Mercurial > repos > ryotas > cypher_tools
changeset 0:aa7a5cc0f59b default tip
commit
| author | ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp> |
|---|---|
| date | Tue, 30 Dec 2014 18:27:26 +0900 |
| parents | |
| children | |
| files | db.sqlite3 graph2db.xml neo4j_driver.js neo4j_loader.js neo4j_remove.js sqlite_lib.py sqlite_lib.pyc tab2graph.py tab2graph.xml test_node.dat test_relation.dat viewer.xml |
| diffstat | 12 files changed, 13023 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graph2db.xml Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,19 @@ +<tool id="graph2db" name="Graph-to-DB" version="0.2.1"> + <description>Loader</description> + <command interpreter="node"> + neo4j_loader.js $input_file_n $input_file_r $namespace $host $port 1 > $log_file + </command> + <inputs> + <param name="host" type="text" size="50" value="localhost" label="Neo4j Host"/> + <param name="port" type="text" size="10" value="7474" label="Neo4j Port"/> + <param name="namespace" type="text" size="50" value="http://sem4j.org/" label="Namespace"/> + <param name="input_file_n" type="data" format="txt" label="Input Node File (txt)"/> + <param name="input_file_r" type="data" format="txt" label="Input Relation File (txt)"/> + </inputs> + <outputs> + <data name="log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> + </outputs> + <help> +**What it does** + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neo4j_driver.js Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,76 @@ +/*** + * Excerpted from "Seven Databases in Seven Weeks", + * published by The Pragmatic Bookshelf. + * Copyrights apply to this code. It may not be used to create training material, + * courses, books, articles, and the like. Contact us if you are in doubt. + * We make no guarantees that this code is fit for any purpose. + * Visit http://www.pragmaticprogrammer.com/titles/rwdata for more book information. +***/ +var http = require('http'); + +exports.createClient = function(options) { + + options = options || {}; + + var + running = 0, + backlog = [], + host = options.host || 'localhost', + port = options.port || 7474, + limit = options.limit || 10; + + function dequeue() { + if (backlog.length && running < limit) { + req.apply(null, backlog.shift()); + } + } + + function req(method, path, data, callback) { + running += 1; + return http + .request({ + host: host, + port: port, + path: '/db/data/' + (path.join ? path.join('/') : path), + headers: {'Content-Type':'application/json'}, + method: method + }, function(res){ + var buffer = ''; + res.on('data', function(chunk){ + buffer += chunk; + }); + res.on('end', function(){ + var output; + if (callback && buffer != '') { + try { + output = JSON.parse(buffer); + } catch (err) { + console.error(err); + } + callback(output, res); + } + running -= 1; + dequeue(); + }); + }) + .on('error', function(){ + running -= 1; + backlog.push([method, path, data, callback]); + dequeue(); + }) + .end(data ? JSON.stringify(data) : undefined); + }; + + return { + get: function(path, callback) { + backlog.push(['GET', path, null, callback]); + dequeue(); + }, + post: function(path, data, callback) { + backlog.push(['POST', path, data, callback]); + dequeue(); + } + }; + +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neo4j_loader.js Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,291 @@ + +// REQUIRE +var esc = require('querystring').escape, + neo4j = require('./neo4j_driver.js'), + fs = require('fs'), + readline = require('readline'), + mysql = require('mysql'); + +// ARGUMENTS +var file_nodes = process.argv[2], + file_relations = process.argv[3], + namespace = process.argv[4], + host = process.argv[5], + port = process.argv[6], + debug = Number(process.argv[7]); + +// VARIABLES +var neo4jClient = neo4j.createClient({'host':host, 'port':port}), + uri_base = 'http://' + host + ':' + port + '/db/data/', + start = process.hrtime(); + +// MAIN +getBaseId(function(nid_base, rid_base){ + console.log('BASE NODE ID:', nid_base); + console.log('BASE RELATIONSHIP ID:', rid_base); + // ADD EMPTY NODES FIRST, THEN ADD PROPERTIES TO THE NODES WITH APPROPRIATE ID. + // OTHERWISE, CANNOT GET CORRECT ID BECAUSE ADD NODE REQUESTS FINISHES IN NO ORDER. + addNodes(file_nodes, nid_base, function(nnum){ + if(debug) elapsed_time('elapsed'); + addNodeProperties(file_nodes, nid_base, function(nnum2){ + if(debug) elapsed_time('elapsed'); + addRelations(file_relations, nid_base, function(rnum){ + if(debug) elapsed_time("elapsed"); + saveMetadata(file_nodes, file_relations, nid_base, rid_base, nnum, rnum); + + }); + }); + }); +}); + +// MYSQL CONNECTION +function connect(callback){ + var conn = mysql.createConnection({ + 'host': host, + 'database':'sem4j', + 'user':'sem4j', + 'password':'sem4j' + }); + callback(conn); +} +function saveMetadata(file_nodes, file_relations, nid_base, rid_base, nnum, rnum){ + connect(function(conn){ + //console.log(conn); + conn.query( + "INSERT INTO load_info VALUES(null,?,?,?,?,?,?,?);", + [getTime(), file_nodes, file_relations, nid_base, rid_base, nnum, rnum], + function (err, results) { + if (err) { + console.log(err); + } + console.log('--- results ---'); + console.log(results); + conn.end(function(){ + console.log('connection end'); + }) + }); + }); +} +function getTime() { + var str = ""; + + var currentTime = new Date() + var hours = currentTime.getHours() + var minutes = currentTime.getMinutes() + var seconds = currentTime.getSeconds() + + if (minutes < 10) { + minutes = "0" + minutes + } + if (seconds < 10) { + seconds = "0" + seconds + } + str += hours + ":" + minutes + ":" + seconds + " "; + return str; +} + +function elapsed_time(note){ +//var elapsed_time = function(note){ + var precision = 3; // 3 decimal places + var elapsed = process.hrtime(start)[1] / 1000000; // divide by a million to get nano to milli + console.log(process.hrtime(start)[0] + " s, " + elapsed.toFixed(precision) + " ms - " + note); // print message + time + start = process.hrtime(); // reset the timer +} +function getBaseId(callback){ + // CREATE TEST NODE + neo4jClient.post('node', '', function(obj){ + // NODE ID IS NOT REUSED, SO THIS IS THE BASE ID + var nid_base = Number(obj.self.split('/')[6]); + // CREATE TEST RELATIONSHIP + var data = { 'to' : uri_base + 'node/' + nid_base, 'type':'test', 'data':{} }; + neo4jClient.post('node/' + nid_base + '/relationships/', data, function(obj) { + var rid_base = Number(obj.self.split('/')[6]); + // DELETE TEST RELATIONSHIP FIRST + // USE BATCH BECAUSE DELETE METHOD IS NOT DEFINED IN THE DRIVER + var data = [{'method':'DELETE', 'to':'relationship/' + rid_base, 'body':'', 'id':0}]; + neo4jClient.post('batch/', data, function(){ + // DELETE TEST NODE + var data = [{'method':'DELETE', 'to':'node/' + nid_base, 'body':'', 'id':0}]; + neo4jClient.post('batch/', data, function(){ + callback(nid_base, rid_base); + }) + }); + }); + }); +} +function addNodes(file, nid_base, callback){ + var rs = fs.ReadStream(file); + var rl = readline.createInterface({'input': rs, 'output': {}}); + var cnt_added = 0; + var cnt_line = 0; + var num_line = 0; + rl.on('line', function(line){ + cnt_line += 1; + line = line.split("\t"); + addNode(function(){ + cnt_added += 1; + if(cnt_added % 100 == 0){ + if(debug) console.log('ADDING EMPTY NODES STATUS:', cnt_added); + } + if(cnt_added == num_line){ + console.log('ADDING EMPTY NODES FINISHED:', cnt_added); + callback(num_line); + } + }); + }).on('pause', function(){ + num_line = cnt_line; + console.log('ADDING EMPTY NODES START:', num_line); + }); + rl.resume(); +} +function addNode(callback){ + neo4jClient.post('node', '', function(obj){ + callback(); + }); +}; +function addNodeProperties(file, nid_base, callback){ + var rs = fs.ReadStream(file); + var rl = readline.createInterface({'input': rs, 'output': {}}); + var cnt_added = 0; + var cnt_line = 0; + var num_line = 0; + rl.on('line', function(line){ + cnt_line += 1; + line = line.split("\t"); + addNodeProperty(Number(line[0]) + nid_base, line[1], line[2], line[3], namespace, file, function(){ + cnt_added += 1; + if(cnt_added % 100 == 0){ + if(debug) console.log('ADDING NODE PROPERTIES STATUS:', cnt_added); + } + if(cnt_added == num_line){ + console.log('ADDING NODE PROPERTIES FINISHED:', cnt_added); + callback(num_line); + } + }); + }).on('pause', function(){ + num_line = cnt_line; + console.log('ADDING NODE PROPERTIES START:', num_line); + }); + rl.resume(); +} +function addNodeProperty(node_id, type, name, properties, namespace, filename, callback){ + + var body = JSON.parse(properties); + body['name'] = name; + body['type'] = type; + body['rowid'] = node_id; + body['namespace'] = namespace; + body['filename'] = filename; + var uri_node = uri_base + 'node/' + node_id; + + // USE BATCH BECAUSE PUT METHOD IS NOT DEFINED IN THE DRIVER + var data = [ + {'method':'PUT', 'to':'node/' + node_id + '/properties', 'body':body, 'id':0}, + {'method':'POST', 'to':'index/node/' + esc(namespace), 'body':{uri:uri_node, key:'name', value:name}, 'id':1}]; + //{'method':'POST', 'to':'index/node/' + esc(namespace), 'body':{uri:uri_node, key:'namespace', value:namespace}, 'id':2}, + //{'method':'POST', 'to':'index/node/' + esc(namespace), 'body':{uri:uri_node, key:'filename', value:esc(filename)}, 'id':3}]; + + neo4jClient.post('batch/', data, function(obj){ + //console.log('DEBUG: Added:', obj, node_id, name); + callback(); + }); + + /* + // USE BATCH BECAUSE PUT METHOD IS NOT DEFINED IN THE DRIVER + data = [{'method':'PUT', 'to':'node/' + node_id + '/properties', 'body':body, 'id':0}]; + neo4jClient.post('batch/', data, function(){ + uri_node = uri_base + 'node/' + node_id; + var data = [{'method':'POST', 'to':'index/node/' + esc(index), 'body':{uri:uri_node, key:'name', value:name}, 'id':0}, + {'method':'POST', 'to':'index/node/' + esc(index), 'body':{uri:uri_node, key:'namespace', value:namespace}, 'id':1}, + {'method':'POST', 'to':'index/node/' + esc(index), 'body':{uri:uri_node, key:'filename', value:esc(filename)}, 'id':2}]; + neo4jClient.post('batch/', data, function(obj){ + console.log('DEBUG: Added:', obj, node_id, name); + callback(); + }); + }); + */ +}; +function addRelations(file, nid_base, callback){ + var rs = fs.ReadStream(file); + var rl = readline.createInterface({'input': rs, 'output': {}}); + var cnt_added = 0, cnt_line = 0, num_line = 0; + rl.on('line', function(line){ + cnt_line += 1; + line = line.split("\t"); + addRelation(Number(line[0]) + nid_base, Number(line[1]) + nid_base, line[2], line[3], 'sem4j.org', file, function(){ + cnt_added += 1; + if(cnt_added % 100 == 0){ + if(debug) console.log('ADDING RELATIONS STATUS:', cnt_added); + } + if(cnt_added == num_line){ + console.log('ADDING RELATIONS FINISHED:', cnt_added); + callback(cnt_added); + } + }); + }).on('pause', function(){ + num_line = cnt_line; + console.log('ADDING RELATIONS START:', num_line); + }); + rl.resume(); +} +function addRelation(source, target, type, properties, namespace, filename, callback){ + var index = 'users'; + var body = JSON.parse(properties); + var relation = { 'to' : uri_base + 'node/' + target, 'type': type, 'data' : body }; + neo4jClient.post('node/' + source + '/relationships/', relation, function() { + callback(); + }); + /* + var data = [ + {'method':'POST', 'to':'node/' + source + '/relationships/', 'body':relation, 'id':0}, + {'method':'POST', 'to':'index/relationship/' + esc(index), 'body':{'uri':'{0}', key:'namespace', value:namespace}, 'id':1}, + {'method':'POST', 'to':'index/relationship/' + esc(index), 'body':{'uri':'{0}', key:'filename', value:esc(filename)}, 