List of usage examples for com.mongodb BasicDBObject getString
public String getString(final String key)
From source file:org.opencb.cellbase.mongodb.db.regulatory.TfbsMongoDBAdaptor.java
License:Apache License
@Override public List<QueryResult> getAllByTargetGeneIdList(List<String> targetGeneIdList, QueryOptions options) { // DBCollection coreMongoDBCollection = db.getCollection("gene"); List<DBObject[]> commandList = new ArrayList<>(); for (String targetGeneId : targetGeneIdList) { DBObject[] commands = new DBObject[3]; DBObject match = new BasicDBObject("$match", new BasicDBObject("transcripts.xrefs.id", targetGeneId)); DBObject unwind = new BasicDBObject("$unwind", "$transcripts"); BasicDBObject projectObj = new BasicDBObject("_id", 0); projectObj.append("transcripts.id", 1); projectObj.append("transcripts.tfbs", 1); DBObject project = new BasicDBObject("$project", projectObj); commands[0] = match;/*from w ww .j a va 2s . com*/ commands[1] = unwind; commands[2] = project; commandList.add(commands); } // List<QueryResult> queryResults = executeAggregationList(targetGeneIdList, commandList, options, coreMongoDBCollection); List<QueryResult> queryResults = new ArrayList<>(); for (int i = 0; i < targetGeneIdList.size(); i++) { String targetGeneId = targetGeneIdList.get(0); // QueryResult queryResult = queryResults.get(0); QueryResult queryResult = new QueryResult(); BasicDBList list = (BasicDBList) queryResult.getResult(); for (int j = 0; j < list.size(); j++) { BasicDBObject gene = (BasicDBObject) list.get(j); BasicDBObject transcript = (BasicDBObject) gene.get("transcripts"); String transcriptId = transcript.getString("id"); if (transcriptId.toUpperCase().equals(targetGeneId)) { BasicDBList tfbs = (BasicDBList) transcript.get("tfbs"); queryResult.setResult(tfbs); break; } } } return queryResults; }
From source file:org.opencb.cellbase.server.ws.feature.GeneWSServer.java
License:Apache License
@GET @Path("/{geneId}/snp") @ApiOperation(httpMethod = "GET", value = "Get all SNPs within the specified gene(s)") public Response getSNPByGeneId(@PathParam("geneId") String query) { try {/* ww w.ja v a 2 s . c o m*/ parseQueryParams(); GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly); VariationDBAdaptor variationDBAdaptor = dbAdaptorFactory.getVariationDBAdaptor(this.species, this.assembly); List<QueryResult> qrList; if (queryOptions.containsKey("count") && queryOptions.getBoolean("count")) { queryOptions.remove("count"); qrList = geneDBAdaptor.getAllByIdList(Splitter.on(",").splitToList(query), queryOptions); queryOptions.put("count", true); } else { qrList = geneDBAdaptor.getAllByIdList(Splitter.on(",").splitToList(query), queryOptions); } List<QueryResult> queryResults = new ArrayList<>(); for (QueryResult qr : qrList) { QueryResult queryResult = new QueryResult(); queryResult.setId(qr.getId()); // FIXME MongoDB code should not be here BasicDBObject gene = (BasicDBObject) qr.getResult().get(0); QueryResult variationQueryResult = variationDBAdaptor.getAllByRegion(gene.getString("chromosome"), gene.getInt("start"), gene.getInt("end"), queryOptions); queryResult.setNumResults(variationQueryResult.getNumResults()); queryResult.setResult(variationQueryResult.getResult()); queryResults.add(queryResult); } return createOkResponse(queryResults); } catch (Exception e) { return createErrorResponse(e); } }
From source file:org.opendaylight.controller.samples.onftappingapp.MatchCriteria.java
License:Apache License
public MatchCriteria(DBObject matchCriteriaObj) { this.setName((String) matchCriteriaObj.get("name")); this.setReferenceCount((long) matchCriteriaObj.get("refCount")); ObjectId oid = (ObjectId) matchCriteriaObj.get("_id"); this.setObjectId(oid.toString()); this.setEnabled((Boolean) matchCriteriaObj.get("enabled")); this.setReflexive((Boolean) matchCriteriaObj.get("reflexive")); this.setPriority((int) matchCriteriaObj.get("priority")); BasicDBList mfList = (BasicDBList) matchCriteriaObj.get("matchFields"); BasicDBObject[] mfArray = mfList.toArray(new BasicDBObject[0]); for (BasicDBObject dbObj : mfArray) { MatchField matchField = new MatchField(); matchField.setType(dbObj.getString("type")); matchField.setValue(dbObj.getString("value")); // Add the match field to the match criteria this.addMatchField(matchField); }//w w w . j a va2 s . c o m }
From source file:org.opendaylight.controller.samples.onftappingapp.RewriteParams.java
License:Apache License
public RewriteParams(BasicDBObject objDoc) throws UnknownHostException { this.setName(objDoc.getString("name")); this.setIPAddress((String) objDoc.get("IPAddress")); this.setMacAddr((String) objDoc.getString("MACAddress")); this.setVlanId((int) objDoc.getInt("VLAN_ID")); }
From source file:org.openhab.persistence.mongodb.internal.MongoDBPersistenceService.java
License:Open Source License
