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Added SBOLTestSuite as git submodule. Updated Python unit tests and e…
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…xample script.
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Bryan Bartley committed Dec 20, 2017
1 parent 0deaf1b commit ad76d10
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Showing 11 changed files with 282 additions and 371 deletions.
2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
[submodule "test/SBOLTestSuite"]
path = test/SBOLTestSuite
url = https://github.com/SynBioDex/SBOLTestSuite.git
url = https://github.com/SynBioDex/SBOLTestSuite
6 changes: 3 additions & 3 deletions manual/installation.dox
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Expand Up @@ -39,7 +39,7 @@
///
/// 2. Clone the repository by running the following command in git application or command console or get the stable source [here](https://github.com/SynBioDex/libSBOL/releases/latest):
/// ```
/// git clone https://github.com/SynBioDex/libSBOL.git
/// git clone https://github.com/SynBioDex/libSBOL --recursive
/// ```
/// This will create a libSBOL directory with the source.
///
Expand Down Expand Up @@ -83,7 +83,7 @@
///
/// 2. Clone the repository by running the following command in terminal or get the stable source [here](https://github.com/SynBioDex/libSBOL/releases/latest).
/// ```
/// git clone https://github.com/SynBioDex/libSBOL.git
/// git clone https://github.com/SynBioDex/libSBOL --recursive
/// ```
/// This will create a libSBOL directory with the source.
///
Expand Down Expand Up @@ -141,7 +141,7 @@
///
/// 3. Clone the repository by running the following command in terminal or get the stable source [here](https://github.com/SynBioDex/libSBOL/releases/latest).
/// ```
/// git clone https://github.com/SynBioDex/libSBOL.git
/// git clone https://github.com/SynBioDex/libSBOL.git --recursive
/// ```
/// This will create a libSBOL directory with the source.
///
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2 changes: 1 addition & 1 deletion source/document.cpp
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Expand Up @@ -1460,7 +1460,7 @@ Identified& Identified::simpleCopy(string uri)
// Initialize the object's URI, this code is same as Identified's constructor
if(Config::getOption("sbol_compliant_uris").compare("True") == 0)
{
if (compliantTypesEnabled())
if (Config::getOption("sbol_typed_uris").compare("True") == 0)
{
new_obj.identity.set(getHomespace() + "/" + getClassName(type) + "/" + uri + "/" + VERSION_STRING);
new_obj.persistentIdentity.set(getHomespace() + "/" + uri);
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2 changes: 1 addition & 1 deletion source/identified.h
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Expand Up @@ -53,7 +53,7 @@ namespace sbol
{
if(Config::getOption("sbol_compliant_uris").compare("True") == 0)
{
if (compliantTypesEnabled())
if (Config::getOption("sbol_typed_uris").compare("True") == 0)
{
identity.set(getHomespace() + "/" + getClassName(type) + "/" + uri + "/" + version);
persistentIdentity.set(getHomespace() + "/" + uri);
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2 changes: 1 addition & 1 deletion source/toplevel.h
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Expand Up @@ -44,7 +44,7 @@ namespace sbol
if (Config::getOption("sbol_compliant_uris").compare("True") == 0)
{
displayId.set(uri);
if (compliantTypesEnabled())
if (Config::getOption("sbol_typed_uris").compare("True") == 0)
{
identity.set(getHomespace() + "/" + getClassName(type) + "/" + displayId.get() + "/" + version);
persistentIdentity.set(getHomespace() + "/" + getClassName(type) + "/" + displayId.get());
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8 changes: 4 additions & 4 deletions test/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ IF ( ${CMAKE_SYSTEM_NAME} MATCHES "Windows" )
Ws2_32.lib
)
file(MAKE_DIRECTORY "${CMAKE_INSTALL_PREFIX}/test")
add_custom_command(TARGET sbol_test PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/roundtrip ${CMAKE_INSTALL_PREFIX}/test/roundtrip)
add_custom_command(TARGET sbol_test PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/SBOLTestSuite/SBOL2 ${CMAKE_INSTALL_PREFIX}/test/roundtrip)
set_target_properties(sbol_test PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_INSTALL_PREFIX}/test")
ELSE ()
# build test executable
Expand All @@ -64,8 +64,8 @@ ELSE ()
${LIBXSLT_LIBRARIES}
${JsonCpp_LIBRARY}
)
file(MAKE_DIRECTORY "${CMAKE_INSTALL_PREFIX}/test")
add_custom_command(TARGET sbol_test PRE_BUILD COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/roundtrip ${CMAKE_INSTALL_PREFIX}/test/roundtrip)
set_target_properties(sbol_test PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_INSTALL_PREFIX}/test")
file(MAKE_DIRECTORY "${SBOL_RELEASE_DIR}/test")
add_custom_command(TARGET sbol_test PRE_BUILD COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/SBOLTestSuite/SBOL2 ${SBOL_RELEASE_DIR}/test/roundtrip)
