New upstream version 10.9.20190219+ds

2 files changed, 125 insertions, 5 deletions

diff --git a/nquire b/nquire
index 717996d..e41fe4b 100755
--- a/nquire
+++ b/nquire
@@ -84,6 +84,7 @@ sub clearflags {
   $debug = false;
   $http = "";
   $j2x = false;
+  $x2j = false;
   $output = "";
 }
 
@@ -492,12 +493,12 @@ BioThings Queries
 EDirect Expansion
 
   ExtractIDs() {
-    xtract -pattern BIO_THINGS -block Id -tab "\\n" -element "Id"
+    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 -wrp BIO_THINGS -pattern opt -wrp Type -lbl "\$1" \\
+      -wrp Count -num "\$2" -block "\$2" -wrp Id -element "\$3" |
     xtract -format
   }
 
@@ -584,6 +585,7 @@ sub nquire {
     '-gene'     =>  'http://mygene.info/v3',
     '-variant'  =>  'http://myvariant.info/v1',
     '-chem'     =>  'http://mychem.info/v1',
+    '-disease'  =>  'http://mydisease.info/v1',
     '-drug'     =>  'http://c.biothings.io/v1',
     '-taxon'    =>  'http://t.biothings.io/v1',
   );
@@ -695,6 +697,19 @@ sub nquire {
     }
   }
 
+  # if present, -j2x or -x2j must be next argument (undocumented)
+
+  if ( $i < $max ) {
+    $pat = $args[$i];
+    if ( $pat eq "-j2x" ) {
+      $i++;
+      $j2x = true;
+    } elsif ( $pat eq "-x2j" ) {
+      $i++;
+      $x2j = true;
+    }
+  }
+
   # read file of keyword shortcuts for URL expansion
 
   if ( $i < $max ) {
@@ -920,6 +935,16 @@ sub nquire {
     binmode(STDOUT, ":utf8");
   }
 
+  if ( $x2j ) {
+    my $xc = new XML::Simple(KeepRoot => 1);
+    my $conv = $xc->XMLin($output);
+    convert_bools($conv);
+    my $jc = JSON::PP->new->ascii->pretty->allow_nonref;
+    my $result = $jc->encode($conv);
+
+    $output = "$result";
+  }
+
   print "$output";
 }
 
diff --git a/xtract.go b/xtract.go
index 1441dca..82fd193 100644
--- a/xtract.go
+++ b/xtract.go
@@ -112,6 +112,7 @@ String Constraints
 
   -equals          String must match exactly
   -contains        Substring must be present
+  -is-within       String must be present
   -starts-with     Substring must be at beginning
   -ends-with       Substring must be at end
   -is-not          String must not match
@@ -1675,6 +1676,7 @@ const (
 	OR
 	EQUALS
 	CONTAINS
+	ISWITHIN
 	STARTSWITH
 	ENDSWITH
 	ISNOT
@@ -1778,6 +1780,7 @@ var argTypeIs = map[string]ArgumentType{
 	"-or":          CONDITIONAL,
 	"-equals":      CONDITIONAL,
 	"-contains":    CONDITIONAL,
+	"-is-within":   CONDITIONAL,
 	"-starts-with": CONDITIONAL,
 	"-ends-with":   CONDITIONAL,
 	"-is-not":      CONDITIONAL,
@@ -1893,6 +1896,7 @@ var opTypeIs = map[string]OpType{
 	"-or":          OR,
 	"-equals":      EQUALS,
 	"-contains":    CONTAINS,
+	"-is-within":   ISWITHIN,
 	"-starts-with": STARTSWITH,
 	"-ends-with":   ENDSWITH,
 	"-is-not":      ISNOT,
@@ -2586,7 +2590,7 @@ func ParseArguments(cmdargs []string, pttrn string) *Block {
 				cond = append(cond, op)
 				parseStep(op, elementColonValue)
 				status = UNSET
-			case EQUALS, CONTAINS, STARTSWITH, ENDSWITH, ISNOT:
+			case EQUALS, CONTAINS, ISWITHIN, STARTSWITH, ENDSWITH, ISNOT:
 				if op != nil {
 					if len(str) > 1 && str[0] == '\\' {
 						// first character may be backslash protecting dash (undocumented)
@@ -4729,7 +4733,7 @@ func ConditionsAreSatisfied(conditions []*Operation, curr *Node, mask string, in
 			stat := constraint.Type
 