@Override public Iterable<HistoricItem> query(FilterCriteria filter) { if (!initialized) { return Collections.emptyList(); }/*from ww w. j a v a 2 s . c o m*/ if (!isConnected()) { connectToDatabase(); } if (!isConnected()) { return Collections.emptyList(); } String name = filter.getItemName(); Item item = getItem(name); List<HistoricItem> items = new ArrayList<HistoricItem>(); DBObject query = new BasicDBObject(); if (filter.getItemName() != null) { query.put(FIELD_ITEM, filter.getItemName()); } if (filter.getState() != null && filter.getOperator() != null) { String op = convertOperator(filter.getOperator()); Object value = convertValue(filter.getState()); query.put(FIELD_VALUE, new BasicDBObject(op, value)); } if (filter.getBeginDate() != null) { query.put(FIELD_TIMESTAMP, new BasicDBObject("$gte", filter.getBeginDate())); } if (filter.getEndDate() != null) { query.put(FIELD_TIMESTAMP, new BasicDBObject("$lte", filter.getEndDate())); } Integer sortDir = (filter.getOrdering() == Ordering.ASCENDING) ? 1 : -1; DBCursor cursor = this.mongoCollection.find(query).sort(new BasicDBObject(FIELD_TIMESTAMP, sortDir)) .skip(filter.getPageNumber() * filter.getPageSize()).limit(filter.getPageSize()); while (cursor.hasNext()) { BasicDBObject obj = (BasicDBObject) cursor.next(); final State state; if (item instanceof NumberItem) { state = new DecimalType(obj.getDouble(FIELD_VALUE)); } else if (item instanceof DimmerItem) { state = new PercentType(obj.getInt(FIELD_VALUE)); } else if (item instanceof SwitchItem) { state = OnOffType.valueOf(obj.getString(FIELD_VALUE)); } else if (item instanceof ContactItem) { state = OpenClosedType.valueOf(obj.getString(FIELD_VALUE)); } else if (item instanceof RollershutterItem) { state = new PercentType(obj.getInt(FIELD_VALUE)); } else if (item instanceof ColorItem) { state = new HSBType(obj.getString(FIELD_VALUE)); } else if (item instanceof DateTimeItem) { Calendar cal = Calendar.getInstance(); cal.setTime(obj.getDate(FIELD_VALUE)); state = new DateTimeType(cal); } else { state = new StringType(obj.getString(FIELD_VALUE)); } items.add(new MongoDBItem(name, state, obj.getDate(FIELD_TIMESTAMP))); } return items; }
From source file:org.ossmeter.platform.mining.msr14.Extractor.java
License:Open Source License
public static void main(String[] args) throws Exception { long start = System.currentTimeMillis(); Mongo msrMongo = new Mongo(new ServerAddress("localhost", 1234)); // GitHub challenge data Mongo bioMongo = new Mongo(new ServerAddress("localhost", 12345));// Extracted data // Create indexes Biodiversity bio = new Biodiversity(bioMongo.getDB("biodiversity")); bio.setClearPongoCacheOnSync(true);//w ww .j ava2 s. co m bioMongo.getDB("biodiversity").getCollection("users").ensureIndex(new BasicDBObject("login", 1)); BasicDBObject index = new BasicDBObject(); index.put("name", 1); index.put("ownerName", 1); bioMongo.getDB("biodiversity").getCollection("projects").ensureIndex(index); index = new BasicDBObject(); index.put("projectName", 1); index.put("projectOwner", 1); bioMongo.getDB("biodiversity").getCollection("projectMemberships").ensureIndex(index); index = new BasicDBObject(); index.put("projectName", 1); index.put("userName", 1); bioMongo.getDB("biodiversity").getCollection("projectMemberships").ensureIndex(index); bioMongo.getDB("biodiversity").getCollection("projectMemberships") .ensureIndex(new BasicDBObject("userName", 1)); DB msrDb = msrMongo.getDB("msr14"); // #1 User extraction System.out.println("Extracting users..."); DBCursor cursor = msrDb.getCollection("users").find(); cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); Iterator<DBObject> it = cursor.iterator(); int count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // User user = new User(); // user.setGhId(obj.getString("id")); // user.setLogin(obj.getString("login")); // user.setLocation(obj.getString("location")); // user.setPublicRepos(obj.getInt("public_repos", 0)); // user.setJoinedDate(obj.getString("created_at")); // user.setFollowerCount(obj.getInt("followers", 0)); // user.setFollowingCount(obj.getInt("following", 0)); // user.setPublicGists(obj.getInt("public_gists", 0)); // // bio.getUsers().add(user); // // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // //// #1.2 Project extraction // System.out.println("Extracting projects..."); // cursor = msrDb.getCollection("repos").