package net.sourceforge.seqware.common.metadata;
import io.seqware.common.model.ProcessingStatus;
import io.seqware.common.model.SequencerRunStatus;
import io.seqware.common.model.WorkflowRunStatus;
import java.io.Writer;
import java.sql.Connection;
import java.sql.DatabaseMetaData;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import javax.sql.DataSource;
import net.sourceforge.seqware.common.factory.DBAccess;
import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.ExperimentAttribute;
import net.sourceforge.seqware.common.model.ExperimentLibraryDesign;
import net.sourceforge.seqware.common.model.ExperimentSpotDesign;
import net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec;
import net.sourceforge.seqware.common.model.FileAttribute;
import net.sourceforge.seqware.common.model.FileProvenanceParam;
import net.sourceforge.seqware.common.model.IUS;
import net.sourceforge.seqware.common.model.IUSAttribute;
import net.sourceforge.seqware.common.model.Lane;
import net.sourceforge.seqware.common.model.LaneAttribute;
import net.sourceforge.seqware.common.model.LibrarySelection;
import net.sourceforge.seqware.common.model.LibrarySource;
import net.sourceforge.seqware.common.model.LibraryStrategy;
import net.sourceforge.seqware.common.model.Organism;
import net.sourceforge.seqware.common.model.ParentAccessionModel;
import net.sourceforge.seqware.common.model.Platform;
import net.sourceforge.seqware.common.model.Processing;
import net.sourceforge.seqware.common.model.ProcessingAttribute;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.SampleAttribute;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.SequencerRunAttribute;
import net.sourceforge.seqware.common.model.Study;
import net.sourceforge.seqware.common.model.StudyAttribute;
import net.sourceforge.seqware.common.model.StudyType;
import net.sourceforge.seqware.common.model.Workflow;
import net.sourceforge.seqware.common.model.WorkflowAttribute;
import net.sourceforge.seqware.common.model.WorkflowParam;
import net.sourceforge.seqware.common.model.WorkflowRun;
import net.sourceforge.seqware.common.model.WorkflowRunAttribute;
import net.sourceforge.seqware.common.module.FileMetadata;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.common.util.Bool;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.common.util.maptools.MapTools;
import org.apache.commons.dbutils.DbUtils;
import org.apache.commons.dbutils.ResultSetHandler;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.tomcat.dbcp.dbcp.BasicDataSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
// FIXME: Have to record processing event (event), what the workflow it was, etc.
// FIXME: Need to add workflow table, and then have each processing event associated with a workflowID for this particular run of the workflow
/**
* <p>
* MetadataDB class.
* </p>
*
* @author boconnor
* @version $Id: $Id
*/
public class MetadataDB implements Metadata {
private final Connection db; // A connection to the database
private final DatabaseMetaData dbmd; // This is basically info the driver delivers
// about the DB it just connected to. I use
// it to get the DB version to confirm the
// connection in this example.
private final Statement instance_sql;
private final Logger logger = LoggerFactory.getLogger(MetadataDB.class);
public MetadataDB(Connection conn) throws SQLException {
this.db = conn;
this.dbmd = conn.getMetaData();
this.instance_sql = conn.createStatement();
}
public MetadataDB(DataSource ds) throws SQLException {
this(getConnection(ds));
}
public MetadataDB(String url, String username, String password) throws SQLException {
this(getConnection(url, username, password));
}
private static Connection getConnection(String url, String username, String password) throws SQLException {
try {
Class.forName("org.postgresql.Driver");
} catch (ClassNotFoundException e) {
throw new RuntimeException(e);
}
return DriverManager.getConnection(url, username, password);
}
private static Connection getConnection(DataSource ds) throws SQLException {
try {
Class.forName("org.postgresql.Driver");
} catch (ClassNotFoundException e) {
throw new RuntimeException(e);
}
if (ds instanceof BasicDataSource) {
BasicDataSource bds = (BasicDataSource) ds;
Log.info("Tomcat Basic data source init with: Log-abandoned =" + bds.getLogAbandoned() + " Max-active: " + bds.getMaxActive()
+ " Max-wait: " + bds.getMaxWait() + " Remove-abandoned: " + bds.getRemoveAbandoned() + " Remove-abandoned-timeout: "
+ bds.getRemoveAbandonedTimeout() + " Num-active: " + bds.getNumActive() + " Num-idle: " + bds.getNumIdle());
}
return ds.getConnection();
}
@Override
public void fileProvenanceReport(Map<FileProvenanceParam, List<String>> params, Writer out) {
throw new NotImplementedException("This is currently not implemented for a direct DB connection!");
}
@Override
public List<Map<String, String>> fileProvenanceReport(Map<FileProvenanceParam, List<String>> params) {
throw new NotImplementedException("This is currently not implemented for a direct DB connection!");
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue addStudy(String title, String description, String centerName, String centerProjectName, Integer studyTypeId) {
return (new ReturnValue(ReturnValue.NOTIMPLEMENTED));
}
/**
* {@inheritDoc}
*
* @param experiment_library_design_id
* the value of experiment_library_design_id
* @param experiment_spot_design_id
* the value of experiment_spot_design_id
*/
@Override
public ReturnValue addExperiment(Integer studySwAccession, Integer platformId, String description, String title,
Integer experiment_library_design_id, Integer experiment_spot_design_id) {
return (new ReturnValue(ReturnValue.NOTIMPLEMENTED));
}
/**
* {@inheritDoc}
*
* @param parentSampleAccession
*/
@Override
public ReturnValue addSample(Integer experimentAccession, Integer parentSampleAccession, Integer organismId, String description,
String title) {
return (new ReturnValue(ReturnValue.NOTIMPLEMENTED));
}
// FIXME: Need to tune these statements in case of null values. Need to figure
// what we exactly need
// FIXME: to require in a ReturnValue and gracefully exit on missing required
// value.
/**
* Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
*
* @param SequenceID
* a {@link java.lang.String} object.
* @throws java.sql.SQLException
* if any.
* @param sqlQuery
* a {@link java.lang.String} object.
