Merge pull request #214 from SynBioDex/develop

Develop

.travis.yml

@@ -26,8 +26,15 @@ before_install:
   - sudo apt-get update -q=2
 
   # install dependencies
-  - sudo apt-get -y install build-essential libxml2-dev gcc-multilib g++-multilib libraptor2-dev libjsoncpp-dev swig3.0 python-dev
-
+  - sudo apt-get -y install build-essential libxml2-dev gcc-multilib g++-multilib libraptor2-dev swig3.0 python-dev
+  - curl --tlsv1.2 -L https://github.com/open-source-parsers/jsoncpp/archive/1.7.7.tar.gz > jsoncpp-1.7.7.tar.gz
+  - tar -xzf jsoncpp-1.7.7.tar.gz
+  - cd jsoncpp-1.7.7
+  - cmake . -Bbuild -DBUILD_SHARED_LIBS=TRUE
+  - cd build
+  - sudo make install
+  - cd ../..
+  - ls /usr/local/lib
   - echo "TRAVIS_BUILD_DIR $TRAVIS_BUILD_DIR"
   # build 
   - mkdir -p ~/build/libSBOL
@@ -36,7 +43,7 @@ install:
   - cd ~/build/libSBOL
   - sudo apt-get install -q=2 g++-4.8
   - export CXX="g++-5" CC="gcc-5"
-  - cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install_x64 -DSBOL_BUILD_64=ON -DSBOL_BUILD_SHARED=ON -DCURL_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurl.so -DJsonCpp_LIBRARY=/usr/lib/x86_64-linux-gnu/libjsoncpp.so -DLIBXSLT_LIBRARIES=/usr/lib/x86_64-linux-gnu/libxslt.so -DRAPTOR_LIBRARY=/usr/lib/x86_64-linux-gnu/libraptor2.so -DSBOL_BUILD_PYTHON2=ON -DPYTHON_EXECUTABLE=/usr/bin/python -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7.so python2.7 -DSWIG_EXECUTABLE=/usr/bin/swig3.0 "$TRAVIS_BUILD_DIR"
+  - cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/install_x64 -DSBOL_BUILD_64=ON -DSBOL_BUILD_SHARED=ON -DCURL_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurl.so -DLIBXSLT_LIBRARIES=/usr/lib/x86_64-linux-gnu/libxslt.so -DRAPTOR_LIBRARY=/usr/lib/x86_64-linux-gnu/libraptor2.so -DSBOL_BUILD_PYTHON2=ON -DPYTHON_EXECUTABLE=/usr/bin/python -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7.so python2.7 -DSWIG_EXECUTABLE=/usr/bin/swig3.0 "$TRAVIS_BUILD_DIR"
   - make 
   - make install
 
@@ -53,7 +60,8 @@ script:
   - ls ~/build/SynBioDex
   - cd ~/build/SynBioDex/libSBOL/release/wrapper/Linux_64_2
   - python -c "from sbol import *; testSBOL()"
-
+  - python -c "from sbol.unit_tests import *; runRoundTripTests()"
+
 addons:
   apt:
     sources:

source/CMakeLists.txt

@@ -40,6 +40,7 @@ FILE(GLOB SBOL_HEADER_FILES
     properties.h
     object.h
 	identified.h
+    measure.h
 	toplevel.h
 	sequenceannotation.h
 	component.h

source/assembly.cpp

@@ -389,7 +389,10 @@ std::string ComponentDefinition::compile()
     {
         if (Config::getOption("sbol_compliant_uris") == "True")
         {
-            seq = &doc->sequences.create(displayId.get());
+            string display_id = displayId.get();
+            if (Config::getOption("sbol_typed_uris") == "False")
+                display_id = display_id + "_seq";
+            seq = &doc->sequences.create(display_id);
             sequence.set(*seq);
             sequences.set(seq->identity.get());
 
@@ -1979,6 +1982,27 @@ void nest_ranges(std::vector < sbol::Range* > ranges, ComponentDefinition* cdef_
         removed_ann->close();
 }
 
+vector<SequenceAnnotation*> ComponentDefinition::sortSequenceAnnotations()
+{
+    vector<Range*> unsorted_ranges;
+    vector<SequenceAnnotation*> sorted_annotations;
+    for (auto & ann : sequenceAnnotations)
+    {
+        for (auto & l : ann.locations)
+        {
+            if (l.type == SBOL_RANGE)
+                unsorted_ranges.push_back((Range*)&l);
+        }
+    }
+    sort(unsorted_ranges.begin(), unsorted_ranges.end(), compare_ranges);
+    for (auto & r : unsorted_ranges)
+    {
+        sorted_annotations.push_back((SequenceAnnotation*)r->parent);
+    }
+    return sorted_annotations;
+};
+
+
 void disassemble(ComponentDefinition * cdef_node, int range_start)
 {
 //    std::cout << "Dissembling " << cdef_node->identity.get() << " at " << range_start << std::endl;

source/component.h

@@ -28,6 +28,8 @@
 
 #include "identified.h"
 #include "mapsto.h"
+#include "location.h"
+#include "measurement.h"
 
 #include <string>
 
@@ -56,13 +58,17 @@ namespace sbol
         /// The mapsTos property is OPTIONAL and MAY contain a set of MapsTo objects that refer to and link together ComponentInstance objects (both Component objects and FunctionalComponent objects) within a larger design.
 		OwnedObject<MapsTo> mapsTos;
 
+        /// The measurements property links a ComponentInstance to parameters or measurements and their associated units. For example a Measurement attached to a FunctionalComponent might indicate the quantity of a component ingredient in a growth medium recipe.
+        OwnedObject<Measurement> measurements;
+
         virtual ~ComponentInstance() {};
 	protected:
         ComponentInstance(rdf_type type, std::string uri, std::string definition, std::string access, std::string version) :
             Identified(type, uri, version),
             definition(this, SBOL_DEFINITION, SBOL_COMPONENT_DEFINITION, '1', '1', ValidationRules({}), definition),
             access(this, SBOL_ACCESS, '0', '1', ValidationRules({}), access),
-            mapsTos(this, SBOL_MAPS_TOS, '0', '*', ValidationRules({}))
+            mapsTos(this, SBOL_MAPS_TOS, '0', '*', ValidationRules({})),
+            measurements(this, SBOL_MEASUREMENTS, '0', '*', ValidationRules({}))
             {
             };
 
@@ -87,6 +93,10 @@ namespace sbol
         /// | http://sbols.org/v2#mergeRoles     | Use the union of the two sets: both the set of zero or more roles given for this Component as well |
         /// |                                    | as the set of zero or more roles given for the included sub-ComponentDefinition.                   |
         URIProperty roleIntegration;
+
+        /// The sourceLocations property allows only a portion of the Component's sequence to be used when compiling a composite Sequence from a component hierarchy. This serves two related purposes: (1) To support the insertion of parts within a larger plasmid or genome "backbone". Typically, this will replace a small segment of the backbone which, currently, cannot be expressed in SBOL. (2) To support the "trimming" of part boundaries as it may happen during DNA assembly.
+        OwnedObject<Location> sourceLocations;
+
 
         /// Construct a Component. If operating in SBOL-compliant mode, use ComponentDefinition::components::create instead.
         /// @param A full URI including a scheme, namespace, and identifier.  If SBOLCompliance configuration is enabled, then this argument is simply the displayId for the new object and a full URI will automatically be constructed.
@@ -104,7 +114,8 @@ namespace sbol
         Component(rdf_type type, std::string uri, std::string definition, std::string access, std::string version) :
             ComponentInstance(type, uri, definition, access, version),
             roles(this, SBOL_ROLES, '0', '*', ValidationRules({})),
-            roleIntegration(this, SBOL_ROLE_INTEGRATION, '0', '1', ValidationRules({}), SBOL_ROLE_INTEGRATION_MERGE)
+            roleIntegration(this, SBOL_ROLE_INTEGRATION, '0', '1', ValidationRules({}), SBOL_ROLE_INTEGRATION_MERGE),
+            sourceLocations(this, SBOL_LOCATIONS, '0', '*', ValidationRules({}))
             {};
 
 //        Component(sbol_type type, std::string uri_prefix, std::string display_id, std::string version, std::string definition, std::string access) : ComponentInstance(type, uri_prefix, display_id, version, definition, access) {};
@@ -160,4 +171,4 @@ namespace sbol
 	};
 }
 
-#endif
+#endif

source/componentdefinition.h

@@ -234,6 +234,8 @@ namespace sbol
 
         ComponentDefinition& build();
 
+        std::vector<SequenceAnnotation*> sortSequenceAnnotations();
+
         /// A convenience method that assigns a component to participate in a biochemical reaction.  Behind the scenes, it auto-constructs a FunctionalComponent for this ComponentDefinition and assigns it to a Participation
         /// @param species A Participation object (ie, participant species in a biochemical Interaction).
         void participate(Participation& species);

source/config.cpp

@@ -66,7 +66,9 @@ std::map<std::string, std::string> sbol::Config::options {
     {"main_file_name", "main file"},
     {"diff_file_name", "comparison file"},
     {"return_file", "False"},
-    {"verbose", "False"}
+    {"verbose", "False"},
+    {"ca-path", ""}
+
 };
 
 std::map<std::string, std::vector<std::string>> sbol::Config::valid_options {

source/constants.h

@@ -74,7 +74,7 @@
 #define SBOL_IMPLEMENTATION SBOL_URI "#Implementation"
 #define SBOL_EXPERIMENT SBOL_URI "#Experiment"
 #define SBOL_EXPERIMENTAL_DATA SBOL_URI "#ExperimentalData"
-
+#define SBOL_MEASURE SBOL_URI "#Measure"
 #define UNDEFINED SBOL_URI "#Undefined"
 
 /* URIs for SBOL Properties */
@@ -129,6 +129,9 @@
 #define SBOL_STRATEGY SBOL_URI "#strategy"
 #define SBOL_TEMPLATE SBOL_URI "#template"
 #define SBOL_ATTACHMENTS SBOL_URI "#attachment"
+#define SBOL_VALUE SBOL_URI "#hasNumericalValue"
+#define SBOL_UNIT SBOL_URI "#unit"
+#define SBOL_MEASUREMENTS SBOL_URI "#measure"
 
 /* SBOL internal ontologies */
 #define SBOL_ACCESS_PRIVATE SBOL_URI "#private"  ///< Option for Component::access or FunctionalComponent::access property

source/dbtl.cpp

@@ -285,14 +285,13 @@ namespace sbol
                 // If the progenitor object is a Build, set samples property to the Build
                 test.samples.set(this->identity.get());
             }
-            else if (properties[SYSBIO_URI "#type"].front() == "<" SYSBIO_TEST ">")
-            {
-                // The progenitor object is another Test
-                Test& progenitor = *(Test*)this;
-                test.samples.copy(progenitor.samples);
-            }
         }
-
+        else if (this->type == SBOL_TEST)
+        {
+            // The progenitor object is another Test
+            Test& progenitor = *(Test*)this;
+            test.samples.copy(progenitor.samples);
+        }
         // Form URI for auto-constructing an Activity
         std::string id;
         if (Config::getOption("sbol_compliant_uris") == "True")
@@ -544,16 +543,16 @@ namespace sbol
 
     }
 
-    template<>
-    void Document::add<Test>(Test& sbol_obj)
-    {
-        // Call recursive adder
-        add<Collection>((Collection&)sbol_obj);
-        
-        // Move from Collection store to Test store
-        this->owned_objects[SBOL_COLLECTION].pop_back();
-        this->owned_objects[SYSBIO_TEST].push_back(&sbol_obj);
-    }
+//    template<>
+//    void Document::add<Test>(Test& sbol_obj)
+//    {
+//        // Call recursive adder
+//        add<Collection>((Collection&)sbol_obj);
+//
+//        // Move from Collection store to Test store
+//        this->owned_objects[SBOL_COLLECTION].pop_back();
+//        this->owned_objects[SYSBIO_TEST].push_back(&sbol_obj);
+//    }
 
 //    template<>
 //    Build& OwnedObject<Build>::get(std::string uri)
@@ -635,67 +634,67 @@ namespace sbol
         }
     }
 