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // Project project = new Project(); // project.setName(obj.getString("name")); // project.setGhId(obj.getString("id")); // project.setCreatedAt(obj.getString("created_at")); // project.setSize(obj.getInt("size", 0)); // project.setWatchersCount(obj.getInt("watchers",0)); // project.setWatchersCount2(obj.getInt("watchers_count",0)); // project.setLanguage(obj.getString("language")); // project.setForks(obj.getInt("forks", 0)); // project.setForksCount(obj.getInt("forks_count", 0)); // project.setOpenIssues(obj.getInt("open_issues",0)); // project.setOpenIssuesCount(obj.getInt("open_issues_count",0)); // project.setOpenIssues(obj.getInt("open_issues",0)); // project.setNetworkCount(obj.getInt("network_count", 0)); // // BasicDBObject ownerObj = (BasicDBObject) obj.get("owner"); // User owner = null; // if (ownerObj != null) { // owner = bio.getUsers().findOne(User.LOGIN.eq(ownerObj.getString("login"))); // if (owner !=null) { // project.setOwner(owner); // project.setOwnerName(owner.getLogin()); // } // } // bio.getProjects().add(project); // // if (owner != null) { // This comes here as to reference the project, we need to have added to the project list first // ProjectMembership pm = getProjectMembership(bio, owner, project); // pm.setOwner(true); // } // // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // // System.exit(0); //// #2 Follower/following extraction // System.out.println("Extracting followers..."); // cursor = msrDb.getCollection("followers").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String followerLogin = obj.getString("login"); // String followedLogin = obj.getString("follows"); // // User follower = bio.getUsers().findOne(User.LOGIN.eq(followerLogin)); // User followed = bio.getUsers().findOne(User.LOGIN.eq(followedLogin)); // // if (follower != null && followed != null) { // follower.getFollowing().add(followed); // followed.getFollowers().add(follower); // } else{ //// System.err.println("Follower or followed is null. Follower: " +follower + ". followed: " + followed); // } // if (follower != null) follower.setFollowingCount(follower.getFollowingCount()+1); // if (followed != null) followed.setFollowerCount(followed.getFollowerCount()+1); // // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // // System.exit(0); System.out.println("Clearing ProjectMembership commit data"); for (ProjectMembership pm : bio.getProjectMemberships()) { pm.setCommitCount(0); pm.setCommitTotalChanges(0); pm.setCommitAdditions(0); pm.setCommitDeletions(0); pm.setCommitsAsAuthor(0); pm.setCommitsAsCommitter(0); pm.setCommitTotalFiles(0); pm.setAverageFilesPerCommit(0); pm.getCommitTimes().clear(); } bio.sync(); System.out.println("cleared."); // #3 Commits System.out.println("Extracting commits..."); cursor = msrDb.getCollection("commits").find(); cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); it = cursor.iterator(); count = 0; while (it.hasNext()) { BasicDBObject obj = (BasicDBObject) it.next(); // Author and committer BasicDBObject commitAuthor = (BasicDBObject) obj.get("author"); BasicDBObject commitCommitter = (BasicDBObject) obj.get("committer"); String authorLogin = ""; if (commitAuthor != null) authorLogin = commitAuthor.getString("login"); String committerLogin = ""; if (commitCommitter != null) committerLogin = commitCommitter.getString("login"); // Stats BasicDBObject stats = (BasicDBObject) obj.get("stats"); if (stats == null) stats = new BasicDBObject(); // Create a new one so we can get zeroed values int total = stats.getInt("total", 0); int additions = stats.getInt("additions", 0); int deletions = stats.getInt("deletions", 0); String commitDate = ((BasicDBObject) ((BasicDBObject) obj.get("commit")).get("author")) .getString("date"); BasicDBList files = (BasicDBList) obj.get("files"); String[] url = convertUrlIntoProjectNameAndOwner(obj.getString("url")); ProjectMembership authorPm = null; ProjectMembership committerPm = null; if (authorLogin != null) { authorPm = getProjectMembership(bio, authorLogin, url[1], url[0]); authorPm.setCommitCount(authorPm.getCommitCount() + 1); authorPm.setCommitTotalChanges(authorPm.getCommitTotalChanges() + total); authorPm.setCommitAdditions(authorPm.getCommitAdditions() + additions); authorPm.setCommitDeletions(authorPm.getCommitDeletions() + deletions); authorPm.setCommitsAsAuthor(authorPm.getCommitsAsAuthor() + 1); if (files != null) authorPm.setCommitTotalFiles(authorPm.getCommitTotalChanges() + files.size()); authorPm.setAverageFilesPerCommit(authorPm.getCommitTotalFiles() / authorPm.getCommitCount()); authorPm.getCommitTimes().add(commitDate); } if (authorLogin != null && !authorLogin.equals(committerLogin)) { committerPm = getProjectMembership(bio, committerLogin, url[1], url[0]); committerPm.setCommitCount(committerPm.getCommitCount() + 1); // committerPm.setCommitTotalChanges(committerPm.getCommitTotalChanges()+total); // committerPm.setCommitAdditions(committerPm.getCommitAdditions()+additions); // committerPm.setCommitDeletions(committerPm.getCommitDeletions()+deletions); committerPm.setCommitsAsCommitter(committerPm.getCommitsAsCommitter() + 1); committerPm.setCommitTotalFiles(committerPm.getCommitTotalChanges() + files.size()); committerPm.setAverageFilesPerCommit(committerPm.getCommitTotalFiles() / authorPm.getCommitCount()); if (files != null) committerPm.setCommitTotalFiles(committerPm.getCommitTotalChanges() + files.size()); committerPm .setAverageFilesPerCommit(committerPm.getCommitTotalFiles() / committerPm.getCommitCount()); committerPm.getCommitTimes().add(commitDate); } bio.sync(); count++; if (count % 1000 == 0) { System.out.print(count + ", "); bio.sync(); } } cursor.close(); bio.sync(); System.out.println(); System.exit(0); // if (author != null) { //// if (author.getCommits() ==null) author.setCommits(new Commits()); // author.setCommitCount(author.getCommitCount()+1); // author.setCommitTotalChanges(author.getCommitTotalChanges()+total); // author.setCommitAdditions(author.getCommitAdditions()+additions); // author.setCommitDeletions(author.getCommitDeletions()+deletions); // author.setCommitsAsAuthor(author.getCommitsAsAuthor()+1); // author.getCommitTimes().add(commitDate); // } // if (committer != null) { //// if (committer.getCommits() ==null) committer.setCommits(new Commits()); // committer.setCommitCount(committer.getCommitCount()+1); // committer.setCommitTotalChanges(committer.getCommitTotalChanges()+total); // committer.setCommitAdditions(committer.getCommitAdditions()+additions); // committer.setCommitDeletions(committer.getCommitDeletions()+deletions); // committer.setCommitsAsCommitter(committer.getCommitsAsCommitter()+1); // committer.getCommitTimes().add(commitDate); // } // // ProjectMembership authorPm = null; // ProjectMembership committerPm = null; // //// Only a very small number of commit comments actually reference the repo //// Instead we're going to have to strip the string // String[] url = convertUrlIntoProjectNameAndOwner(obj.getString("url")); // Project project = null; // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(url[1]), Project.OWNERNAME.eq(url[0])).iterator(); // if (repoIt.hasNext()) { // project = repoIt.next(); // if (project != null) { // // project.setCommitCount(project.getCommitCount()+1); // project.setCommitTotalChanges(project.getCommitTotalChanges()+total); // project.setCommitAdditions(project.getCommitAdditions()+additions); // project.setCommitDeletions(project.getCommitDeletions()+deletions); // project.getCommitTimes().add(commitDate); // // if (author != null) { // authorPm = getProjectMembership(bio, author, project); // authorPm.setCommitCount(authorPm.getCommitCount()+1); // authorPm.setCommitTotalChanges(authorPm.getCommitTotalChanges()+total); // authorPm.setCommitAdditions(authorPm.getCommitAdditions()+additions); // authorPm.setCommitDeletions(authorPm.getCommitDeletions()+deletions); // authorPm.setCommitsAsAuthor(authorPm.getCommitsAsAuthor()+1); // // // Avoid duplicating information // if (committer != null && author.getLogin().equals(committer.getLogin())) { // authorPm.setCommitsAsCommitter(authorPm.getCommitsAsCommitter()+1); // } // // authorPm.getCommitTimes().add(commitDate); // } // if (committer != null && author != null && !author.getLogin().equals(committer.getLogin())) { // committerPm = getProjectMembership(bio, committer, project); // committerPm.setCommitCount(committerPm.getCommitCount()+1); // committerPm.setCommitTotalChanges(committerPm.getCommitTotalChanges()+total); // committerPm.setCommitAdditions(committerPm.getCommitAdditions()+additions); // committerPm.setCommitDeletions(committerPm.getCommitDeletions()+deletions); // committerPm.setCommitsAsCommitter(committerPm.getCommitsAsCommitter()+1); // // committerPm.getCommitTimes().add(commitDate); // } // } // } // else { // System.err.println("Didn't find project:" + url[0] + ":"+url[1] + ", prestrip: " + obj.getString("url")); // } // bio.getProjectMemberships().sync(); // bio.sync(); // // // // Files // BasicDBList files = (BasicDBList) obj.get("files"); // if (files != null) { // for (Object f : files) { // BasicDBObject file = (BasicDBObject)f; // // String filename = file.getString("filename"); // if (filename.lastIndexOf(".") != -1) { // If it has an extension, we want that. If not, use the entire filename // filename = filename.substring(filename.lastIndexOf(".")); // filename = filename.toLowerCase(); // Ensure consistency // } // // FIXME: Should strip any /'s if there is no '.' - i.e. just the last one // // if (author != null) addArtefact(author, filename); // if (committer != null) addArtefact(committer, filename); //// if (project != null) addArtefact(project, filename); // } // } // // if (author != null && files !=null) { // author.setCommitTotalFiles(author.getCommitTotalFiles()+files.size()); // author.setAverageFilesPerCommit(author.getCommitTotalFiles()/author.getCommitCount()); // } // if (committer != null && files !