From efcc06df6383636aa4c8096a58d0b44f61f489d0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 26 Oct 2023 07:57:33 +0000 Subject: [PATCH] build: bump org.springframework.boot:spring-boot-starter-validation from 2.7.10 to 3.1.5 (#199) --- mcq-ws/pom.xml | 102 ----- .../java/pl/poznan/put/ws/Application.java | 11 - .../java/pl/poznan/put/ws/Controller.java | 55 --- .../pl/poznan/put/ws/ControllerAdvice.java | 52 --- .../pl/poznan/put/ws/ServicesSupervisor.java | 47 -- .../main/java/pl/poznan/put/ws/WebConfig.java | 52 --- .../pl/poznan/put/ws/components/Version.java | 29 -- .../java/pl/poznan/put/ws/entities/Chain.java | 61 --- .../pl/poznan/put/ws/entities/Residue.java | 422 ------------------ .../put/ws/entities/StructureContent.java | 95 ---- .../entities/TrigonometricRepresentation.java | 150 ------- .../exceptions/NoGitPropertiesException.java | 7 - .../exceptions/ObjectNotFoundException.java | 7 - .../ws/exceptions/PathVariableException.java | 13 - .../put/ws/jpa/StructureContentCrudRepo.java | 12 - .../TrigonometricRepresentationCrudRepo.java | 14 - .../put/ws/services/AnalyzeService.java | 72 --- .../put/ws/services/CompareService.java | 68 --- .../poznan/put/ws/services/UploadService.java | 63 --- .../put/ws/services/VersionService.java | 25 -- .../subservices/ComputationService.java | 27 -- .../src/main/resources/application.properties | 7 - .../src/main/resources/schema/AnglesDTO.yaml | 55 --- .../src/main/resources/schema/ChainDTO.yaml | 14 - .../resources/schema/ModelComparisonDTO.yaml | 26 -- .../src/main/resources/schema/ModelsDTO.yaml | 10 - .../resources/schema/ResidueAngelsDTO.yaml | 12 - .../schema/ResidueComparisonDTO.yaml | 25 -- .../src/main/resources/schema/ResidueDTO.yaml | 25 -- .../resources/schema/StructureContentDTO.yaml | 7 - .../resources/schema/TargetModelsDTO.yaml | 13 - .../TrigonometricRepresentationDTO.yaml | 17 - .../src/main/resources/schema/UploadDTO.yaml | 7 - pom.xml | 35 +- 34 files changed, 1 insertion(+), 1636 deletions(-) delete mode 100644 mcq-ws/pom.xml delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/Application.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/Controller.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/ControllerAdvice.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/ServicesSupervisor.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/WebConfig.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/components/Version.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/entities/Chain.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/entities/Residue.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/entities/StructureContent.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/entities/TrigonometricRepresentation.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/NoGitPropertiesException.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/ObjectNotFoundException.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/PathVariableException.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/jpa/StructureContentCrudRepo.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/jpa/TrigonometricRepresentationCrudRepo.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/services/AnalyzeService.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/services/CompareService.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/services/UploadService.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/services/VersionService.java delete mode 100644 mcq-ws/src/main/java/pl/poznan/put/ws/services/subservices/ComputationService.java delete mode 100644 mcq-ws/src/main/resources/application.properties delete mode 100644 mcq-ws/src/main/resources/schema/AnglesDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ChainDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ModelComparisonDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ModelsDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ResidueAngelsDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ResidueComparisonDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/ResidueDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/StructureContentDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/TargetModelsDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/TrigonometricRepresentationDTO.yaml delete mode 100644 mcq-ws/src/main/resources/schema/UploadDTO.yaml diff --git a/mcq-ws/pom.xml b/mcq-ws/pom.xml deleted file mode 