Concept Profile Generation Pipeline
Created: 2014-04-30 19:14:51
Last updated: 2014-06-15 17:55:11
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Workflow Components
Authors (1)
| Amrish Mahes |
Titles (0)
None
Descriptions (1)
| Requirements: Have MySQL installed with a database called mydb or please create one. Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files. Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool" Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics_bet_dev/downloads Install LVG2013Lite. See: https://trac.nbic.nl/data-mining/wiki/Using%20plain%20jar%20files Copy properties file from production.properties Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to taverna File --> preferences --> Tool invocation --> Edit defaul local --> write in Shell: C:\Windows\system32\cmd.exe /c and save that. Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale. |
Dependencies (1)
| mysql-connector-java-5.1.28-bin.jar |
Inputs (5)
| Name | Description |
|---|---|
| Ontology_input | A Skos formated dictionary/thesaurus of predefined concepts. |
| User_password | Input your sql password to acces as root. |
| abstract_input_depth2 | Give a list with sublist. Each sublist consist out of two elements. Such as [ [ Document_URI, Abstract_URI] ]. For an example please load in the file named: Input_value_for_test_upload_CPGP. Which can be found under the files tab on MyExperiment. |
| Driver_value | The driver needed for all SQL query to run. |
| usr_id | The user ID which is in this case root. |
Processors (56)
| Name | Type | Description |
|---|---|---|
| Indexer_tool | externaltool | Uses a jar peregrine program to index which concept occurs in what document. Change the commands to : java -Dperegrine.config.location=your/path/to/peregrine/production.properties -jar path/to/peregrine-skos-cli.jar ontology abstract_content out1 When using a Windows machine: Go to Location tab select radiobutton "Select an explicit location" and default local then save settings by clicking apply. |
| Split_string_into_string_list_by_regular_expression | localworker |
Uses Regex to split string into string list. ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
| regex_value | stringconstant |
Value[\n] |
| url_value | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Sql_beanshell_query_generator_Concept_Occ_Doc | beanshell |
A Beanshell script that generates a Sql statement to INSERT
the concept URI, occurence URI and document URI in the table named after the timestamp the workflow started.
It uses a database called mydb. It is needed to have a database called mydb. Script/* Generate sql statement which inserts the concept URI, occurence URI and document URI in the table*/
List con_occ_doc = Arrays.asList(in1.split("\\s+"));
out1 = "INSERT INTO mydb."+table_name+"(concept_uri,occurence_uri,doc_uri)VALUES("+"'"+con_occ_doc.get(0)+"','"+con_occ_doc.get(1)+"','"+con_occ_doc.get(2)+"');"; |
| Execute_SQL_Update_INSERT_INTO_first_table | localworker |
Executes the SQL statement generated by the Beanshell script: "Sql_beanshell_query_generator_Concept_occ_Doc" which insert the concept, occurence and document URI into the table. Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| Beanshell_generate_sql_table_occurence_concept_doc | beanshell |
A Beanshell script which generates a sql statement to CREATE a TABLE.
TABLE name is the input of the timestamp.
The table consists out of 4 columns: concept_occ_doc_id, concept_uri, occurence_uri and doc_uri.
Where as concept_occ_doc_id is the PRIMARY KEY and AUTOINCREMENTED.
Every other column has a VARCHAR(200)
ScriptString Table_sql = "CREATE TABLE `mydb`.`"+timeStamp+"` ( `concept_occ_doc_id` INT NOT NULL AUTO_INCREMENT, `concept_uri` VARCHAR(200) NULL, `occurence_uri` VARCHAR(200) NULL, `doc_uri` VARCHAR(200) NULL, PRIMARY KEY (`concept_occ_doc_id`));" /* generate sql statement which create a table with a timestamp as table name*/ |
| Execute_SQL_Update_CREATE_TABLE | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_1 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_get_timestamp | beanshell |
A Beanshell script which retreives the time the program started.
As in year, month, day, hour, minutes and seconds in military time. Scriptimport java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Calender;
String timeStamp = new SimpleDateFormat("yyyy_MM_dd_HH_mm_ss").format(new Date());
/* Retrieve the year, month, day, hour, minutes and seconds in military time at which the program started */ |
| Beanshell_extract_uri_doc_and_abstract | beanshell |
A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs. Scriptdoc_uri= input.get(0); abstracts = input.get(1); |
| Beanshell_generate_sql_statement_Get_destinct_concept | beanshell |
A Beanshell script that oversees if the amount of inserted rows in MySql table is equal to the amount of "triples".
