;
+    my $conv = $jc->decode($output);
+    convert_bools($conv);
+    my $result = XMLout($conv, SuppressEmpty => undef);
+
+    # remove newlines, tabs, space between tokens, compress runs of spaces
+    $result =~ s/\r/ /g;
+    $result =~ s/\n/ /g;
+    $result =~ s/\t//g;
+    $result =~ s/ +/ /g;
+    $result =~ s/> +</></g;
+
+    # remove <opt> flanking object
+    if ( $result =~ /<opt>\s*?</ and $result =~ />\s*?<\/opt>/ ) {
+      $result =~ s/<opt>\s*?</</g;
+      $result =~ s/>\s*?<\/opt>/>/g;
+    }
+
+    $output = "$result";
+
+    # restore newlines between objects
+    $output =~ s/> *?</>\n</g;
+
+    binmode(STDOUT, ":utf8");
+  }
+
   print "$output";
 }
 
diff --git a/xtract.go b/xtract.go
index 7813d24..1441dca 100644
--- a/xtract.go
+++ b/xtract.go
@@ -3497,11 +3497,15 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d
 					}
 				}
 
-				// -nucleic uses direction of range to decide between forward strand or reverse complement
 				doRevComp := false
-				if stat == NUCLEIC && min+1 > max {
-					min, max = max-1, min+1
-					doRevComp = true
+				doUpCase := false
+				if status == NUCLEIC {
+					// -nucleic uses direction of range to decide between forward strand or reverse complement
+					if min+1 > max {
+						min, max = max-1, min+1
+						doRevComp = true
+					}
+					doUpCase = true
 				}
 
 				// numeric range now calculated, apply slice to string
@@ -3509,6 +3513,9 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d
 					if doRevComp {
 						str = reverseComplement(str)
 					}
+					if doUpCase {
+						str = strings.ToUpper(str)
+					}
 					acc(str)
 				} else if max == 0 {
 					if min > 0 && min < len(str) {
@@ -3517,6 +3524,9 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d
 							if doRevComp {
 								str = reverseComplement(str)
 							}
+							if doUpCase {
+								str = strings.ToUpper(str)
+							}
 							acc(str)
 						}
 					}
@@ -3527,6 +3537,9 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d
 							if doRevComp {
 								str = reverseComplement(str)
 							}
+							if doUpCase {
+								str = strings.ToUpper(str)
+							}
 							acc(str)
 						}
 					}
@@ -3537,6 +3550,9 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d
 							if doRevComp {
 								str = reverseComplement(str)
 							}
+							if doUpCase {
+								str = strings.ToUpper(str)
+							}
 							acc(str)
 						}
 					}
@@ -4541,11 +4557,16 @@ func ProcessInstructions(commands []*Operation, curr *Node, mask, tab, ret strin
 		case LBL:
 			lbl := str
 			accum(tab)
+			accum(plg)
+			accum(pfx)
 			if plain {
 				accum(lbl)
 			} else {
 				printInColor(lbl)
 			}
+			accum(sfx)
+			plg = ""
+			lst = elg
 			tab = col
 			ret = lin
 		case PFC: