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Merge pull request #542 from johnjaylward/fixXmlHexEntityParse
Fix xml hex entity parse
This commit is contained in:
Sean Leary
GitHub
commit
880402120c
@ -167,7 +167,7 @@ public class XMLTokener extends JSONTokener {
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// if our entity is an encoded unicode point, parse it.
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if (e.charAt(0) == '#') {
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int cp;
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if (e.charAt(1) == 'x') {
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if (e.charAt(1) == 'x' || e.charAt(1) == 'X') {
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// hex encoded unicode
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cp = Integer.parseInt(e.substring(2), 16);
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} else {
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@ -103,20 +103,18 @@ public class Util {
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*/
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if (!(value instanceof Number && expectedValue instanceof Number)) {
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// Non-Number and non-matching types
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assertTrue("object types should be equal for actual: "+
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value.toString()+" ("+
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value.getClass().toString()+") expected: "+
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expectedValue.toString()+" ("+
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expectedValue.getClass().toString()+")",
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value.getClass().toString().equals(
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expectedValue.getClass().toString()));
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assertEquals("object types should be equal ",
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expectedValue.getClass().toString(),
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value.getClass().toString()
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);
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}
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/**
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* Same types or both Numbers, compare by toString()
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*/
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assertTrue("string values should be equal for actual: "+
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value.toString()+" expected: "+expectedValue.toString(),
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value.toString().equals(expectedValue.toString()));
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assertEquals("values should be equal",
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expectedValue.toString(),
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value.toString()
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);
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}
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}
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}
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@ -34,12 +34,15 @@ import java.io.File;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.io.StringReader;
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import org.json.JSONArray;
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import org.json.JSONException;
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import org.json.JSONObject;
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import org.json.JSONTokener;
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import org.json.XML;
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import org.json.XMLParserConfiguration;
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import org.junit.Rule;
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@ -898,4 +901,57 @@ public class XMLTest {
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final JSONObject json = XML.toJSONObject(originalXml, new XMLParserConfiguration());
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assertEquals(expectedJsonString, json.toString());
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}
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/**
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* Tests to verify that supported escapes in XML are converted to actual values.
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*/
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@Test
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public void testIssue537CaseSensitiveHexEscapeMinimal(){
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String xmlStr =
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"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"+
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"<root>Neutrophils.Hypersegmented | Bld-Ser-Plas</root>";
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String expectedStr =
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"{\"root\":\"Neutrophils.Hypersegmented | Bld-Ser-Plas\"}";
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JSONObject xmlJSONObj = XML.toJSONObject(xmlStr, true);
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JSONObject expected = new JSONObject(expectedStr);
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Util.compareActualVsExpectedJsonObjects(xmlJSONObj, expected);
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}
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/**
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* Tests to verify that supported escapes in XML are converted to actual values.
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*/
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@Test
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public void testIssue537CaseSensitiveHexEscapeFullFile(){
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try {
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try(
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InputStream xmlStream = XMLTest.class.getClassLoader().getResourceAsStream("Issue537.xml");
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Reader xmlReader = new InputStreamReader(xmlStream);
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){
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JSONObject actual = XML.toJSONObject(xmlReader, true);
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try(
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InputStream jsonStream = XMLTest.class.getClassLoader().getResourceAsStream("Issue537.json");
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){
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final JSONObject expected = new JSONObject(new JSONTokener(jsonStream));
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Util.compareActualVsExpectedJsonObjects(actual,expected);
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}
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}
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} catch (IOException e) {
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fail("file writer error: " +e.getMessage());
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}
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}
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/**
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* Tests to verify that supported escapes in XML are converted to actual values.
