src/testutils/refdata-xml.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements reference data XML persistence.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \ingroup module_testutils
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "refdata-xml.h"
  46
  47 #include <tinyxml2.h>
  48
  49 #include "gromacs/utility/exceptions.h"
  50
  51 #include "testutils/refdata-impl.h"
  52 #include "testutils/testexceptions.h"
  53
  54 namespace gmx
  55 {
  56 namespace test
  57 {
  58
  59 namespace
  60 {
  61
  62 //! XML version declaration used when writing the reference data.
  63 const char *const c_VersionDeclarationString = "xml version=\"1.0\"";
  64 //! XML stylesheet declaration used for writing the reference data.
  65 const char *const c_StyleSheetDeclarationString = "xml-stylesheet type=\"text/xsl\" href=\"referencedata.xsl\"";
  66 //! Name of the root element in reference data XML files.
  67 const char *const c_RootNodeName = "ReferenceData";
  68 //! Name of the XML attribute used to store identifying strings for reference data elements.
  69 const char *const c_IdAttrName = "Name";
  70
  71 }       // namespace
  72
  73 /********************************************************************
  74  * XML reading
  75  */
  76
  77 namespace
  78 {
  79
  80 //! Convenience typedef
  81 typedef tinyxml2::XMLDocument *XMLDocumentPtr;
  82 //! Convenience typedef
  83 typedef tinyxml2::XMLNode *XMLNodePtr;
  84 //! Convenience typedef
  85 typedef tinyxml2::XMLElement *XMLElementPtr;
  86 //! Convenience typedef
  87 typedef tinyxml2::XMLText *XMLTextPtr;
  88
  89 //! \name Helper functions for XML reading
  90 //! \{
  91
  92 void readEntry(XMLNodePtr node, ReferenceDataEntry *entry);
  93
  94 XMLNodePtr getCDataChildNode(XMLNodePtr node)
  95 {
  96     XMLNodePtr cdata = node->FirstChild();
  97     while (cdata != nullptr &&
  98            cdata->ToText() != nullptr &&
  99            !cdata->ToText()->CData())
 100     {
 101         cdata = cdata->NextSibling();
 102     }
 103     return cdata;
 104 }
 105
 106 bool hasCDataContent(XMLNodePtr node)
 107 {
 108     return getCDataChildNode(node) != nullptr;
 109 }
 110
 111 //! Return a node convertible to text, either \c childNode or its first such sibling.
 112 XMLNodePtr getNextTextChildNode(XMLNodePtr childNode)
 113 {
 114     // Note that when reading, we don't have to care if it is in a
 115     // CDATA section, or not.
 116     while (childNode != nullptr)
 117     {
 118         if (childNode->ToText() != nullptr)
 119         {
 120             break;
 121         }
 122         childNode = childNode->NextSibling();
 123     }
 124     return childNode;
 125 }
 126
 127 //! Return the concatenation of all the text children of \c node, including multiple CDATA children.
 128 std::string getValueFromLeafElement(XMLNodePtr node)
 129 {
 130     std::string value;
 131
 132     XMLNodePtr  childNode = getNextTextChildNode(node->FirstChild());
 133     while (childNode != nullptr)
 134     {
 135         value += std::string(childNode->Value());
 136
 137         childNode = getNextTextChildNode(childNode->NextSibling());
 138     }
 139
 140     if (hasCDataContent(node))
 141     {
 142         // Prepare to strip the convenience newline added in
 143         // createElementContents, when writing CDATA content for
 144         // StringBlock data.
 145         if (value.empty() || value[0] != '\n')
 146         {
 147             GMX_THROW(TestException("Invalid string block in reference data"));
 148         }
 149         value.erase(0, 1);
 150     }
 151
 152     return value;
 153 }
 154
 155 //! Make a new entry from \c element.
 156 ReferenceDataEntry::EntryPointer createEntry(XMLElementPtr element)
 157 {
 158     const char *id = element->Attribute(c_IdAttrName);
 159     ReferenceDataEntry::EntryPointer entry(new ReferenceDataEntry(element->Value(), id));
 160     return entry;
 161 }
 162
 163 //! Read the child entries of \c parentElement and transfer the contents to \c entry
 164 void readChildEntries(XMLNodePtr parentElement, ReferenceDataEntry *entry)
 165 {
 166     XMLElementPtr childElement = parentElement->FirstChildElement();
 167     while (childElement != nullptr)
 168     {
 169         ReferenceDataEntry::EntryPointer child(createEntry(childElement));
 170         readEntry(childElement, child.get());
 171         entry->addChild(move(child));
 172         childElement = childElement->NextSiblingElement();
 173     }
 174 }
 175
 176 //! Return whether \c node has child XML elements (rather than text content).