* @return a int.
*/
public int InsertAndReturnNewPrimaryKey(String sqlQuery, String SequenceID) throws SQLException {
executeUpdate(sqlQuery);
return executeQuery("select currval('" + SequenceID + "')", new IntByIndex(1, 0));
}
/**
* {@inheritDoc}
*
* @param processingID
* @return
*/
public ReturnValue set_processing_update_tstmp_if_null(int processingID) {
// Create a SQL statement
StringBuilder sql = new StringBuilder();
try {
// FIXME: Update a processing entry from ReturnValue
sql.append("UPDATE processing SET ");
// create_tstmp timestamp and update_tstmp
sql.append("update_tstmp = now()");
sql.append(" WHERE processing_id = ").append(processingID).append(" AND update_tstmp IS NULL");
// Execute above
PreparedStatement ps = null;
try {
Log.info(sql);
ps = this.getDb().prepareStatement(sql.toString());
ps.executeUpdate();
} finally {
DbUtils.closeQuietly(ps);
}
} catch (SQLException e) {
e.printStackTrace();
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
return new ReturnValue();
}
// FIXME: This should all be a transaction. For now, we end up with cruft in
// the DB if something failed.
/*
* FIXME: instead of taking in parentID's here, need to take in tubles to discuss the relationship. Different types of relationships:
* match1 -> variant1 is process match -> variant is algorithm match -> match1, match2, etc is subprocess
*/
/**
* {@inheritDoc}
*/
@Override
public ReturnValue add_empty_processing_event(int[] parentIDs) {
int processingID;
// Create a SQL statement
StringBuffer sql = new StringBuffer();
try {
// FIXME: Add a new processing entry
sql.append("INSERT INTO processing (status, create_tstmp) VALUES( '").append(ProcessingStatus.pending.name())
.append("', now())");
processingID = InsertAndReturnNewPrimaryKey(sql.toString(), "processing_processing_id_seq");
// Associate the processing entry with the zero or more parents
if (parentIDs != null) {
for (int parentID : parentIDs) {
sql = new StringBuffer();
sql.append("INSERT INTO processing_relationship (");
sql.append("parent_id,");
sql.append("child_id,");
sql.append("relationship");
sql.append(") VALUES (");
sql.append(parentID).append(",");
sql.append(processingID).append(",");
sql.append("'parent-child'");
sql.append(")");
executeUpdate(sql.toString());
}
}
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
ReturnValue ret = new ReturnValue();
ret.setReturnValue(processingID);
return ret;
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue add_empty_processing_event_by_parent_accession(int[] parentAccessions) {
int processingID;
ReturnValue ret = new ReturnValue();
ret.setExitStatus(ReturnValue.SUCCESS);
// Create a SQL statement
StringBuilder sql = new StringBuilder();
try {
// FIXME: Add a new processing entry
sql.append("INSERT INTO processing (status, create_tstmp) VALUES( '").append(ProcessingStatus.pending.name())
.append("', now())");
processingID = InsertAndReturnNewPrimaryKey(sql.toString(), "processing_processing_id_seq");
// Associate the processing entry with the zero or more parents
if (parentAccessions != null) {
for (int accession : parentAccessions) {
// LEFT OFF HERE: need to check ius, lane, sequencer_run, processing
// to see which table to populate
if (!linkAccessionAndParent(accession, processingID)) {
ret.setExitStatus(ReturnValue.SQLQUERYFAILED);
ret.setStderr(ret.getStderr() + "\nCouldn't link this processing event: " + processingID + " to accession "
+ accession);
return ret;
}
}
}
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
} finally {
DBAccess.close();
}
/*
* If no error, return success
*/
ret.setReturnValue(processingID);
return ret;
}
/**
* {@inheritDoc}
*
* This maps processing_id to sw_accession for that event.
*/
@Override
public int mapProcessingIdToAccession(int processingId) {
String sql = "select sw_accession from processing where processing_id = " + processingId;
try {
return executeQuery(sql, new IntByName("sw_accession", 0));
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql);
return (-1);
}
}
/**
* {@inheritDoc}
*
* TODO: needs to support more relationship types, but will need to add to the SQL schema to support this
*/
@Override
public boolean linkWorkflowRunAndParent(int workflowRunId, int parentAccession) throws SQLException {
StringBuilder sql = new StringBuilder();
if (findAccessionInTable("ius", "ius_id", parentAccession) != 0) {
int parentId = findAccessionInTable("ius", "ius_id", parentAccession);
sql.append("INSERT INTO ius_workflow_runs (");
sql.append("ius_id, ");
sql.append("workflow_run_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(workflowRunId);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("lane", "lane_id", parentAccession) != 0) {
int parentId = findAccessionInTable("lane", "lane_id", parentAccession);
sql.append("INSERT INTO lane_workflow_runs (");
sql.append("lane_id, ");
sql.append("workflow_run_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(workflowRunId);
sql.append(")");
executeUpdate(sql.toString());
} else {
return (false);
}
return (true);
}
/**
* <p>
* linkAccessionAndParent.
* </p>
*
* @param accession
* a int.
* @param processingID
* a int.
* @return a boolean.
* @throws java.sql.SQLException
* if any.