100644 index c638e482..00000000 --- a/mcq-ws/pom.xml +++ /dev/null @@ -1,102 +0,0 @@ - - - 4.0.0 - - - pl.poznan.put - mcq-parent - 1.8.2 - - - mcq-ws - - - 8 - 8 - - - - - jakarta.persistence - jakarta.persistence-api - - - - javax.annotation - javax.annotation-api - - - - org.modelmapper.extensions - modelmapper-spring - - - - org.springframework - spring-core - - - - org.springframework.boot - spring-boot-maven-plugin - - - - org.springframework.boot - spring-boot-starter-data-jpa - - - - org.springframework.boot - spring-boot-starter-validation - - - - org.springframework.boot - spring-boot-starter-web - - - - com.h2database - h2 - runtime - - - - org.springframework.boot - spring-boot-starter-test - test - - - - - - - com.diffplug.spotless - spotless-maven-plugin - - - - org.jsonschema2pojo - jsonschema2pojo-maven-plugin - - - - generate - - - - - - - org.springframework.boot - spring-boot-maven-plugin - - - - pl.project13.maven - git-commit-id-plugin - - - - diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/Application.java b/mcq-ws/src/main/java/pl/poznan/put/ws/Application.java deleted file mode 100644 index 7e309f51..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/Application.java +++ /dev/null @@ -1,11 +0,0 @@ -package pl.poznan.put.ws; - -import org.springframework.boot.SpringApplication; -import org.springframework.boot.autoconfigure.SpringBootApplication; - -@SpringBootApplication() -public class Application { - public static void main(final String[] args) { - SpringApplication.run(Application.class, args); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/Controller.java b/mcq-ws/src/main/java/pl/poznan/put/ws/Controller.java deleted file mode 100644 index 47ba8bc8..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/Controller.java +++ /dev/null @@ -1,55 +0,0 @@ -package pl.poznan.put.ws; - -import java.util.List; -import javax.validation.Valid; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.web.bind.annotation.*; -import pl.poznan.put.schema.*; -import pl.poznan.put.ws.components.Version; - -@RestController -@RequestMapping("/api") -public class Controller { - - private final ServicesSupervisor servicesSupervisor; - - @Autowired - public Controller(ServicesSupervisor servicesSupervisor) { - this.servicesSupervisor = servicesSupervisor; - } - - @GetMapping("/version") - private Version getVersion() { - return servicesSupervisor.getVersionService().findVersion(); - } - - @PostMapping("/upload") - private UploadDTO postUpload(@RequestBody @Valid StructureContentDTO structureContentDTO) { - return servicesSupervisor.getUploadService().handlePostUpload(structureContentDTO); - } - - @PostMapping("/upload/{pdbId}") - private UploadDTO postUpload(@RequestParam String pdbId) { - return servicesSupervisor.getUploadService().handlePostUpload(pdbId, 1); - } - - @PostMapping("/upload/{pdbId}/{assemblyId}") - private UploadDTO postUpload(@RequestParam String pdbId, @RequestParam int assemblyId) { - return servicesSupervisor.getUploadService().handlePostUpload(pdbId, assemblyId); - } - - @PostMapping("/analyze/{id}") - private List postAnalyze(@PathVariable String id) { - return servicesSupervisor.getAnalyzeService().handleGetAnalyze(id); - } - - @PostMapping("/compare/target") - private List postCompareTarget(@RequestBody TargetModelsDTO targetModelsDTO) { - return servicesSupervisor.getCompareService().handleCompare(targetModelsDTO); - } - - @PostMapping("/compare/models") - private List postCompareModels(@RequestBody ModelsDTO modelsDTO) { - return servicesSupervisor.getCompareService().handleCompare(modelsDTO); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/ControllerAdvice.java b/mcq-ws/src/main/java/pl/poznan/put/ws/ControllerAdvice.java deleted file mode 100644 index 32167ea3..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/ControllerAdvice.java +++ /dev/null @@ -1,52 +0,0 @@ -package pl.poznan.put.ws; - -import org.springframework.http.HttpStatus; -import org.springframework.web.bind.MethodArgumentNotValidException; -import org.springframework.web.bind.annotation.ExceptionHandler; -import org.springframework.web.bind.annotation.ResponseBody; -import org.springframework.web.bind.annotation.ResponseStatus; -import pl.poznan.put.ws.exceptions.NoGitPropertiesException; -import pl.poznan.put.ws.exceptions.ObjectNotFoundException; -import pl.poznan.put.ws.exceptions.PathVariableException; - -@org.springframework.web.bind.annotation.ControllerAdvice -public class ControllerAdvice { - - @ResponseBody - @ResponseStatus(HttpStatus.BAD_REQUEST) - @ExceptionHandler(IllegalArgumentException.class) - private String illegalArgumentExceptionHandler( - IllegalArgumentException illegalArgumentException) { - return illegalArgumentException.getMessage(); - } - - @ResponseBody - @ResponseStatus(HttpStatus.INTERNAL_SERVER_ERROR) - @ExceptionHandler(NoGitPropertiesException.class) - private String NoGitPropertiesExceptionHandler( - NoGitPropertiesException noGitPropertiesException) { - return noGitPropertiesException.getMessage(); - } - - @ResponseBody - @ResponseStatus(HttpStatus.NOT_FOUND) - @ExceptionHandler(ObjectNotFoundException.class) - private String objectNotFoundHandler(ObjectNotFoundException objectNotFoundException) { - return objectNotFoundException.getMessage(); - } - - @ResponseBody - @ResponseStatus(HttpStatus.BAD_REQUEST) - @ExceptionHandler(PathVariableException.class) - private String pathInputExceptionHandler(PathVariableException pathVariableException) { - return pathVariableException.getMessage(); - } - - @ResponseBody - @ResponseStatus(HttpStatus.BAD_REQUEST) - @ExceptionHandler(MethodArgumentNotValidException.class) - private String methodArgumentNotValidExceptionHandler( - MethodArgumentNotValidException methodArgumentNotValidException) { - return methodArgumentNotValidException.getMessage(); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/ServicesSupervisor.java b/mcq-ws/src/main/java/pl/poznan/put/ws/ServicesSupervisor.java deleted file mode 100644 index 62183008..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/ServicesSupervisor.java +++ /dev/null @@ -1,47 +0,0 @@ -package pl.poznan.put.ws; - -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; -import pl.poznan.put.ws.services.AnalyzeService; -import pl.poznan.put.ws.services.CompareService; -import pl.poznan.put.ws.services.UploadService; -import pl.poznan.put.ws.services.VersionService; - -@Service -public class ServicesSupervisor { - private final VersionService versionService; - - private final UploadService uploadService; - - private final AnalyzeService analyzeService; - - private final CompareService compareService; - - @Autowired - public ServicesSupervisor( - VersionService versionService, - UploadService uploadService, - AnalyzeService analyzeService, - CompareService compareService) { - this.versionService = versionService; - this.uploadService = uploadService; - this.analyzeService = analyzeService; - this.compareService = compareService; - } - - public VersionService getVersionService() { - return versionService; - } - - public UploadService getUploadService() { - return uploadService; - } - - public AnalyzeService getAnalyzeService() { - return analyzeService; - } - - public CompareService getCompareService() { - return compareService; - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/WebConfig.java b/mcq-ws/src/main/java/pl/poznan/put/ws/WebConfig.java deleted file mode 100644 index 54c3585b..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/WebConfig.java +++ /dev/null @@ -1,52 +0,0 @@ -package pl.poznan.put.ws; - -import java.time.Instant; -import java.util.UUID; -import org.modelmapper.Converter; -import org.modelmapper.ModelMapper; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; -import org.springframework.context.support.PropertySourcesPlaceholderConfigurer; -import org.springframework.core.io.ClassPathResource; -import pl.poznan.put.schema.StructureContentDTO; -import pl.poznan.put.schema.UploadDTO; -import pl.poznan.put.ws.entities.StructureContent; - -@Configuration -public class WebConfig { - - @Bean - public PropertySourcesPlaceholderConfigurer configurePlaceholder() { - PropertySourcesPlaceholderConfigurer placeholderConfigurer = - new PropertySourcesPlaceholderConfigurer(); - placeholderConfigurer.setLocations(new ClassPathResource("git.properties")); - placeholderConfigurer.setIgnoreResourceNotFound(true); - placeholderConfigurer.setIgnoreUnresolvablePlaceholders(true); - return placeholderConfigurer; - } - - @Bean - public ModelMapper configureModelMapper() { - ModelMapper modelMapper = new ModelMapper(); - - Converter toUUID = ctx -> UUID.fromString(ctx.getSource()); - Converter toString = ctx -> ctx.getSource().toString(); - - modelMapper - .typeMap(StructureContent.class, UploadDTO.class) - .addMappings( - mapper -> { - mapper.using(toString).map(src -> src.getId(), UploadDTO::setId); - }); - - modelMapper - .typeMap(StructureContentDTO.class, StructureContent.class) - .addMappings( - mapper -> { - mapper.map(src -> UUID.randomUUID(), StructureContent::setId); - mapper.map(src -> Instant.now(), StructureContent::setCreatedAt); - }); - - return modelMapper; - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/components/Version.java b/mcq-ws/src/main/java/pl/poznan/put/ws/components/Version.java deleted file mode 100644 index 6d262833..