/*******************************************************************************
* Copyright 2012 University of Southern California
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* This code was developed by the Information Integration Group as part
* of the Karma project at the Information Sciences Institute of the
* University of Southern California. For more information, publications,
* and related projects, please see: http://www.isi.edu/integration
******************************************************************************/
package edu.isi.karma.webserver;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.Random;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.JSONStringer;
import org.json.JSONWriter;
import org.json.XML;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import edu.isi.karma.imp.json.JsonImport;
import edu.isi.karma.rep.HNode;
import edu.isi.karma.rep.HNode.HNodeType;
import edu.isi.karma.rep.HTable;
import edu.isi.karma.rep.RepFactory;
import edu.isi.karma.rep.Row;
import edu.isi.karma.rep.Worksheet;
import edu.isi.karma.rep.Workspace;
import edu.isi.karma.util.FileUtil;
import edu.isi.karma.util.JSONUtil;
public class SampleDataFactory {
private static Logger logger = LoggerFactory
.getLogger(SampleDataFactory.class);
public static Worksheet createSample1(Workspace workspace) {
RepFactory f = workspace.getFactory();
Worksheet w = f.createWorksheet("Complex Smaple Table", workspace, "UTF-8");
String ss = w.addHNode("Social Security", HNodeType.Regular, f).getId();
String personContainer = w.addHNode("Person", HNodeType.Regular, f).getId();
String addressContainer = w.addHNode("Address", HNodeType.Regular, f).getId();
String relativesContainer = w.addHNode("Relatives", HNodeType.Regular, f).getId();
HTable personTable = w.getHeaders().getHNode(personContainer)
.addNestedTable("Person Table", w, f);
String firstName = personTable.addHNode("First Name", HNodeType.Regular, w, f).getId();
String lastName = personTable.addHNode("Last Name", HNodeType.Regular, w, f).getId();
HTable addressTable = w.getHeaders().getHNode(addressContainer)
.addNestedTable("Address Table", w, f);
String what = addressTable.addHNode("What", HNodeType.Regular, w, f).getId();
String address = addressTable.addHNode("Address", HNodeType.Regular, w, f).getId();
HTable relativesTable = w.getHeaders().getHNode(relativesContainer)
.addNestedTable("Relatives Person Table", w, f);
String relFirstName = relativesTable.addHNode("Relatives First Name", HNodeType.Regular,
w, f).getId();
String relLastName = relativesTable.addHNode("Relatives Last Name", HNodeType.Regular, w,
f).getId();
// Row 1
Row r1 = w.addRow(f);
r1.setValue(ss, "123-45-6789", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Pedro", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f)
.setValue(firstName, "P Alejandro", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Pedro A", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Pablo", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Piotr", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Szekeli", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "CK Lee", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Zekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Zsekely", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Szeke", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Peter", f)
.setValue(lastName, "Sequeli", f);
r1.addNestedRow(addressContainer, f).setValue(what, "home", f)
.setValue(address, "1401 E Maple Ave, El Segundo, CA 90245", f);
r1.addNestedRow(addressContainer, f)
.setValue(what, "work", f)
.setValue(address,
"4676 Admiralty Way #1000, Marina del Rey, CA 90292", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Claudia", f)
.setValue(relLastName, "Szekely", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Susana", f)
.setValue(relLastName, "Szekely", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Cristina", f)
.setValue(relLastName, "Sierra", f);
Row r2 = w.addRow(f);
r2.setValue(ss, "007-00-7007", f);
r2.addNestedRow(personContainer, f).setValue(firstName, "Shubham", f)
.setValue(lastName, "Gupta", f);
r2.addNestedRow(addressContainer, f)
.setValue(what, "home", f)
.setValue(address,
