Merge pull request #3 from ncbi/dev

Version 1.0.24 
Includes several requested changes and updated tests

.gitignore

@@ -1,5 +1,6 @@
 *.o
 stxtyper
 fasta_check
+fasta_extract
 stx.prot.*
 *.got

LICENSE

@@ -17,5 +17,6 @@
   warranties of performance, merchantability or fitness for any particular
   purpose.
 
-  Please cite the author in any work or product based on this material.   
-
+  Manuscript in preparation. Please cite https://github.com/ncbi/stxtyper in
+  any work or product based on this material.
+

Makefile

@@ -42,13 +42,6 @@ ifneq '$(INSTALL_DIR)' ''
 	bindir=$(INSTALL_DIR)
 endif
 bindir ?= $(PREFIX)/bin
-ifneq '$(CONDA_DB_DIR)' ''
-	DBDIR := -D'CONDA_DB_DIR="$(CONDA_DB_DIR)"'
-endif
-ifneq '$(DEFAULT_DB_DIR)' ''
-	DBDIR := -D'CONDA_DB_DIR="$(DEFAULT_DB_DIR)"'
-endif
-
 
 # detect system architecture and set appropriate flags
 # this is probably not the best way (i.e. M1 Mac would be arm64)
@@ -74,13 +67,21 @@ endif
 # was: -std=gnu++14 
 
 CXX=g++
-COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c 
+COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) -c 
 
 
 .PHONY: all clean install release test
 
-BINARIES= stxtyper fasta_check 
+BINARIES= stxtyper fasta_check fasta_extract
 DATABASE= stx.prot
+TEST= test/amrfinder_integration.expected   test/cases.expected \
+test/amrfinder_integration.fa         test/cases.fa \
+test/amrfinder_integration2.expected  test/synthetics.expected \
+test/amrfinder_integration2.fa        test/synthetics.fa \
+test/basic.expected                   test/virulence_ecoli.expected \
+test/basic.fa                         test/virulence_ecoli.fa \
+test/basic.nuc_out.expected
+
 
 all:	$(BINARIES)
 
@@ -90,7 +91,7 @@ all:	$(BINARIES)
 common.o:	common.hpp common.inc
 
 stxtyper.o:  common.hpp common.inc 
-stxtyperOBJS=stxtyper.o common.o
+stxtyperOBJS=stxtyper.o common.o tsv.o
 stxtyper:	$(stxtyperOBJS)
 	$(CXX) -o $@ $(stxtyperOBJS) -pthread $(DBDIR)
 
@@ -99,6 +100,10 @@ fasta_checkOBJS=fasta_check.o common.o
 fasta_check:	$(fasta_checkOBJS)
 	$(CXX) -o $@ $(fasta_checkOBJS)
 
+fasta_extract.o:	common.hpp common.inc 
+fasta_extractOBJS=fasta_extract.o common.o 
+fasta_extract:	$(fasta_extractOBJS)
+	$(CXX) -o $@ $(fasta_extractOBJS)
 
 clean:
 	rm -f *.o
@@ -112,23 +117,20 @@ install:
 	$(INSTALL) $(BINARIES) $(DATABASE) $(DESTDIR)$(bindir) 
 
 # stxtyper binaries for github binary release
-GITHUB_FILE=stxtyper_binaries_v$(VERSION_STRING)
-GITHUB_FILES = $(BINARIES) $(DATABASE)
-github_binaries:
+GITHUB_FILE=stxtyper_v$(VERSION_STRING)_$(ARCH)_$(OS)
+GITHUB_FILES = $(BINARIES) $(DATABASE) version.txt test_stxtyper.sh
+binary_dist:
 	@if [ ! -e version.txt ]; \
 	then \
 		echo >&2 "version.txt required to make a distribution file"; \
 		false; \
 	fi
-#   first recompile stxtyper.o to pick up the new version info
-	rm stxtyper.o stxtyper
-	make
 	mkdir $(GITHUB_FILE)
-	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
 	cp $(GITHUB_FILES) $(GITHUB_FILE)
+	mkdir $(GITHUB_FILE)/test
+	cp $(TEST) $(GITHUB_FILE)/test
 	if [ -e $(GITHUB_FILE).tar.gz ]; then rm $(GITHUB_FILE).tar.gz; fi
-	cd $(GITHUB_FILE); tar cvfz ../$(GITHUB_FILE).tar.gz *
-#	tar cvfz $(GITHUB_FILE).tar.gz $(GITHUB_FILE)/*
+	tar cvfz $(GITHUB_FILE).tar.gz $(GITHUB_FILE)/*
 	rm -r $(GITHUB_FILE)/*
 	rmdir $(GITHUB_FILE)
 

common.cpp

@@ -1710,7 +1710,7 @@ void Xml::TextFile::tagStart (const string &tag)
 	string tag_ (tag);
 	replace (tag_, ':', '_');
 	if (! isIdentifier (tag_, true))
-    throw runtime_error (FUNC "Bad tag name: " + strQuote (tag));
+    throw runtime_error (FUNC "Bad textual XML tag name: " + strQuote (tag));
 
 	printRaw ("<" + tag + ">"); 
 }
@@ -3689,14 +3689,11 @@ string Application::key2shortHelp (const string &name) const
 