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/components/Version.java +++ /dev/null @@ -1,29 +0,0 @@ -package pl.poznan.put.ws.components; - -import com.fasterxml.jackson.annotation.JsonProperty; -import com.fasterxml.jackson.annotation.JsonPropertyOrder; -import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Component; - -@JsonPropertyOrder({"version"}) -@Component -public class Version { - - @Value("${git.commit.id.describe-short}") - @JsonProperty("version") - private String version; - - public Version(String version) { - this.version = version; - } - - public Version() {} - - public String getVersion() { - return version; - } - - public void setVersion(String version) { - this.version = version; - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Chain.java b/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Chain.java deleted file mode 100644 index e81386d7..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Chain.java +++ /dev/null @@ -1,61 +0,0 @@ -package pl.poznan.put.ws.entities; - -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.OneToMany; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; -import javax.validation.Valid; - -@Entity -public class Chain { - - @Id private String name; - - @Valid - @OneToMany(targetEntity = Residue.class, mappedBy = "residueNumber") - private List residues = new ArrayList(); - - public Chain() {} - - public Chain(String name, List residues) { - super(); - this.name = name; - this.residues = residues; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public List getResidues() { - return residues; - } - - public void setResidues(List residues) { - this.residues = residues; - } - - @Override - public String toString() { - return "Chain{" + "name='" + name + '\'' + ", residues=" + residues + '}'; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - Chain chain = (Chain) o; - return Objects.equals(name, chain.name) && Objects.equals(residues, chain.residues); - } - - @Override - public int hashCode() { - return Objects.hash(name, residues); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Residue.java b/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Residue.java deleted file mode 100644 index d9a7e110..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/Residue.java +++ /dev/null @@ -1,422 +0,0 @@ -package pl.poznan.put.ws.entities; - -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import java.util.Objects; - -@Entity -public class Residue { - - private boolean isMissing; - - private String standardResidueName; - - private String modifiedResidueName; - - private String oneLetterName; - - private String chain; - - @Id private int residueNumber; - - private String insertionCode; - - private double alpha; - - private double beta; - - private double gamma; - - private double delta; - - private double epsilon; - - private double zeta; - - private double nu0; - - private double nu1; - - private double nu2; - - private double nu3; - - private double nu4; - - private double eta; - - private double theta; - - private double etaPrim; - - private double tehtaPrim; - - private double chi; - - private double pseudophasePucker; - - public Residue() {} - - public Residue( - boolean isMissing, - String standardResidueName, - String modifiedResidueName, - String oneLetterName, - String chain, - int residueNumber, - String insertionCode, - double alpha, - double beta, - double gamma, - double delta, - double epsilon, - double zeta, - double nu0, - double nu1, - double nu2, - double nu3, - double nu4, - double eta, - double theta, - double etaPrim, - double tehtaPrim, - double chi, - double pseudophasePucker) { - super(); - this.isMissing = isMissing; - this.standardResidueName = standardResidueName; - this.modifiedResidueName = modifiedResidueName; - this.oneLetterName = oneLetterName; - this.chain = chain; - this.residueNumber = residueNumber; - this.insertionCode = insertionCode; - this.alpha = alpha; - this.beta = beta; - this.gamma = gamma; - this.delta = delta; - this.epsilon = epsilon; - this.zeta = zeta; - this.nu0 = nu0; - this.nu1 = nu1; - this.nu2 = nu2; - this.nu3 = nu3; - this.nu4 = nu4; - this.eta = eta; - this.theta = theta; - this.etaPrim = etaPrim; - this.tehtaPrim = tehtaPrim; - this.chi = chi; - this.pseudophasePucker = pseudophasePucker; - } - - public boolean isIsMissing() { - return isMissing; - } - - public void setIsMissing(boolean isMissing) { - this.isMissing = isMissing; - } - - public String getStandardResidueName() { - return standardResidueName; - } - - public void setStandardResidueName(String standardResidueName) { - this.standardResidueName = standardResidueName; - } - - public String getModifiedResidueName() { - return modifiedResidueName; - } - - public void setModifiedResidueName(String modifiedResidueName) { - this.modifiedResidueName = modifiedResidueName; - } - - public String getOneLetterName() { - return oneLetterName; - } - - public void setOneLetterName(String oneLetterName) { - this.oneLetterName = oneLetterName; - } - - public String getChain() { - return chain; - } - - public void setChain(String chain) { - this.chain = chain; - } - - public int getResidueNumber() { - return residueNumber; - } - - public void setResidueNumber(int residueNumber) { - this.residueNumber = residueNumber; - } - - public String getInsertionCode() { - return insertionCode; - } - - public void setInsertionCode(String insertionCode) { - this.insertionCode = insertionCode; - } - - public double getAlpha() { - return alpha; - } - - public void setAlpha(double alpha) { - this.alpha = alpha; - } - - public double getBeta() { - return beta; - } - - public void setBeta(double beta) { - this.beta = beta; - } - - public double getGamma() { - return gamma; - } - - public void setGamma(double gamma) { - this.gamma = gamma; - } - - public double getDelta() { - return delta; - } - - public void setDelta(double delta) { - this.delta = delta; - } - - public double getEpsilon() { - return epsilon; - } - - public void setEpsilon(double epsilon) { - this.epsilon = epsilon; - } - - public double getZeta() { - return zeta; - } - - public void setZeta(double zeta) { - this.zeta = zeta; - } - - public double getNu0() { - return nu0; - } - - public void setNu0(double nu0) { - this.nu0 = nu0; - } - - public double getNu1() { - return nu1; - } - - public void setNu1(double nu1) { - this.nu1 = nu1; - } - - public double getNu2() { - return nu2; - } - - public void setNu2(double nu2) { - this.nu2 = nu2; - } - - public double getNu3() { - return nu3; - } - - public void setNu3(double nu3) { - this.nu3 = nu3; - } - - public double getNu4() { - return nu4; - } - - public void setNu4(double nu4) { - this.nu4 = nu4; - } - - public double getEta() { - return eta; - } - - public void setEta(double eta) { - this.eta = eta; - } - - public double getTheta() { - return theta; - } - - public void setTheta(double theta) { - this.theta = theta; - } - - public double getEtaPrim() { - return etaPrim; - } - - public void setEtaPrim(double etaPrim) { - this.etaPrim = etaPrim; - } - - public double getTehtaPrim() { - return tehtaPrim; - } - - public void setTehtaPrim(double tehtaPrim) { - this.tehtaPrim = tehtaPrim; - } - - public double getChi() { - return chi; - } - - public void setChi(double chi) { - this.chi = chi; - } - - public double getPseudophasePucker() { - return pseudophasePucker; - } - - public void setPseudophasePucker(double pseudophasePucker) { - this.pseudophasePucker = pseudophasePucker; - } - - @Override - public String toString() { - return "Residue{" - + "isMissing=" - + isMissing - + ", standardResidueName='" - + standardResidueName - + '\'' - + ", modifiedResidueName='" - + modifiedResidueName - + '\'' - + ", oneLetterName='" - + oneLetterName - + '\'' - + ", chain='" - + chain - + '\'' - + ", residueNumber=" - + residueNumber - + ", insertionCode='" - + insertionCode - + '\'' - + ", alpha=" - + alpha - + ", beta=" - + beta - + ", gamma=" - + gamma - + ", delta=" - + delta - + ", epsilon=" - + epsilon - + ", zeta=" - + zeta - + ", nu0=" - + nu0 - + ", nu1=" - + nu1 - + ", nu2=" - + nu2 - + ", nu3=" - + nu3 - + ", nu4=" - + nu4 - + ", eta=" - + eta - + ", theta=" - + theta - + ", etaPrim=" - + etaPrim - + ", tehtaPrim=" - + tehtaPrim - + ", chi=" - + chi - + ", pseudophasePucker=" - + pseudophasePucker - + '}'; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - Residue residue = (Residue) o; - return isMissing == residue.isMissing - && residueNumber == residue.residueNumber - && Double.compare(residue.alpha, alpha) == 0 - && Double.compare(residue.beta, beta) == 0 - && Double.compare(residue.gamma, gamma) == 0 - && Double.compare(residue.delta, delta) == 0 - && Double.compare(residue.epsilon, epsilon) == 0 - && Double.compare(residue.zeta, zeta) == 0 - && Double.compare(residue.nu0, nu0) == 0 - && Double.compare(residue.nu1, nu1) == 0 - && Double.compare(residue.nu2, nu2) == 0 - && Double.compare(residue.nu3, nu3) == 0 - && Double.compare(residue.nu4, nu4) == 0 - && Double.compare(residue.eta, eta) == 0 - && Double.compare(residue.theta, theta) == 0 - && Double.compare(residue.etaPrim, etaPrim) == 0 - && Double.compare(residue.tehtaPrim, tehtaPrim) == 0 - && Double.compare(residue.chi, chi) == 0 - && Double.compare(residue.pseudophasePucker, pseudophasePucker) == 0 - && Objects.equals(standardResidueName, residue.standardResidueName) - && Objects.equals(modifiedResidueName, residue.modifiedResidueName) - && Objects.equals(oneLetterName, residue.oneLetterName) - && Objects.equals(chain, residue.chain) - && Objects.equals(insertionCode, residue.insertionCode); - } - - @Override - public int hashCode() { - return Objects.hash( - isMissing, - standardResidueName, - modifiedResidueName, - oneLetterName, - chain, - residueNumber, - insertionCode, - alpha, - beta, - gamma, - delta, - epsilon, - zeta, - nu0, - nu1, - nu2, - nu3, - nu4, - eta, - theta, - etaPrim, - tehtaPrim, - chi, - pseudophasePucker); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/StructureContent.java b/mcq-ws/src/main/java/pl/poznan/put/ws/entities/StructureContent.java deleted file mode 100644 index 6b059d28..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/StructureContent.java +++ /dev/null @@ -1,95 +0,0 @@ -package pl.poznan.put.ws.entities; - -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.OneToMany; -import java.time.Instant; -import java.util.List; -import java.util.Objects; -import java.util.UUID; -import org.springframework.data.annotation.CreatedDate; - -@Entity -public class StructureContent { - - public StructureContent(UUID id, Instant createdAt, String data) { - this.id = id; - this.createdAt = createdAt; - this.data = data; - } - - public StructureContent() {} - - @Id private UUID id; - - @CreatedDate private Instant createdAt; - - private String data = ""; - - public UUID getId() { - return id; - } - - public void setId(UUID id) { - this.id = id; - } - - public Instant getCreatedAt() { - return createdAt; - } - - @OneToMany(mappedBy = "inputId") - private List trigonometricRepresentations; - - public void setCreatedAt(Instant createdAt) { - this.createdAt = createdAt; - } - - public String getData() { - return data; - } - - public void setData(String data) { - this.data = data; - } - - public List getTrigonometricRepresentations() { - return trigonometricRepresentations; - } - - public void setTrigonometricRepresentations( - List trigonometricRepresentations) { - this.trigonometricRepresentations = trigonometricRepresentations; - } - - @Override - public String toString() { - return "StructureContent{" - + "id=" - + id - + ", createdAt=" - + createdAt - + ", data='" - + data - + '\'' - + ", trigonometricRepresentations=" - + trigonometricRepresentations - + '}'; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - StructureContent that = (StructureContent) o; - return Objects.equals(id, that.id) - && Objects.equals(createdAt, that.createdAt) - && Objects.equals(data, that.data) - && Objects.equals(trigonometricRepresentations, that.trigonometricRepresentations); - } - - @Override - public int hashCode() { - return Objects.hash(id, createdAt, data, trigonometricRepresentations); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/TrigonometricRepresentation.java b/mcq-ws/src/main/java/pl/poznan/put/ws/entities/TrigonometricRepresentation.java deleted file mode 100644 index 37ff7c57..