=null && (author==null || !committer.getLogin().equals(author.getLogin()))) { // committer.setCommitTotalFiles(committer.getCommitTotalFiles()+files.size()); // committer.setAverageFilesPerCommit(committer.getCommitTotalFiles()/committer.getCommitCount()); // } // if (authorPm !=null && files != null) { // authorPm.setCommitTotalFiles(authorPm.getCommitTotalChanges()+files.size()); // authorPm.setAverageFilesPerCommit(authorPm.getCommitTotalFiles()/authorPm.getCommitCount()); // } // if (committerPm != null && files != null) { // committerPm.setCommitTotalFiles(committerPm.getCommitTotalChanges()+files.size()); // committerPm.setAverageFilesPerCommit(committerPm.getCommitTotalFiles()/committerPm.getCommitCount()); // } // // if (project!=null && files != null) { // project.setCommitTotalFiles(project.getCommitTotalChanges()+files.size()); // project.setAverageFilesPerCommit(project.getCommitTotalFiles()/project.getCommitCount()); // } // bio.getProjectMemberships().sync(); // bio.sync(); // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // cursor.close(); // bio.sync(); // System.out.println(); // // System.exit(0); //// #4 Commit comments // System.out.println("Extracting commit comments..."); // cursor = msrDb.getCollection("commit_comments").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String username = getUserLoginName(bio, "user", "login", obj); // User user = bio.getUsers().findOne(User.LOGIN.eq(username)); // if (user == null) { // System.err.println("Found commit comment with unrecognised user: " + username); // continue; // } // // user.setNumberOfCommitComments(user.getNumberOfCommitComments()+1); // //// if (!user.getDbObject().containsField("commitCommentTimes")) { //// user.getDbObject().put("commitCommentTimes", new BasicDBList()); //// } //// user.getCommitCommentTimes().add(obj.getString("created_at")); // // // Only a very small number of commit comments actually reference the repo // // Instead we're going to have to strip the string // String[] url = convertUrlIntoProjectNameAndOwner(obj.getString("url")); // //// System.out.println("Querying project " + url[1] + " and owner " + url[0]); // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(url[1]), Project.OWNERNAME.eq(url[0])).iterator(); //// if (repoIt.hasNext()) { // Project project = repoIt.next(); // if (project != null) { // project.setNumberOfCommitComments(project.getNumberOfCommitComments()+1); // // if (!project.getDbObject().containsField("commitCommentTimes")) { // project.getDbObject().put("commitCommentTimes", new BasicDBList()); // } // project.getCommitCommentTimes().add(obj.getString("created_at")); // // ProjectMembership pm = getProjectMembership(bio, user, project); // pm.setNumberOfCommitComments(pm.getNumberOfCommitComments()+1); // // if (!pm.getDbObject().containsField("commitCommentTimes")) { // pm.getDbObject().put("commitCommentTimes", new BasicDBList()); // } // pm.getCommitCommentTimes().add(obj.getString("created_at")); // } //// } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // cursor.close(); // bio.sync(); // System.out.println(); // System.exit(0); //// //FIXME: THIS IS CAUSING THE CPU TO HIS 350% AND THEN KILLS THE LAPTOP?!?!?!?!? // #5 Pull requests System.out.println("Extracting pull requests..."); cursor = msrDb.getCollection("pull_requests").find(); cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); it = cursor.iterator(); System.out.println("Clearing previous data"); for (User u : bio.getUsers()) { if (!u.getDbObject().containsField("pullRequestTimes")) { u.getDbObject().put("pullRequestTimes", new BasicDBList()); } u.getPullRequestTimes().clear(); u.setNumberOfPullRequests(0); } bio.sync(); for (Project u : bio.getProjects()) { if (!u.getDbObject().containsField("pullRequestTimes")) { u.getDbObject().put("pullRequestTimes", new BasicDBList()); } u.getPullRequestTimes().clear(); u.setNumberOfPullRequests(0); } bio.sync(); for (ProjectMembership u : bio.getProjectMemberships()) { if (!u.getDbObject().containsField("pullRequestTimes")) { u.getDbObject().put("pullRequestTimes", new BasicDBList()); } u.getPullRequestTimes().clear(); u.setNumberOfPullRequests(0); } bio.sync(); System.out.println("Cleared!"); count = 0; while (it.hasNext()) { BasicDBObject obj = (BasicDBObject) it.next(); String username = getUserLoginName(bio, "user", "login", obj); User user = bio.getUsers().findOne(User.LOGIN.eq(username)); if (user == null) { // System.err.println("Found pull request with unrecognised user:" + username); continue; } if (!user.getDbObject().containsField("pullRequestTimes")) { user.getDbObject().put("pullRequestTimes", new BasicDBList()); } user.getPullRequestTimes().add(obj.getString("created_at")); user.setNumberOfPullRequests(user.getNumberOfPullRequests() + 1); // Project System.out.println(obj.getString("repo") + " " + obj.getString("owner") + obj.getString("_id")); ProjectMembership pm = getProjectMembership(bio, user.getLogin(), obj.getString("repo"), obj.getString("owner")); pm.setNumberOfPullRequests(pm.getNumberOfPullRequests() + 1); if (!pm.getDbObject().containsField("pullRequestTimes")) { pm.getDbObject().put("pullRequestTimes", new BasicDBList()); } pm.getPullRequestTimes().add(obj.getString("created_at")); // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); // if (repoIt.hasNext()) { // FIXME Causes it to run out of heap! // Project project = repoIt.next(); // if (project != null) { // project.setNumberOfPullRequests(project.getNumberOfPullRequests()+1); // // if (!project.getDbObject().containsField("pullRequestTimes")) { // project.getDbObject().put("pullRequestTimes", new BasicDBList()); // } // project.getPullRequestTimes().add(obj.getString("created_at")); // // } // } else { // System.err.println("Didn't find project:" + obj.getString("repo") + ":"+obj.getString("owner")); // } count++; if (count % 1000 == 0) { System.out.print(count + ", "); bio.sync(); System.gc(); } } bio.sync(); System.out.println(); System.exit(0); //// #6 Pull request comments // System.out.println("Extracting pull request comments..."); // cursor = msrDb.getCollection("pull_request_comments").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String username = getUserLoginName(bio, "user", "login", obj); // User user = bio.getUsers().findOne(User.LOGIN.eq(username)); // if (user == null) { //// System.err.println("Found pull request comment with unrecognised user:" + username); // continue; // } // // if (!user.getDbObject().containsField("pullRequestCommentTimes")) { // user.getDbObject().put("pullRequestCommentTimes", new BasicDBList()); // } // user.getPullRequestCommentTimes().add(obj.getString("created_at")); // user.setNumberOfPullRequestComments(user.getNumberOfPullRequestComments()+1); // // // Project // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); //// if (repoIt.hasNext()) { // Project project = repoIt.next(); // if (project != null) { // project.setNumberOfPullRequestComments(project.getNumberOfPullRequestComments()+1); // if (!project.getDbObject().containsField("pullRequestCommentTimes")) { // project.getDbObject().put("pullRequestCommentTimes", new BasicDBList()); // } // project.getPullRequestCommentTimes().add(obj.getString("created_at")); // // ProjectMembership pm = getProjectMembership(bio, user, project); // pm.setNumberOfPullRequestComments(pm.getNumberOfPullRequestComments()+1); // // if (!pm.getDbObject().containsField("pullRequestCommentTimes")) { // pm.getDbObject().put("pullRequestCommentTimes", new BasicDBList()); // } // pm.getPullRequestCommentTimes().add(obj.getString("created_at")); // } //// } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // System.exit(0); //// #7 Issues // System.out.println("Extracting issues..."); // cursor = msrDb.getCollection("issues").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String username = getUserLoginName(bio, "user", "login", obj); // User user = bio.getUsers().findOne(User.LOGIN.eq(username)); // if (user == null) { //// System.err.println("Found issue with unrecognised user:" + username); // continue; // } // // if (!user.getDbObject().containsField("issueTimes")) { // user.getDbObject().put("issueTimes", new BasicDBList()); // } // user.getIssueTimes().add(obj.getString("created_at")); // user.setNumberOfIssues(user.getNumberOfIssues()+1); // // // Project // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); // if (repoIt.hasNext()) { // Project project = repoIt.next(); // if (project != null) { // project.setNumberOfIssues(project.getNumberOfIssues()+1); // // if (!project.getDbObject().containsField("issueTimes")) { // project.getDbObject().put("issueTimes", new BasicDBList()); // } // project.getIssueTimes().add(obj.getString("created_at")); // // ProjectMembership pm = getProjectMembership(bio, user, project); // pm.setNumberOfIssues(pm.getNumberOfIssues()+1); // // if (!pm.getDbObject().containsField("issueTimes")) { // pm.getDbObject().put("issueTimes", new BasicDBList()); // } // pm.getIssueTimes().add(obj.getString("created_at")); // } // } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // System.exit(0); //// #8 Issue comments // System.out.println("Extracting issue comments..."); // cursor = msrDb.getCollection("issue_comments").