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redcap ability to read from a file instead of from just a redcap api
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mem61 committed Feb 16, 2022
1 parent 90c79f0 commit 95a235f
Showing 1 changed file with 54 additions and 22 deletions.
76 changes: 54 additions & 22 deletions edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/dao/redcap/RedcapPuller.java
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Expand Up @@ -68,6 +68,7 @@

import com.google.gson.Gson;

import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
import java.text.DateFormat;
Expand All @@ -78,6 +79,7 @@
import java.util.GregorianCalendar;
import java.util.List;
import java.util.Scanner;
import java.util.stream.Stream;

import javax.xml.bind.JAXBContext;
import javax.xml.datatype.DatatypeConfigurationException;
Expand All @@ -86,7 +88,10 @@
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.stream.XMLStreamException;

import java.math.*;
import java.math.*;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;


public class RedcapPuller {
Expand All @@ -104,6 +109,7 @@ public class RedcapPuller {
//String ontologyFormat = "tree"; //tree = For Tree format, popup = For popup with selection
String api = null;
String redcapApiUrl = null;
String startDateName = null;

public void pullRecordRequest(String redcapUrl, String record, String recordId, String surveyForm, String pid) throws I2B2Exception {
if (record == null || record.isEmpty()) {
Expand Down Expand Up @@ -144,35 +150,46 @@ else if (projectParam.getName().equalsIgnoreCase("REDCAP_PROTECTED_ROLE"))
protectedRole = projectParam.getValue();
else if (projectParam.getName().equalsIgnoreCase("REDCAP_ONTOLOGY_REFRESH"))
refreshOntology = projectParam.getValue();
else if (projectParam.getName().equalsIgnoreCase("REDCAP_STARTDATE_NAME"))
startDateName = projectParam.getValue();

}

if (api == null)
throw new I2B2Exception("Project " + surveyForm + " does not have a param called REDCAP_TOKEN_PID_" + pid + " with the token number.");

List <NameValuePair> apiCall = new ArrayList <NameValuePair>();
apiCall.add(new BasicNameValuePair("token", api));
apiCall.add(new BasicNameValuePair("content", "metadata"));
apiCall.add(new BasicNameValuePair("format", FORMAT));
HttpPost httpPost = new HttpPost(redcapApiUrl);

httpPost.setEntity(new UrlEncodedFormEntity(apiCall, HTTP.UTF_8));
httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");

CloseableHttpClient client = HttpClientBuilder.create().build();
response = client.execute(httpPost);
if (response.getStatusLine().getStatusCode() >= 300) {
throw new I2B2Exception(String.format("failure - received a %d for %s.",
response.getStatusLine().getStatusCode(), httpPost.getURI().toString()));
}

HttpEntity entity = response.getEntity();
responseStr = EntityUtils.toString(entity, "UTF-8");

if (response.getStatusLine().getStatusCode() == HttpStatus.SC_OK) {
if (redcapApiUrl.startsWith("file:")) {
responseStr = readLineByLineJava8( redcapApiUrl.substring(7) ) ;
metadatas = new Gson().fromJson(responseStr, DataCollectionInstrumentMetadata[].class);
if (metadatas != null) {
redcapResult.getMetadata().addAll(Arrays.asList(metadatas));
}
} else {
List <NameValuePair> apiCall = new ArrayList <NameValuePair>();
apiCall.add(new BasicNameValuePair("token", api));
apiCall.add(new BasicNameValuePair("content", "metadata"));
apiCall.add(new BasicNameValuePair("format", FORMAT));
HttpPost httpPost = new HttpPost(redcapApiUrl);

httpPost.setEntity(new UrlEncodedFormEntity(apiCall, HTTP.UTF_8));
httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");

CloseableHttpClient client = HttpClientBuilder.create().build();
response = client.execute(httpPost);
if (response.getStatusLine().getStatusCode() >= 300) {
throw new I2B2Exception(String.format("failure - received a %d for %s.",
response.getStatusLine().getStatusCode(), httpPost.getURI().toString()));
}

HttpEntity entity = response.getEntity();
responseStr = EntityUtils.toString(entity, "UTF-8");

if (response.getStatusLine().getStatusCode() == HttpStatus.SC_OK) {
metadatas = new Gson().fromJson(responseStr, DataCollectionInstrumentMetadata[].class);
if (metadatas != null) {
redcapResult.getMetadata().addAll(Arrays.asList(metadatas));
}
}
}

} catch (Exception e) {
Expand Down Expand Up @@ -236,6 +253,21 @@ else if (projectParam.getName().equalsIgnoreCase("REDCAP_ONTOLOGY_REFRESH"))
}
}

private static String readLineByLineJava8(String filePath)
{
StringBuilder contentBuilder = new StringBuilder();

try (Stream<String> stream = Files.lines( Paths.get(filePath), StandardCharsets.UTF_8))
{
stream.forEach(s -> contentBuilder.append(s).append("\n"));
}
catch (IOException e)
{
e.printStackTrace();
}

return contentBuilder.toString();
}

private void insertI2B2(SurveyRecord[] records, APISurveyResponse redcapResult, String surveyForm, ProjectType projectParams
, SecurityType securityType, DataCollectionInstrumentMetadata[] metadatas ) throws I2B2Exception, DatatypeConfigurationException, AxisFault, XMLStreamException, JAXBUtilException {
Expand Down Expand Up @@ -631,7 +663,7 @@ else if (metadata.getFieldContent().equals("datetime_seconds_mdy"))
FORMATER = "yyyy-MM-dd kk:mm:ss";
else if (metadata.getFieldContent().equals("datetime_seconds_dmy"))
FORMATER = "yyyy-MM-dd kk:mm:ss";

DateFormat format = new SimpleDateFormat(FORMATER);
Date date = format.parse(record.getValue());

Expand Down

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