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Fix journal citation issues #149 and #151
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@rogerdahl
rogerdahl committed Nov 13, 2024
1 parent f128e62 commit ce70dde
Showing 1 changed file with 148 additions and 124 deletions.
272 changes: 148 additions & 124 deletions DataPackageManager/src/edu/lternet/pasta/datapackagemanager/DataPackageRegistry.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4465,27 +4465,26 @@ public ArrayList<Integer> listWorkingOnIdentifiers(String scope)
public void addJournalCitation(JournalCitation journalCitation)
throws ClassNotFoundException, SQLException
{
Connection connection = null;
int journalCitationId = 0;
int journalCitationId = 0;

if (journalCitation != null) {
String packageId = journalCitation.getPackageId();
String principalOwner = journalCitation.getPrincipalOwner();
String articleDoi = journalCitation.getArticleDoi();
String articleTitle = journalCitation.getArticleTitle();
String articleUrl = journalCitation.getArticleUrl();
LocalDateTime dateCreated = journalCitation.getDateCreated();
String journalTitle = journalCitation.getJournalTitle();
String relationType = journalCitation.getRelationType();
Integer journalPubYear = journalCitation.getJournalPubYear();
String journalIssue = journalCitation.getJournalIssue();
String journalVolume = journalCitation.getJournalVolume();
String articlePages = journalCitation.getArticlePages();

if (journalCitation != null) {
String packageId = journalCitation.getPackageId();
String principalOwner = journalCitation.getPrincipalOwner();
String articleDoi = journalCitation.getArticleDoi();
String articleTitle = journalCitation.getArticleTitle();
String articleUrl = journalCitation.getArticleUrl();
LocalDateTime dateCreated = journalCitation.getDateCreated();
String journalTitle = journalCitation.getJournalTitle();
String relationType = journalCitation.getRelationType();
Integer journalPubYear = journalCitation.getJournalPubYear();
String journalIssue = journalCitation.getJournalIssue();
String journalVolume = journalCitation.getJournalVolume();
String articlePages = journalCitation.getArticlePages();

// fmt:off
// language=PostgreSQL
String queryStr = String.format(
"INSERT INTO %s ( " +
// fmt:off
// language=PostgreSQL
String queryStr = String.format(
"INSERT INTO %s ( " +
"package_id, " +
"principal_owner, " +
"article_doi, " +
Expand All @@ -4498,53 +4497,59 @@ public void addJournalCitation(JournalCitation journalCitation)
"journal_issue, " +
"journal_volume, " +
"article_pages " +
" ) " +
" ) " +
"VALUES(?,?,?,?,?,?,?,?::datapackagemanager.relation_type,?,?,?,?) ",
JOURNAL_CITATION);
// fmt:on

logger.debug("queryStr: " + queryStr);
JOURNAL_CITATION);
// fmt:on

try {
connection = getConnection();
PreparedStatement pstmt =
connection.prepareStatement(queryStr, Statement.RETURN_GENERATED_KEYS);
pstmt.setString(1, packageId);
pstmt.setString(2, principalOwner);
pstmt.setString(3, Objects.toString(articleDoi, ""));
pstmt.setString(4, Objects.toString(articleTitle, ""));
pstmt.setString(5, Objects.toString(articleUrl, ""));
pstmt.setTimestamp(6, Timestamp.valueOf(dateCreated));
pstmt.setString(7, Objects.toString(journalTitle, ""));
pstmt.setString(8, Objects.toString(relationType, "IsCitedBy"));
pstmt.setObject(9, journalPubYear, java.sql.Types.INTEGER);
pstmt.setString(10, Objects.toString(journalIssue, ""));
pstmt.setString(11, Objects.toString(journalVolume, ""));
pstmt.setString(12, Objects.toString(articlePages, ""));
logger.debug("queryStr: " + queryStr);

pstmt.executeUpdate();
try (
Connection connection = getConnection();
PreparedStatement pstmt = connection.prepareStatement(queryStr, Statement.RETURN_GENERATED_KEYS)
) {
pstmt.setString(1, packageId);
pstmt.setString(2, principalOwner);
pstmt.setString(3, Objects.toString(articleDoi, ""));
pstmt.setString(4, Objects.toString(articleTitle, ""));
pstmt.setString(5, Objects.toString(articleUrl, ""));
pstmt.setTimestamp(6, Timestamp.valueOf(dateCreated));
pstmt.setString(7, Objects.toString(journalTitle, ""));
pstmt.setString(8, Objects.toString(relationType, "IsCitedBy"));
pstmt.setObject(9, journalPubYear, java.sql.Types.INTEGER);
pstmt.setString(10, Objects.toString(journalIssue, ""));
pstmt.setString(11, Objects.toString(journalVolume, ""));
pstmt.setString(12, Objects.toString(articlePages, ""));

pstmt.executeUpdate();

try (ResultSet rs = pstmt.getGeneratedKeys()) {
while (rs.next()) {
journalCitationId = rs.getInt(1);
}
}
} catch (SQLException e) {
logger.error(
"Error inserting JOURNAL_CITATION record for JournalCitation object:\n" +
journalCitation.toXML(true));
throw (e);
}

