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Michael Halagan
authored
Merge pull request #13 from fscheel/ChangePersistanceLayer
Use a relational persistance layer and other things
2 parents fdf9153 + e2b6fec commit d514829

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-330
lines changed

‎pom.xml‎

Lines changed: 11 additions & 3 deletions
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@@ -25,12 +25,20 @@
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-data-mongodb</artifactId>
28+
<artifactId>spring-boot-starter-tomcat</artifactId>
29+
<scope>provided</scope>
30+
</dependency>
31+
<dependency>
32+
<groupId>com.h2database</groupId>
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<artifactId>h2</artifactId>
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</dependency>
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<dependency>
36+
<groupId>org.springframework.data</groupId>
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<artifactId>spring-data-jpa</artifactId>
2938
</dependency>
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<dependency>
3140
<groupId>org.springframework.boot</groupId>
32-
<artifactId>spring-boot-starter-tomcat</artifactId>
33-
<scope>provided</scope>
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<artifactId>spring-boot-starter-data-jpa</artifactId>
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</dependency>
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<!--SpringFox dependencies -->
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<dependency>

‎src/main/java/io/swagger/api/ApiException.java‎

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package io.swagger.api;
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@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
4+
5+
public class ApiException extends Exception{
6+
private int code;
7+
public ApiException (int code, String msg) {
8+
super(msg);
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this.code = code;
10+
}
11+
}

‎src/main/java/io/swagger/api/ApiOriginFilter.java‎

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package io.swagger.api;
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import java.io.IOException;
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import javax.servlet.*;
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import javax.servlet.http.HttpServletResponse;
7+
8+
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
9+
10+
public class ApiOriginFilter implements javax.servlet.Filter {
11+
@Override
12+
public void doFilter(ServletRequest request, ServletResponse response,
13+
FilterChain chain) throws IOException, ServletException {
14+
HttpServletResponse res = (HttpServletResponse) response;
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res.addHeader("Access-Control-Allow-Origin", "*");
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res.addHeader("Access-Control-Allow-Methods", "GET, POST, DELETE, PUT");
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res.addHeader("Access-Control-Allow-Headers", "Content-Type");
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chain.doFilter(request, response);
19+
}
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@Override
22+
public void destroy() {
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}
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@Override
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public void init(FilterConfig filterConfig) throws ServletException {
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}
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}

‎src/main/java/io/swagger/api/ApiResponseMessage.java‎

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package io.swagger.api;
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import javax.xml.bind.annotation.XmlTransient;
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@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
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7+
@javax.xml.bind.annotation.XmlRootElement
8+
public class ApiResponseMessage {
9+
public static final int ERROR = 1;
10+
public static final int WARNING = 2;
11+
public static final int INFO = 3;
12+
public static final int OK = 4;
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public static final int TOO_BUSY = 5;
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15+
int code;
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String type;
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String message;
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public ApiResponseMessage(){}
20+
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public ApiResponseMessage(int code, String message){
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this.code = code;
23+
switch(code){
24+
case ERROR:
25+
setType("error");
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break;
27+
case WARNING:
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setType("warning");
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break;
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case INFO:
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setType("info");
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break;
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case OK:
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setType("ok");
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break;
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case TOO_BUSY:
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setType("too busy");
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break;
39+
default:
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setType("unknown");
41+
break;
42+
}
43+
this.message = message;
44+
}
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46+
@XmlTransient
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public int getCode() {
48+
return code;
49+
}
50+
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public void setCode(int code) {
52+
this.code = code;
53+
}
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55+
public String getType() {
56+
return type;
57+
}
58+
59+
public void setType(String type) {
60+
this.type = type;
61+
}
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63+
public String getMessage() {
64+
return message;
65+
}
66+
67+
public void setMessage(String message) {
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this.message = message;
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}
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}