If this is true it gives an output "COMPLETED" Scriptout1 = "SELECT DISTINCT concept_uri FROM mydb."+table_name+";" ;//occurence_table |
| Execute_SQL_Query | localworker |
Script
import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import javax.sql.rowset.WebRowSet;
import com.sun.rowset.WebRowSetImpl;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
ResultSet rs = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramSize = params.size();
for (int i = 0; i < paramSize; i++) {
ps.setObject(i + 1, params.get(i));
}
rs = ps.executeQuery();
if (provideXmlBoolean) {
WebRowSet webrs = new WebRowSetImpl();
StringWriter sw = new StringWriter();
webrs.writeXml(rs, sw);
xmlresults = sw.toString();
} else {
xmlresults = "";
}
try {
rs.beforeFirst();
} catch (SQLException e) {
// redo the query
rs = ps.executeQuery();
}
ResultSetMetaData rsmd = rs.getMetaData();
int numCols = rsmd.getColumnCount();
resultList = new ArrayList();
// put the results into the results list.
while (rs.next()) {
List row = new ArrayList(numCols);
for (int i = 0; i < numCols; i++) {
String str = rs.getString(i + 1);
row.add(str == null ? "null" : str);
}
resultList.add(row);
}
}
finally {
if (rs != null) {
rs.close();
}
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_2 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Flatten_List | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Beanshell_make_concept_pairs | beanshell |
A Beanshell script that gets as input a list of concepts to create concept pairs Scriptout1 = in1 +","+ input; |
| Flatten_List_2 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Beanshell_generate_sql_for_contingency_table | beanshell |
A Beanshell script that generates a SQL statement to retrieve the amount two concepts co-occur, concept A only occurss
and not concept B, concept B occurs and not concept A and neither concepts occur in litrature. ScriptList concept_pair = Arrays.asList(in1.split(","));
out1="SELECT count(*) AS total FROM " +
"(SELECT doc_uri,count(DISTINCT concept_uri) AS count_conc FROM mydb."+table_name+" " + //occurence_table
"WHERE concept_uri IN ('"+concept_pair.get(0)+"','"+concept_pair.get(1)+"') " +
"GROUP BY doc_uri " +
"HAVING count_conc >=2 ) " +
"AS amount_of_concept_co_occurence " +
"UNION ALL " +
"SELECT count(*) AS total FROM " +
"(SELECT concept_uri,doc_uri FROM mydb."+table_name+" " + //occurence_table
"WHERE concept_uri IN ('"+concept_pair.get(0)+"')) " +
"AS only_concept_A " +
"UNION ALL " +
"SELECT count(*) AS total FROM " +
"(SELECT concept_uri,doc_uri FROM mydb."+table_name+" " + //occurence_table
"WHERE concept_uri IN ('"+concept_pair.get(1)+"')) " +
"AS only_concept_B " +
"UNION ALL " +
"SELECT count(*) AS total FROM " +
"(SELECT doc_uri,count(DISTINCT concept_uri) AS count_conc FROM mydb."+table_name+" " + //occurence_table
"WHERE concept_uri NOT IN ('"+concept_pair.get(0)+"','"+concept_pair.get(1)+"') " +
"GROUP BY doc_uri) " +
"AS non_conceptA_B; "; |
| Execute_SQL_Query_2 | localworker |
Script
import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import javax.sql.rowset.WebRowSet;
import com.sun.rowset.WebRowSetImpl;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
ResultSet rs = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramSize = params.size();
for (int i = 0; i < paramSize; i++) {
ps.setObject(i + 1, params.get(i));
}
rs = ps.executeQuery();
if (provideXmlBoolean) {
WebRowSet webrs = new WebRowSetImpl();
StringWriter sw = new StringWriter();
webrs.writeXml(rs, sw);
xmlresults = sw.toString();
} else {
xmlresults = "";
}
try {
rs.beforeFirst();
} catch (SQLException e) {
// redo the query
rs = ps.executeQuery();
}
ResultSetMetaData rsmd = rs.getMetaData();
int numCols = rsmd.getColumnCount();
resultList = new ArrayList();
// put the results into the results list.