"7077 Alvern St # 118, Los Angeles, CA - 90045", f);
r2.addNestedRow(addressContainer, f)
.setValue(what, "work", f)
.setValue(address,
"4676 Admiralty Way #1000, Marina del Rey, CA 90292", f);
r2.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Anushree", f)
.setValue(relLastName, "Mehra", f);
r2.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Sameer", f)
.setValue(relLastName, "Mohan", f);
r2.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Suhani", f)
.setValue(relLastName, "Gupta", f);
r2.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Sarika", f)
.setValue(relLastName, "Saxena", f);
return w;
}
public static Worksheet createSample1small(Workspace workspace) {
RepFactory f = workspace.getFactory();
Worksheet w = f.createWorksheet("Complex Smaple Table", workspace, "UTF-8");
String ss = w.addHNode("Social Security", HNodeType.Regular, f).getId();
String personContainer = w.addHNode("Person", HNodeType.Regular, f).getId();
String addressContainer = w.addHNode("Address", HNodeType.Regular, f).getId();
String relativesContainer = w.addHNode("Relatives", HNodeType.Regular, f).getId();
HTable personTable = w.getHeaders().getHNode(personContainer)
.addNestedTable("Person Table", w, f);
String firstName = personTable.addHNode("First Name", HNodeType.Regular, w, f).getId();
String lastName = personTable.addHNode("Last Name", HNodeType.Regular, w, f).getId();
HTable addressTable = w.getHeaders().getHNode(addressContainer)
.addNestedTable("Address Table", w, f);
String what = addressTable.addHNode("What", HNodeType.Regular, w, f).getId();
String address = addressTable.addHNode("Address", HNodeType.Regular, w, f).getId();
HTable relativesTable = w.getHeaders().getHNode(relativesContainer)
.addNestedTable("Relatives Person Table", w, f);
String relFirstName = relativesTable.addHNode("Relatives First Name", HNodeType.Regular,
w, f).getId();
String relLastName = relativesTable.addHNode("Relatives Last Name", HNodeType.Regular, w,
f).getId();
// Row 1
Row r1 = w.addRow(f);
r1.setValue(ss, "123-45-6789", f);
r1.addNestedRow(personContainer, f).setValue(firstName, "Pedro", f)
.setValue(lastName, "Szekely", f);
r1.addNestedRow(addressContainer, f).setValue(what, "home", f)
.setValue(address, "1401 E Maple Ave", f);
r1.addNestedRow(addressContainer, f).setValue(what, "work", f)
.setValue(address, "4676 Admiralty", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Claudia", f)
.setValue(relLastName, "Szekely", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Susana", f)
.setValue(relLastName, "Szekely", f);
r1.addNestedRow(relativesContainer, f)
.setValue(relFirstName, "Cristina", f)
.setValue(relLastName, "Sierra", f);
return w;
}
public static Worksheet createFlatWorksheet(Workspace wsp, int numRows,
int numColumns) {
Worksheet w = wsp.getFactory().createWorksheet(
"Table (" + numRows + ", " + numColumns + ")", wsp, "UTF-8");
for (int c = 1; c <= numColumns; c++) {
w.getHeaders().addHNode("Column " + c, HNodeType.Regular, w, wsp.getFactory());
}
int vCount = 1;
for (int r = 1; r <= numRows; r++) {
Row row = w.addRow(wsp.getFactory());
for (HNode hn : w.getHeaders().getSortedHNodes()) {
row.setValue(hn.getId(), "Value " + vCount, wsp.getFactory());
vCount += 1;
}
}
return w;
}
public static Worksheet createFromJsonTextFile(Workspace workspace,
String fileName) {
FileReader r;
try {
r = new FileReader(fileName);
Object o = JSONUtil.createJson(r);
File f = new File(fileName);
JsonImport ji = new JsonImport(o, f.getName(), workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (FileNotFoundException e) {
logger.error("Cannot read file " + fileName + ".");
e.printStackTrace();
} catch (JSONException e) {
logger.error("Could not parse JSON in file " + fileName + ".");
e.printStackTrace();
}
return null;
}
public static Worksheet createFromXMLTextFile(Workspace workspace,
String fileName) {
File xmlFile = new File(fileName);
try {
String fileContents = FileUtil.readFileContentsToString(xmlFile, "UTF-8");
// Converting the XML to JSON
JSONObject json = XML.toJSONObject(fileContents);
JsonImport ji = new JsonImport(json, fileName, workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (FileNotFoundException e) {
logger.error("Cannot read file " + fileName + ".");