ResultSet rs = pstmt.getGeneratedKeys();
while (rs.next()) {
journalCitationId = rs.getInt(1);
}
journalCitation.setJournalCitationId(journalCitationId);

pstmt.close();
} catch (SQLException e) {
logger.error(
"Error inserting JOURNAL_CITATION record for JournalCitation object:\n" +
journalCitation.toXML(true));
throw (e);
} finally {
journalCitation.setJournalCitationId(
journalCitationId); // set the id value of the journal citation
returnConnection(connection);
try {
updateAuthors(journalCitation, journalCitationId);
} catch (SQLException | ClassNotFoundException e) {
logger.error(
"Error updating JOURNAL_CITATION_AUTHOR record for JournalCitation object:\n" +
journalCitation.toXML(true));
throw (e);
}
}
}
}

public void updateJournalCitation(JournalCitation journalCitation)
throws ClassNotFoundException, SQLException {
throws ClassNotFoundException, SQLException
{

if (journalCitation == null) {
return;
Expand All @@ -4556,7 +4561,7 @@ public void updateJournalCitation(JournalCitation journalCitation)
String articleDoi = journalCitation.getArticleDoi();
String articleTitle = journalCitation.getArticleTitle();
String articleUrl = journalCitation.getArticleUrl();
LocalDateTime dateCreated = journalCitation.getDateCreated();
// LocalDateTime dateCreated = journalCitation.getDateCreated();
String journalTitle = journalCitation.getJournalTitle();
String relationType = journalCitation.getRelationType();
Integer journalPubYear = journalCitation.getJournalPubYear();
Expand Down Expand Up @@ -4587,7 +4592,7 @@ public void updateJournalCitation(JournalCitation journalCitation)

try (
Connection connection = getConnection();
PreparedStatement pstmt = connection.prepareStatement(queryStr);
PreparedStatement pstmt = connection.prepareStatement(queryStr)
) {
pstmt.setString(1, packageId);
pstmt.setString(2, principalOwner);
Expand All @@ -4608,58 +4613,72 @@ public void updateJournalCitation(JournalCitation journalCitation)
"Error updating JOURNAL_CITATION record for JournalCitation object:\n" +
journalCitation.toXML(true));
throw (e);
} finally {
journalCitation.setJournalCitationId(journalCitationId);
}
try {
updateAuthors(journalCitation, journalCitationId);
} catch (SQLException | ClassNotFoundException e) {
logger.error(
"Error updating JOURNAL_CITATION_AUTHOR record for JournalCitation object:\n" +
journalCitation.toXML(true));
throw (e);
}
}

// Update authors

queryStr = String.format(
"DELETE FROM %s WHERE journal_citation_id=?",
private void updateAuthors(JournalCitation journalCitation, int journalCitationId) throws SQLException, ClassNotFoundException
{
String queryStr = String.format(
"INSERT INTO %s (journal_citation_id, sequence, given, family, suffix, orcid)\n" +
"VALUES(?,?,?,?,?,?)\n",
SqlEscape.name(JOURNAL_CITATION_AUTHOR)
);

logger.debug("queryStr: " + queryStr);

try (
Connection connection = getConnection();
PreparedStatement pstmt = connection.prepareStatement(queryStr);
PreparedStatement insertPstmt = connection.prepareStatement(queryStr)
) {
pstmt.setInt(1, journalCitationId);
pstmt.executeUpdate();
connection.setAutoCommit(false);

deleteAuthors(journalCitationId);

for (JournalCitation.ArticleAuthor articleAuthor : journalCitation.getArticleAuthorList()) {
setParam(insertPstmt, 1, journalCitationId);
setParam(insertPstmt, 2, articleAuthor.getSequence());
setParam(insertPstmt, 3, articleAuthor.getGiven());
setParam(insertPstmt, 4, articleAuthor.getFamily());
setParam(insertPstmt, 5, articleAuthor.getSuffix());
setParam(insertPstmt, 6, articleAuthor.getShortOrcid());
insertPstmt.addBatch();
}
insertPstmt.executeBatch();

connection.commit();
} catch (SQLException e) {
logger.error(
"Error updating JOURNAL_CITATION_AUTHOR record for JournalCitation object:\n" +
journalCitation.toXML(true));
logger.error("Error updating JOURNAL_CITATION_AUTHOR record: " + e.getMessage());
throw (e);
}
}