while (rs.next()) {
List row = new ArrayList(numCols);
for (int i = 0; i < numCols; i++) {
String str = rs.getString(i + 1);
row.add(str == null ? "null" : str);
}
resultList.add(row);
}
}
finally {
if (rs != null) {
rs.close();
}
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_3 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Flatten_List_3 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Beanshell_correct_contincengy_table | beanshell |
A Beanshell script that correct the output SQL retreived contincengy table. Scriptint co_occure_ab = Integer.parseInt(in1.get(0)); int count_concept_a = Integer.parseInt(in1.get(1)); int count_concept_b = Integer.parseInt(in1.get(2)); int count_non_ab = Integer.parseInt(in1.get(3)); all_concept_a = count_concept_a - co_occure_ab; all_concept_b = count_concept_b - co_occure_ab; List correct_contingencytable = new ArrayList(); correct_contingencytable.add(co_occure_ab); correct_contingencytable.add(all_concept_a); correct_contingencytable.add(all_concept_b); correct_contingencytable.add(count_non_ab); out1 = correct_contingencytable |
| Beanshell_calculate_uncertainty_coefficient | beanshell |
A Beanshell script that calculates the Uncertainty coefficient created by Herman van Haagen. Script//string omzetten naar double! //int co_occure_ab = Integer.parseInt(in1.get(0)); double M11 = Double.parseDouble(input.get(0)); // co-occure A B double M01 = Double.parseDouble(input.get(1)); // Only concept A double M10 = Double.parseDouble(input.get(2)); // Only concept B double M00 = Double.parseDouble(input.get(3)); // None A or B double N = M11+M01+10+M00; double Pxy = M11/N; double Pxnoty = M01/N; double Pnotxy = M10/N; double Pnotxnoty = M00/N; double Px = (M11+M01)/N; double Py = (M11+M10)/N; double Pnotx = (M10+M00)/N; double Pnoty = (M01+M00)/N; double Hx = -Px*Math.log(Px)-Pnotx*Math.log(Pnotx); double Hy = -Py*Math.log(Py)-Pnoty*Math.log(Pnoty); double miA = Pxy*Math.log(Pxy/(Px*Py)); if (Double.isNaN(miA)) miA = 0.0; double miB = Pxnoty*Math.log(Pxnoty/(Px*Pnoty)); if (Double.isNaN(miB)) miB = 0.0; double miC = Pnotxy*Math.log(Pnotxy/(Pnotx*Py)); if (Double.isNaN(miC)) miC = 0.0; double miD = Pnotxnoty*Math.log(Pnotxnoty/(Pnotx*Pnoty)); if (Double.isNaN(miD)) miD = 0.0; double mi = miA+miB+miC+miD; double uc = (2*mi)/(Hx+Hy); output = uc; |
| Beanshell_generate_table_UC | beanshell |
A Beanshell script that generates a table for the uncertainty coefficient values. ScriptString output = "Create table mydb."+time_stamp+"_UC(concept_profile_id INT NOT NULL AUTO_INCREMENT, concept_alpha VARCHAR(200) NULL, concept_beta VARCHAR(200) NULL, Uncertainty_coefficient DOUBLE NULL, PRIMARY KEY (concept_profile_id));" |
| Execute_SQL_Update_Create_table_UC | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_4 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_sql_insert_UC_values_to_table | beanshell |
A Beanshell script which generates a SQL statement to insert the calculated values of uncertainty coefficient per
concept pair into the table. ScriptList concept_pair = Arrays.asList(in1.split(","));
concept_alpha = concept_pair.get(0);
concept_beta = concept_pair.get(1);
output_SQL = "INSERT INTO mydb."+timestamp+"_uc (concept_alpha, concept_beta, Uncertainty_coefficient) VALUES ('"+concept_alpha+"', '"+concept_beta+"', '"+UC_value+"');";
|
| Execute_SQL_Update | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_5 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_generate_SQL_get_inner_product | beanshell |
A Beanshell script that generates a SQL statement to retrieve the Inner product between two concept profiles. ScriptList concept_pair = Arrays.asList(in1.split(","));
concept_alpha = concept_pair.get(0);
concept_beta = concept_pair.get(1);
out1 = "SELECT SUM(cpTable1.Uncertainty_coefficient*cpTable2.Uncertainty_coefficient) FROM mydb."+timestamp+"_uc AS cpTable1, mydb."+timestamp+"_uc AS cpTable2 WHERE cpTable1.concept_alpha = '"+concept_alpha+"' AND cpTable2.concept_alpha = '"+concept_beta+"' AND cpTable1.concept_beta=cpTable2.concept_beta;";
|
| Beanshell_SQL_create_table_co_occurence | beanshell |
ScriptString out1 = "CREATE TABLE mydb."+timestamp+"_co_occurence (concept_id INT NOT NULL AUTO_INCREMENT, concept1 VARCHAR(200) NULL, concept2 VARCHAR(200) NULL, concept_co_occurence VARCHAR(200) NULL,PRIMARY KEY (concept_id));"; |