e.printStackTrace();
} catch (JSONException e) {
logger.error("Could not parse JSON in file " + fileName + ".");
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
public static String getSampleJsonString(int numRows) {
JSONStringer x = new JSONStringer();
Random rand = new Random(0);
try {
JSONWriter top = x.array();
for (int i = 1; i <= numRows; i++) {
JSONWriter o = top.object();
o.key("a").value("a" + i);
o.key("b").value("b" + i);
JSONWriter c = o.key("c").array();
for (int ci = 1; ci <= 10; ci++) {
JSONWriter co = c.object();
co.key("c.1").value("c.1_" + ci);
if (rand.nextBoolean()) {
co.key("c.2").value("c.2_" + ci);
}
if (rand.nextBoolean()) {
JSONWriter c3a = co.key("c.3").array();
for (int c3i = 1; c3i < rand.nextInt(10) + 1; c3i++) {
JSONWriter c3o = c3a.object();
if (rand.nextBoolean()) {
co.key("c.3.1").value(
"c.3.1_" + c3i + "+" + ci + "+" + i);
}
if (rand.nextBoolean()) {
co.key("c.3.2").value("c.3.2_" + c3i);
}
if (rand.nextBoolean()) {
co.key("c.3.3").value("c.3.3_" + c3i);
}
if (rand.nextBoolean()) {
JSONWriter c34o = co.key("c.3.4").object();
c34o.key("c.3.4.1").value("c.3.4.1_X");
c34o.key("c.3.4.2").value("c.3.4.1_Y");
c34o.endObject();
}
c3o.endObject();
}
c3a.endArray();
}
co.endObject();
}
c.endArray();
// List of primitive values.
JSONWriter d = o.key("d").array();
for (int di = 1; di < rand.nextInt(10) + 1; di++) {
d.value("d" + di);
}
d.endArray();
JSONWriter e = o.key("e").array();
for (int ei = 1; ei < rand.nextInt(10) + 1; ei++) {
if (rand.nextBoolean()) {
e.value("e" + ei + "+" + i);
} else {
e.object().key("e.1").value("e.1_" + ei).key("e.2")
.value("e.2_" + ei).endObject();
}
}
e.endArray();
o.endObject();
}
top.endArray();
} catch (JSONException e) {
e.printStackTrace();
return null;
}
return x.toString();
}
public static String getJsonForUnitTest1() {
JSONStringer x = new JSONStringer();
Random rand = new Random(0);
try {
JSONWriter top = x.array();
for (int i = 1; i <= 2; i++) {
JSONWriter o = top.object();
o.key("a").value("a" + i);
o.key("b").value("b" + i);
JSONWriter c = o.key("c").array();
for (int ci = 1; ci <= 10; ci++) {
JSONWriter co = c.object();
co.key("c.1").value("c.1_" + ci);
if (rand.nextBoolean()) {
co.key("c.2").value("c.2_" + ci);
}
if (rand.nextBoolean()) {
//
}
co.endObject();
}
c.endArray();
// List of primitive values.
JSONWriter d = o.key("d").array();
for (int di = 1; di < rand.nextInt(10) + 1; di++) {
d.value("d" + di);
}
d.endArray();
JSONWriter e = o.key("e").array();
for (int ei = 1; ei < rand.nextInt(10) + 1; ei++) {
if (rand.nextBoolean()) {
e.value("e" + ei + "+" + i);
} else {
e.object().key("e.1").value("e.1_" + ei).key("e.2")
.value("e.2_" + ei).endObject();
}
}
e.endArray();
o.endObject();
}
top.endArray();
} catch (JSONException e) {
e.printStackTrace();
return null;
}
return x.toString();
}
public static String getJsonForUnitTest4() {
JSONStringer x = new JSONStringer();
Random rand = new Random(0);
try {
JSONWriter top = x.array();
for (int i = 1; i <= 1; i++) {
JSONWriter o = top.object();
JSONWriter c = o.key("c").array();
for (int ci = 1; ci <= 3; ci++) {
JSONWriter co = c.object();
if (rand.nextBoolean()) {
co.key("c.2").value("c.2_" + ci);
}
if (rand.nextBoolean()) {
JSONWriter c3a = co.key("c.3").array();
for (int c3i = 1; c3i < 3; c3i++) {
JSONWriter c3o = c3a.object();
if (rand.nextBoolean()) {
co.key("c.3.1").value(
"c.3.1_" + c3i + "+" + ci + "+" + i);
}
if (rand.nextBoolean()) {
co.key("c.3.3").value("c.3.3_" + c3i);
}
if (rand.nextBoolean()) {
JSONWriter c34o = co.key("c.3.4").object();
c34o.key("c.3.4.2").value("c.3.4.1_Y");
c34o.endObject();
}
c3o.endObject();
}
c3a.endArray();
}
co.endObject();
}
c.endArray();
o.endObject();
}
top.endArray();
} catch (JSONException e) {
e.printStackTrace();
return null;
}
return x.toString();
}
public static String getJsonForUnitTest5() {
JSONStringer x = new JSONStringer();
Random rand = new Random(0);
try {
JSONWriter top = x.array();
for (int i = 1; i <= 1; i++) {
JSONWriter o = top.object();
JSONWriter c = o.key("c").array();
for (int ci = 1; ci <= 4; ci++) {
JSONWriter co = c.object();
co.key("c.1").value("c.1_" + ci);
if (rand.nextBoolean()) {
// Need the call to rand to make the test come out
// right.