*/
public boolean linkAccessionAndParent(int accession, int processingID) throws SQLException {
StringBuilder sql = new StringBuilder();
Log.debug("Link Accession and Parent accession:" + accession + " processingId:" + processingID);
if (accession == 0) {
Log.warn("This processing event has no parents! " + processingID);
return true;
}
if (findAccessionInTable("ius", "ius_id", accession) != 0) {
int parentId = findAccessionInTable("ius", "ius_id", accession);
sql.append("INSERT INTO processing_ius (");
sql.append("ius_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("lane", "lane_id", accession) != 0) {
int parentId = findAccessionInTable("lane", "lane_id", accession);
sql.append("INSERT INTO processing_lanes (");
sql.append("lane_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("sequencer_run", "sequencer_run_id", accession) != 0) {
int parentId = findAccessionInTable("sequencer_run", "sequencer_run_id", accession);
sql.append("INSERT INTO processing_sequencer_runs (");
sql.append("sequencer_run_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("processing", "processing_id", accession) != 0) {
int parentId = findAccessionInTable("processing", "processing_id", accession);
sql.append("INSERT INTO processing_relationship (");
sql.append("parent_id, ");
sql.append("child_id, ");
sql.append("relationship");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID).append(",");
sql.append("'parent-child'");
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("study", "study_id", accession) != 0) {
int parentId = findAccessionInTable("study", "study_id", accession);
sql.append("INSERT INTO processing_studies (");
sql.append("study_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("experiment", "experiment_id", accession) != 0) {
int parentId = findAccessionInTable("experiment", "experiment_id", accession);
sql.append("INSERT INTO processing_experiments (");
sql.append("experiment_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else if (findAccessionInTable("sample", "sample_id", accession) != 0) {
int parentId = findAccessionInTable("sample", "sample_id", accession);
sql.append("INSERT INTO processing_samples (");
sql.append("sample_id, ");
sql.append("processing_id ");
sql.append(") VALUES (");
sql.append(parentId).append(",");
sql.append(processingID);
sql.append(")");
executeUpdate(sql.toString());
} else {
return (false);
}
return (true);
}
private int findAccessionInTable(String table, String idCol, int accession) throws SQLException {
String sql = "select " + idCol + " from " + table + " where sw_accession = " + accession;
return executeQuery(sql, new IntByName(idCol, 0));
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue processing_event_to_task_group(int processingID, int parentIDs[], int[] childIDs, String algorithm,
String description) {
// Create a SQL statement
StringBuffer sql = new StringBuffer();
try {
sql.append("UPDATE processing SET task_group = true WHERE processing_id = ").append(processingID);
executeUpdate(sql.toString());
if (algorithm != null) {
sql = new StringBuffer();
sql.append("UPDATE processing SET algorithm = '").append(algorithm).append("' WHERE processing_id = ").append(processingID);
executeUpdate(sql.toString());
}
if (description != null) {
sql = new StringBuffer();
sql.append("UPDATE processing SET description = '").append(description).append("' WHERE processing_id = ")
.append(processingID);
executeUpdate(sql.toString());
}
// Associate the processing entry with the zero or more parents
this.associate_processing_event_with_parents_and_child(processingID, parentIDs, childIDs);
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
ReturnValue ret = new ReturnValue();
ret.setReturnValue(processingID);
return ret;
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue add_task_group(int parentIDs[], int[] childIDs, String algorithm, String description) {
int processingID;
// Create a SQL statement
StringBuffer sql = new StringBuffer();
try {
sql.append("INSERT INTO processing (create_tstmp, task_group, algorithm) VALUES( now(), true, '").append(algorithm)
.append("' )");
processingID = InsertAndReturnNewPrimaryKey(sql.toString(), "processing_processing_id_seq");
if (description != null) {
sql = new StringBuffer();
sql.append("UPDATE processing SET description = '").append(description).append("' WHERE processing_id = ")
.append(processingID);
executeUpdate(sql.toString());
}
// Associate the processing entry with the zero or more parents
this.associate_processing_event_with_parents_and_child(processingID, parentIDs, childIDs);
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
ReturnValue ret = new ReturnValue();
ret.setReturnValue(processingID);
return ret;
}
/**
* {@inheritDoc}
*/
@Override
/*
* FIXME: this should check if association is already made, to make duplicates impossible
*/
public ReturnValue associate_processing_event_with_parents_and_child(int processingID, int[] parentIDs, int[] childIDs) {
// Create a SQL statement
StringBuffer sql = new StringBuffer();
try {
// Associate the processing entry with the zero or more parents
if (parentIDs != null) {
for (int parentID : parentIDs) {
sql = new StringBuffer();
sql.append("INSERT INTO processing_relationship (");
sql.append("parent_id,");
sql.append("child_id,");
sql.append("relationship");
sql.append(") VALUES (");
sql.append(parentID).append(",");
sql.append(processingID).append(",");
sql.append("'parent-child'");
sql.append(")");
executeUpdate(sql.toString());
}
}
// Associate the processing entry with the zero or more children
if (childIDs != null) {
for (int childID : childIDs) {
sql = new StringBuffer();
sql.append("INSERT INTO processing_relationship (");
sql.append("parent_id,");
sql.append("child_id,");
sql.append("relationship");
sql.append(") VALUES (");
sql.append(processingID).append(",");
sql.append(childID).append(",");
sql.append("'parent-child'");
sql.append(")");
executeUpdate(sql.toString());
}
}
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString() + ":" + e.getMessage());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
ReturnValue ret = new ReturnValue();
ret.setReturnValue(processingID);
return ret;
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue update_processing_status(int processingID, ProcessingStatus status) {
if (status == null) {
return new ReturnValue(null, "Processing.Status argument cannot be null", ReturnValue.INVALIDARGUMENT);