'id':2}]; + neo4jClient.post('batch/', data, function(obj){ + //console.log(obj); + callback(); + }); + */ +}; + +/* + +function getNodeIDBase(callback){ + var data = { + "query":"start n = node(*) return max(ID(n))", + "params":{} + }; + neo4jClient.post('cypher', data, function(obj){ + if(obj.data[0][0]){ + var nid_base = obj.data[0][0]; + }else{ + var nid_base = 0; + } + callback(nid_base); + }); +} + +function addNodeOld(node_id, type, name, properties, callback){ + + index = 'idx_name'; + + //name = 'Neo'; + //type = 'person'; + var input = JSON.parse(properties); + //console.log(input); + + //input = {'name':name, 'type':type, 'node_id':node_id}; + input['name'] = name; + input['type'] = type; + input['node_id'] = node_id; + console.log(input); + + neo4jClient.post('node', input, function(obj){ + var data = { uri:obj.self, key:'name', value:name }; + neo4jClient.post(['index/node', esc(index)], data, function(){ + console.log('Added:', obj.self, node_id, name); + callback(); + }); + }); +}; + +*/ \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neo4j_remove.js Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,81 @@ +// $ node neo4j_remove.js a a localhost 7474 1 + +var + esc = require('querystring').escape, + neo4j = require('./neo4j_driver.js'); + +var + file_nodes = process.argv[2], + file_relations = process.argv[3], + host = process.argv[4], + port = process.argv[5] + debug = Number(process.argv[6]), + neo4jClient = neo4j.createClient({'host':host, 'port':port}), + uri_base = 'http://' + host + ':' + port + '/db/data/'; + +var start = process.hrtime(); + +var elapsed_time = function(note){ + var precision = 3; // 3 decimal places + var elapsed = process.hrtime(start)[1] / 1000000; // divide by a million to get nano to milli + console.log(process.hrtime(start)[0] + " s, " + elapsed.toFixed(precision) + " ms - " + note); // print message + time + start = process.hrtime(); // reset the timer +} + +deleteRelationships(0, 11694, function(){ + deleteNodes(1, 545, function(){}); +}); + + +function deleteNodes(base, num, callback){ + var cnt = 0; + for(var i = base + 1; i <= base + num; i++){ + deleteNode(i, function(){ + cnt += 1; + if(cnt % 100 == 0){ + if(debug) console.log('DELETING NODES STATUS:', cnt); + } + if(cnt == num){ + console.log('DELETING NODES FINISHED:', cnt); + callback(); + } + }); + } +} +function deleteNode(id, callback){ + // USE BATCH BECAUSE DELETE METHOD IS NOT DEFINED IN THE DRIVER + data = [{'method':'DELETE', 'to':'node/' + id, 'body':'', 'id':0}]; + neo4jClient.post('batch/', data, function(obj){ + console.log(obj); + callback(); + }); +} +function deleteRelationships(base, num, callback){ + var cnt = 0; + for(var i = base + 1; i <= base + num; i++){ + deleteRelationship(i, function(){ + cnt += 1; + if(cnt % 100 == 0){ + if(debug) console.log('DELETING RELATIONSHIPS STATUS:', cnt); + } + if(cnt == num){ + console.log('DELETING RELATIONSHIPS FINISHED:', cnt); + callback(); + } + }); + } +} +function deleteRelationship(id, callback){ + // USE BATCH BECAUSE DELETE METHOD IS NOT DEFINED IN THE DRIVER + data = [{'method':'DELETE', 'to':'relationship/' + id, 'body':'', 'id':0}]; + neo4jClient.post('batch/', data, function(obj){ + //console.log(obj); + callback(); + }); +} + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sqlite_lib.py Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,140 @@ +# -*- coding:utf-8 -*- + +""" +sqlite_lib +""" + +__author__ = 'Sem4j' +__version__ = '0.0.2' +__date__ = '13 Nov 2013' + +import csv, sqlite3, time + +def connect(): + conn = sqlite3.connect(':memory:') + conn.row_factory = sqlite3.Row + conn.text_factory = lambda x: unicode(x, "utf-8", "ignore") + return conn + +def load(conn, table_name, input_file, input_header, str_index): + + cur = conn.cursor() + + with open(input_file,'rb') as infile: + dr = csv.reader(infile, delimiter='\t') + to_db = [] + row_count = 0 + for row in dr: + row_count += 1 + values =[] + col_count = 0 + for col in row: + col_count += 1 + values.append(col) + if input_header == '1' and row_count == 1: + header = values + print('Header:') + else: + to_db.append(values) + + # PREPARE DDL&DML + str_table1 = table_name + '(' + str_table2 = table_name + '(' + str_value = 'VALUES (' + for j in range(col_count): + if input_header == '1': + print(' ' + str(j + 1) + ' ' + header[j]); + col_name = header[j] + else: + col_name = 'c' + str(j + 1) + str_table1 += col_name + ' NUMERIC' + str_table2 += col_name + ' ' + str_value = str_value + '?' + if j != col_count - 1: + str_table1 += ',' + str_table2 += ',' + str_value = str_value + ',' + str_table1 += ')' + str_table2 += ')' + str_value += ')' + print('') + + # CREATE TABLE + str_create = 'CREATE TABLE ' + str_table1 + ';' + print(str_create) + time_start = time.time() + cur.execute(str_create) + print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + + # LOAD DATA + str_insert = 'INSERT INTO ' + str_table2 + ' ' + str_value + ';' + print(str_insert) + time_start = time.time() + cur.executemany(str_insert, to_db) + conn.commit() + print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + + # CREATE INDEX + array_idx = str_index.split(',') + for col_idx in array_idx: + if col_idx != '': + time_start = time.time() + if input_header == '1': + sql_index = 'CREATE INDEX idx_' + table_name +'_c' + col_idx + ' on ' + table_name + '(' + header[int(col_idx) - 1] + ');' + else: + sql_index = 'CREATE INDEX idx_' + table_name +'_c' + col_idx + ' on ' + table_name + '(c' + col_idx + ');' + cur.execute(sql_index) + print(sql_index) + print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + + cur.close() + +def execute(conn, str_select, output_file, output_header, explain_plan): + + cur = conn.cursor() + + # SELECT + time_start = time.time() + print(str_select) + cur.execute(str_select) + print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + + # OUTPUT + out = open(output_file, 'w') + + # HEADER + if output_header == '1': + col_count = 0 + for col in cur.description: + col_count += 1 + if col_count != len(cur.description): + out.write(str(col[0]) + '\t') + else: + out.write(str(col[0]) + '\n') + + # CONTENT + for row in cur: + col_count = 0 + for col in row: + col_count += 1 + if col_count != len(row): + out.write(str(col) + '\t') + else: + out.write(str(col) + '\n') + + out.close() + + # EXPLAIN PLAN + if explain_plan == '1': + #conn.executescript('.explain on') + cur.execute('explain query plan ' + str_select) + for row in cur: + col_count = 0 + for col in row: + col_count += 1 + if col_count != len(row): + print(str(col) + '\t') + else: + print(str(col) + '\n') + + cur.