CatalogPublish.cpp

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidICat/CatalogPublish.h"
#include "MantidICat/CatalogAlgorithmHelper.h"
 
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/CatalogManager.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/MandatoryValidator.h"
 
#include <Poco/Net/AcceptCertificateHandler.h>
#include <Poco/Net/HTTPRequest.h>
#include <Poco/Net/HTTPResponse.h>
#include <Poco/Net/HTTPSClientSession.h>
#include <Poco/Net/PrivateKeyPassphraseHandler.h>
#include <Poco/Net/SSLException.h>
#include <Poco/Net/SSLManager.h>
#include <Poco/SharedPtr.h>
#include <Poco/StreamCopier.h>
#include <Poco/URI.h>
 
#include <boost/regex.hpp>
#include <filesystem>
#include <fstream>
 
namespace Mantid::ICat {
DECLARE_ALGORITHM(CatalogPublish)
 
 
void CatalogPublish::init() {
  declareProperty(std::make_unique<API::FileProperty>("FileName", "", API::FileProperty::OptionalLoad),
                  "The file to publish.");
  declareProperty(std::make_unique<API::WorkspaceProperty<API::Workspace>>(
                      "InputWorkspace", "", Kernel::Direction::Input, API::PropertyMode::Optional),
                  "The workspace to publish.");
  declareProperty("NameInCatalog", "",
                  "The name to give to the file being saved. The file name or workspace "
                  "name is used by default. "
                  "This can only contain alphanumerics, underscores or periods.");
  declareProperty("InvestigationNumber", "", "The investigation number where the published file will be saved to.");
  declareProperty("DataFileDescription", "", "A short description of the datafile you are publishing to the catalog.");
  declareProperty("Session", "", "The session information of the catalog to use.");
}
 
void CatalogPublish::exec() {
  // Used for error checking.
  std::string ws = getPropertyValue("InputWorkspace");
  std::string filePath = getPropertyValue("FileName");
  std::string nameInCatalog = getPropertyValue("NameInCatalog");
  Mantid::API::Workspace_sptr workspace = getProperty("InputWorkspace");
 
  // Prevent invalid/malicious file names being saved to the catalog.
  boost::regex re("^[a-zA-Z0-9_.]*$");
  if (!boost::regex_match(nameInCatalog.begin(), nameInCatalog.end(), re)) {
    throw std::runtime_error("The filename can only contain characters, "
                             "numbers, underscores and periods");
  }
 
  // Error checking to ensure a workspace OR a file is selected. Never both.
  if ((ws.empty() && filePath.empty()) || (!ws.empty() && !filePath.empty())) {
    throw std::runtime_error("Please select a workspace or a file to publish. Not both.");
  }
 
  // Cast a catalog to a catalogInfoService to access publishing functionality.
  auto catalogInfoService = std::dynamic_pointer_cast<API::ICatalogInfoService>(
      API::CatalogManager::Instance().getCatalog(getPropertyValue("Session")));
 
  // Check if the catalog created supports publishing functionality.
  if (!catalogInfoService)
    throw std::runtime_error("The catalog that you are using does not support "
                             "publishing to the archives.");
 
  // The user want to upload a file.
  if (!filePath.empty()) {
    std::filesystem::path path(filePath);
    std::string fileName = path.filename().string();
    // If the user has not set the name to save the file as, then use the
    // filename of the file being uploaded.
    if (nameInCatalog.empty()) {
      setProperty("NameInCatalog", fileName);
      g_log.notice("NameInCatalog has not been set. Using filename instead: " + fileName + ".");
    }
  } else // The user wants to upload a workspace.
  {
    if (nameInCatalog.empty()) {
      setProperty("NameInCatalog", workspace->getName());
      g_log.notice("NameInCatalog has not been set. Using workspace name instead: " + workspace->getName() + ".");
    }
 
    // Save workspace to a .nxs file in the user's default directory.
    saveWorkspaceToNexus(workspace);
    // Overwrite the filePath string to the location of the file (from which the
    // workspace was saved to).
    filePath =
        Mantid::Kernel::ConfigService::Instance().getString("defaultsave.directory") + workspace->getName() + ".nxs";
  }
 
  // Obtain the mode to used base on file extension.
  std::ios_base::openmode mode = isDataFile(filePath) ? std::ios_base::binary : std::ios_base::in;
  // Stream the contents of the file the user wants to publish & store it in
  // file.
  std::ifstream fileStream(filePath.c_str(), mode);
  // Verify that the file can be opened correctly.
  if (fileStream.rdstate() & std::ios::failbit)
    throw Mantid::Kernel::Exception::FileError("Error on opening file at: ", filePath);
  // Publish the contents of the file to the server.
  publish(fileStream,
          catalogInfoService->getUploadURL(getPropertyValue("InvestigationNumber"), getPropertyValue("NameInCatalog"),
                                           getPropertyValue("DataFileDescription")));
  // If a workspace was published, then we want to also publish the history of a
  // workspace.
  if (!ws.empty())
    publishWorkspaceHistory(catalogInfoService, workspace);
}
 
void CatalogPublish::publish(std::istream &fileContents, const std::string &uploadURL) {
  try {
    Poco::URI uri(uploadURL);
    std::string path(uri.getPathAndQuery());
 