‎src/main/java/io/swagger/api/HfcApi.java‎

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package io.swagger.api;
22

3-
import io.swagger.model.CohortData;
4-
import io.swagger.model.Error;
5-
import io.swagger.model.HFCurationListResponse;
6-
import io.swagger.model.HFCurationRequest;
7-
import io.swagger.model.HFCurationResponse;
8-
import io.swagger.model.HaplotypeFrequencyData;
9-
import io.swagger.model.LabelData;
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import io.swagger.model.PopulationData;
11-
import io.swagger.model.PopulationResponse;
12-
import io.swagger.model.PopulationSubmissionResponse;
13-
import io.swagger.model.ScopeData;
3+
import io.swagger.model.*;
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155
import io.swagger.annotations.*;
16-
import org.springframework.http.HttpStatus;
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import org.springframework.http.ResponseEntity;
187
import org.springframework.web.bind.annotation.PathVariable;
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import org.springframework.web.bind.annotation.RequestBody;
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import org.springframework.web.bind.annotation.RequestHeader;
219
import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RequestMethod;
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import org.springframework.web.bind.annotation.RequestParam;
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import org.springframework.web.bind.annotation.RequestPart;
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import org.springframework.web.multipart.MultipartFile;
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import java.util.List;
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import javax.validation.constraints.*;
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@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-26T11:57:21.787-05:00")
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@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
3013

3114
@Api(value = "hfc", description = "the hfc API")
3215
public interface HfcApi {
3316

34-
@ApiOperation(value = "", notes = "Gets a list of all submission data sets ", response = HFCurationListResponse.class, tags={ })
17+
@ApiOperation(value = "", notes = "Gets a list of all submission data sets ", response = HFCurationResponseList.class, tags={ })
3518
@ApiResponses(value = {
36-
@ApiResponse(code = 200, message = "Successful response", response = HFCurationListResponse.class),
37-
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = HFCurationListResponse.class) })
19+
@ApiResponse(code = 200, message = "Successful response", response = HFCurationResponseList.class),
20+
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = HFCurationResponseList.class) })
3821
@RequestMapping(value = "/hfc",
3922
method = RequestMethod.GET)
40-
default ResponseEntity<HFCurationListResponse> hfcGet() {
41-
// do some magic!
42-
return new ResponseEntity<HFCurationListResponse>(HttpStatus.OK);
43-
}
23+
ResponseEntity<HFCurationResponseList> hfcGet();
4424

4525

4626
@ApiOperation(value = "", notes = "Get a list of all populations ", response = PopulationResponse.class, tags={ })
@@ -49,10 +29,7 @@ default ResponseEntity<HFCurationListResponse> hfcGet() {
4929
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = PopulationResponse.class) })
5030
@RequestMapping(value = "/hfc/population",
5131
method = RequestMethod.GET)
52-
default ResponseEntity<PopulationResponse> hfcPopulationGet() {
53-
// do some magic!
54-
return new ResponseEntity<PopulationResponse>(HttpStatus.OK);
55-
}
32+
ResponseEntity<PopulationResponse> hfcPopulationGet();
5633

5734

5835
@ApiOperation(value = "", notes = "Returns a population with its attached submissions", response = PopulationSubmissionResponse.class, tags={ })
@@ -61,10 +38,7 @@ default ResponseEntity<PopulationResponse> hfcPopulationGet() {
6138
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = PopulationSubmissionResponse.class) })
6239
@RequestMapping(value = "/hfc/population/{populationId}",
6340
method = RequestMethod.GET)
64-
default ResponseEntity<PopulationSubmissionResponse> hfcPopulationPopulationIdGet(@ApiParam(value = "The population id",required=true ) @PathVariable("populationId") String populationId) {
65-
// do some magic!
66-
return new ResponseEntity<PopulationSubmissionResponse>(HttpStatus.OK);
67-
}
41+
ResponseEntity<PopulationSubmissionResponse> hfcPopulationPopulationIdGet(@ApiParam(value = "The population id",required=true ) @PathVariable("populationId") String populationId);
6842

6943

7044
@ApiOperation(value = "", notes = "Storing of a new Haplotype Frequency set. ", response = HFCurationResponse.class, tags={ })
@@ -73,10 +47,7 @@ default ResponseEntity<PopulationSubmissionResponse> hfcPopulationPopulationIdGe
7347
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = HFCurationResponse.class) })
7448
@RequestMapping(value = "/hfc",
7549
method = RequestMethod.POST)
76-
default ResponseEntity<HFCurationResponse> hfcPost(@ApiParam(value = "Haplotype Frequency Curation Data" ,required=true ) @RequestBody HFCurationRequest hfCurationRequest) {
77-
// do some magic!
78-
return new ResponseEntity<HFCurationResponse>(HttpStatus.OK);
79-
}
50+
ResponseEntity<HFCurationResponse> hfcPost(@ApiParam(value = "Haplotype Frequency Curation Data" ,required=true ) @RequestBody HFCurationRequest hfCurationRequest);
8051

8152

8253
@ApiOperation(value = "", notes = "Returns the list of haplotypes attached to the given submission", response = CohortData.class, tags={ })
@@ -85,10 +56,7 @@ default ResponseEntity<HFCurationResponse> hfcPost(@ApiParam(value = "Haplotype
8556
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = CohortData.class) })
8657
@RequestMapping(value = "/hfc/{submissionId}/cohort",
8758
method = RequestMethod.GET)
88-
default ResponseEntity<CohortData> hfcSubmissionIdCohortGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId) {
89-
// do some magic!
90-
return new ResponseEntity<CohortData>(HttpStatus.OK);
91-
}
59+
ResponseEntity<CohortData> hfcSubmissionIdCohortGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId);
9260

9361

9462
@ApiOperation(value = "", notes = "Returns a submission of haplotypes", response = HFCurationResponse.class, tags={ })
@@ -97,10 +65,7 @@ default ResponseEntity<CohortData> hfcSubmissionIdCohortGet(@ApiParam(value = "T
9765
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = HFCurationResponse.class) })
9866
@RequestMapping(value = "/hfc/{submissionId}",
9967
method = RequestMethod.GET)
100-
default ResponseEntity<HFCurationResponse> hfcSubmissionIdGet(@ApiParam(value = "The submission id that the haplotype frequencies were submitted under",required=true ) @PathVariable("submissionId") String submissionId) {
101-
// do some magic!
102-
return new ResponseEntity<HFCurationResponse>(HttpStatus.OK);
103-
}
68+
ResponseEntity<HFCurationResponse> hfcSubmissionIdGet(@ApiParam(value = "The submission id that the haplotype frequencies were submitted under",required=true ) @PathVariable("submissionId") String submissionId);
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10570

10671
@ApiOperation(value = "", notes = "Returns the list of haplotypes attached to the given submission", response = HaplotypeFrequencyData.class, tags={ })
@@ -109,10 +74,7 @@ default ResponseEntity<HFCurationResponse> hfcSubmissionIdGet(@ApiParam(value =
10974
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = HaplotypeFrequencyData.class) })
11075
@RequestMapping(value = "/hfc/{submissionId}/haplotypes",
11176
method = RequestMethod.GET)
112-
default ResponseEntity<HaplotypeFrequencyData> hfcSubmissionIdHaplotypesGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId) {
113-
// do some magic!
114-
return new ResponseEntity<HaplotypeFrequencyData>(HttpStatus.OK);
115-
}
77+
ResponseEntity<HaplotypeFrequencyData> hfcSubmissionIdHaplotypesGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId);
11678

11779

11880
@ApiOperation(value = "", notes = "Returns the labels associated to the submission", response = LabelData.class, tags={ })
@@ -121,10 +83,7 @@ default ResponseEntity<HaplotypeFrequencyData> hfcSubmissionIdHaplotypesGet(@Api
12183
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = LabelData.class) })
12284
@RequestMapping(value = "/hfc/{submissionId}/labels",
12385
method = RequestMethod.GET)
124-
default ResponseEntity<LabelData> hfcSubmissionIdLabelsGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId) {
125-
// do some magic!
126-
return new ResponseEntity<LabelData>(HttpStatus.OK);
127-
}
86+
ResponseEntity<LabelData> hfcSubmissionIdLabelsGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId);
12887

12988

13089
@ApiOperation(value = "", notes = "Returns the population of the given submission", response = PopulationData.class, tags={ })
@@ -133,10 +92,7 @@ default ResponseEntity<LabelData> hfcSubmissionIdLabelsGet(@ApiParam(value = "Th
13392
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = PopulationData.class) })
13493
@RequestMapping(value = "/hfc/{submissionId}/population",
13594
method = RequestMethod.GET)
136-
default ResponseEntity<PopulationData> hfcSubmissionIdPopulationGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId) {
137-
// do some magic!
138-
return new ResponseEntity<PopulationData>(HttpStatus.OK);
139-
}
95+
ResponseEntity<PopulationData> hfcSubmissionIdPopulationGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId);
14096

14197

14298
@ApiOperation(value = "", notes = "Returns the scope of the genotypes used for creating the submitted haplotypes", response = ScopeData.class, tags={ })
@@ -145,9 +101,6 @@ default ResponseEntity<PopulationData> hfcSubmissionIdPopulationGet(@ApiParam(va
145101
@ApiResponse(code = 500, message = "An unexpected error ocurred", response = ScopeData.class) })
146102
@RequestMapping(value = "/hfc/{submissionId}/scope",
147103
method = RequestMethod.GET)
148-
default ResponseEntity<ScopeData> hfcSubmissionIdScopeGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId) {
149-
// do some magic!
150-
return new ResponseEntity<ScopeData>(HttpStatus.OK);
151-
}
104+
ResponseEntity<ScopeData> hfcSubmissionIdScopeGet(@ApiParam(value = "The submission id",required=true ) @PathVariable("submissionId") String submissionId);
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153106
}

‎src/main/java/io/swagger/api/NotFoundException.java‎

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package io.swagger.api;
2+
3+
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
4+
5+
public class NotFoundException extends ApiException {
6+
private int code;
7+
public NotFoundException (int code, String msg) {
8+
super(code, msg);
9+
this.code = code;
10+
}
11+
}

‎src/main/java/io/swagger/model/AccessData.java‎

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55
import com.fasterxml.jackson.annotation.JsonCreator;
66
import io.swagger.annotations.ApiModel;
77
import io.swagger.annotations.ApiModelProperty;
8-
import java.io.Serializable;
98
import javax.validation.constraints.*;
109
/**
1110
* AccessData
1211
*/
13-
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-26T11:57:21.787-05:00")
12+
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
1413

15-
public class AccessData implements Serializable {
14+
public class AccessData {
1615
@JsonProperty("typeOfAccess")
1716
private String typeOfAccess = null;
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‎src/main/java/io/swagger/model/CohortData.java‎

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import io.swagger.annotations.ApiModel;
77
import io.swagger.annotations.ApiModelProperty;
88
import io.swagger.model.GenotypeList;
9-
import java.io.Serializable;
109
import javax.validation.constraints.*;
1110
/**
1211
* CohortData
1312
*/
14-
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-26T11:57:21.787-05:00")
13+
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
1514

16-
public class CohortData implements Serializable {
15+
public class CohortData {
1716
@JsonProperty("GenotypeList")
1817
private GenotypeList genotypeList = null;
1918

@@ -26,8 +25,7 @@ public CohortData genotypeList(GenotypeList genotypeList) {
2625
* Get genotypeList
2726
* @return genotypeList
2827
**/
29-
@ApiModelProperty(required = true, value = "")
30-
@NotNull
28+
@ApiModelProperty(value = "")
3129
public GenotypeList getGenotypeList() {
3230
return genotypeList;
3331
}

‎src/main/java/io/swagger/model/Error.java‎

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import com.fasterxml.jackson.annotation.JsonCreator;
66
import io.swagger.annotations.ApiModel;
77
import io.swagger.annotations.ApiModelProperty;
8-
import java.io.Serializable;
98
import javax.validation.constraints.*;
109
/**
1110
* Error
1211
*/
13-
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-26T11:57:21.787-05:00")
12+
@javax.annotation.Generated(value = "io.swagger.codegen.languages.SpringCodegen", date = "2017-05-30T13:04:33.940Z")
1413

15-
public class Error implements Serializable {
14+
public class Error {
1615
@JsonProperty("code")
1716
private String code = null;
1817

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