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tab2graph.py Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,104 @@ +# USAGE: +# python tab2graph.py test/tab2graph_input.dat 0 output_n.dat output_r.dat \ +# '[{"column":"c1","name":"person","properties":[{"column":"c2","name":"sex"},{"column":"c3","name":"age"}]}, {"column":"c4","name":"dept","properties":[{"column":"c5","name":"tel"}]}]' \ +# '[{"source":"c1","target":"c4","name":"belongs_to","properties":[{"column":"c7","name":"year"}]}]' + +import sys, time, json, sqlite_lib + +argvs = sys.argv + +input_file = argvs[1] +input_header = argvs[2] +output_file_n = argvs[3] +output_file_r = argvs[4] +nodes_json = argvs[5] +relations_json = argvs[6] + +nodes = json.loads(nodes_json) +relations = json.loads(relations_json) + +print(nodes_json) +print(nodes) +print(relations_json) +print(relations) + +conn = sqlite_lib.connect() +sqlite_lib.load(conn, 'input_table', input_file, input_header, '') +cur = conn.cursor() + +# CREATE NODE TABLE +str_create_n = 'CREATE TABLE node_table (id, type);' +print(str_create_n) +time_start = time.time() +cur.execute(str_create_n) +print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + +# LOAD DATA (NODE_TABLE) +str_insert_n = "INSERT INTO node_table" +for n in nodes: + str_insert_n += " SELECT DISTINCT " + n['column'] + ", '" + n['name'] + "' FROM input_table" + if n != nodes[-1]: + str_insert_n += " UNION" + else: + str_insert_n += ";" +print(str_insert_n) +time_start = time.time() +cur.execute(str_insert_n) +conn.commit() +print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + +# CREATE INDEX (NODE_TABLE) +str_index_n = 'CREATE INDEX idx_node ON node_table(id);' +print(str_index_n) +time_start = time.time() +cur.execute(str_index_n) +print('Elapsed Time: ' + str(time.time() - time_start) + '\n') + +# SELECT (NODE) +sql = "" +for n in nodes: + properties = n['properties'] + if len(properties) == 0: + sql_properties = ", '{}'" + else: + sql_properties = ", '{'||" + for p in properties: + sql_properties += "'\"" + p['name'] + "\":\"'||i." + p['column'] + "||'\"'" + if p != properties[-1]: + sql_properties += "||','||" + else: + sql_properties += "||'}'" + sql += "SELECT DISTINCT n.rowid, n.type, n.id" + sql_properties + "\n" + sql += "FROM input_table i, node_table n\n" + sql += "WHERE n.id = i." + n['column'] + " AND type = '" + n['name'] + "'\n" + if n != nodes[-1]: + sql += " UNION ALL\n" + else: + sql += ";" +sqlite_lib.execute(conn, sql, output_file_n, '0', '0') + +# SELECT (RELATION) +sql = "" +for r in relations: + properties = r['properties'] + if len(properties) == 0: + sql_properties = ", '{}'" + else: + sql_properties = ", '{'||" + for p in properties: + sql_properties += "'\"" + p['name'] + "\":\"'||i." + p['column'] + "||'\"'" + if p != properties[-1]: + sql_properties += "||','||" + else: + sql_properties += "||'}'" + sql += "SELECT DISTINCT n1.rowid, n2.rowid, '" + r['name'] + "'" + sql_properties + "\n" + sql += "FROM input_table i, node_table n1, node_table n2\n" + sql += "WHERE n1.id = i." + r['source'] + " AND n2.id = i." + r['target'] + "\n" + if r != relations[-1]: + sql += " UNION ALL\n" + else: + sql += ";" +sqlite_lib.execute(conn, sql, output_file_r, '0', '0') + +cur.close(); +conn.close();
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tab2graph.xml Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,37 @@ +<tool id="tab2graph" name="Tab-to-Graph" version="0.2"> + <description>Converter 2</description> + <command interpreter="python"> + tab2graph.py $input_file $h $output_file_n $output_file_r '$def_n' '$def_r' + </command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Input File (tabular)"/> + <param name="h" label="Check to neglect the first row of the input." type="boolean" truevalue="1" falsevalue="0" checked="False"/> + <param name="def_n" type="text" area="true" size="10x70" label="Definition for Nodes"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param name="def_r" type="text" area="true" size="10x70" label="Definition for Relations"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="output_file_n" format="tabular" label="${tool.name} on ${on_string} (node)"/> + <data name="output_file_r" format="tabular" label="${tool.name} on ${on_string} (relation)"/> + </outputs> + <help> +**What it does** + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_node.dat Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,545 @@ +1 cell_line 697 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +2 cell_line 5637 {"cancer_type":"URINARY_TRACT"} +3 cell_line 1321N1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +5 cell_line 22RV1 {"cancer_type":"PROSTATE"} +6 cell_line 42MGBA {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +7 cell_line 639V {"cancer_type":"URINARY_TRACT"} +8 cell_line 769P {"cancer_type":"KIDNEY"} +9 cell_line 786O {"cancer_type":"KIDNEY"} +10 cell_line 8305C {"cancer_type":"THYROID"} +11 