// fmt:off
// language=PostgreSQL
queryStr = String.format(
"INSERT INTO %s (journal_citation_id, sequence, given, family, suffix, orcid)\n" +
"VALUES(?,?,?,?,?,?)\n",
SqlEscape.name(JOURNAL_CITATION_AUTHOR));
// fmt:on
private void deleteAuthors(int journalCitationId) throws SQLException, ClassNotFoundException
{
String queryStr = String.format(
"DELETE FROM %s WHERE journal_citation_id=?",
SqlEscape.name(JOURNAL_CITATION_AUTHOR)
);

logger.debug("queryStr: " + queryStr);

try (
Connection connection = getConnection();
PreparedStatement pstmt = connection.prepareStatement(queryStr);
PreparedStatement deletePstmt = connection.prepareStatement(queryStr);
) {
for (JournalCitation.ArticleAuthor articleAuthor : journalCitation.getArticleAuthorList()) {
setParam(pstmt, 1, journalCitationId);
setParam(pstmt, 2, articleAuthor.getSequence());
setParam(pstmt, 3, articleAuthor.getGiven());
setParam(pstmt, 4, articleAuthor.getFamily());
setParam(pstmt, 5, articleAuthor.getSuffix());
setParam(pstmt, 6, articleAuthor.getShortOrcid());
pstmt.addBatch();
}
pstmt.executeBatch();
deletePstmt.setInt(1, journalCitationId);
deletePstmt.executeUpdate();
} catch (SQLException e) {
logger.error(
"Error updating JOURNAL_CITATION_AUTHOR record for JournalCitation object:\n" +
journalCitation.toXML(true));
logger.error("Error deleting JOURNAL_CITATION_AUTHOR records: " + e.getMessage());
throw (e);
}
}
Expand Down Expand Up @@ -4690,53 +4709,58 @@ static void setParam(PreparedStatement stmt, int paramIndex, String value) throw


public Integer deleteJournalCitation(Integer id, String userId)
throws ClassNotFoundException, SQLException, NotFoundException {
throws ClassNotFoundException, SQLException, NotFoundException
{
if (!hasJournalCitation(id)) {
throw new NotFoundException(String.format("No journal citation with id value '%d' was found.", id));
}

if (!isJournalCitationOwner(id, userId)) {
throw new UnauthorizedException(String
.format("Journal citation with id value '%d' is not owned by user '%s'.", id, userId));
}

String queryStr = String.format(
"DELETE FROM %s WHERE journal_citation_id=? AND principal_owner=?",
SqlEscape.name(JOURNAL_CITATION)
);

logger.debug("queryStr: " + queryStr);

Integer deletedId = null;
Connection connection = null;
Statement stmt = null;
Integer rowCount = null;

try {
if (hasJournalCitation(id)) {
if (isJournalCitationOwner(id, userId)) {
connection = getConnection();
String queryStr = String.format(
"DELETE FROM %s " +
"WHERE journal_citation_id=%s and principal_owner=%s",
SqlEscape.name(JOURNAL_CITATION),
SqlEscape.integer(id),
SqlEscape.str(userId)
);
try (
Connection connection = getConnection();
PreparedStatement pstmt = connection.prepareStatement(queryStr)
) {
// getConnection() returns a connection with autoCommit = true.
// We start a transaction here to ensure that the delete is atomic. as getConnection() does not use a pool,
// this does not persist after the connection is closed.
connection.setAutoCommit(false);

logger.debug("queryStr: " + queryStr);
deleteAuthors(id);

stmt = connection.createStatement();
rowCount = stmt.executeUpdate(queryStr);
setParam(pstmt, 1, id);
setParam(pstmt, 2, userId);

if (rowCount < 1) {
String gripe = "Delete failed: " + queryStr;
throw new SQLException(gripe);
} else {
deletedId = id;
}
} else {
throw new UnauthorizedException(String
.format("Journal citation with id value '%d' is not owned by user '%s'.", id, userId));
}
Integer rowCount = pstmt.executeUpdate();

if (rowCount < 1) {
String gripe = "Delete failed: " + queryStr;
throw new SQLException(gripe);
} else {
throw new NotFoundException(String.format("No journal citation with id value '%d' was found.", id));
deletedId = id;
}

connection.commit();
} catch (SQLException e) {
logger.error("Error deleting JOURNAL_CITATION record: " + e.getMessage());
throw (e);
} finally {
returnConnection(connection);
}

return deletedId;
}


public ArrayList<JournalCitation> getCitationWithId (Integer journalCitationId)
throws ClassNotFoundException, SQLException, IllegalArgumentException {
ArrayList<JournalCitation> journalCitations = new ArrayList<JournalCitation>();
Expand Down

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