}
if (rand.nextBoolean()) {
JSONWriter c3a = co.key("c.3").array();
for (int c3i = 1; c3i < rand.nextInt(10) + 1; c3i++) {
JSONWriter c3o = c3a.object();
if (rand.nextBoolean()) {
co.key("c.3.1").value(
"c.3.1_" + c3i + "+" + ci + "+" + i);
}
if (rand.nextBoolean()) {
co.key("c.3.2").value("c.3.2_" + c3i);
}
if (rand.nextBoolean()) {
co.key("c.3.3").value("c.3.3_" + c3i);
}
if (rand.nextBoolean()) {
JSONWriter c34o = co.key("c.3.4").object();
c34o.key("c.3.4.1").value("c.3.4.1_X");
c34o.key("c.3.4.2").value("c.3.4.1_Y");
c34o.endObject();
}
c3o.endObject();
}
c3a.endArray();
}
co.endObject();
}
c.endArray();
JSONWriter e = o.key("e").array();
for (int ei = 1; ei < 6; ei++) {
if (rand.nextBoolean()) {
e.value("e" + ei + "+" + i);
} else {
e.object().key("e.1").value("e.1_" + ei).endObject();
}
}
e.endArray();
o.endObject();
}
top.endArray();
} catch (JSONException e) {
e.printStackTrace();
return null;
}
return x.toString();
}
public static String getJsonForUnitTest6() {
JSONStringer x = new JSONStringer();
Random rand = new Random(0);
try {
JSONWriter top = x.array();
for (int i = 1; i <= 1; i++) {
JSONWriter o = top.object();
JSONWriter c = o.key("c").array();
for (int ci = 1; ci <= 1; ci++) {
JSONWriter co = c.object();
// co.key("c.1").value("c.1_" + ci);
if (rand.nextBoolean()) {
// Need the call to rand to make the test come out
// right.