cell_line 8505C {"cancer_type":"THYROID"} +12 cell_line 8MGBA {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +13 cell_line A172 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +14 cell_line A204 {"cancer_type":"SOFT_TISSUE"} +15 cell_line A2058 {"cancer_type":"SKIN"} +16 cell_line A253 {"cancer_type":"SALIVARY_GLAND"} +17 cell_line A2780 {"cancer_type":"OVARY"} +18 cell_line A375 {"cancer_type":"SKIN"} +19 cell_line A549 {"cancer_type":"LUNG"} +20 cell_line A673 {"cancer_type":"BONE"} +22 cell_line ACHN {"cancer_type":"KIDNEY"} +25 cell_line ALLSIL {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +26 cell_line AMO1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +27 cell_line AN3CA {"cancer_type":"ENDOMETRIUM"} +28 cell_line ASPC1 {"cancer_type":"PANCREAS"} +29 cell_line AU565 {"cancer_type":"BREAST"} +30 cell_line AZ521 {"cancer_type":"STOMACH"} +33 cell_line BCPAP {"cancer_type":"THYROID"} +34 cell_line BDCM {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +35 cell_line BFTC909 {"cancer_type":"KIDNEY"} +36 cell_line BGC823 {"cancer_type":"STOMACH"} +37 cell_line BL41 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +38 cell_line BL70 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +39 cell_line BT20 {"cancer_type":"BREAST"} +40 cell_line BT474 {"cancer_type":"BREAST"} +41 cell_line BT549 {"cancer_type":"BREAST"} +42 cell_line BXPC3 {"cancer_type":"PANCREAS"} +43 cell_line C2BBE1 {"cancer_type":"LARGE_INTESTINE"} +44 cell_line C32 {"cancer_type":"SKIN"} +45 cell_line C3A {"cancer_type":"LIVER"} +46 cell_line CAKI2 {"cancer_type":"KIDNEY"} +47 cell_line CAL12T {"cancer_type":"LUNG"} +48 cell_line CAL27 {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +49 cell_line CAL78 {"cancer_type":"BONE"} +50 cell_line CAL851 {"cancer_type":"BREAST"} +51 cell_line CALU1 {"cancer_type":"LUNG"} +52 cell_line CALU3 {"cancer_type":"LUNG"} +53 cell_line CALU6 {"cancer_type":"LUNG"} +54 cell_line CAMA1 {"cancer_type":"BREAST"} +55 cell_line CAPAN2 {"cancer_type":"PANCREAS"} +56 cell_line CAS1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +57 cell_line CCK81 {"cancer_type":"LARGE_INTESTINE"} +59 cell_line CHL1 {"cancer_type":"SKIN"} +60 cell_line CHP212 {"cancer_type":"AUTONOMIC_GANGLIA"} +61 cell_line CI1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +62 cell_line CMK86 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +63 cell_line COLO201 {"cancer_type":"LARGE_INTESTINE"} +64 cell_line COLO205 {"cancer_type":"LARGE_INTESTINE"} +65 cell_line COLO320 {"cancer_type":"LARGE_INTESTINE"} +66 cell_line COLO677 {"cancer_type":"LUNG"} +67 cell_line COLO678 {"cancer_type":"LARGE_INTESTINE"} +68 cell_line COLO679 {"cancer_type":"SKIN"} +69 cell_line COLO699 {"cancer_type":"LUNG"} +70 cell_line COLO741 {"cancer_type":"SKIN"} +71 cell_line CORL105 {"cancer_type":"LUNG"} +72 cell_line CORL23 {"cancer_type":"LUNG"} +73 cell_line COV318 {"cancer_type":"OVARY"} +74 cell_line COV504 {"cancer_type":"OVARY"} +75 cell_line DAOY {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +76 cell_line DBTRG05MG {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +77 cell_line DEL {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +78 cell_line DETROIT562 {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +79 cell_line DKMG {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +80 cell_line DMS114 {"cancer_type":"LUNG"} +81 cell_line DOHH2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +82 cell_line DOV13 {"cancer_type":"OVARY"} +83 cell_line DU145 {"cancer_type":"PROSTATE"} +84 cell_line DV90 {"cancer_type":"LUNG"} +85 cell_line EB1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +86 cell_line EB2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +87 cell_line EBC1 {"cancer_type":"LUNG"} +88 cell_line EFE184 {"cancer_type":"ENDOMETRIUM"} +89 cell_line EFM19 {"cancer_type":"BREAST"} +90 cell_line EFO21 {"cancer_type":"OVARY"} +91 cell_line EFO27 {"cancer_type":"OVARY"} +93 cell_line EM2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +94 cell_line EN {"cancer_type":"ENDOMETRIUM"} +95 cell_line ES2 {"cancer_type":"OVARY"} +96 cell_line ESS1 {"cancer_type":"ENDOMETRIUM"} +98 cell_line F36P {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +99 cell_line FADU {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +101 cell_line FU97 {"cancer_type":"STOMACH"} +102 cell_line FUOV1 {"cancer_type":"OVARY"} +103 cell_line G361 {"cancer_type":"SKIN"} +104 cell_line G401 {"cancer_type":"SOFT_TISSUE"} +105 cell_line G402 {"cancer_type":"SOFT_TISSUE"} +106 cell_line GAMG {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +107 cell_line GB1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +108 cell_line GCIY {"cancer_type":"STOMACH"} +109 cell_line GCT {"cancer_type":"SOFT_TISSUE"} +110 cell_line GI1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +111 cell_line GLC82 {"cancer_type":"LUNG"} +112 cell_line GMS10 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +113 cell_line GRANTA519 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +115 cell_line H4 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +116 cell_line HARA {"cancer_type":"LUNG"} +117 cell_line HCC1187 {"cancer_type":"BREAST"} +118 cell_line HCC1395 {"cancer_type":"BREAST"} +119 cell_line HCC15 {"cancer_type":"LUNG"} +120 cell_line HCC1569 {"cancer_type":"BREAST"} +121 cell_line HCC1806 {"cancer_type":"BREAST"} +122 cell_line HCC1954 {"cancer_type":"BREAST"} +123 cell_line HCC2935 {"cancer_type":"LUNG"} +124 cell_line HCC4006 {"cancer_type":"LUNG"} +125 cell_line HCC44 {"cancer_type":"LUNG"} +126 cell_line HCC56 {"cancer_type":"LARGE_INTESTINE"} +127 cell_line HCC70 {"cancer_type":"BREAST"} +128 cell_line HCC78 {"cancer_type":"LUNG"} +129 cell_line HCC827 {"cancer_type":"LUNG"} +130 