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