}
if (rand.nextBoolean()) {
JSONWriter c3a = co.key("c.3").array();
for (int c3i = 1; c3i <= 2; c3i++) {
JSONWriter c3o = c3a.object();
if (rand.nextBoolean()) {
co.key("c.3.1").value(
"c.3.1_" + c3i + "+" + ci + "+" + i);
}
if (rand.nextBoolean()) {
JSONWriter c34o = co.key("c.3.4").object();
c34o.key("c.3.4.1").value("c.3.4.1_X");
c34o.endObject();
}
c3o.endObject();
}
c3a.endArray();
}
co.endObject();
}
c.endArray();
JSONWriter e = o.key("e").array();
for (int ei = 1; ei <= 3; ei++) {
e.object().key("e.1").value("e.1_" + ei).endObject();
}
e.endArray();
o.endObject();
}
top.endArray();
} catch (JSONException e) {
e.printStackTrace();
return null;
}
return x.toString();
}
public static Worksheet createUnitTest1(Workspace workspace) {
return createWorksheetFromJsonString("unit-test-1",
getJsonForUnitTest1(), workspace);
}
public static Worksheet createUnitTest2(Workspace workspace) {
String s = "[{\"e\":[],\"c\":[{\"c.1\":\"c.1_1\"}]},{\"d\":[\"d1\"],\"e\":[\"e1+2\"],\"c\":[{\"c.1\":\"c.1_1\"}]}]";
return createWorksheetFromJsonString("unit-test-2", s, workspace);
}
public static Worksheet createUnitTest3(Workspace workspace) {
String s = "[{\"d\":[\"d4\"],\"e\":[],\"c\":[{\"c.1\":\"c.1_1\"}]},{\"d\":[\"d1\"],\"e\":[\"e1+2\"],\"c\":[{\"c.1\":\"c.1_1\"}]}]";
return createWorksheetFromJsonString("unit-test-3", s, workspace);
}
public static Worksheet createUnitTest4(Workspace workspace) {
return createWorksheetFromJsonString("unit-test-4",
getJsonForUnitTest4(), workspace);
}
public static Worksheet createUnitTest5(Workspace workspace) {
return createWorksheetFromJsonString("unit-test-5",
getJsonForUnitTest5(), workspace);
}
public static Worksheet createUnitTest6(Workspace workspace) {
return createWorksheetFromJsonString("unit-test-6",
getJsonForUnitTest6(), workspace);
}
public static Worksheet createWorksheetFromJsonString(String name,
String jsonString, Workspace workspace) {
try {
Object o = JSONUtil.createJson(jsonString);
JSONUtil.writeJsonFile(o, name + ".json");
JsonImport ji = new JsonImport(o, name, workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJson(Workspace workspace, int numRows) {
try {
Object o = JSONUtil.createJson(getSampleJsonString(numRows));
JsonImport ji = new JsonImport(o, "Sample JSON", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createJsonWithFunnyCharacters(Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
String html = "<ul><li>item 1</li></ul>";
x.object().key("double quote")
.value("string with \"double quotes\"")
.key("single quotes")
.value("'starts has ' and \"ends\" with '").key("tabs")
.value("there is a tab between \"x\" and \"y\": x\ty")
.key("newlines").value("there sho\nuld be a newline")
.key("HTML").value(html).key("URL").value("http://cnn.com")
.endObject();
JsonImport ji = new JsonImport(x.toString(),
"Funny Characters", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithEmptyNestedTable1(
Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a_1").key("b").array()
//
.object().key("b.1").value("b.1_1").key("b.2")
.value("b.2_1").endObject()
//
// .object().key("b.1").value("b.1_2").key("b.2")
// .value("b.2_2").endObject()
//
.endArray().endObject();
topA.object().key("a").value("a_2").endObject();
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Empty Nested Table 1", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithEmptyNestedTable2(
Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a_1").key("b").array()
//
.object().key("b.1").value("b.1_1").key("b.2")