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*/
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@Test
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public void testIssue537CaseSensitiveHexUnEscapeDirect(){
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String origStr =
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"Neutrophils.Hypersegmented | Bld-Ser-Plas";
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String expectedStr =
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"Neutrophils.Hypersegmented | Bld-Ser-Plas";
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String actualStr = XML.unescape(origStr);
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assertEquals("Case insensitive Entity unescape", expectedStr, actualStr);
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}
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}
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189
src/test/resources/Issue537.json
Normal file
189
src/test/resources/Issue537.json
Normal file
@ -0,0 +1,189 @@
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{
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"clinical_study": {
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"brief_summary": {
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"textblock": "CLEAR SYNERGY is an international multi center 2x2 randomized placebo controlled trial of"
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},
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"brief_title": "CLEAR SYNERGY Neutrophil Substudy",
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"overall_status": "Recruiting",
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"eligibility": {
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"study_pop": {
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"textblock": "Patients who are randomized to the drug RCT portion of the CLEAR SYNERGY (OASIS 9) trial"
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},
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"minimum_age": "19 Years",
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"sampling_method": "Non-Probability Sample",
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"gender": "All",
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"criteria": {
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"textblock": "Inclusion Criteria:"
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},
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"healthy_volunteers": "No",
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"maximum_age": "110 Years"
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},
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"number_of_groups": "2",
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"source": "NYU Langone Health",
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"location_countries": {
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"country": "United States"
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},
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"study_design_info": {
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"time_perspective": "Prospective",
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"observational_model": "Other"
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},
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"last_update_submitted_qc": "September 10, 2019",
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"intervention_browse": {
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"mesh_term": "Colchicine"
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},
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"official_title": "Studies on the Effects of Colchicine on Neutrophil Biology in Acute Myocardial Infarction: A Substudy of the CLEAR SYNERGY (OASIS 9) Trial",
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"primary_completion_date": {
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"type": "Anticipated",
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"content": "February 1, 2021"
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},
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"sponsors": {
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"lead_sponsor": {
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"agency_class": "Other",
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"agency": "NYU Langone Health"
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},
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"collaborator": [
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{
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"agency_class": "Other",
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"agency": "Population Health Research Institute"
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},
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{
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"agency_class": "NIH",
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"agency": "National Heart, Lung, and Blood Institute (NHLBI)"
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}
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]
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},
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"overall_official": {
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"role": "Principal Investigator",
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"affiliation": "NYU School of Medicine",
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"last_name": "Binita Shah, MD"
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},
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"overall_contact_backup": {
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"last_name": "Binita Shah, MD"
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},
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"condition_browse": {
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"mesh_term": [
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"Myocardial Infarction",
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"ST Elevation Myocardial Infarction",
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"Infarction"
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]
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},
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"overall_contact": {
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"phone": "646-501-9648",
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"last_name": "Fatmira Curovic",
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"email": "fatmira.curovic@nyumc.org"
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},
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"responsible_party": {
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"responsible_party_type": "Principal Investigator",
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"investigator_title": "Assistant Professor of Medicine",
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"investigator_full_name": "Binita Shah",
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"investigator_affiliation": "NYU Langone Health"
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},
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"study_first_submitted_qc": "March 12, 2019",
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"start_date": {
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"type": "Actual",
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"content": "March 4, 2019"
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},
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"has_expanded_access": "No",
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"study_first_posted": {
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"type": "Actual",
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"content": "March 14, 2019"
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},
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"arm_group": [
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{
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"arm_group_label": "Colchicine"
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},
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{
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"arm_group_label": "Placebo"
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}
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],
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"primary_outcome": {
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"measure": "soluble L-selectin",
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"time_frame": "between baseline and 3 months",
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"description": "Change in soluble L-selectin between baseline and 3 mo after STEMI in the placebo vs. colchicine groups."
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},
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"secondary_outcome": [
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{
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"measure": "Other soluble markers of neutrophil activity",
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"time_frame": "between baseline and 3 months",
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"description": "Other markers of neutrophil activity will be evaluated at baseline and 3 months after STEMI (myeloperoxidase, matrix metalloproteinase-9, neutrophil gelatinase-associated lipocalin, neutrophil elastase, intercellular/vascular cellular adhesion molecules)"
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},
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{
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"measure": "Markers of systemic inflammation",
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"time_frame": "between baseline and 3 months",
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"description": "Markers of systemic inflammation will be evaluated at baseline and 3 months after STEMI (high sensitive CRP, IL-1β)"