 
 
-string Application::getInstruction (bool coutP) const
+string Application::getInstruction (bool screen) const
 {
   string instr (description);
 
-  if (isRedirected (cout))
-    coutP = false;
-
-  instr += "\n\n" + colorize ("USAGE", coutP) + ":   " + programName; 
+  instr += "\n\n" + colorize ("USAGE", screen) + ":   " + programName; 
 
   for (const Positional& p : positionalArgs)
     instr += " " + p. str ();
@@ -3728,10 +3725,10 @@ string Application::getInstruction (bool coutP) const
 	if (! requiredGroup_prev. empty ())
 		instr += ")";
 
-  instr += "\n" + colorize ("HELP", coutP) + ":    " + programName + " " + ifS (gnu, "-") + "-" + helpS;
+  instr += "\n" + colorize ("HELP", screen) + ":    " + programName + " " + ifS (gnu, "-") + "-" + helpS;
   if (gnu)
     instr += " or " + programName + " -" + helpS [0];
-  instr += "\n" + colorize ("VERSION", coutP) + ": " + programName + " " + ifS (gnu, "-") + "-" + versionS;
+  instr += "\n" + colorize ("VERSION", screen) + ": " + programName + " " + ifS (gnu, "-") + "-" + versionS;
   if (gnu)
     instr += " or " + programName + " -" + versionS [0];
 
@@ -3740,42 +3737,43 @@ string Application::getInstruction (bool coutP) const
 
 
 
-string Application::getDocumentation () const
+string Application::getDocumentation (bool screen) const
 {
   if (documentationUrl. empty ())
     return noString;
-  return "\n\n" + colorize ("DOCUMENTATION", true) + "\n    See " + documentationUrl + " for full documentation";    
+  return "\n\n" + colorize ("DOCUMENTATION", screen) + "\n    See " + colorizeUrl (documentationUrl, screen) + " for full documentation";    
 }
 
 
 
-string Application::getUpdates () const
+string Application::getUpdates (bool screen) const
 {
   if (updatesDoc. empty ())
     return noString;
-  return "\n\n" + colorize ("UPDATES", true) + "\n" + updatesDoc;
+  string s ("\n\n" + colorize ("UPDATES", screen) + "\n" + updatesDoc);
+  if (! updatesUrl. empty ())
+    s += ": " + colorizeUrl (updatesUrl, screen);
+  return s;
 }
 
 
 
-string Application::getHelp () const
+string Application::getHelp (bool screen) const
 {
-  string instr (getInstruction (true));
+  string instr (getInstruction (screen));
 
   const string par ("\n    ");
 
-  const bool coutP = ! isRedirected (cout);
-
   if (! positionalArgs. empty ())
   {
-	  instr += "\n\n" + colorize ("POSITIONAL PARAMETERS", coutP) /*+ ":"*/;
+	  instr += "\n\n" + colorize ("POSITIONAL PARAMETERS", screen) /*+ ":"*/;
 	  for (const Positional& p : positionalArgs)
 	    instr += "\n" + p. str () + par + p. description;
 	}
 
   if (! keyArgs. empty ())
   {
-	  instr += "\n\n" + colorize ("NAMED PARAMETERS", coutP) /*+ ":"*/;
+	  instr += "\n\n" + colorize ("NAMED PARAMETERS", screen) /*+ ":"*/;
 	  for (const Key& key : keyArgs)
 	  {
 	    instr += "\n" + key. getShortHelp () + par + key. description;
@@ -3875,7 +3873,8 @@ int Application::run (int argc,
 
           if (name == helpS || (name. empty () && c == helpS [0] && gnu))
           {
-            cout << getHelp () << getDocumentation () << getUpdates () << endl;
+	          const bool screen = ! isRedirected (cout);
+            cout << getHelp (screen) << getDocumentation (screen) << getUpdates (screen) << endl;
             return 0;
           }
           if (name == versionS || (name. empty () && c == versionS [0] && gnu))
@@ -3921,7 +3920,8 @@ int Application::run (int argc,
 
 	    if (programArgs. size () == 1 && (! positionalArgs. empty () || needsArg))
 	    {
-	      cout << getInstruction (true) << getDocumentation () << endl;
+	      const bool screen = ! isRedirected (cout);
+	      cout << getInstruction (screen) << getDocumentation (screen) << endl;
 	      return 1;
 	    }
 
@@ -4032,7 +4032,7 @@ int Application::run (int argc,
 	}
 	catch (const std::exception &e) 
 	{ 
-	  errorExit ((e. what () + ifS (errno, string ("\n") + strerror (errno))). c_str ());
+	  errorExit ((ifS (errno, strerror (errno) + string ("\n")) + e. what ()). c_str ());
   }
 
 
@@ -4142,9 +4142,9 @@ void ShellApplication::initVar ()
 
 
 
-string ShellApplication::getHelp () const 
+string ShellApplication::getHelp (bool screen) const 
 {
-  string help (Application::getHelp ());
+  string help (Application::getHelp (screen));
   if (useTmp)
     help += "\n\nTemporary directory used is $TMPDIR or \"/tmp\"";
   return help;