}
// Create a SQL statement
StringBuilder sql = new StringBuilder();
try {
sql.append("UPDATE processing SET status = ");
sql.append("'").append(status.name()).append("'");
sql.append(", update_tstmp='").append(new Timestamp(System.currentTimeMillis())).append("' ");
sql.append(" WHERE processing_id = ").append(processingID);
executeUpdate(sql.toString());
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString() + ":" + e.getMessage());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
// On sucess, return empty ReturnValue
return new ReturnValue();
}
/**
* {@inheritDoc}
*/
@Override
public int add_workflow_run(int workflowAccession) {
int workflowId = 0;
int id = 0;
try {
workflowId = findAccessionInTable("workflow", "workflow_id", workflowAccession);
StringBuilder sql = new StringBuilder();
sql.append("insert into workflow_run (workflow_id, create_tstmp, update_tstmp)");
sql.append(" values (").append(workflowId).append(", now(), now())");
id = InsertAndReturnNewPrimaryKey(sql.toString(), "workflow_run_workflow_run_id_seq");
} catch (Exception e) {
e.printStackTrace();
return (0);
}
return (id);
}
/**
* {@inheritDoc}
*/
@Override
public int get_workflow_run_accession(int workflowRunId) {
String sql = "select sw_accession from workflow_run where workflow_run_id = " + workflowRunId;
try {
return executeQuery(sql, new IntByName("sw_accession", 0));
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
return (-1);
}
}
/**
* {@inheritDoc}
*/
@Override
public int get_workflow_run_id(int workflowRunAccession) {
String sql = "select workflow_run_id from workflow_run where sw_accession = " + workflowRunAccession;
try {
return executeQuery(sql, new IntByName("workflow_run_id", 0));
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
return (-1);
}
}
/**
* {@inheritDoc}
*/
@Override
public WorkflowRun getWorkflowRun(int workflowRunAccession) {
String sql = "select workflow_run_id, name, ini_file, cmd, workflow_template, dax, "
+ "status, status_cmd, seqware_revision, host, stderr, stdout, "
+ "current_working_dir, username, create_tstmp from workflow_run where sw_accession = " + workflowRunAccession;
try {
return executeQuery(sql, new ResultSetHandler<WorkflowRun>() {
@Override
public WorkflowRun handle(ResultSet rs) throws SQLException {
WorkflowRun wr = null;
if (rs.next()) {
wr = new WorkflowRun();
wr.setWorkflowRunId(rs.getInt("workflow_run_id"));
wr.setName(rs.getString("name"));
wr.setIniFile(rs.getString("ini_file"));
wr.setCommand(rs.getString("cmd"));
wr.setTemplate(rs.getString("workflow_template"));
wr.setDax(rs.getString("dax"));
wr.setStatus(WorkflowRunStatus.valueOf(rs.getString("status")));
wr.setStatusCmd(rs.getString("status_cmd"));
wr.setHost(rs.getString("host"));
wr.setCurrentWorkingDir(rs.getString("current_working_dir"));
wr.setStdErr(rs.getString("stderr"));
wr.setStdOut(rs.getString("stdout"));
wr.setCreateTimestamp(rs.getDate("create_tstmp"));
}
return wr;
}
});
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
return null;
}
}
/**
* {@inheritDoc}
*/
@Override
public void add_workflow_run_ancestor(int workflowRunAccession, int processingId) {
int workflowRunId = 0;
try {
workflowRunId = findAccessionInTable("workflow_run", "workflow_run_id", workflowRunAccession);
StringBuilder sql = new StringBuilder();
sql.append("update processing set ancestor_workflow_run_id = ").append(workflowRunId).append(", update_tstmp='")
.append(new Timestamp(System.currentTimeMillis())).append("' where processing_id = ").append(processingId);
executeUpdate(sql.toString());
} catch (Exception e) {
logger.error("SQL Command failed: " + e.getMessage() + ":" + e.getMessage());
}
}
/**
* {@inheritDoc}
*
* @param workflowRunAccession
*/
@Override
public ReturnValue update_processing_workflow_run(int processingID, int workflowRunAccession) {
// Create a SQL statement
int workflowRunId = 0;
StringBuilder sql = new StringBuilder();
try {
workflowRunId = findAccessionInTable("workflow_run", "workflow_run_id", workflowRunAccession);
sql.append("UPDATE processing SET workflow_run_id = ");
sql.append(workflowRunId);
sql.append(", update_tstmp='").append(new Timestamp(System.currentTimeMillis())).append("' ");
sql.append(" WHERE processing_id = ").append(processingID);
executeUpdate(sql.toString());
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql.toString() + ":" + e.getMessage());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
// On sucess, return empty ReturnValue
return new ReturnValue();
}
/**
* {@inheritDoc}
*
* @param inputFiles
* @param workflowengine
*/
@Override
public ReturnValue update_workflow_run(int workflowRunId, String pegasusCmd, String workflowTemplate, WorkflowRunStatus status,
String statusCmd, String workingDirectory, String dax, String ini, String host, String stdErr, String stdOut,
String workflowengine, Set<Integer> inputFiles) {
// metadata.update_workflow_run(workflowRunId, pegasusCmd, template,
// "pending", statusCmd, wi.getWorkflowDir(), daxReader.toString(),
// mapBuffer.toString());
ReturnValue ret = new ReturnValue(ReturnValue.SUCCESS);
// Create a SQL statement
// TODO: need to add the currStep, stderr, etc
//
String sql = "UPDATE workflow_run SET status = " + formatSQL(status.name(), WorkflowRunStatus.pending.name()) + ", cmd = "
+ formatSQL(pegasusCmd, null) + ", workflow_template = " + formatSQL(workflowTemplate, null) + ", dax = "
+ formatSQL(dax, null) + ", status_cmd = " + formatSQL(statusCmd, null) + ", current_working_dir = "
+ formatSQL(workingDirectory, null) + ", ini_file = " + formatSQL(ini, null) + ", host = " + formatSQL(host, null)
+ ", stderr = " + formatSQL(stdErr, null) + ", stdout = " + formatSQL(stdOut, null) + ", workflow_engine = "
+ formatSQL(workflowengine, null) + ", update_tstmp='" + new Timestamp(System.currentTimeMillis())
+ "' where workflow_run_id = " + workflowRunId;
try {
executeUpdate(sql);
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + "\n" + e.getMessage());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
return ret;
}
@Override
public void updateWorkflowRun(WorkflowRun wr) {
throw new NotImplementedException("This is currently not implemented for a direct DB connection!");
}
/**
* <p>
* linkProcessingAndFile.
* </p>
*
* @param processingID
* a int.
* @param fileID
* a int.
* @throws java.sql.SQLException
* if any.