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},
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{
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"measure": "Neutrophil-driven responses that may further propagate injury",
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"time_frame": "between baseline and 3 months",
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"description": "Neutrophil-driven responses that may further propagate injury will be evaluated at baseline and 3 months after STEMI (neutrophil extracellular traps, neutrophil-derived microparticles)"
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}
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],
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"oversight_info": {
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"is_fda_regulated_drug": "No",
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"is_fda_regulated_device": "No",
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"has_dmc": "No"
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},
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"last_update_posted": {
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"type": "Actual",
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"content": "September 12, 2019"
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},
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"id_info": {
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"nct_id": "NCT03874338",
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"org_study_id": "18-01323",
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"secondary_id": "1R01HL146206"
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},
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"enrollment": {
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"type": "Anticipated",
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"content": "670"
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},
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"study_first_submitted": "March 12, 2019",
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"condition": [
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"Neutrophils.Hypersegmented | Bld-Ser-Plas",
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"STEMI - ST Elevation Myocardial Infarction"
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],
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"study_type": "Observational",
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"required_header": {
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"download_date": "ClinicalTrials.gov processed this data on July 19, 2020",
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"link_text": "Link to the current ClinicalTrials.gov record.",
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"url": "https://clinicaltrials.gov/show/NCT03874338"
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},
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"last_update_submitted": "September 10, 2019",
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"completion_date": {
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"type": "Anticipated",
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"content": "February 1, 2022"
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},
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"location": {
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"contact": {
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"phone": "646-501-9648",
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"last_name": "Fatmira Curovic",
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"email": "fatmira.curovic@nyumc.org"
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},
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"facility": {
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"address": {
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"zip": "10016",
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"country": "United States",
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"city": "New York",
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"state": "New York"
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},
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"name": "NYU School of Medicine"
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},
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"status": "Recruiting",
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"contact_backup": {
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"last_name": "Binita Shah, MD"
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}
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},
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"intervention": {
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"intervention_type": "Drug",
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"arm_group_label": [
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"Colchicine",
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"Placebo"
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],
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"description": "Participants in the main CLEAR SYNERGY trial are randomized to colchicine/spironolactone versus placebo in a 2x2 factorial design. The substudy is interested in the evaluation of biospecimens obtained from patients in the colchicine vs placebo group.",
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"intervention_name": "Colchicine Pill"
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},
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"patient_data": {
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"sharing_ipd": "No"
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},
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"verification_date": "September 2019"
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}
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}
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169
src/test/resources/Issue537.xml
Normal file
169
src/test/resources/Issue537.xml
Normal file
@ -0,0 +1,169 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<clinical_study>
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<!-- This xml conforms to an XML Schema at:
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https://clinicaltrials.gov/ct2/html/images/info/public.xsd -->
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<required_header>
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<download_date>ClinicalTrials.gov processed this data on July 19, 2020</download_date>
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<link_text>Link to the current ClinicalTrials.gov record.</link_text>
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<url>https://clinicaltrials.gov/show/NCT03874338</url>
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</required_header>
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<id_info>
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<org_study_id>18-01323</org_study_id>
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<secondary_id>1R01HL146206</secondary_id>
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<nct_id>NCT03874338</nct_id>
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</id_info>
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<brief_title>CLEAR SYNERGY Neutrophil Substudy</brief_title>
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<official_title>Studies on the Effects of Colchicine on Neutrophil Biology in Acute Myocardial Infarction: A Substudy of the CLEAR SYNERGY (OASIS 9) Trial</official_title>
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<sponsors>
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<lead_sponsor>
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<agency>NYU Langone Health</agency>
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<agency_class>Other</agency_class>
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</lead_sponsor>
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<collaborator>
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<agency>Population Health Research Institute</agency>
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<agency_class>Other</agency_class>
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</collaborator>
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<collaborator>
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<agency>National Heart, Lung, and Blood Institute (NHLBI)</agency>
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<agency_class>NIH</agency_class>
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</collaborator>
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</sponsors>
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<source>NYU Langone Health</source>
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<oversight_info>
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<has_dmc>No</has_dmc>
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<is_fda_regulated_drug>No</is_fda_regulated_drug>
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<is_fda_regulated_device>No</is_fda_regulated_device>
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</oversight_info>
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<brief_summary>
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<textblock>
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CLEAR SYNERGY is an international multi center 2x2 randomized placebo controlled trial of
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</textblock>
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</brief_summary>
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<overall_status>Recruiting</overall_status>
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<start_date type="Actual">March 4, 2019</start_date>
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<completion_date type="Anticipated">February 1, 2022</completion_date>
