Java tutorial
/* * Open Advancement Question Answering (OAQA) Project Copyright 2016 Carnegie Mellon University * * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except * in compliance with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software distributed under the License * is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express * or implied. See the License for the specific language governing permissions and limitations * under the License. */ package edu.cmu.lti.oaqa.bioasq.triple.retrieval; import edu.cmu.lti.oaqa.baseqa.providers.query.BagOfPhraseQueryStringConstructor; import edu.cmu.lti.oaqa.baseqa.providers.query.QueryStringConstructor; import edu.cmu.lti.oaqa.baseqa.util.UimaContextHelper; import edu.cmu.lti.oaqa.bio.bioasq.services.GoPubMedService; import edu.cmu.lti.oaqa.bioasq.util.BioASQUtil; import edu.cmu.lti.oaqa.type.retrieval.AbstractQuery; import edu.cmu.lti.oaqa.type.retrieval.QueryConcept; import edu.cmu.lti.oaqa.type.retrieval.TripleSearchResult; import edu.cmu.lti.oaqa.util.TypeUtil; import org.apache.commons.configuration.ConfigurationException; import org.apache.commons.configuration.PropertiesConfiguration; import org.apache.commons.lang.WordUtils; import org.apache.uima.UimaContext; import org.apache.uima.analysis_component.JCasAnnotator_ImplBase; import org.apache.uima.analysis_engine.AnalysisEngineProcessException; import org.apache.uima.fit.util.FSCollectionFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.resource.ResourceInitializationException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.IOException; import java.util.*; /** * A {@link JCasAnnotator_ImplBase} that performs search using a query string, transformed from a * {@link AbstractQuery} by a {@link QueryStringConstructor} to retrieve relevant * {@link TripleSearchResult}s from {@link GoPubMedService}. * * @author <a href="mailto:chiz2@andrew.cmu.edu">Chi Zhang</a>, * <a href="mailto:ziy@cs.cmu.edu">Zi Yang</a> created on 11/3/14 */ public class GoPubMedTripleRetrievalExecutor extends JCasAnnotator_ImplBase { private GoPubMedService service; private int pages; private int hits; private QueryStringConstructor bopQueryStringConstructor; private StringBuilder sb; private Set<String> queryWords; private static final Logger LOG = LoggerFactory.getLogger(GoPubMedTripleRetrievalExecutor.class); @Override public void initialize(UimaContext context) throws ResourceInitializationException { super.initialize(context); String conf = UimaContextHelper.getConfigParameterStringValue(context, "conf"); PropertiesConfiguration gopubmedProperties = new PropertiesConfiguration(); try { gopubmedProperties.load(getClass().getResourceAsStream(conf)); } catch (ConfigurationException e) { throw new ResourceInitializationException(e); } service = new GoPubMedService(gopubmedProperties); pages = UimaContextHelper.getConfigParameterIntValue(context, "pages", 1); hits = UimaContextHelper.getConfigParameterIntValue(context, "hits", 100); bopQueryStringConstructor = new BagOfPhraseQueryStringConstructor(); } private void addQueryWord(String s) { if (s == null) return; if (s.length() == 0) return; if (queryWords.contains(s)) return; else queryWords.add(s); if (sb.length() > 0) sb.append(" OR "); sb.append(s + "[obj] OR " + s + "[subj]"); List<String> ls = new LinkedList<String>(); ls.add(s.toUpperCase()); ls.add(s.toLowerCase()); ls.add(WordUtils.capitalize(s)); for (String x : ls) { sb.append(" OR "); sb.append(x); sb.append("[obj] OR "); sb.append(x); sb.append("[subj]"); } } @Override public void process(JCas jcas) throws AnalysisEngineProcessException { sb = new StringBuilder(); queryWords = new HashSet<String>(); AbstractQuery aquery = TypeUtil.getAbstractQueries(jcas).stream().findFirst().get(); StringBuilder question = new StringBuilder(); question.append(TypeUtil.getQuestion(jcas).getText().toLowerCase().replaceAll("\\p{P}", " ")); for (QueryConcept q : FSCollectionFactory.create(aquery.getConcepts(), QueryConcept.class)) { question.append(" "); question.append(bopQueryStringConstructor.formatQueryText(q).toLowerCase().replaceAll("\\p{P}", " ")); question.append(" "); } Set<String> stopWords = new HashSet<String>(Arrays.asList("or", "emerging", "gold", "being", "text", "global", "mainly", "affect", "oldest", "mining", "alignment", "style", "depended", "recommended", "forms", "to", "treatment", "rich", "main", "do", "affected", "diseases", "food", "could", "safe", "possible", "preferred", "effects", "during", "association", "loss", "modifications", "necessary", "cause", "reduces", "list", "identified", "events", "benefit", "common", "found", "where", "because", "be", "undergoes", "reduce", "prediction", "related", "detection", "frequency", "coss", "are", "images", "depression", "concern", "incontinence", "what", "detect", "for", "pattern", "increase", "models", "does", "health", "between", "newly", "conditions", "mode", "available", "model", "we", "targeted", "analysed", "standard", "reported", "selective", "formation", "analyses", "by", "both", "protect", "benefits", "most", "healthy", "involved", "study", "transition", "commonly", "trial", "preferentially", "action", "advantages", "changes", "top", "frequent", "repair", "major", "computational", "useful", "functional", "down", "underexpression", "defects", "determine", "implicated", "array", "tools", "approximately", "use", "basis", "create", "there", "system", "been", "screened", "their", "intermediate", "treat", "was", "function", "disorder", "life", "families", "that", "bladder", "failure", "favorable", "automated", "known", "encoded", "technologies", "promote", "with", "present", "population", "plants", "states", "has", "embedded", "work", "value", "aim", "patients", "can", "of", "flashes", "region", "examples", "and", "associated", "give", "process", "is", "describe", "binding", "it", "an", "sample", "as", "have", "in", "technology", "any", "approved", "high", "functions", "united", "administration", "mechanism", "how", "hot", "role", "take", "which", "test", "gate", "many", "goat", "used", "altered", "normal", "may", "why", "after", "problems", "shown", "hand", "applications", "chance", "important", "mass", "cleared", "response", "structure", "a", "lead", "effective", "expression", "average", "disease", "analysis", "solve", "quantitative", "the", "sequence", "enrichment")); Set<String> sqlWords = new HashSet<String>(Arrays.asList("a", "abort", "abs", "absolute", "access", "action", "ada", "add", "admin", "after", "aggregate", "alias", "all", "allocate", "also", "alter", "always", "analyse", "analyze", "and", "any", "are", "array", "as", "asc", "asensitive", "assertion", "assignment", "asymmetric", "at", "atomic", "attribute", "attributes", "audit", "authorization", "auto_increment", "avg", "avg_row_length", "backup", "backward", "before", "begin", "bernoulli", "between", "bigint", "binary", "bit", "bit_length", "bitvar", "blob", "bool", "boolean", "both", "breadth", "break", "browse", "bulk", "by", "c", "cache", "call", "called", "cardinality", "cascade", "cascaded", "case", "cast", "catalog", "catalog_name", "ceil", "ceiling", "chain", "change", "char", "char_length", "character", "character_length", "character_set_catalog", "character_set_name", "character_set_schema", "characteristics", "characters", "check", "checked", "checkpoint", "checksum", "class", "class_origin", "clob", "close", "cluster", "clustered", "coalesce", "cobol", "collate", "collation", "collation_catalog", "collation_name", "collation_schema", "collect", "column", "column_name", "columns", "command_function", "command_function_code", "comment", "commit", "committed", "completion", "compress", "compute", "condition", "condition_number", "connect", "connection", "connection_name", "constraint", "constraint_catalog", "constraint_name", "constraint_schema", "constraints", "constructor", "contains", "containstable", "continue", "conversion", "convert", "copy", "corr", "corresponding", "count", "covar_pop", "covar_samp", "create", "createdb", "createrole", "createuser", "cross", "csv", "cube", "cume_dist", "current", "current_date", "current_default_transform_group", "current_path", "current_role", "current_time", "current_timestamp", "current_transform_group_for_type", "current_user", "cursor", "cursor_name", "cycle", "data", "database", "databases", "date", "datetime", "datetime_interval_code", "datetime_interval_precision", "day", "day_hour", "day_microsecond", "day_minute", "day_second", "dayofmonth", "dayofweek", "dayofyear", "dbcc", "deallocate", "dec", "decimal", "declare", "default", "defaults", "deferrable", "deferred", "defined", "definer", "degree", "delay_key_write", "delayed", "delete", "delimiter", "delimiters", "dense_rank", "deny", "depth", "deref", "derived", "desc", "describe", "descriptor", "destroy", "destructor", "deterministic", "diagnostics", "dictionary", "disable", "disconnect", "disk", "dispatch", "distinct", "distinctrow", "distributed", "div", "do", "domain", "double", "drop", "dual", "dummy", "dump", "dynamic", "dynamic_function", "dynamic_function_code", "each", "element", "else", "elseif", "enable", "enclosed", "encoding", "encrypted", "end", "end-exec", "enum", "equals", "errlvl", "escape", "escaped", "every", "except", "exception", "exclude", "excluding", "exclusive", "exec", "execute", "existing", "exists", "exit", "exp", "explain", "external", "extract", "false", "fetch", "fields", "file", "fillfactor", "filter", "final", "first", "float", "float4", "float8", "floor", "flush", "following", "for", "force", "foreign", "fortran", "forward", "found", "free", "freetext", "freetexttable", "freeze", "from", "full", "fulltext", "function", "fusion", "g", "general", "generated", "get", "global", "go", "goto", "grant", "granted", "grants", "greatest", "group", "grouping", "handler", "having", "header", "heap", "hierarchy", "high_priority", "hold", "holdlock", "host", "hosts", "hour", "hour_microsecond", "hour_minute", "hour_second", "identified", "identity", "identity_insert", "identitycol", "if", "ignore", "ilike", "immediate", "immutable", "implementation", "implicit", "in", "include", "including", "increment", "index", "indicator", "infile", "infix", "inherit", "inherits", "initial", "initialize", "initially", "inner", "inout", "input", "insensitive", "insert", "insert_id", "instance", "instantiable", "instead", "int", "int1", "int2", "int3", "int4", "int8", "integer", "intersect", "intersection", "interval", "into", "invoker", "is", "isam", "isnull", "isolation", "iterate", "join", "k", "key", "key_member", "key_type", "keys", "kill", "lancompiler", "language", "large", "last", "last_insert_id", "lateral", "leading", "least", "leave", "left", "length", "less", "level", "like", "limit", "lineno", "lines", "listen", "ln", "load", "local", "localtime", "localtimestamp", "location", "locator", "lock", "login", "logs", "long", "longblob", "longtext", "loop", "low_priority", "lower", "m", "map", "match", "matched", "max", "max_rows", "maxextents", "maxvalue", "mediumblob", "mediumint", "mediumtext", "member", "merge", "message_length", "message_octet_length", "message_text", "method", "middleint", "min", "min_rows", "minus", "minute", "minute_microsecond", "minute_second", "minvalue", "mlslabel", "mod", "mode", "modifies", "modify", "module", "month", "monthname", "more", "move", "multiset", "mumps", "myisam", "name", "names", "national", "natural", "nchar", "nclob", "nesting", "new", "next", "no", "no_write_to_binlog", "noaudit", "nocheck", "nocompress", "nocreatedb", "nocreaterole", "nocreateuser", "noinherit", "nologin", "nonclustered", "none", "normalize", "normalized", "nosuperuser", "not", "nothing", "notify", "notnull", "nowait", "null", "nullable", "nullif", "nulls", "number", "numeric", "object", "octet_length", "octets", "of", "off", "offline", "offset", "offsets", "oids", "old", "on", "online", "only", "open", "opendatasource", "openquery", "openrowset", "openxml", "operation", "operator", "optimize", "option", "optionally", "options", "or", "order", "ordering", "ordinality", "others", "out", "outer", "outfile", "output", "over", "overlaps", "overlay", "overriding", "owner", "pack_keys", "pad", "parameter", "parameter_mode", "parameter_name", "parameter_ordinal_position", "parameter_specific_catalog", "parameter_specific_name", "parameter_specific_schema", "parameters", "partial", "partition", "pascal", "password", "path", "pctfree", "percent", "percent_rank", "percentile_cont", "percentile_disc", "placing", "