*/
public void linkProcessingAndFile(int processingID, int fileID) throws SQLException {
StringBuffer sql;
sql = new StringBuffer();
sql.append("INSERT INTO processing_files (");
sql.append("processing_id,");
sql.append("file_id");
sql.append(") VALUES (");
sql.append(processingID).append(",");
sql.append(fileID);
sql.append(")");
executeUpdate(sql.toString());
}
private String sqlQuote(String value) {
return value == null ? "null" : "'" + value + "'";
}
private String sqlQuote(Long value) {
return value == null ? "null" : value.toString();
}
private int insertFileRecord(FileMetadata file) throws SQLException {
String sql = "INSERT INTO FILE (file_path, meta_type, type, description, url, url_label, md5sum, size) "
+ " VALUES (%s, %s, %s, %s, %s, %s, %s, %s)";
sql = String.format(sql, sqlQuote(file.getFilePath()), sqlQuote(file.getMetaType()), sqlQuote(file.getType()),
sqlQuote(file.getDescription()), sqlQuote(file.getUrl()), sqlQuote(file.getUrlLabel()), sqlQuote(file.getMd5sum()),
sqlQuote(file.getSize()));
try {
/*
* Create a processing_files entry
*/
return InsertAndReturnNewPrimaryKey(sql, "file_file_id_seq");
} catch (SQLException e) {
logger.error("Error executing sql: " + sql + ":" + e.getMessage());
throw e;
}
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue update_processing_event(int processingID, ReturnValue retval) {
// Create a SQL statement
StringBuilder sql = new StringBuilder();
ArrayList params = new ArrayList();
try {
// FIXME: Update a processing entry from ReturnValue
sql.append("UPDATE processing SET ");
// FIXME: sql.append("sequencer_run_id,");
// FIXME: sql.append("workflow_id,");
// exit_status integer
if (retval.getExitStatus() != ReturnValue.NULL) {
sql.append("exit_status = ?, ");
params.add(retval.getExitStatus());
}
// process_exit_status integer
if (retval.getProcessExitStatus() != ReturnValue.NULL) {
sql.append("process_exit_status = ?, ");
params.add(retval.getProcessExitStatus());
}
// algorithm = text
if (retval.getAlgorithm() != null) {
sql.append("algorithm = ?, ");
params.add(retval.getAlgorithm());
}
// parameters text
if (retval.getParameters() != null) {
sql.append("parameters = ?, ");
params.add(retval.getParameters());
}
// parameters text
if (retval.getDescription() != null) {
sql.append("description = ?, ");
params.add(retval.getDescription());
}
// version text
if (retval.getVersion() != null) {
sql.append("version = ?, ");
params.add(retval.getVersion());
}
// url text
if (retval.getUrl() != null) {
sql.append("url = ?, ");
params.add(retval.getUrl());
}
// urlLabel text
if (retval.getUrlLabel() != null) {
sql.append("url_label = ?, ");
params.add(retval.getUrlLabel());
}
// stdout text
if (retval.getStdout() != null) {
sql.append("stdout = ?, ");
params.add(retval.getStdout());
}
// stderr text
if (retval.getStderr() != null) {
sql.append("stderr = ?, ");
params.add(retval.getStderr());
}
// run start timestamp
if (retval.getRunStartTstmp() != null) {
sql.append("run_start_tstmp = ?, ");
params.add(new Timestamp(retval.getRunStartTstmp().getTime()));
}
// run stop timestamp
if (retval.getRunStopTstmp() != null) {
sql.append("run_stop_tstmp = ?, ");
params.add(new Timestamp(retval.getRunStopTstmp().getTime()));
}
// create_tstmp timestamp and update_tstmp
sql.append("update_tstmp = now()");
sql.append(" WHERE processing_id = ").append(processingID);
// Execute above
PreparedStatement ps = null;
try {
ps = this.getDb().prepareStatement(sql.toString());
for (int i = 0; i < params.size(); i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
} finally {
DbUtils.closeQuietly(ps);
}
// Add and associate files for each item
if (retval.getFiles() != null) {
for (FileMetadata file : retval.getFiles()) {
// If the file path is empty, warn and skip
if (file.getFilePath().compareTo("") == 0) {
logger.warn("WARNING: Skipping empty FilePath for ProcessingID entry: " + processingID);
continue;
}
// If the meta type is empty, warn and skip
if (file.getMetaType().compareTo("") == 0) {
logger.warn("WARNING: Skipping empty MetaType for ProcessingID entry: " + processingID);
continue;
}
// Add a new file entry
int fileID = insertFileRecord(file);
linkProcessingAndFile(processingID, fileID);
}
}
} catch (SQLException e) {
e.printStackTrace();
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
/*
* If no error, return success
*/
return new ReturnValue();
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue clean_up() {
Log.debug("clean_up() of MetadataDB occured " + Integer.toHexString(this.hashCode()));
Log.debug("clean_up() of statement " + Integer.toHexString(this.getSql().hashCode()));
DbUtils.closeQuietly(this.instance_sql);
Log.debug("clean_up() of connection " + Integer.toHexString(this.getDb().hashCode()));
DbUtils.closeQuietly(this.db);
return new ReturnValue();
}
/**
* <p>
* Getter for the field <code>db</code>.
* </p>
*
* @return a {@link java.sql.Connection} object.
*/
public Connection getDb() {
return db;
}
/**
* <p>
* Getter for the field <code>dbmd</code>.
* </p>
*
* @return a {@link java.sql.DatabaseMetaData} object.
*/
public DatabaseMetaData getDbmd() {
return dbmd;
}
/**
* <p>
* Getter for the field <code>sql</code>.
* </p>
*
* @return a {@link java.sql.Statement} object.