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/entities/TrigonometricRepresentation.java +++ /dev/null @@ -1,150 +0,0 @@ -package pl.poznan.put.ws.entities; - -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.JoinColumn; -import jakarta.persistence.ManyToOne; -import jakarta.persistence.OneToMany; -import java.time.Instant; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; -import java.util.UUID; -import javax.validation.Valid; - -@Entity -public class TrigonometricRepresentation { - - @Id private UUID id; - - private Instant createdAt; - - @ManyToOne - @JoinColumn(name = "input_id") - private StructureContent inputId; - - private String pdbId; - - private int assemblyId; - - private double modelNumber; - - @OneToMany(targetEntity = Chain.class, mappedBy = "name") - @Valid - private List chains = new ArrayList(); - - public TrigonometricRepresentation() {} - - public TrigonometricRepresentation( - UUID id, - Instant createdAt, - StructureContent inputId, - String pdbId, - int assemblyId, - double modelNumber, - List chains) { - this.id = id; - this.createdAt = createdAt; - this.inputId = inputId; - this.pdbId = pdbId; - this.assemblyId = assemblyId; - this.modelNumber = modelNumber; - this.chains = chains; - } - - public UUID getId() { - return id; - } - - public void setId(UUID id) { - this.id = id; - } - - public Instant getCreatedAt() { - return createdAt; - } - - public void setCreatedAt(Instant createdAt) { - this.createdAt = createdAt; - } - - public StructureContent getInputId() { - return inputId; - } - - public void setInputId(StructureContent inputId) { - this.inputId = inputId; - } - - public String getPdbId() { - return pdbId; - } - - public void setPdbId(String pdbId) { - this.pdbId = pdbId; - } - - public int getAssemblyId() { - return assemblyId; - } - - public void setAssemblyId(int assemblyId) { - this.assemblyId = assemblyId; - } - - public double getModelNumber() { - return modelNumber; - } - - public void setModelNumber(double modelNumber) { - this.modelNumber = modelNumber; - } - - public List getChains() { - return chains; - } - - public void setChains(List chains) { - this.chains = chains; - } - - @Override - public String toString() { - return "TrigonometricRepresentation{" - + "id=" - + id - + ", createdAt=" - + createdAt - + ", inputId=" - + inputId - + ", pdbId='" - + pdbId - + '\'' - + ", assemblyId=" - + assemblyId - + ", modelNumber=" - + modelNumber - + ", chains=" - + chains - + '}'; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - TrigonometricRepresentation that = (TrigonometricRepresentation) o; - return assemblyId == that.assemblyId - && Double.compare(that.modelNumber, modelNumber) == 0 - && Objects.equals(id, that.id) - && Objects.equals(createdAt, that.createdAt) - && Objects.equals(inputId, that.inputId) - && Objects.equals(pdbId, that.pdbId) - && Objects.equals(chains, that.chains); - } - - @Override - public int hashCode() { - return Objects.hash(id, createdAt, inputId, pdbId, assemblyId, modelNumber, chains); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/NoGitPropertiesException.java b/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/NoGitPropertiesException.java deleted file mode 100644 index 3649b852..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/NoGitPropertiesException.java +++ /dev/null @@ -1,7 +0,0 @@ -package pl.poznan.put.ws.exceptions; - -public class NoGitPropertiesException extends RuntimeException { - public NoGitPropertiesException() { - super("File git.properties has not been found!"); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/ObjectNotFoundException.java b/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/ObjectNotFoundException.java deleted file mode 100644 index 2a32b32c..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/ObjectNotFoundException.java +++ /dev/null @@ -1,7 +0,0 @@ -package pl.poznan.put.ws.exceptions; - -public class ObjectNotFoundException extends RuntimeException { - public ObjectNotFoundException(String id, Class className) { - super(className.getSimpleName() + " with id: " + id + " has not been found!"); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/PathVariableException.java b/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/PathVariableException.java deleted file mode 100644 index eaf3b6f2..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/exceptions/PathVariableException.java +++ /dev/null @@ -1,13 +0,0 @@ -package pl.poznan.put.ws.exceptions; - -public class PathVariableException extends RuntimeException { - public PathVariableException(String pathName, String pathValue, String problem) { - super( - "Path variable " - + pathName - + " with given value " - + pathValue - + " encountered exception: " - + problem); - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/StructureContentCrudRepo.java b/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/StructureContentCrudRepo.java deleted file mode 100644 index d604e14c..