    Poco::SharedPtr<Poco::Net::InvalidCertificateHandler> certificateHandler =
        new Poco::Net::AcceptCertificateHandler(true);
    // Currently do not use any means of authentication. This should be updated
    // IDS has signed certificate.
    const Poco::Net::Context::Ptr context =
        new Poco::Net::Context(Poco::Net::Context::CLIENT_USE, "", "", "", Poco::Net::Context::VERIFY_NONE);
    // Create a singleton for holding the default context. E.g. any future
    // requests to publish are made to this certificate and context.
    Poco::Net::SSLManager::instance().initializeClient(nullptr, certificateHandler, context);
    Poco::Net::HTTPSClientSession session(uri.getHost(), uri.getPort(), context);
 
    // Send the HTTP request, and obtain the output stream to write to. E.g. the
    // data to publish to the server.
    Poco::Net::HTTPRequest request(Poco::Net::HTTPRequest::HTTP_PUT, path, Poco::Net::HTTPMessage::HTTP_1_1);
    // Sets the encoding type of the request. This enables us to stream data to
    // the server.
    request.setChunkedTransferEncoding(true);
    std::ostream &os = session.sendRequest(request);
    // Copy data from the input stream to the server (request) output stream.
    Poco::StreamCopier::copyStream(fileContents, os);
 
    // Close the request by requesting a response.
    Poco::Net::HTTPResponse response;
    // Store the response for use IF an error occurs (e.g. 404).
    std::istream &responseStream = session.receiveResponse(response);
 
    // Obtain the status returned by the server to verify if it was a success.
    Poco::Net::HTTPResponse::HTTPStatus HTTPStatus = response.getStatus();
    // The error message returned by the IDS (if one exists).
    std::string IDSError = CatalogAlgorithmHelper().getIDSError(HTTPStatus, responseStream);
    // Cancel the algorithm and display the message if it exists.
    if (!IDSError.empty()) {
      // As an error occurred we must cancel the algorithm.
      // We cannot throw an exception here otherwise it is caught below as
      // Poco::Exception catches runtimes,
      // and then the I/O error is thrown as it is generated above first.
      this->cancel();
      // Output an appropriate error message from the JSON object returned by
      // the IDS.
      g_log.error(IDSError);
    }
  } catch (Poco::Net::SSLException &error) {
    throw std::runtime_error(error.displayText());
  }
  // This is bad, but is needed to catch a POCO I/O error.
  // For more info see comments (of I/O error) in CatalogDownloadDataFiles.cpp
  catch (Poco::Exception &) {
  }
}
 
bool CatalogPublish::isDataFile(const std::string &filePath) {
  std::filesystem::path path(filePath);
  std::string extension = path.extension().string();
  if (!extension.empty() && extension[0] == '.') {
    extension = extension.substr(1); // remove leading dot
  }
  std::transform(extension.begin(), extension.end(), extension.begin(), tolower);
  return extension == "raw" || extension == "nxs";
}
 
void CatalogPublish::saveWorkspaceToNexus(Mantid::API::Workspace_sptr &workspace) {
  // Create the save nexus algorithm to use.
  auto saveNexus = Mantid::API::AlgorithmManager::Instance().create("SaveNexus");
  saveNexus->initialize();
  // Set the required properties & execute.
  saveNexus->setProperty("InputWorkspace", workspace->getName());
  saveNexus->setProperty("FileName", Mantid::Kernel::ConfigService::Instance().getString("defaultsave.directory") +
                                         workspace->getName() + ".nxs");
  saveNexus->execute();
}
 
void CatalogPublish::publishWorkspaceHistory(Mantid::API::ICatalogInfoService_sptr &catalogInfoService,
                                             Mantid::API::Workspace_sptr &workspace) {
  std::stringstream ss;
  // Obtain the workspace history as a string.
  ss << generateWorkspaceHistory(workspace);
  // Use the name the use wants to save the file to the server as and append .py
  std::filesystem::path nameInCatalog(getPropertyValue("NameInCatalog"));
  std::string fileName = nameInCatalog.stem().string() + ".py";
  // Publish the workspace history to the server.
  publish(ss, catalogInfoService->getUploadURL(getPropertyValue("InvestigationNumber"), fileName,
                                               getPropertyValue("DataFileDescription")));
}
 
const std::string CatalogPublish::generateWorkspaceHistory(Mantid::API::Workspace_sptr &workspace) {
  auto wsHistory = Mantid::API::AlgorithmManager::Instance().createUnmanaged("GeneratePythonScript");
  wsHistory->initialize();
  wsHistory->setProperty("InputWorkspace", workspace->getName());
  wsHistory->execute();
  return wsHistory->getPropertyValue("ScriptText");
}
} // namespace Mantid::ICat