Adds gzstream stream, exposes to swig (#2314)

* Move RDBoostStreams to RDStreams

* RDBoostStreams->RDStreams

* RDBoostStreams->RDStreams

* Wrap SWIG (with Java test)

* Fix missing declaration

* Use the file that already exists

* Revert to original version

* Revert to CXSMiles version

* Update boost version

* Remove redundant code

* Add zlib

* check for win32

* FileParsers now builds static on windows

Code/JavaWrappers/CMakeLists.txt

@@ -26,7 +26,7 @@ set(swigRDKitLibList "${swigRDKitLibList}"
   "Subgraphs;GraphMol;DataStructs;Trajectory;Descriptors;"
   "PartialCharges;MolTransforms;DistGeomHelpers;DistGeometry;"
   "ForceFieldHelpers;ForceField;EigenSolvers;Optimizer;MolAlign;"
-  "Alignment;SimDivPickers;RDGeometryLib;RDGeneral;"
+  "Alignment;SimDivPickers;RDGeometryLib;RDStreams;RDGeneral;"
 )
 #if(RDK_BUILD_COORDGEN_SUPPORT)
 #  set(swigRDKitLibList "${swigRDKitLibList};${RDK_COORDGEN_LIBS}")
@@ -37,15 +37,21 @@ foreach(swigRDKitLib ${swigRDKitLibList})
 endforeach()
 set(swigRDKitLibs "${swigRDKitLibs}${Boost_SERIALIZATION_LIBRARY};")
 
-if(RDK_BUILD_COORDGEN_SUPPORT)
+
+if(WIN32)
+  find_package(Boost 1.56.0 COMPONENTS system iostreams zlib REQUIRED)
+  set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_ZLIB_LIBRARY};${Boost_SYSTEM_LIBRARY};")
+else()
   find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
   set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_SYSTEM_LIBRARY};")
-endif(RDK_BUILD_COORDGEN_SUPPORT)
+endif()
+
+
 
 set(RDKit_Wrapper_Libs ${swigRDKitLibs})
 
 message("SUFFIX: ${swigRDKitLibSuffix}")
-message("LIBS: ${RDKit_Wrapper_Libs}")
+message("JAVA_LIBS: ${RDKit_Wrapper_Libs}")
 
 
 if(RDK_BUILD_SWIG_JAVA_WRAPPER)

Code/JavaWrappers/MolSupplier.i

@@ -42,6 +42,7 @@
 #include <GraphMol/Substruct/SubstructMatch.h>
 %}
 
+%include "Streams.i"
 
 %newobject RDKit::ForwardSDMolSupplier::next;
 %newobject RDKit::ResonanceMolSupplier::next;
@@ -50,7 +51,22 @@
 %newobject RDKit::TDTMolSupplier::next;
 %newobject RDKit::PDBMolSupplier::next;
 
+
 %include <GraphMol/FileParsers/MolSupplier.h>
+
+%extend RDKit::ForwardSDMolSupplier {
+    ForwardSDMolSupplier(RDKit::gzstream *strm, bool sanitize=true, bool removeHs = true,
+                  bool strictParsing = true) {
+    const bool takeOwnership = false;
+    RDKit::ForwardSDMolSupplier*foo = new RDKit::ForwardSDMolSupplier(
+                                     (std::istream*)strm,
+                                     takeOwnership,
+                                     sanitize, removeHs, strictParsing);
+    PRECONDITION(!foo->atEnd(), "LDJKLJF");
+    return foo;
+  }
+};
+
 %include <GraphMol/Resonance.h>
 
 %extend RDKit::ResonanceMolSupplier {
@@ -60,3 +76,4 @@
     return mv;
   }
 }
+

Code/JavaWrappers/Streams.i

@@ -0,0 +1,74 @@
+
+/*
+ *  Copyright (c) 2019, Novartis Institutes for BioMedical Research Inc.
+ *  All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ *     * Redistributions of source code must retain the above copyright
+ *       notice, this list of conditions and the following disclaimer.
+ *     * Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *     * Neither the name of Novartis Institutes for BioMedical Research Inc.
+ *       nor the names of its contributors may be used to endorse or promote
+ *       products derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+
+%include "std_string.i"
+
+
+%{
+#include <../RDStreams/streams.h>
+#include <sstream> 
+%}
+
+// We just need to pass the pointers around here
+%nodefaultctor istream;
+%nodefaultdtor istream;
+%nodefaultctor filtering_istream;
+%nodefaultdtor filtering_istream;
+
+namespace std {
+class istream;
+}
+
+%extend RDKit::gzstream {
+    std::istream* _GetStream() { return (std::istream*)$self; }
+    std::string Dump() {
+      std::ostringstream stream;
+      std::copy(std::istreambuf_iterator<char>(*$self),
+                std::istreambuf_iterator<char>(),
+                std::ostreambuf_iterator<char>(stream));
+
+      return stream.str();
+    }
+}
+%typemap(javacode) RDKit::gzstream %{
+  private SWIGTYPE_p_std__istream streamRef;
+  public SWIGTYPE_p_std__istream GetStream() {
+     if (streamRef == null)
+       streamRef = _GetStream();
+     return streamRef;
+  }
+%}
+
+%include <../RDStreams/streams.h>
+
+

Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i

@@ -247,6 +247,8 @@ typedef unsigned long long int	uintmax_t;
 %include "../FilterCatalog.i"
 %include "../Trajectory.i"
 %include "../SubstructLibrary.i"
+%include "../Streams.i"
+
 
 // Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java
 #ifdef INCLUDE_ERROR_GENERATOR

Code/JavaWrappers/gmwrapper/GraphMolJava.i

@@ -226,6 +226,7 @@ typedef unsigned long long int	uintmax_t;
 %include "../MolStandardize.i"
 %include "../SubstructLibrary.i"
 %include "../RGroupDecomposition.i"
+%include "../Streams.i"
 
 // Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java
 #ifdef INCLUDE_ERROR_GENERATOR

Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SuppliersTests.java

@@ -167,6 +167,28 @@ public class SuppliersTests extends GraphMolTest {
                 if((i%1000)==0) System.err.printf("Done: %s\n",i);
             }
 	}
+  
+        @Test
+        public void test11GZstream() {
+          // NCI_aids_few.sdf.gz
+          File base = getRdBase();
+          File gzpath  = new File(base, "Code" + File.separator + "GraphMol" + File.separator +
+                                  "FileParsers" + File.separator + "test_data");
+          File fileN = new File(baseTestPath, "NCI_aids_few.sdf.gz");
+          assertTrue(fileN.exists());
+          gzstream stream = new gzstream(fileN.getPath());
+          ForwardSDMolSupplier suppl = new ForwardSDMolSupplier(stream);
+          assertFalse(suppl.atEnd());
+          ArrayList<ROMol> ms = new ArrayList<ROMol>();
+          ROMol m;
+          do {
+            m = suppl.next();
+            if (m != null)
+              ms.add(m);
+          } while (!suppl.atEnd());
+          assertEquals(16, ms.size());
+
+        }
 
 	public static void main(String args[]) {
 		org.junit.runner.JUnitCore.main("org.RDKit.SuppliersTests");