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<primary_completion_date type="Anticipated">February 1, 2021</primary_completion_date>
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<study_type>Observational</study_type>
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<has_expanded_access>No</has_expanded_access>
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<study_design_info>
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<observational_model>Other</observational_model>
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<time_perspective>Prospective</time_perspective>
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</study_design_info>
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<primary_outcome>
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<measure>soluble L-selectin</measure>
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<time_frame>between baseline and 3 months</time_frame>
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<description>Change in soluble L-selectin between baseline and 3 mo after STEMI in the placebo vs. colchicine groups.</description>
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</primary_outcome>
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<secondary_outcome>
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<measure>Other soluble markers of neutrophil activity</measure>
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<time_frame>between baseline and 3 months</time_frame>
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<description>Other markers of neutrophil activity will be evaluated at baseline and 3 months after STEMI (myeloperoxidase, matrix metalloproteinase-9, neutrophil gelatinase-associated lipocalin, neutrophil elastase, intercellular/vascular cellular adhesion molecules)</description>
|
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</secondary_outcome>
|
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<secondary_outcome>
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<measure>Markers of systemic inflammation</measure>
|
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<time_frame>between baseline and 3 months</time_frame>
|
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<description>Markers of systemic inflammation will be evaluated at baseline and 3 months after STEMI (high sensitive CRP, IL-1β)</description>
|
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</secondary_outcome>
|
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<secondary_outcome>
|
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<measure>Neutrophil-driven responses that may further propagate injury</measure>
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<time_frame>between baseline and 3 months</time_frame>
|
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<description>Neutrophil-driven responses that may further propagate injury will be evaluated at baseline and 3 months after STEMI (neutrophil extracellular traps, neutrophil-derived microparticles)</description>
|
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</secondary_outcome>
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<number_of_groups>2</number_of_groups>
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<enrollment type="Anticipated">670</enrollment>
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<condition>Neutrophils.Hypersegmented | Bld-Ser-Plas</condition>
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<condition>STEMI - ST Elevation Myocardial Infarction</condition>
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<arm_group>
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<arm_group_label>Colchicine</arm_group_label>
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</arm_group>
|
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<arm_group>
|
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<arm_group_label>Placebo</arm_group_label>
|
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</arm_group>
|
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<intervention>
|
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<intervention_type>Drug</intervention_type>
|
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<intervention_name>Colchicine Pill</intervention_name>
|
||||
<description>Participants in the main CLEAR SYNERGY trial are randomized to colchicine/spironolactone versus placebo in a 2x2 factorial design. The substudy is interested in the evaluation of biospecimens obtained from patients in the colchicine vs placebo group.</description>
|
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<arm_group_label>Colchicine</arm_group_label>
|
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<arm_group_label>Placebo</arm_group_label>
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</intervention>
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<eligibility>
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<study_pop>
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<textblock>
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Patients who are randomized to the drug RCT portion of the CLEAR SYNERGY (OASIS 9) trial
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</textblock>
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</study_pop>
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<sampling_method>Non-Probability Sample</sampling_method>
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<criteria>
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<textblock>
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Inclusion Criteria:
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</textblock>
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</criteria>
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<gender>All</gender>
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<minimum_age>19 Years</minimum_age>
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<maximum_age>110 Years</maximum_age>
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<healthy_volunteers>No</healthy_volunteers>
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</eligibility>
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<overall_official>
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<last_name>Binita Shah, MD</last_name>
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<role>Principal Investigator</role>
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<affiliation>NYU School of Medicine</affiliation>
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</overall_official>
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<overall_contact>
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<last_name>Fatmira Curovic</last_name>
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<phone>646-501-9648</phone>
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||||
<email>fatmira.curovic@nyumc.org</email>
|
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</overall_contact>
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<overall_contact_backup>
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<last_name>Binita Shah, MD</last_name>
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</overall_contact_backup>
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<location>
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<facility>
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<name>NYU School of Medicine</name>
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<address>
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<city>New York</city>
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<state>New York</state>
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<zip>10016</zip>
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<country>United States</country>
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</address>
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</facility>
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<status>Recruiting</status>
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<contact>
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||||
<last_name>Fatmira Curovic</last_name>
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<phone>646-501-9648</phone>
|
||||
<email>fatmira.curovic@nyumc.org</email>
|
||||
</contact>
|
||||
<contact_backup>
|
||||
<last_name>Binita Shah, MD</last_name>
|
||||
</contact_backup>
|
||||
</location>
|
||||
<location_countries>
|
||||
<country>United States</country>
|
||||
</location_countries>
|
||||
<verification_date>September 2019</verification_date>
|
||||
<study_first_submitted>March 12, 2019</study_first_submitted>
|
||||
<study_first_submitted_qc>March 12, 2019</study_first_submitted_qc>
|
||||
<study_first_posted type="Actual">March 14, 2019</study_first_posted>
|
||||
<last_update_submitted>September 10, 2019</last_update_submitted>
|
||||
<last_update_submitted_qc>September 10, 2019</last_update_submitted_qc>
|
||||
<last_update_posted type="Actual">September 12, 2019</last_update_posted>
|
||||
<responsible_party>
|
||||
<responsible_party_type>Principal Investigator</responsible_party_type>
|
||||
<investigator_affiliation>NYU Langone Health</investigator_affiliation>
|
||||
<investigator_full_name>Binita Shah</investigator_full_name>
|
||||
<investigator_title>Assistant Professor of Medicine</investigator_title>
|
||||
</responsible_party>
|
||||
<condition_browse>
|
||||
<!-- CAUTION: The following MeSH terms are assigned with an imperfect algorithm -->
|
||||
<mesh_term>Myocardial Infarction</mesh_term>
|
||||
<mesh_term>ST Elevation Myocardial Infarction</mesh_term>
|
||||
<mesh_term>Infarction</mesh_term>
|
||||
</condition_browse>
|
||||
<intervention_browse>
|
||||
<!-- CAUTION: The following MeSH terms are assigned with an imperfect algorithm -->
|
||||
<mesh_term>Colchicine</mesh_term>
|
||||
</intervention_browse>
|
||||
<patient_data>
|
||||
<sharing_ipd>No</sharing_ipd>
|
||||
</patient_data>
|
||||
<!-- Results have not yet been posted for this study -->
|
||||
</clinical_study>
|
||||
Loading…
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Reference in New Issue
Block a user