| Execute_SQL_Update_CREATE_TABLE_co_occurence | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_6 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_SQL_insert_into_co_occurence_table | beanshell |
ScriptList concept_pair = Arrays.asList(concept_pairs.split(","));
concept_alpha = concept_pair.get(0);
concept_beta = concept_pair.get(1);
String co_occurence = contingency_values.get(0);
String out1 = "INSERT INTO mydb."+timestamp+"_co_occurence (concept1, concept2, concept_co_occurence)VALUES('"+concept_alpha+"','"+concept_beta+"','"+co_occurence+"');"; |
| Execute_SQL_Update_3 | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_7 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_generate_sql_table_inner_product | beanshell |
ScriptString out1 = "CREATE TABLE mydb."+timestamp+"_inner_product ( concept_profile_id INT NOT NULL AUTO_INCREMENT, concept_1 VARCHAR(200) NULL, concept_2 VARCHAR(200) NULL, Inner_product DOUBLE NULL, PRIMARY KEY (concept_profile_id));"; |
| Execute_SQL_Update_CREATE_TABLE_inner_product | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_8 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| url_value_9 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Execute_SQL_Query_3 | localworker |
Script
import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import javax.sql.rowset.WebRowSet;
import com.sun.rowset.WebRowSetImpl;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
ResultSet rs = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramSize = params.size();
for (int i = 0; i < paramSize; i++) {
ps.setObject(i + 1, params.get(i));
}
rs = ps.executeQuery();
if (provideXmlBoolean) {
WebRowSet webrs = new WebRowSetImpl();
StringWriter sw = new StringWriter();
webrs.writeXml(rs, sw);
xmlresults = sw.toString();
} else {
xmlresults = "";
}
try {
rs.beforeFirst();
} catch (SQLException e) {
// redo the query
rs = ps.executeQuery();
}
ResultSetMetaData rsmd = rs.getMetaData();
int numCols = rsmd.getColumnCount();
resultList = new ArrayList();
// put the results into the results list.
while (rs.next()) {
List row = new ArrayList(numCols);
for (int i = 0; i < numCols; i++) {
String str = rs.getString(i + 1);
row.add(str == null ? "null" : str);
}
resultList.add(row);
}
}
finally {
if (rs != null) {
rs.close();
}
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| Flatten_List_4 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Flatten_List_5 | localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Beanshell_insert_into_inner_product_table | beanshell |
ScriptList concept_pair = Arrays.asList(in1.split(","));
concept_1 = concept_pair.get(0);
concept_2 = concept_pair.get(1);
String out1 = "INSERT INTO mydb."+timestamp+"_inner_product ( concept_1,concept_2,Inner_product) VALUES('"+concept_1+"','"+concept_2+"','"+inner_product_value+"');" |
| Execute_SQL_Update_2 | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_10 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_SQL_statement_get_last_table_data_input | beanshell |
A Beanshell that generates SQL statements to retreive the inner product of two concept profiles, the co-occurence of the concepts and the uncertainty coefficient. ScriptString out1 = "SELECT distinct inner_product.concept_1, " + "inner_product.concept_2, " + "inner_product.Inner_product, " + "uc.Uncertainty_coefficient, " + "Co_occurence_table.concept_co_occurence " + "FROM mydb."+timestamp+"_inner_product AS inner_product, " + "mydb."+timestamp+"_uc AS uc, " + "mydb."+timestamp+"_co_occurence AS Co_occurence_table " + "WHERE inner_product.concept_profile_id = uc.concept_profile_id " + "AND " + "inner_product.concept_profile_id = Co_occurence_table.concept_id; "; |
| Execute_SQL_Query_4 | localworker |
Script
import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import javax.sql.rowset.WebRowSet;
import com.sun.rowset.WebRowSetImpl;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
ResultSet rs = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramSize = params.size();
for (int i = 0; i < paramSize; i++) {
ps.setObject(i + 1, params.get(i));
}
rs = ps.executeQuery();
if (provideXmlBoolean) {
WebRowSet webrs = new WebRowSetImpl();
StringWriter sw = new StringWriter();
webrs.writeXml(rs, sw);
xmlresults = sw.toString();
} else {
xmlresults = "";
}
try {
rs.beforeFirst();
} catch (SQLException e) {
// redo the query
rs = ps.executeQuery();
}
ResultSetMetaData rsmd = rs.getMetaData();
int numCols = rsmd.getColumnCount();
resultList = new ArrayList();
// put the results into the results list.