set_target_properties(sbol_test PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${SBOL_RELEASE_DIR}/test")
ENDIF ()

2 changes: 1 addition & 1 deletion test/SBOLTestSuite
Submodule SBOLTestSuite updated 35 files
+26 −26 SBOL2/BBa_I0462.xml
+24 −24 SBOL2/BBa_I0462_orig.xml
+688 −688 SBOL2/BBa_T9002.xml
+550 −550 SBOL2/BBa_T9002_orig.xml
+66 −66 SBOL2/ComponentDefinitionOutput.xml
+261 −261 SBOL2/ModuleDefinitionOutput.xml
+16 −16 SBOL2/SBOL1and2Test.xml
+8 −8 SBOL2/SequenceConstraintOutput.xml
+9 −9 SBOL2/SimpleModuleDefinition.xml
+1,415 −1,415 SBOL2/igem1.xml
+2,273 −2,273 SBOL2/igem2.xml
+4,346 −4,346 SBOL2/igem3.xml
+1,421 −1,421 SBOL2/pIKE_pTAK_cassettes 2.xml
+1,210 −1,210 SBOL2/pIKE_pTAK_cassettes 2_orig.xml
+1,421 −1,421 SBOL2/pIKE_pTAK_cassettes.xml
+1,210 −1,210 SBOL2/pIKE_pTAK_cassettes_orig.xml
+1,421 −1,421 SBOL2/pIKE_pTAK_left_right_cassettes.xml
+1,210 −1,210 SBOL2/pIKE_pTAK_left_right_cassettes_orig.xml
+2,472 −2,472 SBOL2/pIKE_pTAK_toggle_switches.xml
+2,214 −2,214 SBOL2/pIKE_pTAK_toggle_switches_orig.xml
+32 −32 SBOL2/partial_pIKE_left_cassette.xml
+77 −77 SBOL2/partial_pIKE_left_cassette_orig.xml
+104 −104 SBOL2/partial_pIKE_right_casette.xml
+131 −131 SBOL2/partial_pIKE_right_casette_orig.xml
+104 −104 SBOL2/partial_pIKE_right_cassette.xml
+131 −131 SBOL2/partial_pIKE_right_cassette_orig.xml
+33 −33 SBOL2/partial_pTAK_left_cassette.xml
+60 −60 SBOL2/partial_pTAK_left_cassette_orig.xml
+160 −160 SBOL2/partial_pTAK_right_cassette.xml
+142 −142 SBOL2/partial_pTAK_right_cassette_orig.xml
+91 −91 SBOL2/sequence1.xml
+149 −149 SBOL2/sequence2.xml
+165 −165 SBOL2/sequence3.xml
+1,928 −1,928 SBOL2/sequence4.xml
+410 −410 SBOL2/toggle.xml
16 changes: 8 additions & 8 deletions wrapper/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ IF (SBOL_BUILD_PYTHON3)
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR})
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol32_3 PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${PROJECT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol32_3 PRE_BUILD
COMMAND cp ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/__init__.py)
add_custom_command(TARGET _libsbol32_3 PRE_BUILD
Expand Down Expand Up @@ -136,7 +136,7 @@ IF (SBOL_BUILD_PYTHON3)
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR})
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol64_3 PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${PROJECT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol64_3 PRE_BUILD
COMMAND cp ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/__init__.py)
add_custom_command(TARGET _libsbol64_3 PRE_BUILD
Expand Down Expand Up @@ -190,7 +190,7 @@ IF (SBOL_BUILD_PYTHON3)
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/unit_tests.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol POST_BUILD
COMMAND cp -r ${CMAKE_SWIG_OUTDIR}/libsbol.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol POST_BUILD
Expand Down Expand Up @@ -234,7 +234,7 @@ IF (SBOL_BUILD_PYTHON3)
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/unit_tests.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol POST_BUILD
COMMAND cp -r ${CMAKE_SWIG_OUTDIR}/libsbol.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol POST_BUILD
Expand Down Expand Up @@ -372,7 +372,7 @@ IF (SBOL_BUILD_PYTHON2)
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR})
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol32_2 PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${PROJECT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol32_2 PRE_BUILD
COMMAND cp ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/__init__.py)
add_custom_command(TARGET _libsbol32_2 PRE_BUILD
Expand Down Expand Up @@ -419,7 +419,7 @@ IF (SBOL_BUILD_PYTHON2)
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR})
file(MAKE_DIRECTORY ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol64_2 PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${PROJECT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol64_2 PRE_BUILD
COMMAND cp ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py ${CMAKE_SWIG_OUTDIR}/${PYSBOL_TARGET_DIR}/__init__.py)
add_custom_command(TARGET _libsbol64_2 PRE_BUILD
Expand Down Expand Up @@ -469,7 +469,7 @@ IF (SBOL_BUILD_PYTHON2)
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/unit_tests.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol POST_BUILD
COMMAND cp -r ${CMAKE_SWIG_OUTDIR}/libsbol.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol POST_BUILD
Expand Down Expand Up @@ -510,7 +510,7 @@ IF (SBOL_BUILD_PYTHON2)
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/unit_tests.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol PRE_BUILD
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/test/SBOLTestSuite/* ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR}/test)
add_custom_command(TARGET _libsbol POST_BUILD
COMMAND cp -r ${CMAKE_SWIG_OUTDIR}/libsbol.py ${CMAKE_INSTALL_PREFIX}/wrapper/${PYSBOL_TARGET_DIR})
add_custom_command(TARGET _libsbol POST_BUILD
Expand Down
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