public void importFromFile(String filePath) throws IOException {
Map<String, Long> cache = new HashMap<String, Long>(COUNT);
final File storeDir = new File(this.path);
org.apache.commons.io.FileUtils.deleteDirectory(storeDir);
BatchInserter batchInserter = new BatchInserterImpl(storeDir.getAbsolutePath());
final BatchInserterIndexProvider indexProvider =
new LuceneBatchInserterIndexProvider(batchInserter);
final BatchInserterIndex index =
indexProvider.nodeIndex("nodes", MapUtil.stringMap("type", "exact"));
BufferedReader reader = new BufferedReader(new FileReader(filePath));
String line = null;
int nodes = 0;
long time = System.currentTimeMillis();
long batchTime = time;
while ((line = reader.readLine()) != null) {
final String[] nodeNames = line.split("\\|");
final String name = nodeNames[0];
final Map<String, Object> props = MapUtil.map("name", name);
final long node = batchInserter.createNode(props);
index.add(node, props);
cache.put(name, node);
nodes++;
if ((nodes % REPORT_COUNT) == 0) {
System.out.printf(
"%d nodes created. Took %d %n", nodes, (System.currentTimeMillis() - batchTime));
batchTime = System.currentTimeMillis();
}
}
System.out.println("Creating nodes took " + (System.currentTimeMillis() - time) / 1000);
index.flush();
reader.close();
reader = new BufferedReader(new FileReader(filePath));
int rels = 0;
time = System.currentTimeMillis();
batchTime = time;
String relationshipType = "KNOWS";
while ((line = reader.readLine()) != null) {
final String[] nodeNames = line.split("\\|");
final String name = nodeNames[0];
// final Long from = index.get("name", name).getSingle();
Long from = cache.get(name);
for (int j = 1; j < nodeNames.length; j++) {
// final Long to = index.get("name", nodeNames[j]).getSingle();
final Long to = cache.get(name);
batchInserter.createRelationship(
from, to, DynamicRelationshipType.withName(relationshipType), null);
}
rels++;
if ((rels % REPORT_COUNT) == 0) {
System.out.printf(
"%d relationships created. Took %d %n", rels, (System.currentTimeMillis() - batchTime));
batchTime = System.currentTimeMillis();
}
}
System.out.println("Creating relationships took " + (System.currentTimeMillis() - time) / 1000);
indexProvider.shutdown();
batchInserter.shutdown();
}
public <T extends Element> Index<T> createManualIndex(
final String indexName, final Class<T> indexClass, final Parameter... indexParameters) {
final Neo4jBatchIndex<T> index;
final Map<String, String> map = generateParameterMap(indexParameters);
if (indexParameters.length == 0) {
map.put(Neo4jBatchTokens.TYPE, Neo4jBatchTokens.EXACT);
}
map.put(Neo4jBatchTokens.BLUEPRINTS_TYPE, Index.Type.MANUAL.toString());
if (Vertex.class.isAssignableFrom(indexClass)) {
index =
new Neo4jBatchIndex<T>(
this, indexProvider.nodeIndex(indexName, map), indexName, indexClass);
} else {
index =
new Neo4jBatchIndex<T>(
this, indexProvider.relationshipIndex(indexName, map), indexName, indexClass);
}
this.indices.put(indexName, index);
return index;
}
public <T extends Element> AutomaticIndex<T> createAutomaticIndex(
final String indexName,
final Class<T> indexClass,
final Set<String> indexKeys,
final Parameter... indexParameters) {
final Neo4jBatchAutomaticIndex<T> index;
final Map<String, String> map = generateParameterMap(indexParameters);
if (indexParameters.length == 0) {
map.put(Neo4jBatchTokens.TYPE, Neo4jBatchTokens.EXACT);
}
map.put(Neo4jBatchTokens.BLUEPRINTS_TYPE, Index.Type.AUTOMATIC.toString());
map.put(Neo4jBatchTokens.BLUEPRINTS_AUTOKEYS, makeAutoIndexKeys(indexKeys));
if (indexClass.equals(Vertex.class)) {
index =
new Neo4jBatchAutomaticIndex<T>(
this, indexProvider.nodeIndex(indexName, map), indexName, indexClass, indexKeys);
} else {
index =
new Neo4jBatchAutomaticIndex<T>(
this,
indexProvider.relationshipIndex(indexName, map),
indexName,
indexClass,
indexKeys);
}
this.indices.put(indexName, index);
if (Vertex.class.isAssignableFrom(indexClass)) {
this.automaticVertexIndices.put(
indexName, (Neo4jBatchAutomaticIndex<Neo4jBatchVertex>) index);
} else {
this.automaticEdgeIndices.put(indexName, (Neo4jBatchAutomaticIndex<Neo4jBatchEdge>) index);
}
return index;
}
public static void main(String[] args) {
File currentFolder = new File(".");
File[] files = currentFolder.listFiles();
BatchInserter inserter = null;
BatchInserterIndexProvider indexProvider = null;
// ----------------------------------------------------------------------------------
// ---------------------initializing node type properties----------------------------
