Added support for validating NeXus files without an application defin…

…ition.

As implemented now, validation happens against a minimal application definition containing
just an NXentry.

Refs #13

nxvmain.c

@@ -68,9 +68,9 @@ int main(int argc, char *argv[])
 	/*
 		should all be 0 in production
 	*/
-	filt.warnOpt = 1;
-	filt.warnBase = 1;
-	filt.warnUndefined = 1;
+	filt.warnOpt = 0;
+	filt.warnBase = 0;
+	filt.warnUndefined = 0;
 	filt.debug = 0;
 
 

src/minimal.c

@@ -0,0 +1,17 @@
+/*
+ Just a morsel of code to define the minimal application definition. For 
+ checking NeXus files without an application definition
+*/
+
+static const char xmlMinimal[] = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\
+<?xml-stylesheet type=\"text/xsl\" href=\"nxdlformat.xsl\" ?>\
+<definition name=\"NXminimal\" extends=\"NXobject\" type=\"group\"\
+  category=\"application\"\
+  xmlns=\"http://definition.nexusformat.org/nxdl/3.1\"\
+    xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\
+    xsi:schemaLocation=\"http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd\"\
+    version=\"1.0b\"\
+    >\
+    <group type=\"NXentry\" name=\"entry\">\
+   </group>\
+</definition>";

src/nxdlutil.c

@@ -242,6 +242,7 @@ static void mergeInheritance(pNXVcontext self)
 	mergeInheritance(self);
 
 }
+#include "minimal.c"
 /*--------------------------------------------------------------*/
 int NXVloadAppDef(pNXVcontext self, char *nxdlFile)
 {
@@ -257,7 +258,11 @@ int NXVloadAppDef(pNXVcontext self, char *nxdlFile)
 		pPtr = nxdlFile;
 	}
 
-  xmlData = self->nxdlRetriever(pPtr,self->retrieverUserData);
+	if(strstr(pPtr,"NXminimal") == NULL){
+	  xmlData = self->nxdlRetriever(pPtr,self->retrieverUserData);
+	} else {
+	  xmlData = strdup(xmlMinimal);
+	}
 	if(xmlData == NULL){
 		NXVsetLog(self,"sev","fatal");
 		NXVsetLog(self,"message","Failed to load application definition");

src/nxvcontext.h

@@ -78,3 +78,15 @@ int testISO8601(char *date);
  * strings are not properly read by this HDF5 function. Implemented in nxvutil.c 
  */
 herr_t H5NXget_attribute_string( hid_t loc_id, const char *obj_name, const char *attr_name,  char *data );
+
+/*
+ * validate a base class filed as fas as this is possible. Implemented in nxvfield.c
+ */
+void validateBaseClassField(pNXVcontext self, hid_t groupID, hid_t dataID);
+
+/*
+  validation of the depends_on chain. In nxvgroup.c
+*/
+void validateDependsOn(pNXVcontext self, hid_t groupID,
+		       hid_t fieldID);
+

src/nxvfield.c

@@ -1060,3 +1060,49 @@ int NXVvalidateField(pNXVcontext self, hid_t fieldID,
 	self->nxdlPath = myPath;
 	return 0;
 }
+/*-----------------------------------------------------------------------*/
+void validateBaseClassField(pNXVcontext self, hid_t groupID, hid_t dataID)
+{
+  char fName[512];
+
+  H5Iget_name(dataID,fName,sizeof(fName));
+  NXVsetLog(self,"sev","debug");
+  NXVsetLog(self,"message","Validating field");
+  NXVsetLog(self,"dataPath",fName);
+  NXVlog(self);
+
+  validateDataOffsetStride(self, dataID);
+  validateAxes(self, dataID); 
+  validateInterpretation(self,dataID);
+  validateCalibration(self,dataID);
+
+  if(H5LTfind_attribute(dataID,"depends_on") == 1){
+    validateDependsOn(self,groupID,dataID);
+  }
+
+  if(H5LTfind_attribute(dataID,"axis") == 1 &&
+      testAttType(dataID,"axis",H5T_INTEGER) == 0 &&
+     testAttType(dataID,"axis",H5T_STRING) == 0){
+    NXVsetLog(self,"sev","error");
+    NXVprintLog(self,"message","Attribute %s to %s has wrong type", "axis",fName);
+    NXVlog(self);
+  }
+
+  if(H5LTfind_attribute(dataID,"signal") == 1 &&
+      testAttType(dataID,"signal",H5T_INTEGER) == 0 &&
+     testAttType(dataID,"signal",H5T_STRING) == 0){
+    NXVsetLog(self,"sev","error");
+    NXVprintLog(self,"message","Attribute %s to %s has wrong type", "signal",fName);
+    NXVlog(self);
+  }
+
+  if(H5LTfind_attribute(dataID,"primary") == 1 &&
+      testAttType(dataID,"primary",H5T_INTEGER) == 0 &&
+     testAttType(dataID,"primary",H5T_STRING) == 0){
+    NXVsetLog(self,"sev","error");
+    NXVprintLog(self,"message","Attribute %s to %s has wrong type", "primary",fName);
+    NXVlog(self);
+  }
+
+}
+