while (rs.next()) {
List row = new ArrayList(numCols);
for (int i = 0; i < numCols; i++) {
String str = rs.getString(i + 1);
row.add(str == null ? "null" : str);
}
resultList.add(row);
}
}
finally {
if (rs != null) {
rs.close();
}
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_11 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_CREATE_last_big_table | beanshell |
ScriptString out1 = "CREATE TABLE mydb."+timestamp+"_big_table ( concept_profile_id INT NOT NULL AUTO_INCREMENT, concept_profile_A VARCHAR(255) NULL, concept_profile_B VARCHAR(255) NULL, Inner_product DOUBLE NULL, Uncertainty_coefficient DOUBLE NULL, Co_occurence VARCHAR(255) NULL, PRIMARY KEY (concept_profile_id));"; |
| Beanshell_Generate_SQL_insert_into_big_table | beanshell |
Scriptconcept_profile_A = in1.get(0);
concept_profile_B = in1.get(1);
inner_product = in1.get(2);
uncertainty_coefficient = in1.get(3);
co_occurence = in1.get(4);
String out1 = "INSERT INTO mydb."+timestamp+"_big_table (concept_profile_A, concept_profile_B, Inner_product, Uncertainty_coefficient, Co_occurence) " +
"VALUES ('"+concept_profile_A+"','"+concept_profile_B+"','"+inner_product+"','"+uncertainty_coefficient+"','"+co_occurence+"');"; |
| Execute_SQL_Update_4 | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_12 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Execute_SQL_Update_5 | localworker |
Scriptimport java.sql.Driver;
import java.sql.DriverManager;
import java.sql.Connection;
import java.sql.PreparedStatement;
if ((driver == void) || (driver == null) || driver.equals("")) {
throw new RuntimeException("The driver must be specified");
}
if ((url == void) || (url == null) || url.equals("")) {
throw new RuntimeException("The url must be specified");
}
if ((params == void) || (params == null)) {
params = new ArrayList();
}
if ((sql == void) || (sql == null) || sql.equals("")) {
throw new RuntimeException("The sql must be specified");
}
Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
if (c == null) {
throw new RuntimeException("Class " + driver + " not found");
}
Driver d = c.newInstance();
if (d == null) {
throw new RuntimeException("Could not create instance of driver");
}
Properties p = new Properties();
if ((userid == void) || (userid == null)) {
userid = "";
}
p.setProperty("user", userid);
if ((password == void) || (password == null)) {
password = "";
}
p.setProperty("password", password);
Connection con = null;
PreparedStatement ps = null;
try {
con = d.connect(url, p);
ps = con.prepareStatement(sql);
int paramsSize = params.size();
for (int i = 0; i < paramsSize; i++) {
ps.setObject(i + 1, params.get(i));
}
ps.executeUpdate();
resultList = "update successful";
}
finally {
if (ps != null) {
ps.close();
}
if (con != null) {
con.close();
}
}
|
| url_value_13 | stringconstant |
Valuejdbc:mysql://localhost:3306/mydb |
| Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc | beanshell |
A Beanshell script that replaces the temp created Taverna file with the correct Document URI. ScriptList con_occ_doc = Arrays.asList(triple.split("\\s+"));
concept = con_occ_doc.get(0);
occurs = con_occ_doc.get(1);
doc = con_occ_doc.get(2);
element = doc.substring(doc.indexOf('.')+1,doc.lastIndexOf('.'));
int element = Integer.parseInt(element);
correct_doc_uri = doc_uri.get(element);
String out1 = concept+" "+occurs+" "+correct_doc_uri; |
Beanshells (20)
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| Sql_beanshell_query_generator_Concept_Occ_Doc | A Beanshell script that generates a Sql statement to INSERT the concept URI, occurence URI and document URI in the table named after the timestamp the workflow started. It uses a database called mydb. It is needed to have a database called mydb. |
table_name in1 |
wordList out1 |
| Beanshell_generate_sql_table_occurence_concept_doc | A Beanshell script which generates a sql statement to CREATE a TABLE. TABLE name is the input of the timestamp. The table consists out of 4 columns: concept_occ_doc_id, concept_uri, occurence_uri and doc_uri. Where as concept_occ_doc_id is the PRIMARY KEY and AUTOINCREMENTED. Every other column has a VARCHAR(200) | timeStamp | Table_sql |
