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ALS-7883: Fix issues from checkmarx report #213

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merged 2 commits into from
Nov 25, 2024
Merged

ALS-7883: Fix issues from checkmarx report #213

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cbc658b
ALS-7883: Fix issues from checkmarx report
ramari16 Nov 22, 2024
d52a28d
ALS-7883: Remove unused logger
ramari16 Nov 25, 2024
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8 changes: 6 additions & 2 deletions pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,13 @@
import javax.persistence.*;

import edu.harvard.dbmi.avillach.util.PicSureStatus;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

@Entity(name = "query")
public class Query extends BaseEntity {

private static final Logger logger = LoggerFactory.getLogger(Query.class);
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Delete


//TODO may not need these two things
private Date startTime;
Expand Down Expand Up @@ -89,7 +93,7 @@ public String getQuery() {
outStr += line;
}
} catch (IOException e) {
e.printStackTrace();
throw new UncheckedIOException(e);
}
return outStr;
}
Expand All @@ -106,7 +110,7 @@ public void setQuery(String queryStr) {
gzip.close();
this.query = obj.toByteArray();
} catch (IOException e) {
e.printStackTrace();
throw new UncheckedIOException(e);
}
}

Expand Down
12 changes: 2 additions & 10 deletions ...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java
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Expand Up @@ -142,13 +142,8 @@ public List<T> getByColumns(CriteriaQuery query, Root root, Predicate... predica
query.select(root);
if (predicates != null && predicates.length > 0)
query.where(predicates);
try{
return em().createQuery(query)
.getResultList();
} catch (PersistenceException e) {
e.printStackTrace();
return null;
}
return em().createQuery(query)
.getResultList();

}

Expand All @@ -168,9 +163,6 @@ public T getUniqueResultByColumns(CriteriaQuery query, Root root, Predicate... p
.getSingleResult();
} catch (NoResultException e){
return null;
} catch (PersistenceException e){
e.printStackTrace();
return null;
}
}

Expand Down
2 changes: 1 addition & 1 deletion pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java
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Expand Up @@ -102,7 +102,7 @@ public String status() {
lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED;
}
} catch (Exception e) {
e.printStackTrace();
logger.error("One or more components degraded", e);
lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED;
}
return lastStatus;
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33 changes: 0 additions & 33 deletions pic-sure-initializer/README.md
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58 changes: 0 additions & 58 deletions pic-sure-initializer/pom.xml
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103 changes: 0 additions & 103 deletions pic-sure-initializer/src/main/java/edu/harvard/hms/dbmi/avillach/PicSureInitializer.java
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8 changes: 0 additions & 8 deletions pic-sure-initializer/src/main/resources/log4j.properties
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51 changes: 10 additions & 41 deletions ...ources/pic-sure-ga4gh-dos/src/main/java/edu/harvard/hms/dbmi/avillach/HttpClientUtil.java
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Original file line number Diff line number Diff line change
@@ -1,31 +1,26 @@
package edu.harvard.hms.dbmi.avillach;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonNode;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
import edu.harvard.dbmi.avillach.util.exception.ResourceCommunicationException;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.HttpClientBuilder;

import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;

import edu.harvard.dbmi.avillach.util.exception.ResourceCommunicationException;
import org.apache.http.util.EntityUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

public class HttpClientUtil {
private final static ObjectMapper json = new ObjectMapper();

private static final Logger logger = LoggerFactory.getLogger(HttpClientUtil.class);

public static HttpResponse retrieveGetResponse(String uri, String token) {
try {
HttpClient client = HttpClientBuilder.create().build();
Expand All @@ -39,32 +34,6 @@ public static HttpResponse retrieveGetResponse(String uri, String token) {
}
}

public static HttpResponse retrievePostResponse(String uri, String token) {
try {
HttpClient client = HttpClientBuilder.create().build();
HttpPost post = new HttpPost(uri);
if (token != null) {
Map<String, String> clientCredentials = new HashMap<String, String>();
clientCredentials.put("BEARER_TOKEN", token);
post.setEntity(new StringEntity(json.writeValueAsString(clientCredentials)));
}
post.setHeader("Content-type","application/json");
return client.execute(post);
} catch (IOException e) {
throw new ResourceCommunicationException(uri, e);
}
}

public static <T> List<T> readListFromResponse(HttpResponse response, Class<T> expectedElementType) {
try {
String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
return json.readValue(responseBody, new TypeReference<List<T>>() {});
} catch (IOException e) {
e.printStackTrace();
return new ArrayList<T>();
}
}

public static <T> List<T> readDataObjectsFromResponse(HttpResponse response, Class<T> expectedElementType) {
try {
String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
Expand All @@ -79,7 +48,7 @@ public static <T> List<T> readDataObjectsFromResponse(HttpResponse response, Cla
return json.readValue(jn.get("data_objects").toString(), new TypeReference<List<T>>() {});
}
} catch (IOException e) {
e.printStackTrace();
logger.error("Error reading object from response, returning empty list", e);
return new ArrayList<T>();
}
}
Expand Down
1 change: 0 additions & 1 deletion ...a/edu/harvard/hms/dbmi/avillach/resource/visualization/service/DataProcessingService.java
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Expand Up @@ -283,7 +283,6 @@ private String createXAxisLabel(String title) {
return title.substring(title.lastIndexOf(" ") + 1);
} catch (IndexOutOfBoundsException e) {
logger.error("Error getting cross counts: " + e.getMessage());
e.printStackTrace();
return title;
}
}
Expand Down
6 changes: 5 additions & 1 deletion .../java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package edu.harvard.dbmi.avillach.util.exception.mapper;

import edu.harvard.dbmi.avillach.util.response.PICSUREResponse;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.ws.rs.core.Response;
import javax.ws.rs.ext.ExceptionMapper;
Expand All @@ -9,9 +11,11 @@
@Provider
public class IllegalArgumentExceptionMapper implements ExceptionMapper<IllegalArgumentException>{

private static final Logger logger = LoggerFactory.getLogger(IllegalArgumentExceptionMapper.class);

@Override
public Response toResponse(IllegalArgumentException exception) {
exception.printStackTrace();
logger.error("Uncaught exception", exception);
return PICSUREResponse.protocolError(exception.getMessage());
}
}
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