/**
* This function makes the call to the XML database and retrieves all the file metadata for use in
* ECGridToolkit. The data is first retrieved in a series of XML blocks, and then they are
* converted into StudyEntry Objects and returned to the user
*
* @param userID - The ID of the user. This is used to check which files the user has submitted
* and thus has access to
* @return The list of StudyEntry Objects taken from the file metadata in the XML database
*/
public ArrayList<StudyEntry> getEntries(String userID) {
ArrayList<StudyEntry> tempList = new ArrayList<StudyEntry>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
String sQuery =
studyBuilder.defaultFor()
+ studyBuilder.defaultWhere(userID)
+ studyBuilder.defaultOrderBy()
+ studyBuilder.defaultReturn();
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
Resource fileSelection = null;
int listIndex = 0;
int subjectCount = 1;
while (iter.hasMoreResources()) {
selection = iter.nextResource();
String studyEntryResult = (selection.getContent()).toString();
// Now we will create an XStream object and then put that into our StudyEntry objects
// the StudyEntry objects are de-serialized versions of the studyEntry blocks.
XStream xmlStream = new XStream();
xmlStream.alias("studyEntry", StudyEntry.class);
xmlStream.alias("recordDetails", RecordDetails.class);
xmlStream.alias("fileDetails", FileDetails.class);
xmlStream.addImplicitCollection(RecordDetails.class, "fileDetails");
StudyEntry newStudy = (StudyEntry) xmlStream.fromXML(studyEntryResult);
// System.out.println(newStudy);
// Add it to the return array
tempList.add(newStudy);
}
} catch (Exception ex) {
System.out.println(
"StudyEntryUtility.getEntries(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
public ArrayList<String> queryStudyTypes(String userID, String dataName) {
System.out.println("In function queryStudyTypes");
ArrayList<String> tempList = new ArrayList<String>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
System.out.println("queryDatatypes:");
String sQuery =
studyBuilder.forStudyEntry()
+ studyBuilder.customNameBracket(dataName, EnumStudyTreeNode.DATATYPE)
+ studyBuilder.userDefinedWhere(userID)
+ studyBuilder.customOrderBySubjectID()
+ studyBuilder.returnTreeNodeDistinct(EnumStudyTreeNode.STUDY);
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
tempList = this.checkForDuplicates(iter, selection);
for (String listing : tempList) {
int i = 1;
System.out.println("Entry " + i + " = " + listing);
i++;
}
} catch (Exception ex) {
System.out.println(
"ExistMainDatabase.queryStudies(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
/**
* This function makes the call to the XML database and retrieves all the file metadata for use in
* ECGridToolkit. The data is first retrieved in a series of XML blocks, and then they are
* converted into StudyEntry Objects and returned to the user
*
* @param userID - The ID of the user. This is used to check which files the user has submitted
* and thus has access to
* @param studyID - The ID of the study selected to search
* @param datatype - The type of data that will be observed
* @return The list of StudyEntry Objects taken from the file metadata in the XML database
*/
public ArrayList<StudyEntry> getEntries(String userID, String studyID, String datatype) {
System.out.println("In function getEntries");
ArrayList<StudyEntry> tempList = new ArrayList<StudyEntry>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
// CompiledExpression query = subjectQuery.compile("for $x in collection('" +
// allConstants.getDBCollection() + "')//record where collection('" +
// allConstants.getDBCollection() + "')//record/studyEntry/submitterID=\"" + userID + "\"
// order by $x/studyEntry/subjectID return $x/studyEntry");
// ***
// 02/25/2013 - Brandon Benitez: Commented this out temporarily in case the query builder
// version of this failed.
// ***
// String sQuery = "for $x in collection('" + dbHandle.getMainCollection() +
// "')//record/studyEntry[studyID=\"" + studyID + "\"] where $x/submitterID=\"" + userID + "\"
// return $x[datatype=\"" + datatype + "\"]";
String sQuery =
studyBuilder.forStudyEntry()
+
// studyBuilder.customNameBracket(studyID, EnumStudyTreeNode.STUDY) +
studyBuilder.whereUser2(userID)
+ studyBuilder.andWhereStudy(studyID)
+ studyBuilder.customOrderBySubjectID()
+ studyBuilder.returnX()
+ studyBuilder.customNameBracket(datatype, EnumStudyTreeNode.DATATYPE);
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
Resource fileSelection = null;
int listIndex = 0;
int subjectCount = 1;
while (iter.hasMoreResources()) {
selection = iter.nextResource();
String studyEntryResult = (selection.getContent()).toString();
// Now we will create an XStream object and then put that into our StudyEntry objects
// the StudyEntry objects are de-serialized versions of the studyEntry blocks.
XStream xmlStream = new XStream();
xmlStream.alias("studyEntry", StudyEntry.class);
xmlStream.alias("recordDetails", RecordDetails.class);
xmlStream.alias("fileDetails", FileDetails.class);
xmlStream.addImplicitCollection(RecordDetails.class, "fileDetails");
StudyEntry newStudy = (StudyEntry) xmlStream.fromXML(studyEntryResult);
// System.out.println(newStudy);
// Add it to the return array
tempList.add(newStudy);
}
} catch (Exception ex) {
System.out.println(
"StudyEntryUtility.getEntries(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