.value("b.2_1").endObject()
//
.object().key("b.1").value("b.1_2").endObject()
//
.endArray().endObject();
topA.object().key("a").value("a_2").endObject();
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Empty Nested Table 2", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithEmptyNestedTable3(
Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a_1").key("b").array()
//
.object().key("b.1").value("b.1_1").key("b.2")
.value("b.2_1").endObject()
//
.endArray().endObject();
topA.object().key("b").array().endArray().endObject();
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Empty Nested Table 3", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithEmptyNestedTable4(
Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a_1").key("b").array()
//
.object().key("b.1").value("b.1_1").key("b.2")
.value("b.2_1").endObject()
//
.object().key("b.2").value("b.2_2").endObject()
//
.object().key("b.1").value("b.1_3").endObject()
//
.endArray().endObject();
topA.object().key("a").value("a_2").endObject();
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Empty Nested Table 4", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithNestedTable1(Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a/1").key("b")
.array()
//
.object().key("b.1").value("b.1/1,1").key("b.2")
.value("b.2/1,1").endObject()
//
.object().key("b.1").value("b.1/1,2").key("b.2")
.value("b.2/1,2").endObject()
//
.endArray().endObject();
topA.object().key("a").value("a/2").key("b")
.array()
//
.object().key("b.1").value("b.1/2,1").key("b.2")
.value("b.2/2,1").endObject()
//
.object().key("b.1").value("b.1/2,2").key("b.2")
.value("b.2/2,2").endObject()
//
.endArray().endObject();
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Nested Table 1", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSampleJsonWithNestedTable2(
boolean hasTwoRows, Workspace workspace) {
try {
JSONStringer x = new JSONStringer();
JSONWriter topA = x.array();
topA.object().key("a").value("a/1").key("b").array()
//
.object()//
.key("b.1").value("b.1/1,1")//
.key("b.2").array()//
.object()//
.key("b.2.1").value("b.2.1/1,1,1")//
.key("b.2.2").value("b.2.2/1,1,1")//
.endObject()//
.object()//
.key("b.2.1").value("b.2.1/1,1,2")//
.key("b.2.2").value("b.2.2/1,1,2")//
.endObject()//
.endArray()//
.endObject()//
//
.object()//
.key("b.1").value("b.1/1,2")//
.key("b.2").array()//
.object()//
.key("b.2.1").value("b.2.1/1,2,1")//
.key("b.2.2").value("b.2.2/1,2,1")//
.endObject()//
.endArray()//
.endObject();//
topA.endArray().endObject();
if (hasTwoRows) {
topA.object().key("a").value("a/2").key("b").array()
//
.object()//
.key("b.1").value("b.1/2,1")//
.key("b.2").array()//
.object()//
.key("b.2.1").value("b.2.1/2,1,1")//
.key("b.2.2").value("b.2.2/2,1,1")//
.endObject()//
.endArray()//
.endObject()//
//
.object()//
.key("b.1").value("b.1/2,2")//
.key("b.2").array()//
.object()//
.key("b.2.1").value("b.2.1/2,2,1")//
.key("b.2.2").value("b.2.2/2,2,1")//
.endObject()//
.endArray()//
.endObject()//
//
;
topA.endArray().endObject();
}
topA.endArray();
JsonImport ji = new JsonImport(x.toString(),
"Nested Table 2", workspace, "UTF-8", -1);
Worksheet w = ji.generateWorksheet();
return w;
} catch (JSONException e) {
e.printStackTrace();
return null;
}
}
public static Worksheet createSamplePathwaysWorksheet(Workspace workspace) {
String json = "["
+ "{"
+ "\"ACCESSION_ID\": \"PA2039\","
+ "\"NAME\": \"Methotrexate Pathway\","
+ "\"DRUG_ID\": \"PA452621\","
+ "\"DRUG_NAME\": \"antineoplastic agents\","
