Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in / Register
Toggle navigation
Menu
Open sidebar
INB
eTRANSAFE
pretox-rest-api
Commits
106b7e59
Commit
106b7e59
authored
Oct 08, 2021
by
Javi Corvi
Browse files
rest api development
parent
4fdaa188
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
View file @
106b7e59
package
es.bsc.inb.ades.rest.api.controllers
;
import
java.security.Principal
;
import
java.util.List
;
import
org.springframework.beans.factory.annotation.Autowired
;
...
...
@@ -8,28 +7,23 @@ import org.springframework.http.HttpHeaders;
import
org.springframework.http.HttpStatus
;
import
org.springframework.http.MediaType
;
import
org.springframework.http.ResponseEntity
;
import
org.springframework.ui.Model
;
import
org.springframework.web.bind.annotation.CrossOrigin
;
import
org.springframework.web.bind.annotation.PathVariable
;
import
org.springframework.web.bind.annotation.RequestMapping
;
import
org.springframework.web.bind.annotation.RestController
;
import
es.bsc.inb.ades.rest.api.model.Document
;
import
es.bsc.inb.ades.rest.api.model.DocumentAnnotations
;
import
es.bsc.inb.ades.rest.api.services.DocumentService
;
@RestController
@CrossOrigin
@CrossOrigin
()
public
class
DocumentController
{
@Autowired
public
DocumentService
documentService
;
@RequestMapping
(
"/api/v1/basicauth"
)
public
String
validateLogin
(
Model
model
,
Principal
principal
)
{
return
"login correct"
;
}
@RequestMapping
(
"/documents/"
)
public
List
<
Document
>
findAll
()
{
return
documentService
.
findAll
();
...
...
src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
View file @
106b7e59
...
...
@@ -200,6 +200,7 @@ public class SRDomainFinding implements Cloneable{
public
Boolean
getExport
()
{
if
(
export
==
null
)
return
true
;
return
export
;
}
public
void
setExport
(
Boolean
export
)
{
...
...
src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
View file @
106b7e59
...
...
@@ -5,7 +5,7 @@ import org.springframework.web.bind.annotation.GetMapping;
import
org.springframework.web.bind.annotation.RestController
;
//Controller
@CrossOrigin
(
origins
={
"http://localhost:3000"
,
"http://localhost:4200"
,
"http://localhost:8081"
}
)
@CrossOrigin
()
@RestController
public
class
BasicAuthenticationController
{
...
...
src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
View file @
106b7e59
...
...
@@ -11,7 +11,8 @@ import org.springframework.security.config.annotation.web.configuration.WebSecur
public
class
SecurityConfig
extends
WebSecurityConfigurerAdapter
{
@Override
protected
void
configure
(
HttpSecurity
http
)
throws
Exception
{
http
.
csrf
().
disable
().
http
.
cors
().
and
().
csrf
().
disable
().
//http.csrf().disable().
authorizeRequests
().
antMatchers
(
HttpMethod
.
OPTIONS
,
"/**"
).
permitAll
().
anyRequest
().
authenticated
()
.
and
().
httpBasic
();
...
...
src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
View file @
106b7e59
...
...
@@ -256,77 +256,80 @@ public class DocumentServiceImpl implements DocumentService {
for
(
Finding
finding
:
relevantSentences
.
getFindings
())
{
if
(
finding
.
getSrDomainFindings
()!=
null
)
{
for
(
SRDomainFinding
srDomainFinding
:
finding
.
getSrDomainFindings
())
{
//STUDYID -- > Study Identifier
retStr
.
append
(
id
);
retStr
.
append
(
"|"
);
//DOMAIN -- > Domain Abbreviation, always SR
retStr
.
append
(
"SR"
);
retStr
.
append
(
"|"
);
//SRSEQ -- > Sequence number
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD
retStr
.
append
(
srDomainFinding
.
getSRRISK
()==
null
?
""
:
srDomainFinding
.
getSRRISK
());
retStr
.
append
(
"|"
);
//SPGRPCD --> Sponsor-defined Group Code, group 1 , A
retStr
.
append
(
srDomainFinding
.
getSPGRPCD
()==
null
?
""
:
srDomainFinding
.
getSPGRPCD
());
retStr
.
append
(
"|"
);
//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
retStr
.
append
(
srDomainFinding
.
getGRPLBL
()==
null
?
""
:
srDomainFinding
.
getGRPLBL
());
retStr
.
append
(
"|"
);
//SRGRPDOS --> Group Dose Level, "20 mg/kg"
retStr
.
append
(
srDomainFinding
.
getSRGRPDOS
()==
null
?
""
:
srDomainFinding
.
getSRGRPDOS
());
retStr
.
append
(
"|"
);
//SRSEX -- > Sex
retStr
.
append
(
srDomainFinding
.
getSRSEX
()==
null
?
""
:
srDomainFinding
.
getSRSEX
());
retStr
.
append
(
"|"
);
//SRSTDY --> Study Day of Start of Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SROBSTDY --> Start Phase Day of Observation
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRENPHSE -->Study Phase of last Observation
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRDOMAIN --> Domain of Finding
retStr
.
append
(
srDomainFinding
.
getSRDOMAIN
()==
null
?
""
:
srDomainFinding
.
getSRDOMAIN
());
retStr
.
append
(
"|"
);
//SRSPEC --> Specimen of Finding
retStr
.
append
(
srDomainFinding
.
getSRSPEC
()==
null
?
""
:
srDomainFinding
.
getSRSPEC
());
retStr
.
append
(
"|"
);
//SRTSTCD --> Test Short Name
retStr
.
append
(
srDomainFinding
.
getSRTSTCD
()==
null
?