*/
public Statement getSql() {
return instance_sql;
}
@Override
public ReturnValue addWorkflow(String name, String version, String description, String baseCommand, String configFile,
String templateFile, String provisionDir, boolean storeProvisionDir, String archiveZip, boolean storeArchiveZip,
String workflowClass, String workflowType, String workflowEngine, String seqwareVersion) {
ReturnValue ret = new ReturnValue(ReturnValue.SUCCESS);
// figure out the correct command
String command = baseCommand + " ";
command = command.replaceAll("\\$\\{workflow_bundle_dir\\}", provisionDir);
// make the base workflow row
int workflowId = 0;
// Create a SQL statement
StringBuilder sql = new StringBuilder();
try {
sql.append(
"INSERT INTO workflow (name, description, version, base_ini_file, cmd, current_working_dir, permanent_bundle_location, workflow_template, create_tstmp, update_tstmp, workflow_engine, workflow_class, workflow_type) "
+ "VALUES( '").append(name).append("', '").append(description).append("', '").append(version).append("', '")
.append(configFile).append("', '").append(command).append("', '").append(provisionDir).append("', '")
.append(archiveZip).append("', '").append(templateFile).append("', '" + "now()" + "', '" + "now()" + "', '")
.append(workflowEngine).append("', '").append(workflowClass).append("', '").append(workflowType).append(")");
// get back last ID value
workflowId = InsertAndReturnNewPrimaryKey(sql.toString(), "workflow_workflow_id_seq");
ret.setReturnValue(workflowId);
// open the ini file and parse each item
// FIXME: this assumes there is one ini file which is generally fine for
// bundled workflows but we could make this more flexible
HashMap<String, Map<String, String>> hm = new HashMap<>();
MapTools.ini2RichMap(configFile, hm);
// foreach workflow param add an entry in the workflow_param table
for (String key : hm.keySet()) {
Map<String, String> details = hm.get(key);
boolean display = Bool.parse(details.get("display"));
String insert = "insert into workflow_param (workflow_id, type, key, display, display_name, file_meta_type, default_value) values ( "
+ workflowId
+ ", "
+ formatSQL(details.get("type"), "text")
+ ", "
+ formatSQL(details.get("key"), null)
+ ", "
+ display
+ ", "
+ formatSQL(details.get("display_name"), details.get("key"))
+ ", "
+ formatSQL(details.get("file_meta_type"), null) + ", " + formatSQL(details.get("default_value"), null) + ")";
int workflowParamId = InsertAndReturnNewPrimaryKey(insert, "workflow_param_workflow_param_id_seq");
// at this point everything should be setup unless it's of type
// "pulldown", in which case we need to populate the pulldown table
if ("pulldown".equals(details.get("type")) && details.get("pulldown_items") != null) {
String[] pulldowns = details.get("pulldown_items").split(";");
for (String pulldown : pulldowns) {
String[] kv = pulldown.split("\\|");
if (kv.length == 2) {
String pulldownInsert = "insert into workflow_param_value (workflow_param_id, display_name, value) values ( "
+ workflowParamId + ", " + formatSQL(kv[0], kv[0]) + ", " + formatSQL(kv[1], kv[1]) + ")";
int workflowParamValueId = InsertAndReturnNewPrimaryKey(pulldownInsert,
"workflow_param_value_workflow_param_value_id_seq");
}
}
}
}
// TODO: need to add support for pulldowns!
} catch (SQLException e) {
logger.error("SQL Command failed: " + e.getMessage() + ":" + e.getMessage());
return new ReturnValue(null, "Could not execute one of the SQL commands: " + sql.toString() + "\nException: " + e.getMessage(),
ReturnValue.SQLQUERYFAILED);
}
// add default params in workflow_param table
return ret;
}
private String formatSQL(String variable, String defaultStr) {
if ((variable == null || "".equals(variable)) && (defaultStr != null && !"".equals(defaultStr))) {
String newDefaultStr = defaultStr.replaceAll("'", "");
return ("'" + newDefaultStr + "'");
} else if ((variable == null || "".equals(variable)) && (defaultStr == null || "".equals(defaultStr))) {
return ("NULL");
} else {
String newVariable = variable.replaceAll("'", "");
return ("'" + newVariable + "'");
}
}
/**
* {@inheritDoc}
*/
@Override
public Map<String, String> get_workflow_info(final int workflowAccession) {
String sql = "SELECT name, description, version, base_ini_file, cmd, current_working_dir, workflow_template, create_tstmp, update_tstmp, permanent_bundle_location, workflow_engine, workflow_type, workflow_class FROM workflow where sw_accession = "
+ workflowAccession;
try {
return executeQuery(sql, new ResultSetHandler<Map<String, String>>() {
@Override
public Map<String, String> handle(ResultSet rs) throws SQLException {
HashMap<String, String> map = new HashMap<>();
if (rs.next()) {
map.put("name", rs.getString("name"));
map.put("description", rs.getString("description"));
map.put("version", rs.getString("version"));
map.put("base_ini_file", rs.getString("base_ini_file"));
map.put("cmd", rs.getString("cmd"));
map.put("current_working_dir", rs.getString("current_working_dir"));
map.put("workflow_template", rs.getString("workflow_template"));
map.put("create_tstmp", rs.getString("create_tstmp"));
map.put("update_tstmp", rs.getString("update_tstmp"));
map.put("workflow_accession", Integer.toString(workflowAccession));
map.put("permanent_bundle_location", rs.getString("permanent_bundle_location"));
map.put("workflow_engine", rs.getString("workflow_engine"));
map.put("workflow_type", rs.getString("workflow_type"));
map.put("workflow_class", rs.getString("workflow_class"));
}
return map;
}
});
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
return null;
}
}
/**
* {@inheritDoc}
*/
@Override
public Boolean isDuplicateFile(String filepath) {
String sql = "SELECT sw_accession FROM file WHERE file_path = '" + filepath + "';";
try {
return executeQuery(sql, new ResultSetHandler<Boolean>() {
@Override
public Boolean handle(ResultSet rs) throws SQLException {
return rs.next();
}
});
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
throw new RuntimeException(e);
}
}
/**
* {@inheritDoc}
*/
@Override
public ReturnValue updateWorkflow(int workflowId, String permanentBundleLocation) {
String sql = "UPDATE workflow SET " + "permanent_bundle_location = '" + permanentBundleLocation + "'," + " update_tstmp='"
+ new Timestamp(System.currentTimeMillis()) + "' " + "WHERE workflow_id = " + workflowId;
ReturnValue ret = new ReturnValue();
try {
executeUpdate(sql);
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
e.printStackTrace();
ret.setExitStatus(ReturnValue.SQLQUERYFAILED);
}
return ret;
}
/**
* <p>
* listInstalledWorkflows.
* </p>
*
* @return a {@link java.lang.String} object.
