/**
* This method creates map of latest version of ontology with contexts as key. It uses virtual
* ontology ids associated with contexts.
*
* @param structure {@code Structure} for given resource
* @return {@code HashMap} of latest local ontology id with context as key.
*/
private HashMap<String, String> createLocalOntologyIDMap(Structure structure) {
HashMap<String, String> localOntologyIDMap = new HashMap<String, String>();
String virtualOntologyID;
for (String contextName : structure.getOntoIds().keySet()) {
virtualOntologyID = structure.getOntoIds().get(contextName);
if (!virtualOntologyID.equals(Structure.FOR_CONCEPT_RECOGNITION)
&& !virtualOntologyID.equals(Structure.NOT_FOR_ANNOTATION)) {
localOntologyIDMap.put(
contextName, ontlogyService.getLatestLocalOntologyID(virtualOntologyID));
}
}
return localOntologyIDMap;
}
/**
* This method is used to get all elements from resource site.
*
* @return HashSet<Element>
*/
private HashSet<Element> getAllElements() {
logger.info("* Get All Elements for NIF CTD ChemDisease ... ");
HashSet<Element> elementSet = new HashSet<Element>();
int nbAdded;
int offset = 0;
int totalCount = 0;
try {
// get all elements from _ET table
HashSet<String> allElementsInET = this.resourceUpdateService.getAllLocalElementIDs();
Map<String, Map<String, String>> allRowsData = new HashMap<String, Map<String, String>>();
// int rowcnt = 1;
// parsing data
do {
Document dom = queryFederation(nifId, query, offset);
if (dom != null) {
Node tableData = dom.getFirstChild().getChildNodes().item(1);
// get total records
totalCount =
Integer.parseInt(tableData.getAttributes().getNamedItem(resultCount).getNodeValue());
offset += rowCount;
Node results = tableData.getChildNodes().item(1);
// Iterate over the returned structure
NodeList rows = results.getChildNodes();
for (int i = 0; i < rows.getLength(); i++) {
String localElementId = EMPTY_STRING;
Map<String, String> elementAttributes = new HashMap<String, String>();
Node row = rows.item(i);
for (int j = 0; j < row.getChildNodes().getLength(); j++) {
NodeList vals = row.getChildNodes().item(j).getChildNodes();
String name = null;
String value = null;
for (int k = 0; k < vals.getLength(); k++) {
if (nodeName.equals(vals.item(k).getNodeName())) {
name = vals.item(k).getTextContent();
} else if (nodeValue.equals(vals.item(k).getNodeName())) {
value = vals.item(k).getTextContent();
}
}
if (name.equalsIgnoreCase(Disease)) {
localElementId =
value.substring(
value.indexOf(ELT_URL) + ELT_URL.length(), value.indexOf(endTag));
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[0]),
Jsoup.parse(value).text());
} else if (name.equalsIgnoreCase(ChemicalName)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[1]),
Jsoup.parse(value).text());
} else if (name.equalsIgnoreCase(Inference_Gene_Symbol)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[2]), value);
} else if (name.equalsIgnoreCase(Inference_Score)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[3]), value);
} else if (name.equalsIgnoreCase(Direct_Evidence)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[4]), value);
} else if (name.equalsIgnoreCase(OMIM_IDs)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[5]),
Jsoup.parse(value).text());
} else if (name.equalsIgnoreCase(References)) {
elementAttributes.put(
Structure.generateContextName(RESOURCEID, ITEMKEYS[6]),
Jsoup.parse(value).text());
}
}
// Check if elementId is present in database.
if (allElementsInET.contains(localElementId)) {
} else {
// localElementId += SLASH_STRING + rowcnt;
// rowcnt++;
allRowsData.put(localElementId, elementAttributes);
}
}
} else {
offset += rowCount;
}
} while (offset < totalCount);
// parsing ends
// Second phase: creation of elements
for (String localElementID : allRowsData.keySet()) {
Map<String, String> elementAttributes;
elementAttributes = allRowsData.get(localElementID);
// PUT DATA INTO A STRUCTURE++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Structure elementStructure = new Structure(STRUCTURE.getContextNames());
for (String contextName : STRUCTURE.getContextNames()) {
boolean attributeHasValue = false;
for (String att : elementAttributes.keySet()) {
if (contextName.equals(att)) {
// not an existing annotation
if (STRUCTURE.getOntoID(contextName).equals(Structure.FOR_CONCEPT_RECOGNITION)
|| STRUCTURE.getOntoID(contextName).equals(Structure.NOT_FOR_ANNOTATION)) {
elementStructure.putContext(contextName, elementAttributes.get(att));
attributeHasValue = true;
}
}
}
// to avoid null value in the structure
if (!attributeHasValue) {
elementStructure.putContext(contextName, EMPTY_STRING);
}
}
// put the element structure in a new element
try {
Element exp = new Element(localElementID, elementStructure);
elementSet.add(exp);
} catch (Element.BadElementStructureException e) {
logger.error(EMPTY_STRING, e);
}
}
} catch (Exception e) {
logger.error("** PROBLEM ** Problem in getting rows.", e);
}
nbAdded = elementSet.size();
logger.info((nbAdded) + " rows found.");
return elementSet;
}