genomeElementProperties.put(GenomeElementNode.NODE_TYPE_PROPERTY, GenomeElementNode.NODE_TYPE);
geneProperties.put(GeneNode.NODE_TYPE_PROPERTY, GeneNode.NODE_TYPE);
cdsProperties.put(CDSNode.NODE_TYPE_PROPERTY, CDSNode.NODE_TYPE);
miscRnaProperties.put(MiscRNANode.NODE_TYPE_PROPERTY, MiscRNANode.NODE_TYPE);
mRnaProperties.put(MRNANode.NODE_TYPE_PROPERTY, MRNANode.NODE_TYPE);
ncRnaProperties.put(NcRNANode.NODE_TYPE_PROPERTY, NcRNANode.NODE_TYPE);
rRnaProperties.put(RRNANode.NODE_TYPE_PROPERTY, RRNANode.NODE_TYPE);
tmRnaProperties.put(TmRNANode.NODE_TYPE_PROPERTY, TmRNANode.NODE_TYPE);
tRnaProperties.put(TRNANode.NODE_TYPE_PROPERTY, TRNANode.NODE_TYPE);
// ----------------------------------------------------------------------------------
// ----------------------------------------------------------------------------------
try {
// This block configures the logger with handler and formatter
fh = new FileHandler("ImportGenbank.log", false);
SimpleFormatter formatter = new SimpleFormatter();
fh.setFormatter(formatter);
logger.addHandler(fh);
logger.setLevel(Level.ALL);
// create the batch inserter
inserter =
new BatchInserterImpl(
CommonData.DATABASE_FOLDER,
BatchInserterImpl.loadProperties(CommonData.PROPERTIES_FILE_NAME));
// create the batch index service
indexProvider = new LuceneBatchInserterIndexProvider(inserter);
// -----------------create batch indexes----------------------------------
// ----------------------------------------------------------------------
BatchInserterIndex genomeElementVersionIndex =
indexProvider.nodeIndex(
GenomeElementNode.GENOME_ELEMENT_VERSION_INDEX,
MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST));
for (File file : files) {
if (file.getName().endsWith(".gbff")) {
BufferedReader reader = new BufferedReader(new FileReader(file));
String line = null;
while ((line = reader.readLine()) != null) {
// this is the first line where the locus is
String accessionSt = "";
String definitionSt = "";
String versionSt = "";
String commentSt = "";
StringBuilder seqStBuilder = new StringBuilder();
ArrayList<String> cdsList = new ArrayList<String>();
ArrayList<String> geneList = new ArrayList<String>();
ArrayList<String> miscRnaList = new ArrayList<String>();
ArrayList<String> mRnaList = new ArrayList<String>();
ArrayList<String> ncRnaList = new ArrayList<String>();
ArrayList<String> rRnaList = new ArrayList<String>();
ArrayList<String> tmRnaList = new ArrayList<String>();
ArrayList<String> tRnaList = new ArrayList<String>();
boolean originFound = false;
// Now I get all the lines till I reach the string '//'
do {
boolean readLineFlag = true;
if (line.startsWith(GBCommon.LOCUS_STR)) {
// do nothing right now
} else if (line.startsWith(GBCommon.ACCESSION_STR)) {
accessionSt = line.split(GBCommon.ACCESSION_STR)[1].trim();
} else if (line.startsWith(GBCommon.VERSION_STR)) {
versionSt = line.split(GBCommon.VERSION_STR)[1].trim().split(" ")[0];
} else if (line.startsWith(GBCommon.DEFINITION_STR)) {
definitionSt += line.split(GBCommon.DEFINITION_STR)[1].trim();
do {
line = reader.readLine();
if (line.startsWith(" ")) {
definitionSt += line.trim();
}
} while (line.startsWith(" "));
readLineFlag = false;
} else if (line.startsWith(GBCommon.COMMENT_STR)) {
commentSt += line.split(GBCommon.COMMENT_STR)[1].trim();
do {
line = reader.readLine();
if (line.startsWith(" ")) {
commentSt += "\n" + line.trim();
}
} while (line.startsWith(" "));
readLineFlag = false;
} else if (line.startsWith(GBCommon.FEATURES_STR)) {
do {
line = reader.readLine();
if (line.trim().startsWith(GBCommon.CDS_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.CDS_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
cdsList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.GENE_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.GENE_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
geneList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.MISC_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.MISC_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
miscRnaList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.TM_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.TM_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
tmRnaList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.R_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.R_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
rRnaList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.M_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.M_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
