From f4e9982365bbe2b9fd7341d283300a220b18e36c Mon Sep 17 00:00:00 2001
From: Mirco Nasuti <mirco.nasuti@chuv.ch>
Date: Mon, 1 Feb 2016 12:19:15 +0100
Subject: [PATCH] CSV file loaded from within the JAR + Bugfixes
---
.../org/hbp/mip/controllers/ModelsApi.java | 7 ++++-
.../org/hbp/mip/controllers/RequestsApi.java | 4 +--
src/main/java/org/hbp/mip/model/Group.java | 2 +-
src/main/java/org/hbp/mip/model/Model.java | 13 ++++++--
src/main/java/org/hbp/mip/model/Query.java | 14 ++++-----
src/main/java/org/hbp/mip/model/Tag.java | 13 --------
src/main/java/org/hbp/mip/model/Variable.java | 2 +-
src/main/java/org/hbp/mip/utils/CSVUtil.java | 31 ++++++++++++-------
8 files changed, 45 insertions(+), 41 deletions(-)
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 08fd2acdb..d6fd6834a 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -18,7 +18,9 @@ import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.*;
import java.security.Principal;
-import java.util.*;
+import java.util.Date;
+import java.util.LinkedList;
+import java.util.List;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -158,6 +160,9 @@ public class ModelsApi {
model.getDataset().getData().put("MidTemp", values);
model.getDataset().getHeader().add("MidTemp");
+ System.out.println("queryID" + model.getQuery().getId());
+ System.out.println("dataset id" + model.getDataset().getCode());
+
return new ResponseEntity<Model>(HttpStatus.OK).ok(model);
}
diff --git a/src/main/java/org/hbp/mip/controllers/RequestsApi.java b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
index 0dc71cd77..0d41fe609 100644
--- a/src/main/java/org/hbp/mip/controllers/RequestsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
@@ -21,8 +21,6 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/queries/requests", description = "the requests API")
public class RequestsApi {
- private final String VALUES_FILE = "/home/mirco/Workspace/GitLab/portal-backend/src/main/resources/data/values.csv";
-
@ApiOperation(value = "Send a request", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.POST)
@@ -30,7 +28,7 @@ public class RequestsApi {
@RequestBody @ApiParam(value = "Query to process", required = true) Query query
) throws NotFoundException {
- Dataset dataset = CSVUtil.parseValues(VALUES_FILE, query);
+ Dataset dataset = CSVUtil.parseValues("data/values.csv", query);
return new ResponseEntity<Dataset>(HttpStatus.OK).ok(dataset);
}
diff --git a/src/main/java/org/hbp/mip/model/Group.java b/src/main/java/org/hbp/mip/model/Group.java
index 76b6fbd6f..d5d61c435 100644
--- a/src/main/java/org/hbp/mip/model/Group.java
+++ b/src/main/java/org/hbp/mip/model/Group.java
@@ -21,7 +21,7 @@ public class Group {
@Id
private String code = null;
private String label = null;
- @OneToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+ @OneToMany(fetch = FetchType.EAGER)
private List<Group> groups = new LinkedList<Group>();
public Group() {
diff --git a/src/main/java/org/hbp/mip/model/Model.java b/src/main/java/org/hbp/mip/model/Model.java
index 67db5e085..6d0257a03 100644
--- a/src/main/java/org/hbp/mip/model/Model.java
+++ b/src/main/java/org/hbp/mip/model/Model.java
@@ -8,8 +8,12 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
+import org.hibernate.annotations.*;
+import org.hibernate.annotations.CascadeType;
import javax.persistence.*;
+import javax.persistence.Entity;
+import javax.persistence.Table;
import java.util.Date;
@Entity
@@ -24,11 +28,14 @@ public class Model {
private Boolean valid = null;
private Date createdAt = null;
private Date updatedAt = null;
- @ManyToOne(cascade = CascadeType.ALL)
+ @ManyToOne
+ @Cascade(CascadeType.SAVE_UPDATE)
private Query query = null;
- @ManyToOne(cascade = CascadeType.ALL)
+ @ManyToOne
+ @Cascade(CascadeType.SAVE_UPDATE)
private Dataset dataset = null;
- @ManyToOne(cascade = CascadeType.ALL)
+ @ManyToOne
+ @Cascade(CascadeType.SAVE_UPDATE)
private Chart chart = null;
@ManyToOne
private User createdBy = null;
diff --git a/src/main/java/org/hbp/mip/model/Query.java b/src/main/java/org/hbp/mip/model/Query.java
index 10ac94510..7543d62c6 100644
--- a/src/main/java/org/hbp/mip/model/Query.java
+++ b/src/main/java/org/hbp/mip/model/Query.java
@@ -24,26 +24,26 @@ public class Query {
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id = null;
private String request = null;
- @ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+ @ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "query_variable", joinColumns = {
@JoinColumn(name = "id", nullable = false, updatable = false) },
inverseJoinColumns = { @JoinColumn(name = "code",
nullable = false, updatable = false) })
- private List<Variable> variables = new LinkedList<Variable>();