| Beanshell_get_timestamp | A Beanshell script which retreives the time the program started. As in year, month, day, hour, minutes and seconds in military time. | timeStamp | |
| Beanshell_extract_uri_doc_and_abstract | A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs. | input |
doc_uri abstracts |
| Beanshell_generate_sql_statement_Get_destinct_concept | A Beanshell script that oversees if the amount of inserted rows in MySql table is equal to the amount of "triples". If this is true it gives an output "COMPLETED" | table_name | out1 |
| Beanshell_make_concept_pairs | A Beanshell script that gets as input a list of concepts to create concept pairs |
input in1 |
out1 |
| Beanshell_generate_sql_for_contingency_table | A Beanshell script that generates a SQL statement to retrieve the amount two concepts co-occur, concept A only occurss and not concept B, concept B occurs and not concept A and neither concepts occur in litrature. |
in1 table_name |
out1 |
| Beanshell_correct_contincengy_table | A Beanshell script that correct the output SQL retreived contincengy table. | in1 | out1 |
| Beanshell_calculate_uncertainty_coefficient | A Beanshell script that calculates the Uncertainty coefficient created by Herman van Haagen. | input | output |
| Beanshell_generate_table_UC | A Beanshell script that generates a table for the uncertainty coefficient values. | time_stamp | output |
| Beanshell_sql_insert_UC_values_to_table | A Beanshell script which generates a SQL statement to insert the calculated values of uncertainty coefficient per concept pair into the table. |
timestamp in1 UC_value |
output_SQL |
| Beanshell_generate_SQL_get_inner_product | A Beanshell script that generates a SQL statement to retrieve the Inner product between two concept profiles. |
in1 timestamp |
out1 |
| Beanshell_SQL_create_table_co_occurence | timestamp | out1 | |
| Beanshell_SQL_insert_into_co_occurence_table |
contingency_values timestamp concept_pairs |
out1 | |
| Beanshell_generate_sql_table_inner_product | timestamp | out1 | |
| Beanshell_insert_into_inner_product_table |
in1 timestamp inner_product_value |
out1 | |
| Beanshell_SQL_statement_get_last_table_data_input | A Beanshell that generates SQL statements to retreive the inner product of two concept profiles, the co-occurence of the concepts and the uncertainty coefficient. | timestamp | out1 |
| Beanshell_CREATE_last_big_table | timestamp | out1 | |
| Beanshell_Generate_SQL_insert_into_big_table |
timestamp in1 |
out1 | |
| Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc | A Beanshell script that replaces the temp created Taverna file with the correct Document URI. |
triple doc_uri |
out1 |
Outputs (2)
| Name | Description |
|---|---|
| einde | |
| Beanshell_generate_sql_statement_Get_destinct_concept_out1 |
Datalinks (112)
| Source | Sink |
|---|---|
| Ontology_input | Indexer_tool:ontology |
| Beanshell_extract_uri_doc_and_abstract:abstracts | Indexer_tool:abstract_content |
| Indexer_tool:out1 | Split_string_into_string_list_by_regular_expression:string |
| regex_value:value | Split_string_into_string_list_by_regular_expression:regex |
| Beanshell_get_timestamp:timeStamp | Sql_beanshell_query_generator_Concept_Occ_Doc:table_name |
| Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc:out1 | Sql_beanshell_query_generator_Concept_Occ_Doc:in1 |
| url_value:value | Execute_SQL_Update_INSERT_INTO_first_table:url |
| User_password | Execute_SQL_Update_INSERT_INTO_first_table:password |
| Driver_value | Execute_SQL_Update_INSERT_INTO_first_table:driver |
| usr_id | Execute_SQL_Update_INSERT_INTO_first_table:userid |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_sql_table_occurence_concept_doc:timeStamp |
| User_password | Execute_SQL_Update_CREATE_TABLE:password |
| url_value_1:value | Execute_SQL_Update_CREATE_TABLE:url |
| Driver_value | Execute_SQL_Update_CREATE_TABLE:driver |
| usr_id | Execute_SQL_Update_CREATE_TABLE:userid |
