OME ontologies: schemas and samples reorganization

cmake/XsdFu.cmake

@@ -52,7 +52,7 @@ set(XSD_FU python ${XSD_FU_SCRIPT})
 set(MODEL_VERSION 2016-06)
 
 # Path to the model within the source tree
-set(MODEL_PATH ${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/${MODEL_VERSION})
+set(MODEL_PATH ${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/${MODEL_VERSION})
 
 # Files to use within the model directory
 set(MODEL_FILES

ome-xml/CMakeLists.txt

@@ -39,7 +39,7 @@
 function(ome_xml_add_test)
   add_test(${ARGV})
   set_tests_properties(${ARGV0}
-    PROPERTIES ENVIRONMENT "OME_XML_SCHEMADIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema;OME_XML_TRANSFORMDIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/transforms;OME_XML_SAMPLEDIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/samples")
+    PROPERTIES ENVIRONMENT "OME_XML_SCHEMADIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas;OME_XML_TRANSFORMDIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/transforms;OME_XML_SAMPLEDIR=${PROJECT_SOURCE_DIR}/specification/src/main/resources/samples")
 endfunction()
 
 add_subdirectory(src/main/cpp)

ome-xml/src/main/cpp/ome/xml/CMakeLists.txt

@@ -239,15 +239,15 @@ add_custom_target(gensrc DEPENDS
   ${OME_XML_GENERATED_MODEL_ENUMS_HEADERS})
 
 # Find and install all schemas
-file(GLOB OME_SCHEMAS RELATIVE "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/"
-     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/catalog.xml"
-     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/2*/*.xsd"
-     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/2*/catalog.xml"
-     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/external/*.xsd"
-     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/external/catalog.xml")
+file(GLOB OME_SCHEMAS RELATIVE "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/"
+     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/catalog.xml"
+     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/2*/*.xsd"
+     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/2*/catalog.xml"
+     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/external/*.xsd"
+     "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/external/catalog.xml")
 foreach(schema ${OME_SCHEMAS})
   get_filename_component(SCHEMA_RELEASE ${schema} PATH)
-  install(FILES "${PROJECT_SOURCE_DIR}/specification/src/main/resources/released-schema/${schema}"
+  install(FILES "${PROJECT_SOURCE_DIR}/specification/src/main/resources/schemas/${schema}"
           DESTINATION "${OME_XML_INSTALL_SCHEMADIR}/${SCHEMA_RELEASE}"
           COMPONENT "runtime")
 endforeach(schema)
@@ -263,10 +263,10 @@ foreach(transform ${OME_TRANSFORMS})
 endforeach(transform)
 
 # Find and install all samples
-file(GLOB_RECURSE OME_SAMPLES RELATIVE "${PROJECT_SOURCE_DIR}/specification/samples/" "${PROJECT_SOURCE_DIR}/specification/samples/*")
+file(GLOB_RECURSE OME_SAMPLES RELATIVE "${PROJECT_SOURCE_DIR}/specification/src/main/resources/samples/" "${PROJECT_SOURCE_DIR}/specification/src/main/resources/samples/*")
 foreach(sample ${OME_SAMPLES})
   get_filename_component(SAMPLE_FILE ${sample} PATH)
-  install(FILES "${PROJECT_SOURCE_DIR}/specification/samples/${sample}"
+  install(FILES "${PROJECT_SOURCE_DIR}/specification/src/main/resources/samples/${sample}"
           DESTINATION "${OME_XML_INSTALL_SAMPLEDIR}/${SAMPLE_FILE}"
           COMPONENT "runtime")
 endforeach(sample)

ome-xml/src/test/cpp/model.cpp

@@ -83,7 +83,7 @@ namespace
 
     /// @todo Use the correct model version when available.
     /// @todo Use all model versions when transforms available.
-    path dir(PROJECT_SOURCE_DIR "/specification/samples/" "2015-01");
+    path dir(PROJECT_SOURCE_DIR "/specification/src/main/resources/samples/" "2015-01");
     if (exists(dir) && is_directory(dir))
       {
         for(directory_iterator i(dir); i != directory_iterator(); ++i)

ome-xml/src/test/cpp/transform.cpp

@@ -80,7 +80,7 @@ namespace
     ome::xml::OMETransformResolver tr;
     std::set<std::string> versions = tr.schema_versions();
 
-    path samplesdir(PROJECT_SOURCE_DIR "/specification/samples");
+    path samplesdir(PROJECT_SOURCE_DIR "/specification/src/main/resources/samples");
     if (exists(samplesdir) && is_directory(samplesdir))
       {
         for (directory_iterator si(samplesdir); si != directory_iterator(); ++si)

pom.xml

@@ -120,7 +120,7 @@
     <ome-common.version>${ome_common.version}</ome-common.version>
 
     <ome.model.schemaver>2016-06</ome.model.schemaver>
-    <ome.model.schemapath>specification/src/main/resources/released-schema/${ome.model.schemaver}</ome.model.schemapath>
+    <ome.model.schemapath>specification/src/main/resources/schemas/${ome.model.schemaver}</ome.model.schemapath>
     <ome.model.omeschema>${ome.model.schemapath}/ome.xsd</ome.model.omeschema>
 