cell_line HCT116 {"cancer_type":"LARGE_INTESTINE"} +131 cell_line HCT15 {"cancer_type":"LARGE_INTESTINE"} +133 cell_line HDMYZ {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +134 cell_line HDQP1 {"cancer_type":"BREAST"} +135 cell_line HEC151 {"cancer_type":"ENDOMETRIUM"} +136 cell_line HEC1A {"cancer_type":"ENDOMETRIUM"} +137 cell_line HEC1B {"cancer_type":"ENDOMETRIUM"} +138 cell_line HEC251 {"cancer_type":"ENDOMETRIUM"} +139 cell_line HEC265 {"cancer_type":"ENDOMETRIUM"} +140 cell_line HEC59 {"cancer_type":"ENDOMETRIUM"} +141 cell_line HEC6 {"cancer_type":"ENDOMETRIUM"} +142 cell_line HEL9217 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +143 cell_line HEP3B217 {"cancer_type":"LIVER"} +144 cell_line HEPG2 {"cancer_type":"LIVER"} +145 cell_line HEYA8 {"cancer_type":"OVARY"} +146 cell_line HGC27 {"cancer_type":"STOMACH"} +147 cell_line HH {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +148 cell_line HLE {"cancer_type":"LIVER"} +149 cell_line HLF {"cancer_type":"LIVER"} +150 cell_line HMC18 {"cancer_type":"BREAST"} +151 cell_line HMCB {"cancer_type":"SKIN"} +152 cell_line HOS {"cancer_type":"BONE"} +153 cell_line HPAC {"cancer_type":"PANCREAS"} +154 cell_line HPAFII {"cancer_type":"PANCREAS"} +155 cell_line HS229T {"cancer_type":"LUNG"} +156 cell_line HS294T {"cancer_type":"SKIN"} +157 cell_line HS578T {"cancer_type":"BREAST"} +158 cell_line HS683 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +159 cell_line HS695T {"cancer_type":"SKIN"} +160 cell_line HS729 {"cancer_type":"SOFT_TISSUE"} +161 cell_line HS739T {"cancer_type":"BREAST"} +162 cell_line HS746T {"cancer_type":"STOMACH"} +163 cell_line HS766T {"cancer_type":"PANCREAS"} +164 cell_line HS840T {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +165 cell_line HS852T {"cancer_type":"SKIN"} +166 cell_line HS895T {"cancer_type":"SKIN"} +167 cell_line HS936T {"cancer_type":"SKIN"} +168 cell_line HS939T {"cancer_type":"SKIN"} +169 cell_line HS944T {"cancer_type":"SKIN"} +170 cell_line HSC2 {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +172 cell_line HT {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +173 cell_line HT1080 {"cancer_type":"SOFT_TISSUE"} +174 cell_line HT1197 {"cancer_type":"URINARY_TRACT"} +175 cell_line HT1376 {"cancer_type":"URINARY_TRACT"} +176 cell_line HT144 {"cancer_type":"SKIN"} +177 cell_line HT29 {"cancer_type":"LARGE_INTESTINE"} +178 cell_line HUCCT1 {"cancer_type":"BILIARY_TRACT"} +179 cell_line HUH1 {"cancer_type":"LIVER"} +180 cell_line HUPT3 {"cancer_type":"PANCREAS"} +181 cell_line HUPT4 {"cancer_type":"PANCREAS"} +182 cell_line HUT78 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +183 cell_line IALM {"cancer_type":"LUNG"} +185 cell_line IGR37 {"cancer_type":"SKIN"} +186 cell_line IGR39 {"cancer_type":"SKIN"} +187 cell_line IGROV1 {"cancer_type":"OVARY"} +188 cell_line IM95 {"cancer_type":"STOMACH"} +189 cell_line IMR32 {"cancer_type":"AUTONOMIC_GANGLIA"} +190 cell_line IPC298 {"cancer_type":"SKIN"} +191 cell_line ISHIKAWAHERAKLIO02ER {"cancer_type":"ENDOMETRIUM"} +192 cell_line ISTMES1 {"cancer_type":"PLEURA"} +193 cell_line ISTMES2 {"cancer_type":"PLEURA"} +195 cell_line J82 {"cancer_type":"URINARY_TRACT"} +196 cell_line JHH2 {"cancer_type":"LIVER"} +197 cell_line JHH4 {"cancer_type":"LIVER"} +198 cell_line JHH5 {"cancer_type":"LIVER"} +199 cell_line JHH6 {"cancer_type":"LIVER"} +200 cell_line JHH7 {"cancer_type":"LIVER"} +201 cell_line JHOS2 {"cancer_type":"OVARY"} +202 cell_line JHOS4 {"cancer_type":"OVARY"} +203 cell_line JHUEM2 {"cancer_type":"ENDOMETRIUM"} +204 cell_line JM1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +205 cell_line JMSU1 {"cancer_type":"URINARY_TRACT"} +206 cell_line JURKAT {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +207 cell_line JVM3 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +208 cell_line K029AX {"cancer_type":"SKIN"} +209 cell_line KALS1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +210 cell_line KARPAS299 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +211 cell_line KARPAS422 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +212 cell_line KARPAS620 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +213 cell_line KASUMI2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +214 cell_line KCIMOH1 {"cancer_type":"PANCREAS"} +215 cell_line KCL22 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +216 cell_line KE39 {"cancer_type":"STOMACH"} +217 cell_line KE97 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +218 cell_line KELLY {"cancer_type":"AUTONOMIC_GANGLIA"} +219 cell_line KG1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +220 cell_line KHM1B {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +221 cell_line KLE {"cancer_type":"ENDOMETRIUM"} +222 cell_line KMBC2 {"cancer_type":"URINARY_TRACT"} +223 cell_line KMM1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +224 cell_line KMRC1 {"cancer_type":"KIDNEY"} +225 cell_line KMRC2 {"cancer_type":"KIDNEY"} +226 cell_line KMS11 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +227 cell_line KMS12BM {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +228 cell_line KMS26 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +229 cell_line KMS34 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +230 cell_line KNS42 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +231 cell_line KNS60 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +232 cell_line KNS62 {"cancer_type":"LUNG"} +233 cell_line KNS81 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +234 cell_line KO52 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +235 cell_line KP1N {"cancer_type":"PANCREAS"} +236 cell_line KP1NL {"cancer_type":"PANCREAS"} +237 cell_line KP2 {"cancer_type":"PANCREAS"} +238 cell_line KP3 {"cancer_type":"PANCREAS"} +239 