| abstract_input_depth2 | Beanshell_extract_uri_doc_and_abstract:input |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_sql_statement_Get_destinct_concept:table_name |
| url_value_2:value | Execute_SQL_Query:url |
| User_password | Execute_SQL_Query:password |
| Beanshell_generate_sql_statement_Get_destinct_concept:out1 | Execute_SQL_Query:sql |
| Driver_value | Execute_SQL_Query:driver |
| usr_id | Execute_SQL_Query:userid |
| Execute_SQL_Query:resultList | Flatten_List:inputlist |
| Flatten_List:outputlist | Beanshell_make_concept_pairs:in1 |
| Flatten_List:outputlist | Beanshell_make_concept_pairs:input |
| Beanshell_make_concept_pairs:out1 | Flatten_List_2:inputlist |
| Flatten_List_2:outputlist | Beanshell_generate_sql_for_contingency_table:in1 |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_sql_for_contingency_table:table_name |
| Beanshell_generate_sql_for_contingency_table:out1 | Execute_SQL_Query_2:sql |
| User_password | Execute_SQL_Query_2:password |
| url_value_3:value | Execute_SQL_Query_2:url |
| Driver_value | Execute_SQL_Query_2:driver |
| usr_id | Execute_SQL_Query_2:userid |
| Execute_SQL_Query_2:resultList | Flatten_List_3:inputlist |
| Flatten_List_3:outputlist | Beanshell_correct_contincengy_table:in1 |
| Beanshell_correct_contincengy_table:out1 | Beanshell_calculate_uncertainty_coefficient:input |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_table_UC:time_stamp |
| Beanshell_generate_table_UC:output | Execute_SQL_Update_Create_table_UC:sql |
| url_value_4:value | Execute_SQL_Update_Create_table_UC:url |
| User_password | Execute_SQL_Update_Create_table_UC:password |
| Driver_value | Execute_SQL_Update_Create_table_UC:driver |
| usr_id | Execute_SQL_Update_Create_table_UC:userid |
| Flatten_List_2:outputlist | Beanshell_sql_insert_UC_values_to_table:in1 |
| Beanshell_get_timestamp:timeStamp | Beanshell_sql_insert_UC_values_to_table:timestamp |
| Beanshell_calculate_uncertainty_coefficient:output | Beanshell_sql_insert_UC_values_to_table:UC_value |
| url_value_5:value | Execute_SQL_Update:url |
| User_password | Execute_SQL_Update:password |
| Beanshell_sql_insert_UC_values_to_table:output_SQL | Execute_SQL_Update:sql |
| Driver_value | Execute_SQL_Update:driver |
| usr_id | Execute_SQL_Update:userid |
| Flatten_List_2:outputlist | Beanshell_generate_SQL_get_inner_product:in1 |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_SQL_get_inner_product:timestamp |
| Beanshell_get_timestamp:timeStamp | Beanshell_SQL_create_table_co_occurence:timestamp |
| Beanshell_SQL_create_table_co_occurence:out1 | Execute_SQL_Update_CREATE_TABLE_co_occurence:sql |
| url_value_6:value | Execute_SQL_Update_CREATE_TABLE_co_occurence:url |
| User_password | Execute_SQL_Update_CREATE_TABLE_co_occurence:password |
| Driver_value | Execute_SQL_Update_CREATE_TABLE_co_occurence:driver |
| usr_id | Execute_SQL_Update_CREATE_TABLE_co_occurence:userid |
| Flatten_List_3:outputlist | Beanshell_SQL_insert_into_co_occurence_table:contingency_values |
| Flatten_List_2:outputlist | Beanshell_SQL_insert_into_co_occurence_table:concept_pairs |
| Beanshell_get_timestamp:timeStamp | Beanshell_SQL_insert_into_co_occurence_table:timestamp |
| Beanshell_SQL_insert_into_co_occurence_table:out1 | Execute_SQL_Update_3:sql |
| User_password | Execute_SQL_Update_3:password |
| url_value_7:value | Execute_SQL_Update_3:url |
| Driver_value | Execute_SQL_Update_3:driver |
| usr_id | Execute_SQL_Update_3:userid |
| Beanshell_get_timestamp:timeStamp | Beanshell_generate_sql_table_inner_product:timestamp |
| Beanshell_generate_sql_table_inner_product:out1 | Execute_SQL_Update_CREATE_TABLE_inner_product:sql |
| url_value_8:value | Execute_SQL_Update_CREATE_TABLE_inner_product:url |
| User_password | Execute_SQL_Update_CREATE_TABLE_inner_product:password |
| Driver_value | Execute_SQL_Update_CREATE_TABLE_inner_product:driver |
| usr_id | Execute_SQL_Update_CREATE_TABLE_inner_product:userid |
| Beanshell_generate_SQL_get_inner_product:out1 | Execute_SQL_Query_3:sql |
| url_value_9:value | Execute_SQL_Query_3:url |
| User_password | Execute_SQL_Query_3:password |
| Driver_value | Execute_SQL_Query_3:driver |