     <!-- NB: Avoid platform encoding warning when copying resources. -->

specification/publish

@@ -40,7 +40,7 @@ curdate() {
 # Get the most recent version of a schema
 # $1=schema name
 mostrecentversion() {
-    echo "$(basename $(dirname $(find src/main/resources/released-schema -name "$1" | grep -v $devmarker | sort | tail -n1)))"
+    echo "$(basename $(dirname $(find src/main/resources/schemas -name "$1" | grep -v $devmarker | sort | tail -n1)))"
 }
 
 # Check if the a schema is the most recent version (return true) or legacy (return false)
@@ -88,7 +88,7 @@ schemastatus() {
 # $1=schema name
 # $2=release to check if current
 schemaversion() {
-        version=$(grep "version=" "src/main/resources/released-schema/$2/$1" | grep -v 'xml' | head -n1 | sed -e 's;^.*version="\([0-9][0-9]*\)".*$;\1;')
+        version=$(grep "version=" "src/main/resources/schemas/$2/$1" | grep -v 'xml' | head -n1 | sed -e 's;^.*version="\([0-9][0-9]*\)".*$;\1;')
         if [ -z "$version" ]; then
             version="1"
         fi
@@ -155,7 +155,7 @@ root=target/published
 rm -rf "$root"
 mkdir -p "$root"
 
-for dir in src/main/resources/released-schema/20*
+for dir in src/main/resources/schemas/20*
 do
 
     if contains $dir $devmarker; then
@@ -407,11 +407,11 @@ the
 <ul>
 EOF
 
-    for release in $(ls -1d src/main/resources/released-schema/20* | grep -v 2003 | grep -v $devmarker | xargs $XARGSOPTS -n1 basename | sort -r); do
+    for release in $(ls -1d src/main/resources/schemas/20* | grep -v 2003 | grep -v $devmarker | xargs $XARGSOPTS -n1 basename | sort -r); do
         reldate=$(parsedate "$release")
         echo "<li>$reldate - namespace /$release/</li>"
     done
-    for release in $(ls -1d src/main/resources/released-schema/20* | grep 2003 | xargs $XARGSOPTS -n1 basename | sort -r | grep FC | sed -e 's;2003-\(.*\);\1;') $(ls -1d src/main/resources/released-schema/20* | grep 2003 | xargs $XARGSOPTS -n1 basename | sort -r | grep -v FC | sed -e 's;2003-\(.*\);\1;'); do
+    for release in $(ls -1d src/main/resources/schemas/20* | grep 2003 | xargs $XARGSOPTS -n1 basename | sort -r | grep FC | sed -e 's;2003-\(.*\);\1;') $(ls -1d src/main/resources/schemas/20* | grep 2003 | xargs $XARGSOPTS -n1 basename | sort -r | grep -v FC | sed -e 's;2003-\(.*\);\1;'); do
         reldate="2003 ($release)"
         echo "<li>$reldate - namespace /$release/*.xsd</li>"
     done

specification/src/main/java/ome/specification/SchemaResolver.java

@@ -57,7 +57,7 @@ public class SchemaResolver implements LSResourceResolver
     private static String GIT_MASTER_PATH  = "http://git.openmicroscopy.org/src/master/components/specification";
     private static String GIT_DEVELOP_PATH = "http://git.openmicroscopy.org/src/develop/components/specification";
     private static String MAIN_PATH = "http://www.openmicroscopy.org/Schemas/";
-    private static String MAIN_SEARCH_PATH = "/released-schema/";
+    private static String MAIN_SEARCH_PATH = "/schemas/";
     private static String LEGACY_AC_PATH = "http://www.openmicroscopy.org/XMLschemas/AnalysisChain/RC1/";
     private static String LEGACY_AM_PATH = "http://www.openmicroscopy.org/XMLschemas/AnalysisModule/RC1/";
     private static String LEGACY_BF_PATH = "http://www.openmicroscopy.org/XMLschemas/BinaryFile/RC1/";
@@ -67,7 +67,7 @@ public class SchemaResolver implements LSResourceResolver
     private static String LEGACY_ML_PATH = "http://www.openmicroscopy.org/XMLschemas/MLI/IR2/";
     private static String LEGACY_OM_PATH = "http://www.openmicroscopy.org/XMLschemas/OME/FC/";
     private static String LEGACY_ST_PATH = "http://www.openmicroscopy.org/XMLschemas/STD/RC2/";
-    private static String LEGACY_SEARCH_PATH = "/released-schema/2003-FC/";
+    private static String LEGACY_SEARCH_PATH = "/schemas/2003-FC/";
 
     public SchemaResolver() throws ClassNotFoundException, InstantiationException, IllegalAccessException
     {
@@ -136,7 +136,7 @@ public LSInput  resolveResource(
         // Match the requested schema locations and create the appropriate LSInput object
         if (systemId.equals("http://www.w3.org/2001/xml.xsd"))
         {
-            theResult = makeSubstutionStream("/released-schema/external/xml.xsd", systemId);
+            theResult = makeSubstutionStream("/schemas/external/xml.xsd", systemId);
         }
         else if (systemId.startsWith(GIT_MASTER_PATH))
         {