cell_line KP4 {"cancer_type":"PANCREAS"} +240 cell_line KPNSI9S {"cancer_type":"AUTONOMIC_GANGLIA"} +241 cell_line KU812 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +242 cell_line KURAMOCHI {"cancer_type":"OVARY"} +243 cell_line KYM1 {"cancer_type":"SOFT_TISSUE"} +244 cell_line KYSE140 {"cancer_type":"OESOPHAGUS"} +245 cell_line KYSE150 {"cancer_type":"OESOPHAGUS"} +246 cell_line KYSE180 {"cancer_type":"OESOPHAGUS"} +247 cell_line KYSE30 {"cancer_type":"OESOPHAGUS"} +248 cell_line KYSE410 {"cancer_type":"OESOPHAGUS"} +249 cell_line KYSE450 {"cancer_type":"OESOPHAGUS"} +250 cell_line KYSE510 {"cancer_type":"OESOPHAGUS"} +251 cell_line KYSE520 {"cancer_type":"OESOPHAGUS"} +252 cell_line KYSE70 {"cancer_type":"OESOPHAGUS"} +254 cell_line L33 {"cancer_type":"PANCREAS"} +255 cell_line L363 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +256 cell_line L428 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +258 cell_line LC1SQSF {"cancer_type":"LUNG"} +259 cell_line LCLC103H {"cancer_type":"LUNG"} +260 cell_line LN18 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +261 cell_line LN229 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +262 cell_line LOUNH91 {"cancer_type":"LUNG"} +263 cell_line LOXIMVI {"cancer_type":"SKIN"} +264 cell_line LP1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +265 cell_line LS123 {"cancer_type":"LARGE_INTESTINE"} +266 cell_line LS411N {"cancer_type":"LARGE_INTESTINE"} +267 cell_line LS513 {"cancer_type":"LARGE_INTESTINE"} +268 cell_line LU99 {"cancer_type":"LUNG"} +269 cell_line LUDLU1 {"cancer_type":"LUNG"} +271 cell_line M059J {"cancer_type":""} +272 cell_line MALME3M {"cancer_type":"SKIN"} +273 cell_line MB157 {"cancer_type":"BREAST"} +274 cell_line MC116 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +275 cell_line MCAS {"cancer_type":"OVARY"} +276 cell_line MCF7 {"cancer_type":"BREAST"} +277 cell_line 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{"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +299 cell_line MKN45 {"cancer_type":"STOMACH"} +300 cell_line MKN7 {"cancer_type":"STOMACH"} +301 cell_line MKN74 {"cancer_type":"STOMACH"} +302 cell_line MOGGCCM {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +303 cell_line MOLP8 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +304 cell_line MOLT16 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +305 cell_line MONOMAC1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +306 cell_line MORCPR {"cancer_type":"LUNG"} +307 cell_line MPP89 {"cancer_type":"PLEURA"} +308 cell_line MSTO211H {"cancer_type":"PLEURA"} +309 cell_line NCIH1048 {"cancer_type":"LUNG"} +310 cell_line NCIH1092 {"cancer_type":"LUNG"} +311 cell_line NCIH1155 {"cancer_type":"LUNG"} +312 cell_line NCIH1184 {"cancer_type":"LUNG"} +313 cell_line NCIH1299 {"cancer_type":"LUNG"} +314 cell_line NCIH1339 {"cancer_type":"LUNG"} +315 cell_line NCIH1341 {"cancer_type":"LUNG"} +316 cell_line NCIH1355 {"cancer_type":"LUNG"} 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cell_line OE33 {"cancer_type":"OESOPHAGUS"} +381 cell_line ONCODG1 {"cancer_type":"OVARY"} +382 cell_line ONS76 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +383 cell_line OPM2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +384 cell_line OV90 {"cancer_type":"OVARY"} +385 cell_line OVCAR4 {"cancer_type":"OVARY"} +386 cell_line OVCAR8 {"cancer_type":"OVARY"} +387 cell_line OVMANA {"cancer_type":"OVARY"} +388 cell_line OVSAHO {"cancer_type":"OVARY"} +389 cell_line OVTOKO {"cancer_type":"OVARY"} +390 cell_line P12ICHIKAWA {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +391 cell_line P31FUJ {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +392 cell_line P3HR1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +393 cell_line PANC0203 {"cancer_type":"PANCREAS"} +394 cell_line PANC0327 {"cancer_type":"PANCREAS"} +395 cell_line PANC0403 {"cancer_type":"PANCREAS"} +396 cell_line PANC1005 {"cancer_type":"PANCREAS"} +397 cell_line PATU8902 {"cancer_type":"PANCREAS"} +398 cell_line PC14 {"cancer_type":"LUNG"} +399 cell_line PC3 {"cancer_type":"PROSTATE"} +403 cell_line PFEIFFER {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +405 cell_line PK1 {"cancer_type":"PANCREAS"} +406 cell_line PK45H {"cancer_type":"PANCREAS"} +407 cell_line PK59 {"cancer_type":"PANCREAS"} +408 cell_line PL45 {"cancer_type":"PANCREAS"} +409 cell_line PLCPRF5 {"cancer_type":"LIVER"} +411 cell_line PSN1 {"cancer_type":"PANCREAS"} +414 cell_line QGP1 {"cancer_type":"PANCREAS"} +417 cell_line RAJI {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +418 cell_line RD {"cancer_type":"SOFT_TISSUE"} +419 cell_line REH {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +420 cell_line RERFGC1B {"cancer_type":"STOMACH"} +421 cell_line RERFLCAI {"cancer_type":"LUNG"} +422 cell_line RERFLCMS {"cancer_type":"LUNG"} +423 cell_line RKN {"cancer_type":"OVARY"} +424 cell_line RKO {"cancer_type":"LARGE_INTESTINE"} +425 cell_line RL952 {"cancer_type":"ENDOMETRIUM"} +426 cell_line RPMI7951 {"cancer_type":"SKIN"} +427 cell_line RPMI8402 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +428 cell_line RT112 {"cancer_type":"URINARY_TRACT"} +429 cell_line RT4 {"cancer_type":"URINARY_TRACT"} +431 cell_line RVH421 {"cancer_type":"SKIN"} +432 cell_line SAOS2 {"cancer_type":"BONE"} +433 cell_line SBC5 {"cancer_type":"LUNG"} +434 cell_line SCABER {"cancer_type":"URINARY_TRACT"} +435 cell_line SCC25 {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +436 cell_line SCC9 {"cancer_type":"UPPER_AERODIGESTIVE_TRACT"} +437 cell_line SF126 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +438 cell_line SF295 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +439 cell_line SF8657 {"cancer_type":""} +440 cell_line SH10TC {"cancer_type":"STOMACH"} +441 cell_line SHP77 {"cancer_type":"LUNG"} +442 cell_line SIGM5 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +443 cell_line SIMA {"cancer_type":"AUTONOMIC_GANGLIA"} +444 cell_line SJRH30 {"cancer_type":"SOFT_TISSUE"} +445 cell_line SJSA1 {"cancer_type":"BONE"} +446 cell_line SKBR3 {"cancer_type":"BREAST"} +447 cell_line SKCO1 {"cancer_type":"LARGE_INTESTINE"} +448 cell_line SKES1 {"cancer_type":"BONE"} +449 cell_line SKHEP1 {"cancer_type":"LIVER"} +450 cell_line SKLMS1 {"cancer_type":"SOFT_TISSUE"} +451 cell_line SKLU1 {"cancer_type":"LUNG"} +452 cell_line SKMEL2 {"cancer_type":"SKIN"} +453 cell_line SKMEL24 {"cancer_type":"SKIN"} +454 cell_line SKMEL30 {"cancer_type":"SKIN"} +455 cell_line SKMEL31 {"cancer_type":"SKIN"} +456 cell_line SKMEL5 {"cancer_type":"SKIN"} +457 cell_line SKMES1 {"cancer_type":"LUNG"} +458 cell_line SKMM2 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +459 cell_line SKNAS {"cancer_type":"AUTONOMIC_GANGLIA"} +460 cell_line SKNBE2 {"cancer_type":"AUTONOMIC_GANGLIA"} +461 cell_line SKNDZ {"cancer_type":"AUTONOMIC_GANGLIA"} +462 cell_line SKNFI {"cancer_type":"AUTONOMIC_GANGLIA"} +463 cell_line SKNSH {"cancer_type":"AUTONOMIC_GANGLIA"} +464 cell_line SKOV3 {"cancer_type":"OVARY"} +465 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{"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +484 cell_line SUPT1 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +485 cell_line SW1088 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +486 cell_line SW1271 {"cancer_type":"LUNG"} +487 cell_line SW1353 {"cancer_type":"BONE"} +488 cell_line SW1417 {"cancer_type":"LARGE_INTESTINE"} +489 cell_line SW1573 {"cancer_type":"LUNG"} +490 cell_line SW1990 {"cancer_type":"PANCREAS"} +491 cell_line SW403 {"cancer_type":"LARGE_INTESTINE"} +492 cell_line SW48 {"cancer_type":"LARGE_INTESTINE"} +493 cell_line SW480 {"cancer_type":"LARGE_INTESTINE"} +494 cell_line SW579 {"cancer_type":"THYROID"} +495 cell_line SW620 {"cancer_type":"LARGE_INTESTINE"} +496 cell_line SW780 {"cancer_type":"URINARY_TRACT"} +497 cell_line SW900 {"cancer_type":"LUNG"} +499 cell_line T24 {"cancer_type":"URINARY_TRACT"} +500 cell_line T3M10 {"cancer_type":"LUNG"} +501 cell_line T47D {"cancer_type":"BREAST"} +502 cell_line T84 {"cancer_type":"LARGE_INTESTINE"} +503 cell_line T98G {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +505 cell_line TC71 {"cancer_type":"BONE"} +506 cell_line TCCSUP {"cancer_type":"URINARY_TRACT"} +507 cell_line TE1 {"cancer_type":"OESOPHAGUS"} +508 cell_line TE11 {"cancer_type":"OESOPHAGUS"} +509 cell_line TE15 {"cancer_type":"OESOPHAGUS"} +510 cell_line TE5 {"cancer_type":"OESOPHAGUS"} +511 cell_line TE617T {"cancer_type":"SOFT_TISSUE"} +512 cell_line TE9 {"cancer_type":"OESOPHAGUS"} +513 cell_line TEN {"cancer_type":"ENDOMETRIUM"} +515 cell_line TOLEDO {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +517 cell_line TOV112D {"cancer_type":"OVARY"} +518 cell_line TOV21G {"cancer_type":"OVARY"} +519 cell_line TT2609C02 {"cancer_type":"THYROID"} +521 cell_line TYKNU {"cancer_type":"OVARY"} +523 cell_line U118MG {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +524 cell_line U2OS {"cancer_type":"BONE"} +525 cell_line U87MG {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +526 cell_line U937 {"cancer_type":"HAEMATOPOIETIC_AND_LYMPHOID_TISSUE"} +527 cell_line UACC257 {"cancer_type":"SKIN"} +528 cell_line UACC62 {"cancer_type":"SKIN"} +529 cell_line UACC812 {"cancer_type":"BREAST"} +530 cell_line UMUC3 {"cancer_type":"URINARY_TRACT"} +531 cell_line VMRCLCD {"cancer_type":"LUNG"} +532 cell_line VMRCRCW {"cancer_type":"KIDNEY"} +533 cell_line VMRCRCZ {"cancer_type":"KIDNEY"} +534 cell_line WM115 {"cancer_type":"SKIN"} +535 cell_line WM1799 {"cancer_type":"SKIN"} +536 cell_line WM2664 {"cancer_type":"SKIN"} +537 cell_line WM793 {"cancer_type":"SKIN"} +538 cell_line WM88 {"cancer_type":"SKIN"} +539 cell_line WM983B {"cancer_type":"SKIN"} +541 cell_line YKG1 {"cancer_type":"CENTRAL_NERVOUS_SYSTEM"} +543 cell_line ZR751 {"cancer_type":"BREAST"} +544 cell_line ZR7530 {"cancer_type":"BREAST"} +4 drug 17-AAG {} +23 drug AEW541 {} +31 drug AZD0530 {} +32 drug AZD6244 {} +97 drug Erlotinib {} +194 drug Irinotecan {} +253 drug L-685458 {} +257 drug LBW242 {} +270 drug Lapatinib {} +370 drug Nilotinib {} +371 drug Nutlin-3 {} +400 drug PD-0325901 {} +401 drug PD-0332991 {} +402 drug PF2341066 {} +404 drug PHA-665752 {} +410 drug PLX4720 {} +412 drug Paclitaxel {} +413 drug Panobinostat {} +416 drug RAF265 {} +498 drug Sorafenib {} +504 drug TAE684 {} +514 drug TKI258 {} +522 drug Topotecan {} +542 drug ZD-6474 {} +21 protein ABL {} +24 protein ALK {} +58 protein CDK4 {} +92 protein EGFR {} +100 protein FGFR {} +114 protein GS {} +132 protein HDAC {} +171 protein HSP90 {} +184 protein IGF1R {} +284 protein MDM2 {} +287 protein MEK {} +415 protein RAF {} +430 protein RTK {} +516 protein TOP1 {} +520 protein TUBB1 {} +540 protein XIAP {} +545 protein c-MET {}
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/viewer.xml Tue Dec 30 18:27:26 2014 +0900 @@ -0,0 +1,36 @@ +<tool name="Graph Viewer" id="graph_viewer" tool_type="data_source"> + <description></description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://localhost/viewer/index.html" check_values="false" method="get"> + <display>go to Graph Viewer $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="primaryTable" /> + <value galaxy_value="auto" remote_value="selectedFields" /> + <value galaxy_value="wig" remote_value="wigData" /> + <value galaxy_value="interval" remote_value="tab" /> + <value galaxy_value="html" remote_value="hyperlinks" /> + <value galaxy_value="fasta" remote_value="sequence" /> + <value galaxy_value="gtf" remote_value="gff" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>