*/
@Override
public String listInstalledWorkflows() {
String sql = "SELECT name, version, sw_accession, create_tstmp, permanent_bundle_location FROM workflow";
try {
return executeQuery(sql, new ResultSetHandler<String>() {
@Override
public String handle(ResultSet rs) throws SQLException {
StringBuilder sb = new StringBuilder();
while (rs.next()) {
sb.append(rs.getString("name")).append("\t");
sb.append(rs.getString("version")).append("\t");
sb.append(rs.getString("create_tstmp")).append("\t");
sb.append(rs.getString("sw_accession")).append("\t");
sb.append(rs.getString("permanent_bundle_location")).append("\n");
}
return sb.toString();
}
});
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
throw new RuntimeException(e);
}
}
/**
* {@inheritDoc}
*/
@Override
// FIXME: need to implement this for this backend type
public String listInstalledWorkflowParams(String workflowAccession) {
return null;
}
/**
* {@inheritDoc}
*/
@Override
public int getWorkflowAccession(String name, String version) {
String sql = "select sw_accession from workflow where name = '" + name + "' AND version = '" + version + "'";
try {
return executeQuery(sql, new IntByName("sw_accession", 0));
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
return (-1);
}
}
@Override
public List<Study> getStudyByName(String name) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public void fileProvenanceReportTrigger() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Sample> getSampleByName(String name) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public SequencerRun getSequencerRunByName(String name) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public Processing getProcessing(int processingAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public String getWorkflowRunReport(WorkflowRunStatus status, Date earliestDate, Date latestDate) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public String getWorkflowRunReport(Integer workflowSWID, WorkflowRunStatus status, Date earliestDate, Date latestDate) {
throw new UnsupportedOperationException("Not supported yet."); // To change body of generated methods, choose Tools | Templates.
}
@Override
public List<WorkflowRun> getWorkflowRunsByStatusCmd(String statusCmd) {
throw new UnsupportedOperationException("Not supported yet."); // To change body of generated methods, choose Tools | Templates.
}
@Override
public Map<String, String> getEnvironmentReport() {
throw new UnsupportedOperationException("Not supported yet."); // To change body of generated methods, choose Tools | Templates.
}
@Override
public boolean checkClientServerMatchingVersion() {
throw new UnsupportedOperationException("Not supported yet."); // To change body of generated methods, choose Tools | Templates.
}
@Override
public IUS getIUS(int swAccession) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
@Override
public Sample getSample(int swAccession) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
@Override
public Study getStudy(int swAccession) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
public static class IntByIndex implements ResultSetHandler<Integer> {
private final int col;
private final int defaultVal;
public IntByIndex(int col, int defaultVal) {
this.col = col;
this.defaultVal = defaultVal;
}
@Override
public Integer handle(ResultSet rs) throws SQLException {
if (rs.next()) {
return rs.getInt(col);
} else {
return defaultVal;
}
}
}
public static class IntByName implements ResultSetHandler<Integer> {
private final String col;
private final int defaultVal;
public IntByName(String col, int defaultVal) {
this.col = col;
this.defaultVal = defaultVal;
}
@Override
public Integer handle(ResultSet rs) throws SQLException {
if (rs.next()) {
return rs.getInt(col);
} else {
return defaultVal;
}
}
}
/**
* <p>
* executeQuery.
* </p>
*
* @param <T>
* @param s
* a {@link java.lang.String} object.
* @param h
* @return a {@link java.sql.ResultSet} object.
* @throws java.sql.SQLException
* if any.
*/
public <T> T executeQuery(String s, ResultSetHandler<T> h) throws SQLException {
Statement sql1 = getSql();
Log.debug("MetadataDB executeQuery: \"" + s + "\" on connection + " + Integer.toHexString(this.getDb().hashCode()));
Log.debug("MetadataDB executeQuery: query is " + (s == null ? "null" : "not null"));
if (sql1 == null) {
Log.debug("MetadataDB executeQuery: statement is null");
} else {
Log.debug("MetadataDB executeQuery: statement " + Integer.toHexString(sql1.hashCode()) + " is not null");
ResultSet rs = sql1.executeQuery(s);
try {
return h.handle(rs);
} finally {
DbUtils.closeQuietly(rs);
}
}
throw new RuntimeException("could not get sql object");
}
/**
* <p>
* executeUpdate.
* </p>
*
* @param s
* a {@link java.lang.String} object.
* @return a int.
* @throws java.sql.SQLException
* if any.
*/
public int executeUpdate(String s) throws SQLException {
logger.debug("MetadataDB executeUpdate:" + s);
return getSql().executeUpdate(s);
}
/**
* {@inheritDoc}
*/
@Override
public List<WorkflowRun> getWorkflowRunsByStatus(WorkflowRunStatus status) {
String sql = "select workflow_run_id, name, ini_file, cmd, workflow_template, dax, status, status_cmd, seqware_revision, host, current_working_dir, username, create_tstmp from workflow_run where status = '"
+ status.name() + "'";
try {
return executeQuery(sql, new ResultSetHandler<List<WorkflowRun>>() {
@Override
public List<WorkflowRun> handle(ResultSet rs) throws SQLException {
ArrayList<WorkflowRun> results = new ArrayList<>();
while (rs.next()) {
WorkflowRun wr = new WorkflowRun();
wr.setWorkflowRunId(rs.getInt("workflow_run_id"));
wr.setName(rs.getString("name"));
wr.setIniFile(rs.getString("ini_file"));
wr.setCommand(rs.getString("cmd"));
wr.setTemplate(rs.getString("workflow_template"));
wr.setDax(rs.getString("dax"));
wr.setStatus(WorkflowRunStatus.valueOf(rs.getString("status")));
wr.setStatusCmd(rs.getString("status_cmd"));
wr.setHost(rs.getString("host"));
wr.setCurrentWorkingDir(rs.getString("current_working_dir"));
wr.setCreateTimestamp(rs.getDate("create_tstmp"));
// FIXME: need to update with workflow engine etc
results.add(wr);
}
return results;
}
});
} catch (SQLException e) {
logger.error("SQL Command failed: " + sql + ":" + e.getMessage());
throw new RuntimeException(e);
}
}
/**
* {@inheritDoc}
*/
@Override
public WorkflowRun getWorkflowRunWithWorkflow(String workflowRunAccession) {
throw new NotImplementedException("This is currently not implemented for a direct DB connection!");
}
/**
* <p>
* getAllStudies.