- @ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+ private List<Variable> variables = new LinkedList<>();
+ @ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "query_covariable", joinColumns = {
@JoinColumn(name = "id", nullable = false, updatable = false) },
inverseJoinColumns = { @JoinColumn(name = "code",
nullable = false, updatable = false) })
- private List<Variable> covariables = new LinkedList<Variable>();
- @ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+ private List<Variable> covariables = new LinkedList<>();
+ @ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "query_grouping", joinColumns = {
@JoinColumn(name = "id", nullable = false, updatable = false) },
inverseJoinColumns = { @JoinColumn(name = "code",
nullable = false, updatable = false) })
- private List<Variable> grouping = new LinkedList<Variable>();
+ private List<Variable> grouping = new LinkedList<>();
@ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
- private List<Filter> filters = new LinkedList<Filter>();
+ private List<Filter> filters = new LinkedList<>();
public Query() {
}
diff --git a/src/main/java/org/hbp/mip/model/Tag.java b/src/main/java/org/hbp/mip/model/Tag.java
index eba34ccb7..e61cbf017 100644
--- a/src/main/java/org/hbp/mip/model/Tag.java
+++ b/src/main/java/org/hbp/mip/model/Tag.java
@@ -24,19 +24,6 @@ public class Tag {
public Tag() {
}
- /**
- * Unique identifier
- **/
- /*@ApiModelProperty(value = "Unique identifier")
- @JsonProperty("id")
- public Long getId() {
- return id;
- }
-
- public void setId(Long id) {
- this.id = id;
- }*/
-
/**
* Name
**/
diff --git a/src/main/java/org/hbp/mip/model/Variable.java b/src/main/java/org/hbp/mip/model/Variable.java
index 694b0d8d1..37c15697b 100644
--- a/src/main/java/org/hbp/mip/model/Variable.java
+++ b/src/main/java/org/hbp/mip/model/Variable.java
@@ -38,7 +38,7 @@ public class Variable {
@ManyToOne(fetch = FetchType.EAGER)
private Group group = null;
@ManyToMany(fetch = FetchType.EAGER)
- private List<Value> values = new LinkedList<Value>();
+ private List<Value> values = new LinkedList<>();
@ManyToMany(fetch = FetchType.EAGER, mappedBy = "variables")
private List<Query> queries = new LinkedList<>();
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index ab7df6054..756479051 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -21,10 +21,9 @@ public class CSVUtil {
public static Dataset parseValues(String filename, Query query)
{
+ List<String[]> rows = getFilteredRows(filename, query.getFilters());
+
Dataset result = new Dataset();
- File file = new File(filename);
- List<String[]> rows = getFilteredRows(file, query.getFilters());
- System.out.println("nb of filtered rows : "+rows.size());
String code = GenerateDSCode(query);
Date date = new Date();
List<String> header = new LinkedList<>();
@@ -38,11 +37,13 @@ public class CSVUtil {
header.addAll(variables.stream().map(Variable::getCode).collect(Collectors.toList()));
try {
- FileReader fr = new FileReader(file);
- BufferedReader br = new BufferedReader(fr);
+ InputStream is = Dataset.class.getClassLoader().getResourceAsStream(filename);
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
String[] firstRow = br.readLine().split(SEPARATOR, -1);
br.close();
- fr.close();
+ isr.close();
+ is.close();
for (Variable v : variables) {
String type = getTypeFromDB(v);
@@ -119,9 +120,9 @@ public class CSVUtil {
}
}
// TODO : Remove this limit -> only to avoid bug with Virtua's front-end
- if(l.size() > 100)
+ if(l.size() > 50)
{
- l = l.subList(0, 99);
+ l = l.subList(0, 49);
}
data.put(c, l);
System.out.println("Adding "+l.size()+" values to "+c);
@@ -137,11 +138,12 @@ public class CSVUtil {
return result;
}
- private static List<String[]> getFilteredRows(File file, List<Filter> filters) {
+ private static List<String[]> getFilteredRows(String filename, List<Filter> filters) {
List<String[]> filteredRows = new LinkedList<>();
try {
- FileReader fr = new FileReader(file);
- BufferedReader br = new BufferedReader(fr);
+ InputStream is = Dataset.class.getClassLoader().getResourceAsStream(filename);
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
String[] firstRow = br.readLine().split(SEPARATOR, -1); // 1st row -> headers
for (String line = br.readLine(); line != null; line = br.readLine()) {
String[] row = line.split(SEPARATOR, -1);
@@ -150,7 +152,8 @@ public class CSVUtil {
}
}
br.close();
- fr.close();
+ isr.close();
+ is.close();
} catch (IOException e) {
e.printStackTrace();
}
@@ -304,6 +307,10 @@ public class CSVUtil {
String type = (String) q.uniqueResult();
session.getTransaction().commit();
+ if(type == null)
+ {
+ type = "unknown";
+ }
return type;
}
--
GitLab