/**
* Either display the query builder or redirect to project.sitePrefix.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @return an ActionForward object defining where control goes next
* @exception Exception if the application business logic throws an exception
*/
@Override
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
PathQuery query = SessionMethods.getQuery(session);
boolean showTemplate = (request.getParameter("showTemplate") != null);
if (query == null) {
return new ForwardParameters(
getWebProperties(request).getProperty("project.sitePrefix"), true)
.forward();
}
if (query instanceof TemplateQuery && showTemplate) {
TemplateQuery template = (TemplateQuery) query;
Profile profile = SessionMethods.getProfile(session);
String temporaryName = null;
for (SavedQuery sq : profile.getHistory().values()) {
if (sq.getPathQuery() instanceof TemplateQuery
&& ((TemplateQuery) sq.getPathQuery()).getName().equals(template.getName())) {
temporaryName = sq.getName();
}
}
if (temporaryName != null) {
return new ForwardParameters(mapping.findForward("template"))
.addParameter("loadModifiedTemplate", "true")
.addParameter("name", template.getName())
.addParameter("savedQueryName", temporaryName)
.forward();
}
return new ForwardParameters(mapping.findForward("template"))
.addParameter("name", template.getName())
.forward();
}
if (!(query instanceof TemplateQuery)) {
session.removeAttribute(Constants.EDITING_TEMPLATE);
session.removeAttribute(Constants.NEW_TEMPLATE);
}
return mapping.findForward("query");
}
/**
* Convert a SavedQuery to XML and write XML to given writer.
*
* @param query the SavedQuery
* @param writer the XMLStreamWriter to write to
* @param version the version number of the XML format, an attribute of the ProfileManager
*/
public static void marshal(SavedQuery query, XMLStreamWriter writer, int version) {
try {
writer.writeCharacters("\n");
writer.writeStartElement("saved-query");
writer.writeAttribute("name", query.getName());
if (query.getDateCreated() != null) {
writer.writeAttribute("date-created", "" + query.getDateCreated().getTime());
}
PathQueryBinding.marshal(
query.getPathQuery(),
query.getName(),
query.getPathQuery().getModel().getName(),
writer,
version);
writer.writeEndElement();
} catch (XMLStreamException e) {
throw new RuntimeException(e);
}
}
private static void deleteQueriesThatMentionBag(Profile profile, String bagName) {
// delete query from history
Map<String, SavedQuery> savedQueries = profile.getHistory();
Set<String> savedQueriesNames = new HashSet<String>(profile.getHistory().keySet());
for (String queryName : savedQueriesNames) {
SavedQuery query = (SavedQuery) savedQueries.get(queryName);
if (query.getPathQuery().getBagNames().contains(bagName)) {
profile.deleteHistory(queryName);
}
}
// delete query from saved queries
savedQueries = profile.getSavedQueries();
savedQueriesNames = new HashSet<String>(profile.getSavedQueries().keySet());
for (String queryName : savedQueriesNames) {
SavedQuery query = (SavedQuery) savedQueries.get(queryName);
if (query.getPathQuery().getBagNames().contains(bagName)) {
profile.deleteQuery(queryName);
}
}
}
/**
* Method called to export a saved Query.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @return an ActionForward object defining where control goes next
* @exception Exception if the application business logic throws an exception
*/
@Override
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Profile profile = SessionMethods.getProfile(session);
String type = request.getParameter("type");
String name = request.getParameter("name");
PathQuery query = null;
if (StringUtils.isEmpty(type) || StringUtils.isEmpty(name)) {
query = SessionMethods.getQuery(session);
} else if ("history".equals(type)) {
SavedQuery sq = profile.getHistory().get(name);
if (sq == null) {
recordError(new ActionMessage("errors.query.missing", name), request);
return mapping.findForward("mymine");
}
query = sq.getPathQuery();
} else if ("saved".equals(type)) {
SavedQuery sq = profile.getSavedQueries().get(name);
if (sq == null) {
recordError(new ActionMessage("errors.query.missing", name), request);
return mapping.findForward("mymine");
}
query = sq.getPathQuery();
} else {
LOG.error("Bad type parameter: " + type);
return null;
}
if (query == null) {
LOG.error("Failed to find query " + name + " of type " + type);
return null;
}
if (query.getView().size() == 0) {
response.getWriter().write("Invalid query. No fields selected for output.");
return null;
}
response.setContentType("text/plain; charset=utf-8");
WebResultsExecutor webResultsExecutor = im.getWebResultsExecutor(profile);
String format;
if (!StringUtils.isEmpty(request.getParameter("as"))) {
format = request.getParameter("as").toLowerCase();
} else {
format = "xml";
}
if ("xml".equals(format)) {
String xml = getQueryXML(name, query);
xml = XmlUtil.indentXmlSimple(xml);
response.getWriter().write(xml);
} else if ("iql".equals(format)) {
Query osQuery = webResultsExecutor.makeQuery(query);
response.getWriter().println(osQuery.toString());
} else if ("sql".equals(format)) {
response.getWriter().println(webResultsExecutor.makeSql(query));
} else if ("link".equals(format)) {
String serviceFormat;
if (request.getParameter("serviceFormat") != null) {
serviceFormat = request.getParameter("serviceFormat");
} else {
serviceFormat = "tab";
}
String xml = getQueryXML(name, query);
String link =
new QueryResultLinkGenerator()
.getLink(new URLGenerator(request).getPermanentBaseURL(), xml, serviceFormat);
response.getWriter().write(link);
} else {
response.getWriter().println("Unknown export type: " + request.getParameter("as"));
}
return null;
}