| usr_id | Execute_SQL_Query_3:userid |
| Execute_SQL_Query_3:resultList | Flatten_List_4:inputlist |
| Flatten_List_4:outputlist | Flatten_List_5:inputlist |
| Flatten_List_5:outputlist | Beanshell_insert_into_inner_product_table:inner_product_value |
| Beanshell_get_timestamp:timeStamp | Beanshell_insert_into_inner_product_table:timestamp |
| Flatten_List_2:outputlist | Beanshell_insert_into_inner_product_table:in1 |
| Beanshell_insert_into_inner_product_table:out1 | Execute_SQL_Update_2:sql |
| url_value_10:value | Execute_SQL_Update_2:url |
| User_password | Execute_SQL_Update_2:password |
| Driver_value | Execute_SQL_Update_2:driver |
| usr_id | Execute_SQL_Update_2:userid |
| Beanshell_get_timestamp:timeStamp | Beanshell_SQL_statement_get_last_table_data_input:timestamp |
| Beanshell_SQL_statement_get_last_table_data_input:out1 | Execute_SQL_Query_4:sql |
| User_password | Execute_SQL_Query_4:password |
| url_value_11:value | Execute_SQL_Query_4:url |
| Driver_value | Execute_SQL_Query_4:driver |
| usr_id | Execute_SQL_Query_4:userid |
| Beanshell_get_timestamp:timeStamp | Beanshell_CREATE_last_big_table:timestamp |
| Execute_SQL_Query_4:resultList | Beanshell_Generate_SQL_insert_into_big_table:in1 |
| Beanshell_get_timestamp:timeStamp | Beanshell_Generate_SQL_insert_into_big_table:timestamp |
| Beanshell_CREATE_last_big_table:out1 | Execute_SQL_Update_4:sql |
| url_value_12:value | Execute_SQL_Update_4:url |
| Driver_value | Execute_SQL_Update_4:driver |
| User_password | Execute_SQL_Update_4:password |
| usr_id | Execute_SQL_Update_4:userid |
| Beanshell_Generate_SQL_insert_into_big_table:out1 | Execute_SQL_Update_5:sql |
| User_password | Execute_SQL_Update_5:password |
| url_value_13:value | Execute_SQL_Update_5:url |
| Driver_value | Execute_SQL_Update_5:driver |
| usr_id | Execute_SQL_Update_5:userid |
| Split_string_into_string_list_by_regular_expression:split | Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc:triple |
| Beanshell_extract_uri_doc_and_abstract:doc_uri | Beanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_doc:doc_uri |
| Sql_beanshell_query_generator_Concept_Occ_Doc:out1 | Execute_SQL_Update_INSERT_INTO_first_table:sql |
| Beanshell_generate_sql_table_occurence_concept_doc:Table_sql | Execute_SQL_Update_CREATE_TABLE:sql |
| Execute_SQL_Update_5:resultList | einde |
| Beanshell_generate_sql_statement_Get_destinct_concept:out1 | Beanshell_generate_sql_statement_Get_destinct_concept_out1 |
Coordinations (3)
| Controller | Target |
|---|---|
| Execute_SQL_Update | Beanshell_generate_SQL_get_inner_product |
| Execute_SQL_Update_2 | Execute_SQL_Query_4 |
| Execute_SQL_Update_INSERT_INTO_first_table | Beanshell_generate_sql_statement_Get_destinct_concept |
Workflow Type
Version 1 (earliest)
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Version History
In chronological order:
-
Created by Amrish Mahes on Wednesday 30 April 2014 19:14:47 (UTC)
-
Created by Amrish Mahes on Wednesday 30 April 2014 19:18:01 (UTC)
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Created by Amrish Mahes on Wednesday 30 April 2014 19:18:42 (UTC)
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Created by Amrish Mahes on Wednesday 07 May 2014 15:33:38 (UTC)
Revision comment:New version with comment and the right websites to download dependencies
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Created by Amrish Mahes on Monday 12 May 2014 15:34:00 (UTC)
-
Created by Amrish Mahes on Wednesday 11 June 2014 13:23:36 (UTC)
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Created by Amrish Mahes on Sunday 15 June 2014 17:45:34 (UTC)
Revision comment:Changed Table construction workflow
For peregrine tool invocation it is now mandatory to give path to the prodcution.properties and peregrine-skos-cli.jar
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Created by Amrish Mahes on Sunday 15 June 2014 17:50:32 (UTC)
-
Created by Amrish Mahes on Sunday 15 June 2014 17:55:11 (UTC)
Revision comment:Removed the LIMIT 50 in the sql_value file
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