src/nxvgroup.c

@@ -560,7 +560,7 @@ static void validateDependsOnField(pNXVcontext self,
 	}
 }
 /*--------------------------------------------------------------*/
-static void validateDependsOn(pNXVcontext self, hid_t groupID,
+void validateDependsOn(pNXVcontext self, hid_t groupID,
 	hid_t fieldID)
 {
 	char fname[512], dpData[1024];
@@ -632,6 +632,48 @@ typedef struct {
 	hash_table *baseNames;
 	pNXVcontext self;
 } SecondPassData;
+/*------------------ forward declaration ----------------------------*/
+static herr_t SecondPassIterator(hid_t g_id,
+		const char *name,
+				 const H5L_info_t *info, void *op_data);
+
+/*--------------------------------------------------------------*/
+static void validateBaseClassGroup(pNXVcontext self, hid_t group_id, char *baseClass)
+{
+  SecondPassData spd;
+  char *oldNXDLPath;
+  char myNXDLPath[512], fName[1024];
+  hash_table namesSeen, baseNames;
+  hsize_t idx = 0;
+
+  oldNXDLPath = self->nxdlPath;
+  snprintf(myNXDLPath,sizeof(myNXDLPath),"/BASE/%s", baseClass);
+  self->nxdlPath = myNXDLPath;
+  NXVsetLog(self,"nxdlPath", myNXDLPath);
+
+  H5Iget_name(group_id,fName,sizeof(fName));
+  NXVsetLog(self,"sev","debug");
+  NXVsetLog(self,"dataPath",fName);
+  NXVsetLog(self,"message","Validating group against base class");
+  NXVlog(self);		
+
+  hash_construct_table(&baseNames,100);
+  hash_construct_table(&namesSeen,2);
+  NXVloadBaseClass(self,&baseNames,baseClass);
+  spd.baseNames = &baseNames;
+  spd.namesSeen = &namesSeen;
+  spd.self = self;
+  H5Literate(group_id, H5_INDEX_NAME, H5_ITER_INC, &idx,
+	     SecondPassIterator, &spd);
+
+  /*
+    clean up
+  */
+  hash_free_table(&namesSeen,free);
+  hash_free_table(&baseNames,free);
+  self->nxdlPath = oldNXDLPath;
+  NXVsetLog(self,"nxdlPath", oldNXDLPath);
+}
 /*--------------------------------------------------------------*/
 static herr_t SecondPassIterator(hid_t g_id,
 		const char *name,
@@ -667,13 +709,15 @@ static herr_t SecondPassIterator(hid_t g_id,
 					name, nxClass);
 				NXVlog(spd->self);
 				spd->self->warnCount++;
+				validateBaseClassGroup(spd->self, groupID, nxClass);
 			} else {
 				NXVsetLog(spd->self,"sev","warnbase");
 				NXVprintLog(spd->self,"message",
 					"Additional base class group %s of type %s found",
 					name, nxClass);
 				NXVlog(spd->self);
 				spd->self->warnCount++;
+				validateBaseClassGroup(spd->self, groupID, nxClass);
 			}
 		} else {
 			NXVsetLog(spd->self,"sev","warnundef");
@@ -687,7 +731,6 @@ static herr_t SecondPassIterator(hid_t g_id,
 	} else if (obj_info.type == H5O_TYPE_DATASET) {
 		dataID = H5Dopen(g_id,name,H5P_DEFAULT);
 		H5Iget_name(dataID, fname,sizeof(fname));
-		H5Dclose(dataID);
 		NXVsetLog(spd->self,"dataPath",fname);
 		if(hash_lookup((char *)name,spd->baseNames) == NULL){
 			NXVsetLog(spd->self,"sev","warnundef");
@@ -701,7 +744,10 @@ static herr_t SecondPassIterator(hid_t g_id,
 			name);
 			NXVlog(spd->self);
 			spd->self->warnCount++;
+			validateBaseClassField(spd->self, g_id, dataID);
+
 		}
+		H5Dclose(dataID);
 	}
 
 	return 0;

src/nxvmainloop.c

@@ -82,7 +82,7 @@ static int validatePath(pNXVcontext self, char *path, char *rawNxdlFile)
 	hid_t groupID;
 	xmlNodePtr groupNode = NULL;
 	char nxdlFile[512];
-
+	
 	/*
 		first fix the appDef: the nxdl.xml postfix may be missing
 	*/
@@ -195,7 +195,7 @@ static herr_t NXVrootIterator(hid_t g_id,
 					if(strcmp(nxClass,"NXentry") != 0){
 						NXVsetLog(self,"sev","error");
 						NXVprintLog(self,"dataPath","/%s",name);
-            NXVprintLog(self,"message",
+						NXVprintLog(self,"message",
 							"Wrong root group class %s, expected NXentry",nxClass);
 						NXVlog(self);
 					}
@@ -241,10 +241,11 @@ static herr_t NXVrootIterator(hid_t g_id,
 					NXVsetLog(self,"sev","error");
 					NXVprintLog(self,"dataPath","/%s",name);
 					NXVprintLog(self,"message",
-						"Cannot validate %s, failed to find application definition",
+						"No application definition found for %s, continuing with NXminimal",
 						name);
 					self->errCount++;
-					NXVlog(self);
+				    	NXVlog(self);
+					validatePath(self,nxPath,"NXminimal");
 				}
 			}
 

src/nxvutil.c

@@ -44,11 +44,9 @@ herr_t H5NXget_attribute_string( hid_t loc_id, const char *obj_name, const char
 	This is a memory issue waiting to happen. IMHO, there is a design issue with 
 	H5LTget_attribute_string in itself that it does not pass in the length of the 
 	string. Thus no check can be performed. 
-
-        There is also a mmeory leak with varData. However, if I call the reclaim function 
-        from the HDF5 API on it, I get a core dump.....
       */
       strcpy(data,varData);
+      H5Dvlen_reclaim(attr_type, space, H5P_DEFAULT, &varData);
     } else {
       result = H5Aread(attr_id,attr_type,data);
     }