mRnaList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.NC_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.NC_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
ncRnaList.add(positionsSt);
} else if (line.trim().startsWith(GBCommon.T_RNA_STR)) {
String positionsSt = "";
positionsSt += line.trim().split(GBCommon.T_RNA_STR)[1].trim();
line = reader.readLine();
while (!line.trim().startsWith("/")) {
positionsSt += line.trim();
line = reader.readLine();
}
tRnaList.add(positionsSt);
}
} while (line.startsWith(" "));
readLineFlag = false;
} else if (line.startsWith(GBCommon.ORIGIN_STR)) {
// sequence
originFound = true;
do {
line = reader.readLine();
String[] tempArray = line.trim().split(" ");
for (int i = 1; i < tempArray.length; i++) {
seqStBuilder.append(tempArray[i]);
}
} while (line.startsWith(" "));
readLineFlag = false;
}
if (readLineFlag) {
line = reader.readLine();
}
} while (line != null && !line.startsWith(GBCommon.LAST_LINE_STR));
// -----we only save the data when the sequence is found------------
if (originFound) {
System.out.println("accessionSt = " + accessionSt);
System.out.println("versionSt = " + versionSt);
System.out.println("definitionSt = " + definitionSt);
System.out.println("commentSt = " + commentSt);
System.out.println("sequence.length = " + seqStBuilder.toString().length());
System.out.println("geneList = " + geneList);
System.out.println("cdsList = " + cdsList);
System.out.println("miscRnaList = " + miscRnaList);
System.out.println("mRnaList = " + mRnaList);
System.out.println("ncRnaList = " + ncRnaList);
System.out.println("rRnaList = " + rRnaList);
System.out.println("tmRnaList = " + tmRnaList);
System.out.println("tRnaList = " + tRnaList);
// --------create genome element node--------------
long genomeElementId =
createGenomeElementNode(
versionSt, commentSt, definitionSt, inserter, genomeElementVersionIndex);
// -----------genes-----------------
for (String genePositionsSt : geneList) {
geneProperties.put(GeneNode.POSITIONS_PROPERTY, genePositionsSt);
long geneId = inserter.createNode(geneProperties);
inserter.createRelationship(genomeElementId, geneId, genomeElementGeneRel, null);
}
// -----------CDS-----------------
for (String cdsPositionsSt : cdsList) {
cdsProperties.put(CDSNode.POSITIONS_PROPERTY, cdsPositionsSt);
long cdsID = inserter.createNode(cdsProperties);
inserter.createRelationship(genomeElementId, cdsID, genomeElementCDSRel, null);
}
// -----------misc rna-----------------
for (String miscRnaPositionsSt : miscRnaList) {
miscRnaProperties.put(MiscRNANode.POSITIONS_PROPERTY, miscRnaPositionsSt);
long miscRnaID = inserter.createNode(miscRnaProperties);
inserter.createRelationship(
genomeElementId, miscRnaID, genomeElementMiscRnaRel, null);
}
// -----------m rna-----------------
for (String mRnaPositionsSt : mRnaList) {
mRnaProperties.put(MRNANode.POSITIONS_PROPERTY, mRnaPositionsSt);
long mRnaID = inserter.createNode(mRnaProperties);
inserter.createRelationship(genomeElementId, mRnaID, genomeElementMRnaRel, null);
}
// -----------nc rna-----------------
for (String ncRnaPositionsSt : ncRnaList) {
ncRnaProperties.put(NcRNANode.POSITIONS_PROPERTY, ncRnaPositionsSt);
long ncRnaID = inserter.createNode(ncRnaProperties);
inserter.createRelationship(genomeElementId, ncRnaID, genomeElementNcRnaRel, null);
}
// -----------r rna-----------------
for (String rRnaPositionsSt : rRnaList) {
rRnaProperties.put(RRNANode.POSITIONS_PROPERTY, rRnaPositionsSt);
long rRnaID = inserter.createNode(rRnaProperties);
inserter.createRelationship(genomeElementId, rRnaID, genomeElementRRnaRel, null);
}
// -----------tm rna-----------------
for (String tmRnaPositionsSt : tmRnaList) {
tmRnaProperties.put(TmRNANode.POSITIONS_PROPERTY, tmRnaPositionsSt);
long tmRnaID = inserter.createNode(tmRnaProperties);
inserter.createRelationship(genomeElementId, tmRnaID, genomeElementTmRnaRel, null);
}
// -----------t rna-----------------
for (String tRnaPositionsSt : tRnaList) {
tRnaProperties.put(TRNANode.POSITIONS_PROPERTY, tRnaPositionsSt);
long tRnaID = inserter.createNode(tRnaProperties);
inserter.createRelationship(genomeElementId, tRnaID, genomeElementTRnaRel, null);
}
}
}
}
}
} catch (Exception e) {
logger.log(Level.SEVERE, e.getMessage());
StackTraceElement[] trace = e.getStackTrace();
for (StackTraceElement stackTraceElement : trace) {
logger.log(Level.SEVERE, stackTraceElement.toString());
}
} finally {
// shutdown, makes sure all changes are written to disk
indexProvider.shutdown();
inserter.shutdown();
// closing logger file handler
fh.close();
}
}