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String username = getUserLoginName(bio, "user", "login", obj); // User user = bio.getUsers().findOne(User.LOGIN.eq(username)); // if (user == null) { //// System.err.println("Found issue comment with unrecognised user:" + username); // continue; // } // // if (!user.getDbObject().containsField("issueCommentTimes")) { // user.getDbObject().put("issueCommentTimes", new BasicDBList()); // } // user.getIssueCommentTimes().add(obj.getString("created_at")); // user.setNumberOfIssueComments(user.getNumberOfIssueComments()+1); // // // Project // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); // if (repoIt.hasNext()) { // Project project = repoIt.next(); // if (project != null) { // project.setNumberOfIssueComments(project.getNumberOfIssueComments()+1); // // if (!project.getDbObject().containsField("issueCommentTimes")) { // project.getDbObject().put("issueCommentTimes", new BasicDBList()); // } // project.getIssueCommentTimes().add(obj.getString("created_at")); // // ProjectMembership pm = getProjectMembership(bio, user, project); // pm.setNumberOfIssueComments(pm.getNumberOfIssueComments()+1); // // if (!pm.getDbObject().containsField("issueCommentTimes")) { // pm.getDbObject().put("issueCommentTimes", new BasicDBList()); // } // pm.getIssueCommentTimes().add(obj.getString("created_at")); // } // } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // System.exit(0); //// #9 Issue events // System.out.println("Extracting issue events..."); // cursor = msrDb.getCollection("issue_events").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String username = getUserLoginName(bio, "actor", "login", obj); // User user = bio.getUsers().findOne(User.LOGIN.eq(username)); // if (user == null) { //// System.err.println("Found issue event with unrecognised user:" + username); // continue; // } // // String eventKind = obj.getString("event"); // IssueEventKind kind = null; //FIXME // // switch (eventKind) { // case "closed": kind = IssueEventKind.CLOSED; break; // case "assigned": kind = IssueEventKind.ASSIGNED; break; // case "mentioned": kind = IssueEventKind.MENTIONED; break; // case "merged": kind = IssueEventKind.MERGED; break; // case "referenced": kind = IssueEventKind.REFERENCED; break; // case "reopened": kind = IssueEventKind.REOPENED; break; // case "subscribed": kind = IssueEventKind.SUBSCRIBED; break; // case "head_ref_deleted" : kind = IssueEventKind.HEAD_REF_DELETED; break; // case "head_ref_restored" : kind = IssueEventKind.HEAD_REF_RESTORED; break; // case "head_ref_cleaned" : kind = IssueEventKind.HEAD_REF_CLEANED; break; // case "unsubscribed" : kind = IssueEventKind.UNSUBSCRIBED; break; // default: // System.err.println("Unrecognised issue event kind: " + eventKind); // } // if (kind == null) continue; // // boolean eventKindFound = false; // // if (!user.getDbObject().containsField("issueEvents")) { // user.getDbObject().put("issueEvents", new BasicDBList()); // } // // for (IssueEvent ie : user.getIssueEvents()) { // if (ie.getEventKind().equals(kind)) { // ie.setCount(ie.getCount()+1); // eventKindFound = true; // break; // } // } // if (!eventKindFound) { // IssueEvent ie = new IssueEvent(); // ie.setEventKind(kind); // ie.setCount(1); // user.getIssueEvents().add(ie); // } // // // Project // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); // if (repoIt.hasNext()) { // Project project = repoIt.next(); // // if (!project.getDbObject().containsField("issueEvents")) { // project.getDbObject().put("issueEvents", new BasicDBList()); // } // // eventKindFound = false; // for (IssueEvent ie : project.getIssueEvents()) { // if (ie.getEventKind().equals(kind)) { // ie.setCount(ie.getCount()+1); // eventKindFound = true; // break; // } // } // if (!eventKindFound) { // IssueEvent ie = new IssueEvent(); // ie.setEventKind(kind); // ie.setCount(1); // project.getIssueEvents().add(ie); // } // // ProjectMembership pm = getProjectMembership(bio, user, project); // // if (!pm.getDbObject().containsField("issueEvents")) { // pm.getDbObject().put("issueEvents", new BasicDBList()); // } // // eventKindFound = false; // for (IssueEvent ie : pm.getIssueEvents()) { // if (ie.getEventKind().equals(kind)) { // ie.setCount(ie.getCount()+1); // eventKindFound = true; // break; // } // } // if (!eventKindFound) { // IssueEvent ie = new IssueEvent(); // ie.setEventKind(kind); // ie.setCount(1); // pm.getIssueEvents().add(ie); // } // } // // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); // System.exit(0); // //// Watchers // System.out.println("Extracting watchers..."); // cursor = msrDb.getCollection("watchers").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // User user = bio.getUsers().findOne(User.LOGIN.eq(obj.getString("login"))); // if (user == null) continue; // // Iterator<Project> repoIt = bio.getProjects().find(Project.NAME.eq(obj.getString("repo")), Project.OWNERNAME.eq(obj.getString("owner"))).iterator(); // if (repoIt.hasNext()) { // Project project = repoIt.next(); // if (project != null && !project.getWatchers().contains(user)) project.getWatchers().add(user); // if (!user.getWatches().contains(project)) user.getWatches().add(project); // } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // System.out.println(); //// Org members FIXME: INCOMPLETE: Cannot match the org name against ANYTHING.... // System.out.println("Extracting org members..."); // cursor = msrDb.getCollection("org_members").