 			switch stat {
-			case EQUALS, CONTAINS, STARTSWITH, ENDSWITH, ISNOT:
+			case EQUALS, CONTAINS, ISWITHIN, STARTSWITH, ENDSWITH, ISNOT:
 				// substring test on element values
 				str = strings.ToUpper(str)
 				val = strings.ToUpper(val)
@@ -4743,6 +4747,10 @@ func ConditionsAreSatisfied(conditions []*Operation, curr *Node, mask string, in
 					if strings.Contains(str, val) {
 						return true
 					}
+				case ISWITHIN:
+					if strings.Contains(val, str) {
+						return true
+					}
 				case STARTSWITH:
 					if strings.HasPrefix(str, val) {
 						return true
@@ -6039,6 +6047,70 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {
 	return acc
 }
 
+// BIOTHINGS EXTRACTION COMMAND GENERATOR
+
+// ProcessBiopath generates extraction commands for BioThings resources (undocumented)
+func ProcessBiopath(args []string, isPipe bool) []string {
+
+	// nquire -variant variant "chr6:g.26093141G>A" | xtract -biopath "clinvar.rcv.conditions.identifiers.omim"
+
+	// xtract -pattern opt -division clinvar -group rcv -branch conditions -block identifiers -sep "\n" -tab "\n" -element "omim,@omim"
+
+	var acc []string
+
+	max := len(args)
+	if max < 1 {
+		fmt.Fprintf(os.Stderr, "\nERROR: Insufficient command-line arguments supplied to xtract -biopath\n")
+		os.Exit(1)
+	}
+
+	path := args[0]
+
+	dirs := strings.Split(path, ".")
+	max = len(dirs)
+	if max < 1 {
+		fmt.Fprintf(os.Stderr, "\nERROR: Insufficient command-line arguments supplied to xtract -biopath\n")
+		os.Exit(1)
+	}
+
+	expname := []string{
+		"-division",
+		"-group",
+		"-branch",
+		"-block",
+		"-section",
+		"-subset",
+		"-unit",
+	}
+
+	acc = append(acc, "-pattern", "opt")
+
+	max--
+	if max > 7 {
+		fmt.Fprintf(os.Stderr, "\nERROR: Too many nodes in argument supplied to xtract -biopath\n")
+		os.Exit(1)
+	}
+
+	for i, str := range dirs {
+		if i < max {
+			acc = append(acc, expname[i], str)
+		} else {
+			if isPipe {
+				acc = append(acc, "-sep", "\\n", "-tab", "\\n")
+			} else {
+				acc = append(acc, "-sep", "\"\\n\"", "-tab", "\"\\n\"")
+			}
+			if isPipe {
+				acc = append(acc, "-element", str+",@"+str)
+			} else {
+				acc = append(acc, "-element", "\""+str+",@"+str+"\"")
+			}
+		}
+	}
+
+	return acc
+}
+
 // HYDRA CITATION MATCHER COMMAND GENERATOR
 
 // ProcessHydra generates extraction commands for NCBI's in-house citation matcher (undocumented)
@@ -8471,6 +8543,29 @@ func main() {
 		args = hydra
 	}
 
+	// BIOTHINGS EXTRACTION COMMAND GENERATOR
+
+	// -biopath takes a dotted exploration path for BioThings resources (undocumented)
+	if args[0] == "-biopath" {
+
+		args = args[1:]
+
+		biopath := ProcessBiopath(args, isPipe || usingFile)
+
+		if !isPipe && !usingFile {
+			// no piped input, so write output instructions
+			fmt.Printf("xtract")
+			for _, str := range biopath {
+				fmt.Printf(" %s", str)
+			}
+			fmt.Printf("\n")
+			return
+		}
+
+		// data in pipe, so replace arguments, execute dynamically
+		args = biopath
+	}
+
 	// ENTREZ2INDEX COMMAND GENERATOR
 
 	// -e2index shortcut for experimental indexing code (documented in rchive.go)