* </p>
*
* @return a {@link java.util.List} object.
*/
@Override
public List<Study> getAllStudies() {
throw new NotImplementedException("All studies must be retrieved through webservice");
}
/**
* <p>
* getSequencerRunReport.
* </p>
*
* @return a {@link java.lang.String} object.
*/
@Override
public String getSequencerRunReport() {
return null;
}
/**
* {@inheritDoc}
*
* @param iusSWID
*/
@Override
public void annotateIUS(int iusSWID, IUSAttribute iusAtt, Boolean skip) {
throw new NotImplementedException("Updating IUSes must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateLane(int laneSWID, LaneAttribute laneAtt, Boolean skip) {
throw new NotImplementedException("Updating Lanes must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateSequencerRun(int sequencerRunSWID, SequencerRunAttribute sequencerRunAtt, Boolean skip) {
throw new NotImplementedException("Updating Sequencer Runs must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateExperiment(int experimentSWID, ExperimentAttribute att, Boolean skip) {
throw new NotImplementedException("Updating Experiment annotation must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateProcessing(int processingSWID, ProcessingAttribute att, Boolean skip) {
throw new NotImplementedException("Updating processing attribute must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateSample(int sampleSWID, SampleAttribute att, Boolean skip) {
throw new NotImplementedException("Updating sample attribute must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateStudy(int studySWID, StudyAttribute att, Boolean skip) {
throw new NotImplementedException("Updating Study attribute must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public String getWorkflowRunReport(int workflowRunSWID) {
throw new NotImplementedException("Retrieving workflow run reports must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public String getWorkflowRunReport(int workflowSWID, Date earliestDate, Date latestDate) {
throw new NotImplementedException("Retrieving workflow run reports must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public String getWorkflowRunReport(Date earliestDate, Date latestDate) {
throw new NotImplementedException("Retrieving workflow run reports must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public net.sourceforge.seqware.common.model.File getFile(int swAccession) {
throw new NotImplementedException("Retrieving files must be performed through the webservice");
}
/**
* {@inheritDoc}
*/
@Override
public SortedSet<WorkflowParam> getWorkflowParams(String swAccession) {
throw new NotImplementedException("Retrieving workflow params must be performed through the webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateWorkflow(int workflowSWID, WorkflowAttribute att, Boolean skip) {
throw new NotImplementedException("Updating processing attribute must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateWorkflowRun(int workflowrunSWID, WorkflowRunAttribute att, Boolean skip) {
throw new NotImplementedException("Updating processing attribute must be performed through webservice");
}
/**
* {@inheritDoc}
*/
@Override
public void annotateIUS(int laneSWID, Set<IUSAttribute> iusAtts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateLane(int laneSWID, Set<LaneAttribute> laneAtts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateSequencerRun(int sequencerRunSWID, Set<SequencerRunAttribute> sequencerRunAtts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateExperiment(int experimentSWID, Set<ExperimentAttribute> atts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateProcessing(int processingSWID, Set<ProcessingAttribute> atts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateSample(int sampleSWID, Set<SampleAttribute> atts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateStudy(int studySWID, Set<StudyAttribute> atts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateWorkflow(int workflowSWID, Set<WorkflowAttribute> atts) {
// TODO Auto-generated method stub
}
/**
* {@inheritDoc}
*/
@Override
public void annotateWorkflowRun(int workflowSWID, Set<WorkflowRunAttribute> atts) {
// TODO Auto-generated method stub
}
@Override
public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip,
String filePath, SequencerRunStatus status) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public ReturnValue addLane(Integer sequencerRunAccession, Integer studyTypeId, Integer libraryStrategyId, Integer librarySelectionId,
Integer librarySourceId, String name, String description, String cycleDescriptor, boolean skip, Integer laneNumber) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public ReturnValue addIUS(Integer laneAccession, Integer sampleAccession, String name, String description, String barcode, boolean skip) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Platform> getPlatforms() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Organism> getOrganisms() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<StudyType> getStudyTypes() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<LibraryStrategy> getLibraryStrategies() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<LibrarySelection> getLibrarySelections() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<LibrarySource> getLibrarySource() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public String getProcessingRelations(String swAccession) {
return null;
}
@Override
public String getWorkflowRunReportStdErr(int workflowRunSWID) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public String getWorkflowRunReportStdOut(int workflowRunSWID) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public Workflow getWorkflow(int workflowAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<SequencerRun> getAllSequencerRuns() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Lane> getLanesFrom(int sequencerRunAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<IUS> getIUSFrom(int laneOrSampleAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Experiment> getExperimentsFrom(int studyAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Sample> getSamplesFrom(int experimentAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Sample> getChildSamplesFrom(int parentSampleAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Sample> getParentSamplesFrom(int childSampleAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions, List<Integer> workflowAccessions) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<WorkflowRun> getWorkflowRunsAssociatedWithFiles(List<Integer> fileAccessions, String search_type) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public void annotateFile(int laneSWID, FileAttribute iusAtt, Boolean skip) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public void annotateFile(int fileSWID, Set<FileAttribute> iusAtts) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public Lane getLane(int laneAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public SequencerRun getSequencerRun(int sequencerRunAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<ExperimentLibraryDesign> getExperimentLibraryDesigns() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<ExperimentSpotDesignReadSpec> getExperimentSpotDesignReadSpecs() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<ExperimentSpotDesign> getExperimentSpotDesigns() {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public Experiment getExperiment(int swAccession) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<ParentAccessionModel> getViaParentAccessions(int[] potentialParentAccessions) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
@Override
public List<Object> getViaAccessions(int[] accessions) {
throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
}
}