private ArrayList<ExtractPropertyBean> findExtractProperties() throws OpenClinicaSystemException {
ArrayList<ExtractPropertyBean> ret = new ArrayList<ExtractPropertyBean>();
// ExtractPropertyBean epbean = new ExtractPropertyBean();
int i = 1;
while (!getExtractField("extract." + i + ".file").equals("")) {
ExtractPropertyBean epbean = new ExtractPropertyBean();
epbean.setId(i);
// we will implement a find by id function in the front end
// check to make sure the file exists, if not throw an exception and system will abort to
// start.
checkForFile(getExtractFields("extract." + i + ".file"));
epbean.setFileName(getExtractFields("extract." + i + ".file"));
// file name of the xslt stylesheet
epbean.setFiledescription(getExtractField("extract." + i + ".fileDescription"));
// description of the choice of format
epbean.setHelpText(getExtractField("extract." + i + ".helptext"));
// help text, currently in the alt-text of the link
epbean.setLinkText(getExtractField("extract." + i + ".linkText"));
// link text of the choice of format
// epbean.setRolesAllowed(getExtractField("xsl.allowed." + i).split(","));
// which roles are allowed to see the choice?
epbean.setFileLocation(getExtractField("extract." + i + ".location"));
// destination of the copied files
// epbean.setFormat(getExtractField("xsl.format." + i));
// if (("").equals(epbean.getFormat())) {
// }
// formatting choice. currently permenantly set at oc1.3
/*
* String clinica = getExtractField("extract."+i+".odmType"); if(clinica!=null) {
* if(clinica.equalsIgnoreCase("clinical_data")) epbean.setFormat("occlinical_data"); else
* epbean.setFormat("oc1.3"); } else
*/
epbean.setOdmType(getExtractField("extract." + i + ".odmType"));
epbean.setFormat("oc1.3");
// destination file name of the copied files
epbean.setExportFileName(getExtractFields("extract." + i + ".exportname"));
// post-processing event after the creation
// System.out.println("found post function: " + whichFunction);
String whichFunction = getExtractField("extract." + i + ".post").toLowerCase();
// added by JN: Zipformat comes from extract properties returns true by default
epbean.setZipFormat(getExtractFieldBoolean("extract." + i + ".zip"));
epbean.setDeleteOld(getExtractFieldBoolean("extract." + i + ".deleteOld"));
epbean.setSuccessMessage(getExtractField("extract." + i + ".success"));
epbean.setFailureMessage(getExtractField("extract." + i + ".failure"));
epbean.setZipName(getExtractField("extract." + i + ".zipName"));
if (epbean.getFileName().length != epbean.getExportFileName().length)
throw new OpenClinicaSystemException(
"The comma seperated values of file names and export file names should correspond 1 on 1 for the property number"
+ i);
if ("sql".equals(whichFunction)) {
// set the bean within, so that we can access the file locations etc
SqlProcessingFunction function = new SqlProcessingFunction(epbean);
String whichSettings = getExtractField("xsl.post." + i + ".sql");
if (!"".equals(whichSettings)) {
function.setDatabaseType(getExtractFieldNoRep(whichSettings + ".dataBase").toLowerCase());
function.setDatabaseUrl(getExtractFieldNoRep(whichSettings + ".url"));
function.setDatabaseUsername(getExtractFieldNoRep(whichSettings + ".username"));
function.setDatabasePassword(getExtractFieldNoRep(whichSettings + ".password"));
} else {
// set default db settings here
function.setDatabaseType(getField("dataBase"));
function.setDatabaseUrl(getField("url"));
function.setDatabaseUsername(getField("username"));
function.setDatabasePassword(getField("password"));
}
// also pre-set the database connection stuff
epbean.setPostProcessing(function);
// System.out.println("found db password: "******"pdf".equals(whichFunction)) {
// TODO add other functions here
epbean.setPostProcessing(new PdfProcessingFunction());
} else if ("sas".equals(whichFunction)) {
epbean.setPostProcessing(new SasProcessingFunction());
} else if (!whichFunction.isEmpty()) {
String postProcessorName = getExtractField(whichFunction + ".postProcessor");
if (postProcessorName.equals("pdf")) {
epbean.setPostProcessing(new PdfProcessingFunction());
epbean.setPostProcDeleteOld(getExtractFieldBoolean(whichFunction + ".deleteOld"));
epbean.setPostProcZip(getExtractFieldBoolean(whichFunction + ".zip"));
epbean.setPostProcLocation(getExtractField(whichFunction + ".location"));
epbean.setPostProcExportName(getExtractField(whichFunction + ".exportname"));
}
// since the database is the last option TODO: think about custom post processing options
else {
SqlProcessingFunction function = new SqlProcessingFunction(epbean);
function.setDatabaseType(getExtractFieldNoRep(whichFunction + ".dataBase").toLowerCase());
function.setDatabaseUrl(getExtractFieldNoRep(whichFunction + ".url"));
function.setDatabaseUsername(getExtractFieldNoRep(whichFunction + ".username"));
function.setDatabasePassword(getExtractFieldNoRep(whichFunction + ".password"));
epbean.setPostProcessing(function);
}
} else {
// add a null here
epbean.setPostProcessing(null);
}
ret.add(epbean);
i++;
}
// tbh change to print out properties
// System.out.println("found " + ret.size() + " records in extract.properties");
return ret;
}
