/**
* Obtain the pubmed esummary information for the publications
*
* @param ids the pubMedIds of the publications
* @return a Reader for the information
* @throws Exception if an error occurs
*/
protected Reader getReader(Set<Integer> ids) throws Exception {
String urlString = EFETCH_URL + StringUtil.join(ids, ",");
System.err.println("retrieving: " + urlString);
return new BufferedReader(new InputStreamReader(new URL(urlString).openStream()));
}
/**
* Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor. The Set contains
* all the primary keys that exist on a particular class that are used by the source, without
* performing any recursion. The Model.getClassDescriptorsForClass() method is recommended if you
* wish for all the primary keys of the class' parents as well.
*
* @param cld the ClassDescriptor
* @param source the Source
* @param os the ObjectStore that these PrimaryKeys are used in, for creating indexes
* @return a Set of PrimaryKeys
*/
public static Set<PrimaryKey> getPrimaryKeys(ClassDescriptor cld, Source source, ObjectStore os) {
GetPrimaryKeyCacheKey key = new GetPrimaryKeyCacheKey(cld, source);
synchronized (getPrimaryKeyCache) {
Set<PrimaryKey> keySet = getPrimaryKeyCache.get(key);
if (keySet == null) {
keySet = new LinkedHashSet<PrimaryKey>();
Properties keys = getKeyProperties(source);
if (keys != null) {
if (!verifiedSources.contains(source)) {
String packageNameWithDot =
cld.getName().substring(0, cld.getName().lastIndexOf('.') + 1);
LOG.info(
"Verifying primary key config for source "
+ source
+ ", packageName = "
+ packageNameWithDot);
for (Map.Entry<Object, Object> entry : keys.entrySet()) {
String cldName = (String) entry.getKey();
String keyList = (String) entry.getValue();
if (!cldName.contains(".")) {
ClassDescriptor iCld =
cld.getModel().getClassDescriptorByName(packageNameWithDot + cldName);
if (iCld != null) {
Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(iCld);
String[] tokens = keyList.split(",");
for (int i = 0; i < tokens.length; i++) {
String token = tokens[i].trim();
if (map.get(token) == null) {
throw new IllegalArgumentException(
"Primary key "
+ token
+ " for class "
+ cldName
+ " required by datasource "
+ source.getName()
+ " in "
+ source.getName()
+ "_keys.properties is not defined in "
+ cld.getModel().getName()
+ "_keyDefs.properties");
}
}
} else {
LOG.warn(
"Ignoring entry for "
+ cldName
+ " in file "
+ cld.getModel().getName()
+ "_keyDefs.properties - not in model!");
}
}
}
verifiedSources.add(source);
}
Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(cld);
String cldName = TypeUtil.unqualifiedName(cld.getName());
String keyList = (String) keys.get(cldName);
if (keyList != null) {
String[] tokens = keyList.split(",");
for (int i = 0; i < tokens.length; i++) {
String token = tokens[i].trim();
if (map.get(token) == null) {
throw new IllegalArgumentException(
"Primary key "
+ token
+ " for class "
+ cld.getName()
+ " required by data source "
+ source.getName()
+ " in "
+ source.getName()
+ "_keys.properties is not defined in "
+ cld.getModel().getName()
+ "_keyDefs.properties");
} else {
keySet.add(map.get(token));
}
}
}
for (Map.Entry<Object, Object> entry : keys.entrySet()) {
String propKey = (String) entry.getKey();
String fieldList = (String) entry.getValue();
int posOfDot = propKey.indexOf('.');
if (posOfDot > 0) {
String propCldName = propKey.substring(0, posOfDot);
if (cldName.equals(propCldName)) {
String keyName = propKey.substring(posOfDot + 1);
PrimaryKey pk = new PrimaryKey(keyName, fieldList, cld);
if (!keySet.contains(pk)) {
keySet.add(pk);
if (os instanceof ObjectStoreInterMineImpl) {
ObjectStoreInterMineImpl osimi = (ObjectStoreInterMineImpl) os;
DatabaseSchema schema = osimi.getSchema();
ClassDescriptor tableMaster = schema.getTableMaster(cld);
String tableName = DatabaseUtil.getTableName(tableMaster);
List<String> fields = new ArrayList<String>();
for (String field : pk.getFieldNames()) {
String colName = DatabaseUtil.generateSqlCompatibleName(field);
if (tableMaster.getReferenceDescriptorByName(field, true) != null) {
colName += "id";
}
fields.add(colName);
}
String sql =
"CREATE INDEX "
+ tableName
+ "__"
+ keyName
+ " ON "
+ tableName
+ " ("
+ StringUtil.join(fields, ", ")
+ ")";
System.out.println("Creating index: " + sql);
LOG.info("Creating index: " + sql);
Connection conn = null;
try {
conn = osimi.getConnection();
conn.createStatement().execute(sql);
} catch (SQLException e) {
LOG.warn("Index creation failed", e);
} finally {
if (conn != null) {
osimi.releaseConnection(conn);
}
}
}
}
}
}
}
} else {
throw new IllegalArgumentException(
"Unable to find keys for source "
+ source.getName()
+ " in file "
+ source.getName()
+ "_keys.properties");
}
getPrimaryKeyCache.put(key, keySet);
}
return keySet;
}
}