 177 bool isCompoundElement(XMLNodePtr node)
 178 {
 179     return node->FirstChildElement() != nullptr;
 180 }
 181
 182 //! Read \c element and transfer the contents to \c entry
 183 void readEntry(XMLNodePtr element, ReferenceDataEntry *entry)
 184 {
 185     if (isCompoundElement(element))
 186     {
 187         readChildEntries(element, entry);
 188     }
 189     else if (hasCDataContent(element))
 190     {
 191         entry->setTextBlockValue(getValueFromLeafElement(element));
 192     }
 193     else
 194     {
 195         entry->setValue(getValueFromLeafElement(element));
 196     }
 197 }
 198
 199 //! \}
 200
 201 }       // namespace
 202
 203 //! \cond internal
 204 ReferenceDataEntry::EntryPointer
 205 readReferenceDataFile(const std::string &path)
 206 {
 207     tinyxml2::XMLDocument document;
 208     document.LoadFile(path.c_str());
 209     if (document.Error())
 210     {
 211         std::string errorString("Error was ");
 212         errorString += document.GetErrorStr1();
 213         errorString += document.GetErrorStr2();
 214         GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + errorString + "\n"));
 215     }
 216     XMLElementPtr rootNode = document.RootElement();
 217     if (rootNode == nullptr)
 218     {
 219         GMX_THROW(TestException("Reference data is empty: " + path));
 220     }
 221     if (std::strcmp(rootNode->Value(), c_RootNodeName) != 0)
 222     {
 223         GMX_THROW(TestException("Invalid root node type in " + path));
 224     }
 225
 226     ReferenceDataEntry::EntryPointer rootEntry(ReferenceDataEntry::createRoot());
 227     readEntry(rootNode, rootEntry.get());
 228     return rootEntry;
 229 }
 230 //! \endcond
 231
 232 /********************************************************************
 233  * XML writing
 234  */
 235
 236 namespace
 237 {
 238
 239 //! \name Helper functions for XML writing
 240 //! \{
 241
 242 void createElementAndContents(XMLElementPtr             parentElement,
 243                               const ReferenceDataEntry &entry);
 244
 245 void setIdAttribute(XMLElementPtr element, const std::string &id)
 246 {
 247     if (!id.empty())
 248     {
 249         element->SetAttribute(c_IdAttrName, id.c_str()); // If this fails, it throws std::bad_alloc
 250     }
 251 }
 252
 253 XMLElementPtr createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry)
 254 {
 255     XMLElementPtr element = parentElement->GetDocument()->NewElement(entry.type().c_str());
 256     parentElement->InsertEndChild(element);
 257     setIdAttribute(element, entry.id()); // If this fails, it throws std::bad_alloc
 258     return element;
 259 }
 260
 261 void createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry)
 262 {
 263     const ReferenceDataEntry::ChildList &children(entry.children());
 264     ReferenceDataEntry::ChildIterator    child;
 265     for (child = children.begin(); child != children.end(); ++child)
 266     {
 267         createElementAndContents(parentElement, **child);
 268     }
 269 }
 270
 271 /*! \brief Handle \c input intended to be written as CDATA
 272  *
 273  * This method searches for any ']]>' sequences embedded in \c input,
 274  * because this must always end a CDATA field. If any are found, it
 275  * breaks the string so that instead multiple CDATA fields will be
 276  * written with that token sequence split across the fields. Note that
 277  * tinyxml2 does not handle such things itself.
 278  *
 279  * This is an edge case that is unimportant for GROMACS refdata, but
 280  * it is preferable to know that the infrastructure won't break.
 281  */
 282 std::vector<std::string> breakUpAnyCdataEndTags(const std::string &input)
 283 {
 284     std::vector<std::string> strings;
 285     std::size_t              startPos = 0;
 286     std::size_t              endPos;
 287
 288     do
 289     {
 290         endPos = input.find("]]>", startPos);
 291         if (endPos != std::string::npos)
 292         {
 293             // We found an embedded CDATA end tag, so arrange to split it into multiple CDATA blocks
 294             endPos++;
 295         }
 296         strings.push_back(input.substr(startPos, endPos));
 297         startPos = endPos;
 298     }
 299     while (endPos != std::string::npos);
 300
 301     return strings;
 302 }
 303
 304 void createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry)
 305 {
 306     // TODO: Figure out if \r and \r\n can be handled without them
 307     // changing to \n in the roundtrip.
 308     if (entry.isCompound())
 309     {
 310         createChildElements(element, entry);
 311     }
 312     else if (entry.isTextBlock())
 313     {
 314         // An extra newline is written in the beginning to make lines align
 315         // in the output xml (otherwise, the first line would be off by the length
 316         // of the starting CDATA tag).
 317         const std::string        adjustedValue = "\n" + entry.value();
 318         std::vector<std::string> cdataStrings  = breakUpAnyCdataEndTags(adjustedValue);
 319         for (auto const &s : cdataStrings)
 320         {
 321             XMLTextPtr textNode = element->GetDocument()->NewText(s.c_str());
 322             textNode->SetCData(true);
 323             element->InsertEndChild(textNode);
 324         }
 325     }
 326     else
 327     {
 328         XMLTextPtr textNode = element->GetDocument()->NewText(entry.value().c_str());
 329         element->InsertEndChild(textNode);
 330     }
 331 }
 332
 333 void createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry)
 334 {
 335     XMLElementPtr element = createElement(parentElement, entry);
 336     createElementContents(element, entry);
 337 }
 338
 339 XMLElementPtr createRootElement(XMLDocumentPtr document)
 340 {
 341     XMLElementPtr rootElement = document->NewElement(c_RootNodeName);
 342     document->InsertEndChild(rootElement);
 343     return rootElement;
 344 }
 345
 346 //! \}
 347
 348 }       // namespace
 349
 350 //! \cond internal
 351 void writeReferenceDataFile(const std::string        &path,
 352                             const ReferenceDataEntry &rootEntry)
 353 {
 354     // TODO: Error checking
 355     tinyxml2::XMLDocument     document;
 356
 357     tinyxml2::XMLDeclaration *declaration = document.NewDeclaration(c_VersionDeclarationString);
 358     document.InsertEndChild(declaration);
 359
 360     declaration = document.NewDeclaration(c_StyleSheetDeclarationString);
 361     document.InsertEndChild(declaration);
 362
 363     XMLElementPtr rootElement = createRootElement(&document);
 364     createChildElements(rootElement, rootEntry);
 365
 366     if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR)
 367     {
 368         GMX_THROW(TestException("Reference data saving failed in " + path));
 369     }
 370 }
 371 //! \endcond
 372
 373 } // namespace test
 374 } // namespace gmx