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String login = obj.getString("login"); // String orgName = obj.getString("org"); // // User user = bio.getUsers().findOne(User.LOGIN.eq(login)); // // User org = bio.getUsers().findOne(User.LOGIN.eq(orgName)); // // if (org!=null){ // System.err.println("Found org! " + orgName); // // } // //// Project project = bio.getProjects().findOne(Project.OWNERNAME.eq("orgName")); //// if (project==null) { //// System.err.println("Didn't find project: " + orgName); //// continue; //// } //// ProjectMembership pm = getProjectMembership(bio, user, project); //// pm.setOrgMember(true); // } // bio.sync(); // System.out.println(); // Repo collaborators // System.out.println("Extracting repo collaborators..."); // cursor = msrDb.getCollection("repo_collaborators").find(); // cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT); // it = cursor.iterator(); // // count = 0; // while(it.hasNext()){ // BasicDBObject obj = (BasicDBObject) it.next(); // // String login = obj.getString("login"); // String projectName = obj.getString("repo"); // String ownerName = obj.getString("owner"); // // User user = bio.getUsers().findOne(User.LOGIN.eq(login)); // Iterator<Project> repoIt = bio.getProjects().find(Project.OWNERNAME.eq(ownerName), Project.NAME.eq(projectName)).iterator(); // if (repoIt.hasNext()) { // Project project = repoIt.next(); // // ProjectMembership pm = getProjectMembership(bio, user, project); // pm.setCollaborator(true); // } else { // System.err.println("Couldn't find repo. owner: " + ownerName + ", repo: " + projectName); // } // count++; // if (count % 1000 == 0) { // System.out.print(count + ", "); // bio.sync(); // } // } // bio.sync(); // long end = System.currentTimeMillis(); System.out.println("Finished at " + new Date()); long duration = end - start; System.out.println("Duration: " + duration); }
From source file:org.ossmeter.platform.mining.msr14.Extractor.java
License:Open Source License
/** * Some 'user' field in commit_comments are Strings. Some are objects. Seriously. * @param bio//from w w w . j a v a2s . co m * @param obj * @return */ protected static String getUserLoginName(Biodiversity bio, String userField, String loginField, BasicDBObject obj) { String username = null; if (obj.get(userField) == null) return null; if (obj.get(userField) instanceof String) { username = obj.getString(userField); } else { username = ((BasicDBObject) obj.get(userField)).getString(loginField); } return username; }
From source file:org.seasr.meandre.components.transform.bson.SelectBsonFields.java
License:Open Source License
@Override public void executeCallBack(ComponentContext cc) throws Exception { BasicDBObject bson = (BasicDBObject) cc.getDataComponentFromInput(IN_BSON); for (int i = 0; i < _fields.length; i++) { String f = bson.getString(_fields[i]); if (f == null) { console.warning(String.format("Got null string for field %s (%s)", i, _fields[i])); f = ""; }//from w ww . j a v a 2s.c o m cc.pushDataComponentToOutput(PARAM_OUT_STRING + (i + 1), BasicDataTypesTools.stringToStrings(f)); } }
From source file:org.sipfoundry.sipxconfig.mongo.MongoReplicaSetManager.java
License:Open Source License
public void checkState() { try {/* w w w . ja v a 2s . c om*/ BasicBSONObject ret = MongoUtil.runCommand(m_localDb.getDb(), CHECK_COMMAND); boolean initialized = false; if (ret != null) { BasicDBList members = (BasicDBList) ret.get(MEMBERS); if (members != null) { BasicDBObject primary = (BasicDBObject) members.get(0); if (primary != null) { initialized = true; String host = primary.getString(HOST); String expected = format(m_primaryFqdn + ':' + MongoSettings.SERVER_PORT); if (!expected.equals(host)) { String rename = format(RENAME_PRIMARY_COMMAND, expected); MongoUtil.runCommand(m_localDb.getDb(), rename); } } } } if (!initialized) { initialize(); } } catch (Exception ex) { LOG.error("Failed to check replica set state!"); } }
From source file:org.sipfoundry.sipxconfig.mongo.MongoServer.java
License:Open Source License
public MongoServer(BasicDBObject dbo) { m_id = dbo.getInt("_id"); m_name = dbo.getString("name"); m_type = SERVER;/*from w ww .ja va 2s . c o m*/ if (StringUtils.contains(m_name, String.valueOf(MongoSettings.ARBITER_PORT))) { m_type = ARBITER; } m_configured = true; m_state = dbo.getString("stateStr"); m_health = UP; if (dbo.containsField(HEALTH)) { if (dbo.getInt(HEALTH) == 0) { m_health = DOWN; } } if (dbo.containsField(ERR_MSG)) { m_errMsg = dbo.getString(ERR_MSG); } try { BSONTimestamp optime = (BSONTimestamp) dbo.get("optime"); if (optime.getTime() != 0) { m_optimeDate = new Date((long) optime.getTime() * 1000).toString(); } } catch (NumberFormatException ex) { m_optimeDate = NA; } }