/** * 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); }