-    template<>
-    Test& OwnedObject<Test>::create(std::string uri)
-    {
-        Test* child_obj = new Test();
-
-        SBOLObject* parent_obj = this->sbol_owner;
-        Document* parent_doc = this->sbol_owner->doc;
-
-        if (Config::getOption("sbol_compliant_uris").compare("True") == 0)
-        {
-            string persistent_id = getHomespace();
-            if (Config::getOption("sbol_typed_uris").compare("True") == 0)
-                persistent_id += "/" + parseClassName(SYSBIO_TEST);
-            string version = VERSION_STRING;
-            
-            string child_persistent_id =  persistent_id + "/" + uri;
-            string child_id = child_persistent_id + "/" + version;
-            
-            // Check for uniqueness of URI in the Document
-            if (parent_doc && parent_doc->find(child_id))
-                throw SBOLError(DUPLICATE_URI_ERROR, "An object with URI " + child_id + " is already in the Document");
-                                                      
-            // Initialize SBOLCompliant properties
-            child_obj->identity.set(child_id);
-            child_obj->persistentIdentity.set(child_persistent_id);
-            child_obj->displayId.set(uri);
-            child_obj->version.set(version);
-
-            // Add the new object to this OwnedObject property
-            // this->add(*child_obj);   Can't use this because the add method is prohibited in SBOLCompliant mode!!!
-            child_obj->parent = parent_obj;  // Set back-pointer to parent object
-            std::vector< sbol::SBOLObject* >& object_store = this->sbol_owner->owned_objects[this->type];
-            object_store.push_back((SBOLObject*)child_obj);
-
-            // The following effectively adds the child object to the Document by setting its back-pointer.  However, the Document itself only maintains a register of TopLevel objects, otherwise the returned object will not be registered
-            if (parent_doc)
-            {
-                child_obj->doc = parent_doc;
-                parent_doc->SBOLObjects[child_id] = (SBOLObject*)child_obj;
-            }
-            this->validate(child_obj);
-            return *child_obj;
-        }
-        else
-        {
-            if (parent_doc && parent_doc->find(uri))
-                throw SBOLError(DUPLICATE_URI_ERROR, "An object with URI " + uri + " is already in the Document");
-            
-            // Add the new object to this OwnedObject property
-            Identified* parent_obj = (Identified*)this->sbol_owner;
-            child_obj->parent = parent_obj;  // Set back-pointer to parent object
-            child_obj->identity.set(uri);
-            child_obj->persistentIdentity.set(uri);
-            
-            this->add(*child_obj);
-            if (parent_doc)
-                child_obj->doc = parent_doc;
-            this->validate(child_obj);
-            return *child_obj;
-        }
-    }
+//    template<>
+//    Test& OwnedObject<Test>::create(std::string uri)
+//    {
+//        Test* child_obj = new Test();
+//
+//        SBOLObject* parent_obj = this->sbol_owner;
+//        Document* parent_doc = this->sbol_owner->doc;
+//
+//        if (Config::getOption("sbol_compliant_uris").compare("True") == 0)
+//        {
+//            string persistent_id = getHomespace();
+//            if (Config::getOption("sbol_typed_uris").compare("True") == 0)
+//                persistent_id += "/" + parseClassName(SYSBIO_TEST);
+//            string version = VERSION_STRING;
+//
+//            string child_persistent_id =  persistent_id + "/" + uri;
+//            string child_id = child_persistent_id + "/" + version;
+//
+//            // Check for uniqueness of URI in the Document
+//            if (parent_doc && parent_doc->find(child_id))
+//                throw SBOLError(DUPLICATE_URI_ERROR, "An object with URI " + child_id + " is already in the Document");
+//
+//            // Initialize SBOLCompliant properties
+//            child_obj->identity.set(child_id);
+//            child_obj->persistentIdentity.set(child_persistent_id);
+//            child_obj->displayId.set(uri);
+//            child_obj->version.set(version);
+//
+//            // Add the new object to this OwnedObject property
+//            // this->add(*child_obj);   Can't use this because the add method is prohibited in SBOLCompliant mode!!!
+//            child_obj->parent = parent_obj;  // Set back-pointer to parent object
+//            std::vector< sbol::SBOLObject* >& object_store = this->sbol_owner->owned_objects[this->type];
+//            object_store.push_back((SBOLObject*)child_obj);
+//
+//            // The following effectively adds the child object to the Document by setting its back-pointer.  However, the Document itself only maintains a register of TopLevel objects, otherwise the returned object will not be registered
+//            if (parent_doc)
+//            {
+//                child_obj->doc = parent_doc;
+//                parent_doc->SBOLObjects[child_id] = (SBOLObject*)child_obj;
+//            }
+//            this->validate(child_obj);
+//            return *child_obj;
+//        }
+//        else
+//        {
+//            if (parent_doc && parent_doc->find(uri))
+//                throw SBOLError(DUPLICATE_URI_ERROR, "An object with URI " + uri + " is already in the Document");
+//
+//            // Add the new object to this OwnedObject property
+//            Identified* parent_obj = (Identified*)this->sbol_owner;
+//            child_obj->parent = parent_obj;  // Set back-pointer to parent object
+//            child_obj->identity.set(uri);
+//            child_obj->persistentIdentity.set(uri);
+//
+//            this->add(*child_obj);
+//            if (parent_doc)
+//                child_obj->doc = parent_doc;
+//            this->validate(child_obj);
+//            return *child_obj;
+//        }
+//    }
 
 //
 //    template<>