diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 54d65150b78876029b49a483e2aa0074fe8bfc23..1c94154b1be8a5e3ab809594d7f66d1a6b84cee9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,13 +1,25 @@
variables:
- DOCKER_USER: javicorvi
- DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+ #DOCKER_USER: javicorvi
+ #DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+
+ DOCKER_REGISTRY: registry.gitlab.bsc.es
+ #any doubts regarind gitlab ci cd enviroment variables go to
+ #https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
+ IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_PATH:$CI_COMMIT_REF_NAME
stages:
- build
build_docker_image:
stage: build
script:
- - docker login -u javicorvi -p $DOCKER_PASS
- - docker build -t $DOCKER_BUILD .
- - docker push $DOCKER_BUILD
+ #- docker login -u javicorvi -p $DOCKER_PASS
+ #- docker build -t registry.gitlab.bsc.es/ .
+ #- docker push $DOCKER_BUILD
+
+ #- docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN $DOCKER_REGISTRY
+ #- docker build -t registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop .
+ #- docker push registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop
+ - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN $DOCKER_REGISTRY
+ - docker build -t $IMAGE_FULL_PATH .
+ - docker push $IMAGE_FULL_PATH
tags:
- build
diff --git a/pom.xml b/pom.xml
index 4563bf929b078810794ba1dd1bf78b7c31e448d9..e875981822d8dfc1ac8ac925d2d812c047bfacf2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,10 @@
spring-boot-devtools
true
-
+
+ org.springframework.boot
+ spring-boot-starter-security
+
Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD
- retStr.append(finding.getRisk_level()==null?"":finding.getRisk_level().getValue());
- retStr.append("|");
- //SPGRPCD --> Sponsor-defined Group Code, group 1 , A
- retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
- retStr.append("|");
- //GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
- retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
- retStr.append("|");
- //SRGRPDOS --> Group Dose Level, "20 mg/kg"
- retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
- retStr.append("|");
- //SRSEX -- > Sex
- retStr.append(finding.getSex()==null?"":finding.getSex().getValue());
- 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(finding.getStudy_domain()==null?"":finding.getStudy_domain().getValue());
- retStr.append("|");
- //SRSPEC --> Specimen of Finding
- retStr.append(finding.getSpecimen()==null?"":finding.getSpecimen().getValue());
- retStr.append("|");
- //SRTSTCD --> Test Short Name
- retStr.append(finding.getStudy_testcd()==null?"":finding.getStudy_testcd().getValue());
- retStr.append("|");
- //SRFNDG --> Finding
- retStr.append(finding.getFinding()==null?"":finding.getFinding().getValue());
- retStr.append("|");
- //SRORES --> Observation (original result)
- retStr.append(finding.getFinding()==null?"":finding.getFinding().getValue());
- retStr.append("|");
- //SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
- retStr.append(finding.getManifestation_finding()==null?"":finding.getManifestation_finding().getValue());
- retStr.append("|");
- //SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
- retStr.append(finding.getObservation_qualification()==null?"":finding.getObservation_qualification().getValue());
- retStr.append("|");
- //SRSEV --> Severity of Finding
- retStr.append("");
- retStr.append("|");
- //SRPCNT --> Scale of this Finding
- retStr.append("");
- retStr.append("|");
- //SRSIGF --> Statistical Significance
- retStr.append(finding.getStatistical_significance()==null?"":finding.getStatistical_significance().getValue());
- retStr.append("|");
- //SRTRTEF --> Treatment-Related
- retStr.append(finding.getIs_treatment_related()==null?"":finding.getIs_treatment_related().getValue());
- retStr.append("|");
- //SRCOMNT --> Comment
- retStr.append("\n");
+ for (Annotation relevantSentences : documentAnnotations.getRelevantSentences()) {
+ for (Finding finding : relevantSentences.getFindings()) {
+ if(finding.getSrDomainFindings()!=null) {
+ for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+ 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");
+ }
+
+ }
+ }
+ }
}
return retStr.toString().getBytes(Charset.forName("UTF-8"));
}
-
- /**
- * Create a plain text file with the given string
- * @param path
- * @param plainText
- * @throws FileNotFoundException
- * @throws IOException
- */
- private void createTxtFile(String path, String plainText) throws FileNotFoundException, IOException {
- File fout = new File(path);
- FileOutputStream fos = new FileOutputStream(fout);
- BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos,StandardCharsets.UTF_8));
- bw.write(plainText);
- bw.flush();
- bw.close();
- }
-
-// /**
-// *
-// * @param text
-// * @param findingSelected
-// * @return
-// */
-// private String generateFindingSnippet(String text, Finding findingSelected) {
-// System.out.println(text);
-// Integer offsetSlicing = 0;
-//
-// List all = findingSelected.generateSortedAnnotations();
-// Collections.sort(all);
-//
-// Annotation relevant_text = findingSelected.getRelevant_text();
-// String init_ = "";
-// String end_ = "";
-//
-// text = text.toString().substring(0, relevant_text.getStartOffset()) + init_ + relevant_text.getText() + end_ + text.toString().substring(relevant_text.getEndOffset());
-// offsetSlicing = init_.length();
-// Object[] data = {text, offsetSlicing};
-// for (Annotation annotation : all) {
-// if(!annotationSuperposition(annotation, all)) {
-// data = addColorToAnnotation(data, this.getAnnotationStyleClass(annotation), annotation);
-// }
-// System.out.println(data[0]);
-// }
-// return data[0].toString();
-// }
-
/**
*
* @param text
diff --git a/src/main/resources/application-prod.properties b/src/main/resources/application-prod.properties
index 840722db475fd216203d203619ef63ecb1b7ab26..289eaeaf7e2a9cd0feba8db16c0e06bade31665e 100644
--- a/src/main/resources/application-prod.properties
+++ b/src/main/resources/application-prod.properties
@@ -1,5 +1,6 @@
spring.application.name =ades_rest_api
#Spring Boot Port
server.port = ${SERVER_PORT}
-#ADES Database
-spring.data.mongodb.uri=${MONGO_URI}/etransafe
+#PRETOX Database
+spring.data.mongodb.uri=${MONGO_URI}
+
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
index 559622be7d732c8ba252b394979fb71d6bdaa0f3..8da406de12f7aae8dd7d524825023b65ba55dc10 100644
--- a/src/main/resources/application.properties
+++ b/src/main/resources/application.properties
@@ -3,7 +3,8 @@ spring.application.name =ades_rest_api
#server.port = ${SERVER_PORT}
server.port = 8090
#ADES Database
-spring.data.mongodb.uri=mongodb://localhost:27017/etransafe
+#spring.data.mongodb.uri=mongodb://localhost:27017/etransafe
+spring.data.mongodb.uri=mongodb://etransafe_rw:etransafe_rw2019!@mdb-login.bsc.es:27017/etransafe
#development enviroment
#docker run -d -p 27017-27019:27017-27019 -v /home/javi/eTRANSAFE_DATA/mongo-data-dev://data/db --name mongodb mongo:4.0.4