""
:
srDomainFinding
.
getSRTSTCD
());
retStr
.
append
(
"|"
);
//SRFNDG --> Finding
retStr
.
append
(
srDomainFinding
.
getSRFNDG
()==
null
?
""
:
srDomainFinding
.
getSRFNDG
());
retStr
.
append
(
"|"
);
//SRORES --> Observation (original result)
retStr
.
append
(
srDomainFinding
.
getSRORES
()==
null
?
""
:
srDomainFinding
.
getSRORES
());
retStr
.
append
(
"|"
);
//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
retStr
.
append
(
srDomainFinding
.
getSROBSV
()==
null
?
""
:
srDomainFinding
.
getSROBSV
());
retStr
.
append
(
"|"
);
//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
retStr
.
append
(
srDomainFinding
.
getSROBSQ
()==
null
?
""
:
srDomainFinding
.
getSROBSQ
());
retStr
.
append
(
"|"
);
//SRSEV --> Severity of Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRPCNT --> Scale of this Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRSIGF --> Statistical Significance
retStr
.
append
(
srDomainFinding
.
getSRSIGF
()==
null
?
""
:
srDomainFinding
.
getSRSIGF
());
retStr
.
append
(
"|"
);
//SRTRTEF --> Treatment-Related
retStr
.
append
(
srDomainFinding
.
getSRTRTEF
()==
null
?
""
:
srDomainFinding
.
getSRTRTEF
());
retStr
.
append
(
"|"
);
//SRCOMNT --> Comment
retStr
.
append
(
"\n"
);
if
(
srDomainFinding
.
getExport
())
{
//STUDYID -- > Study Identifier
retStr
.
append
(
id
);
retStr
.
append
(
"|"
);
//DOMAIN -- > Domain Abbreviation, always SR
retStr
.
append
(
"SR"
);
retStr
.
append
(
"|"
);
//SRSEQ -- > Sequence number
retStr
.
append
(
srDomainFinding
.
getSRSEQ
());
retStr
.
append
(
"|"
);
//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD
retStr
.
append
(
srDomainFinding
.
getSRRISK
()==
null
?
""
:
srDomainFinding
.
getSRRISK
());
retStr
.
append
(
"|"
);
//SPGRPCD --> Sponsor-defined Group Code, group 1 , A
retStr
.
append
(
srDomainFinding
.
getSPGRPCD
()==
null
?
""
:
srDomainFinding
.
getSPGRPCD
());
retStr
.
append
(
"|"
);
//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
retStr
.
append
(
srDomainFinding
.
getGRPLBL
()==
null
?
""
:
srDomainFinding
.
getGRPLBL
());
retStr
.
append
(
"|"
);
//SRGRPDOS --> Group Dose Level, "20 mg/kg"
retStr
.
append
(
srDomainFinding
.
getSRGRPDOS
()==
null
?
""
:
srDomainFinding
.
getSRGRPDOS
());
retStr
.
append
(
"|"
);
//SRSEX -- > Sex
retStr
.
append
(
srDomainFinding
.
getSRSEX
()==
null
?
""
:
srDomainFinding
.
getSRSEX
());
retStr
.
append
(
"|"
);
//SRSTDY --> Study Day of Start of Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SROBSTDY --> Start Phase Day of Observation
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRENPHSE -->Study Phase of last Observation
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRDOMAIN --> Domain of Finding
retStr
.
append
(
srDomainFinding
.
getSRDOMAIN
()==
null
?
""
:
srDomainFinding
.
getSRDOMAIN
());
retStr
.
append
(
"|"
);
//SRSPEC --> Specimen of Finding
retStr
.
append
(
srDomainFinding
.
getSRSPEC
()==
null
?
""
:
srDomainFinding
.
getSRSPEC
());
retStr
.
append
(
"|"
);
//SRTSTCD --> Test Short Name
retStr
.
append
(
srDomainFinding
.
getSRTSTCD
()==
null
?
""
:
srDomainFinding
.
getSRTSTCD
());
retStr
.
append
(
"|"
);
//SRFNDG --> Finding
retStr
.
append
(
srDomainFinding
.
getSRFNDG
()==
null
?
""
:
srDomainFinding
.
getSRFNDG
());
retStr
.
append
(
"|"
);
//SRORES --> Observation (original result)
retStr
.
append
(
srDomainFinding
.
getSRORES
()==
null
?
""
:
srDomainFinding
.
getSRORES
());
retStr
.
append
(
"|"
);
//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
retStr
.
append
(
srDomainFinding
.
getSROBSV
()==
null
?
""
:
srDomainFinding
.
getSROBSV
());
retStr
.
append
(
"|"
);
//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
retStr
.
append
(
srDomainFinding
.
getSROBSQ
()==
null
?
""
:
srDomainFinding
.
getSROBSQ
());
retStr
.
append
(
"|"
);
//SRSEV --> Severity of Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRPCNT --> Scale of this Finding
retStr
.
append
(
""
);
retStr
.
append
(
"|"
);
//SRSIGF --> Statistical Significance
retStr
.
append
(
srDomainFinding
.
getSRSIGF
()==
null
?
""
:
srDomainFinding
.
getSRSIGF
());
retStr
.
append
(
"|"
);
//SRTRTEF --> Treatment-Related
retStr
.
append
(
srDomainFinding
.
getSRTRTEF
()==
null
?
""
:
srDomainFinding
.
getSRTRTEF
());
retStr
.
append
(
"|"
);
//SRCOMNT --> Comment
retStr
.
append
(
"\n"
);
}
}
}
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment