How to use

PsiFileGenerator

in

uk.ac.ebi.intact.application.dataConversion

/**
 * Writes a file containing the PSI XML, for the information contained in the ExperimentListItem
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @param baseDir The base dir where to put the files
 * @param validate whether to validate the xml
 * @throws IOException thrown if there is some problem writing to the file
 * @return a psiValidatorReport
 */
public static PsiValidatorReport writePsiData(ExperimentListItem eli,
                PsiVersion psiVersion,
                CvMapping cvMapping,
                File baseDir, boolean validate) throws IOException
{
  File xmlFile = new File(baseDir, eli.getFilename());
  Document doc = generatePsiData(eli,psiVersion,cvMapping);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlFile, validate);
}

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

interactionsToFilter = filterInteractions(interactions);

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

interactionsToFilter = filterInteractions(interactions);

/**
 * Writes a file containing the PSI XML, for the information contained in the ExperimentListItem
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @param baseDir The base dir where to put the files
 * @param validate whether to validate the xml
 * @throws IOException thrown if there is some problem writing to the file
 * @return a psiValidatorReport
 */
public static PsiValidatorReport writePsiData(ExperimentListItem eli,
                PsiVersion psiVersion,
                CvMapping cvMapping,
                File baseDir, boolean validate) throws IOException
{
  File xmlFile = new File(baseDir, eli.getFilename());
  Document doc = generatePsiData(eli,psiVersion,cvMapping);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlFile, validate);
}

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

interactionsToFilter = filterInteractions(interactions);

/**
 * Writes a file containing the PSI XML, for the information contained in the ExperimentListItem
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @param baseDir The base dir where to put the files
 * @param validate whether to validate the xml
 * @throws IOException thrown if there is some problem writing to the file
 * @return a psiValidatorReport
 */
public static PsiValidatorReport writePsiData(ExperimentListItem eli,
                PsiVersion psiVersion,
                CvMapping cvMapping,
                File baseDir, boolean validate) throws IOException
{
  File xmlFile = new File(baseDir, eli.getFilename());
  Document doc = generatePsiData(eli,psiVersion,cvMapping);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlFile, validate);
}

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}