+ "\"GENE_ID\": \"PA267\","
+ "\"GENE_NAME\": \"ABCB1\","
+ "\"DISEASE_ID\": \"PA443434\","
+ "\"DISEASE_NAME\": \"Arthritis, Rheumatoid\""
+ "},"
+ "{"
+ "\"ACCESSION_ID\": \"PA2040\","
+ "\"NAME\": \"Thiopurine Pathway\","
+ "\"DRUG_ID\": \"PA452621\","
+ "\"DRUG_NAME\": \"antineoplastic agents\","
+ "\"GENE_ID\": \"PA397\","
+ "\"GENE_NAME\": \"ABCC4\","
+ "\"DISEASE_ID\": \"PA446116\","
+ "\"DISEASE_NAME\": \"Inflammatory Bowel Diseases\""
+ "},"
+ "{"
+ "\"ACCESSION_ID\": \"PA145011108\","
+ "\"NAME\": \"Statin Pathway (PK)\","
+ "\"DRUG_ID\": \"PA448500\","
+ "\"DRUG_NAME\": \"atorvastatin\","
+ "\"GENE_ID\": \"PA267\","
+ "\"GENE_NAME\": \"ABCB1\","
+ "\"DISEASE_ID\": \"PA443635\","
+ "\"DISEASE_NAME\": \"Cardiovascular Diseases\""
+ "},"
+ "{"
+ "\"ACCESSION_ID\": \"PA145011115\","
+ "\"NAME\": \"Phenytoin Pathway (PK)\","
+ "\"DRUG_ID\": \"PA450947\","
+ "\"DRUG_NAME\": \"phenytoin\","
+ "\"GENE_ID\": \"PA27093\","
+ "\"GENE_NAME\": \"CYP1A2\","
+ "\"DISEASE_ID\": \"PA444065\","
+ "\"DISEASE_NAME\": \"Epilepsy\""
+ "},"
+ "{"
+ "\"ACCESSION_ID\": \"PA164713560\","
+ "\"NAME\": \"il22 soluble receptor signaling pathway - (BioCarta via Pathway Interaction Database)\","
+ "\"DRUG_ID\": \"\"," + "\"DRUG_NAME\": \"\","
+ "\"GENE_ID\": \"PA29779\"," + "\"GENE_NAME\": \"IL10RA\","
+ "\"DISEASE_ID\": \"\"," + "\"DISEASE_NAME\": \"\"" + "}"
+ "];";
logger.debug(json);
return createWorksheetFromJsonString("PathwaysPharmGKB", json,
workspace);
}
public static Worksheet createSamplePathwaysWithNestingWorksheet(
Workspace workspace) {
String json = "["
+ "{"
+ "\"ACCESSION_ID\": \"PA2039\","
+ "\"NAME\": \"Methotrexate Pathway\","
+ "\"DRUG\": {"
+ "\"DRUG_ID\": \"PA452621\","
+ "\"DRUG_NAME\": ["
+ "\"antineoplastic agents\","
+ "\"TEST1\","
+ "\"TEST2\""
+ "]"
+ "},"
+ "\"GENE_ID\": \"PA267\","
+ "\"GENE_NAME\": \"ABCB1\","
+ "\"DISEASE_ID\": \"PA443434\","
+ "\"DISEASE_NAME\": \"Arthritis, Rheumatoid\""
+ "},"
+
/*
* "{" + "\"ACCESSION_ID\": \"PA2040\"," +
* "\"NAME\": \"Thiopurine Pathway\"," + "\"DRUG\": {"+
* "\"DRUG_ID\": \"PA452621\","+ "\"DRUG_NAME\": ["+
* "\"antineoplastic agents\","+ "\"TEST3\","+ "\"TEST4\""+ "]"+
* "},"+ "\"GENE_ID\": \"PA397\"," + "\"GENE_NAME\": \"ABCC4\","
* + "\"DISEASE_ID\": \"PA446116\"," +
* "\"DISEASE_NAME\": \"Inflammatory Bowel Diseases\"" + "}," +
* "{" + "\"ACCESSION_ID\": \"PA145011108\"," +
* "\"NAME\": \"Statin Pathway (PK)\"," + "\"DRUG\": {"+
* "\"DRUG_ID\": \"PA448500\","+ "\"DRUG_NAME\": ["+
* "\"atorvastatin\","+ "\"TEST5\","+ "\"TEST6\""+ "]"+ "},"+
* "\"GENE_ID\": \"PA267\"," + "\"GENE_NAME\": \"ABCB1\"," +
* "\"DISEASE_ID\": \"PA443635\"," +
* "\"DISEASE_NAME\": \"Cardiovascular Diseases\"" + "}," + "{"
* + "\"ACCESSION_ID\": \"PA145011115\"," +
* "\"NAME\": \"Phenytoin Pathway (PK)\"," + "\"DRUG\": {"+
* "\"DRUG_ID\": \"PA450947\","+ "\"DRUG_NAME\": ["+
* "\"phenytoin\","+ "\"TEST1\","+ "\"TEST2\""+ "]"+ "},"+
* "\"GENE_ID\": \"PA27093\"," + "\"GENE_NAME\": \"CYP1A2\"," +
* "\"DISEASE_ID\": \"PA444065\"," +
* "\"DISEASE_NAME\": \"Epilepsy\"" + "}," +
*/
"{"
+ "\"ACCESSION_ID\": \"PA164713560\","
+ "\"NAME\": \"il22 soluble receptor signaling pathway - (BioCarta via Pathway Interaction Database)\","
+ "\"DRUG\": {" + "\"DRUG_ID\": \"\"," + "\"DRUG_NAME\": ["
+ "\"\"," + "]" + "}," + "\"GENE_ID\": \"PA29779\","
+ "\"GENE_NAME\": \"IL10RA\"," + "\"DISEASE_ID\": \"\","
+ "\"DISEASE_NAME\": \"\"" + "}" + "];";
logger.debug(json);
return createWorksheetFromJsonString("PathwaysPharmGKBNesting", json,
workspace);
}
}