plan", "pli", "position", "postfix", "power", "preceding", "precision", "prefix", "preorder", "prepare", "prepared", "preserve", "primary", "print", "prior", "privileges", "proc", "procedural", "procedure", "process", "processlist", "public", "purge", "quote", "raid0", "raiserror", "range", "rank", "raw", "read", "reads", "readtext", "real", "recheck", "reconfigure", "recursive", "ref", "references", "referencing", "regexp", "regr_avgx", "regr_avgy", "regr_count", "regr_intercept", "regr_r2", "regr_slope", "regr_sxx", "regr_sxy", "regr_syy", "reindex", "relative", "release", "reload", "rename", "repeat", "repeatable", "replace", "replication", "require", "reset", "resignal", "resource", "restart", "restore", "restrict", "result", "return", "returned_cardinality", "returned_length", "returned_octet_length", "returned_sqlstate", "returns", "revoke", "right", "rlike", "role", "rollback", "rollup", "routine", "routine_catalog", "routine_name", "routine_schema", "row", "row_count", "row_number", "rowcount", "rowguidcol", "rowid", "rownum", "rows", "rule", "save", "savepoint", "scale", "schema", "schema_name", "schemas", "scope", "scope_catalog", "scope_name", "scope_schema", "scroll", "search", "second", "second_microsecond", "section", "security", "select", "self", "sensitive", "separator", "sequence", "serializable", "server_name", "session", "session_user", "set", "setof", "sets", "setuser", "share", "show", "shutdown", "signal", "similar", "simple", "size", "smallint", "some", "soname", "source", "space", "spatial", "specific", "specific_name", "specifictype", "sql", "sql_big_result", "sql_big_selects", "sql_big_tables", "sql_calc_found_rows", "sql_log_off", "sql_log_update", "sql_low_priority_updates", "sql_select_limit", "sql_small_result", "sql_warnings", "sqlca", "sqlcode", "sqlerror", "sqlexception", "sqlstate", "sqlwarning", "sqrt", "ssl", "stable", "start", "starting", "state", "statement", "static", "statistics", "status", "stddev_pop", "stddev_samp", "stdin", "stdout", "storage", "straight_join", "strict", "string", "structure", "style", "subclass_origin", "sublist", "submultiset", "substring", "successful", "sum", "superuser", "symmetric", "synonym", "sysdate", "sysid", "system", "system_user", "table", "table_name", "tables", "tablesample", "tablespace", "temp", "template", "temporary", "terminate", "terminated", "text", "textsize", "than", "then", "ties", "time", "timestamp", "timezone_hour", "timezone_minute", "tinyblob", "tinyint", "tinytext", "to", "toast", "top", "top_level_count", "trailing", "tran", "transaction", "transaction_active", "transactions_committed", "transactions_rolled_back", "transform", "transforms", "translate", "translation", "treat", "trigger", "trigger_catalog", "trigger_name", "trigger_schema", "trim", "true", "truncate", "trusted", "tsequal", "type", "uescape", "uid", "unbounded", "uncommitted", "under", "undo", "unencrypted", "union", "unique", "unknown", "unlisten", "unlock", "unnamed", "unnest", "unsigned", "until", "update", "updatetext", "upper", "usage", "use", "user", "user_defined_type_catalog", "user_defined_type_code", "user_defined_type_name", "user_defined_type_schema", "using", "utc_date", "utc_time", "utc_timestamp", "vacuum", "valid", "validate", "validator", "value", "values", "var_pop", "var_samp", "varbinary", "varchar", "varchar2", "varcharacter", "variable", "variables", "varying", "verbose", "view", "volatile", "waitfor", "when", "whenever", "where", "while", "width_bucket", "window", "with", "within", "without", "work", "write", "writetext", "x509", "xor", "year", "year_month", "zerofill", "zone")); for (String word : question.toString().split(" ")) { if (stopWords.contains(word)) continue; if (sqlWords.contains(word)) continue; //skip words like '345' if (word.toUpperCase().equals(word.toLowerCase())) continue; addQueryWord(word); } List<TripleSearchResult> triples; try { triples = BioASQUtil.searchLinkedLifeData(service, jcas, sb.toString(), pages, hits); LOG.info("Retrieved {} triples.", triples.size()); } catch (IOException e) { throw new AnalysisEngineProcessException(e); } triples.forEach(TripleSearchResult::addToIndexes); } }