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/StructureContentCrudRepo.java +++ /dev/null @@ -1,12 +0,0 @@ -package pl.poznan.put.ws.jpa; - -import java.util.Optional; -import java.util.UUID; -import org.springframework.data.repository.CrudRepository; -import org.springframework.stereotype.Repository; -import pl.poznan.put.ws.entities.StructureContent; - -@Repository -public interface StructureContentCrudRepo extends CrudRepository { - Optional findByData(String data); -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/TrigonometricRepresentationCrudRepo.java b/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/TrigonometricRepresentationCrudRepo.java deleted file mode 100644 index 546a9834..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/jpa/TrigonometricRepresentationCrudRepo.java +++ /dev/null @@ -1,14 +0,0 @@ -package pl.poznan.put.ws.jpa; - -import java.util.List; -import java.util.UUID; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.data.repository.query.Param; -import pl.poznan.put.ws.entities.TrigonometricRepresentation; - -public interface TrigonometricRepresentationCrudRepo - extends CrudRepository { - @Query("SELECT t FROM TrigonometricRepresentation t WHERE t.inputId.id = ?1") - List findAllByInputId(@Param("inputId") UUID inputId); -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/services/AnalyzeService.java b/mcq-ws/src/main/java/pl/poznan/put/ws/services/AnalyzeService.java deleted file mode 100644 index 4a33f8e6..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/services/AnalyzeService.java +++ /dev/null @@ -1,72 +0,0 @@ -package pl.poznan.put.ws.services; - -import java.util.List; -import java.util.Optional; -import java.util.UUID; -import java.util.stream.Collectors; -import org.modelmapper.ModelMapper; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; -import pl.poznan.put.schema.StructureContentDTO; -import pl.poznan.put.schema.TrigonometricRepresentationDTO; -import pl.poznan.put.ws.entities.StructureContent; -import pl.poznan.put.ws.entities.TrigonometricRepresentation; -import pl.poznan.put.ws.exceptions.ObjectNotFoundException; -import pl.poznan.put.ws.jpa.StructureContentCrudRepo; -import pl.poznan.put.ws.jpa.TrigonometricRepresentationCrudRepo; -import pl.poznan.put.ws.services.subservices.ComputationService; - -@Service -public class AnalyzeService { - - private final TrigonometricRepresentationCrudRepo trigonometricRepresentationCrudRepo; - - private final StructureContentCrudRepo structureContentCrudRepo; - - private final ModelMapper modelMapper; - - private final ComputationService computationService; - - @Autowired - public AnalyzeService( - TrigonometricRepresentationCrudRepo trigonometricRepresentationCrudRepo, - ModelMapper modelMapper, - ComputationService computationService, - StructureContentCrudRepo structureContentCrudRepo) { - this.trigonometricRepresentationCrudRepo = trigonometricRepresentationCrudRepo; - this.modelMapper = modelMapper; - this.computationService = computationService; - this.structureContentCrudRepo = structureContentCrudRepo; - } - - public List handleGetAnalyze(String id) { - UUID givenId = UUID.fromString(id); - List foundTrigonometricRepresentations = - trigonometricRepresentationCrudRepo.findAllByInputId(givenId); - - if (foundTrigonometricRepresentations.size() > 0) { - return trigonometricRepresentationCrudRepo.findAllByInputId(givenId).stream() - .map(foundTR -> modelMapper.map(foundTR, TrigonometricRepresentationDTO.class)) - .collect(Collectors.toList()); - } else { - Optional structureContentOptional = - structureContentCrudRepo.findById(givenId); - if (structureContentOptional.isPresent()) { - return computationService - .computeTorsionAngles( - modelMapper.map(structureContentOptional.get(), StructureContentDTO.class)) - .stream() - .map( - structureContentDTO -> - modelMapper.map( - trigonometricRepresentationCrudRepo.save( - modelMapper.map( - structureContentDTO, TrigonometricRepresentation.class)), - TrigonometricRepresentationDTO.class)) - .collect(Collectors.toList()); - } else { - throw new ObjectNotFoundException(id, StructureContent.class); - } - } - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/services/CompareService.java b/mcq-ws/src/main/java/pl/poznan/put/ws/services/CompareService.java deleted file mode 100644 index 45719c41..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/services/CompareService.java +++ /dev/null @@ -1,68 +0,0 @@ -package pl.poznan.put.ws.services; - -import java.util.ArrayList; -import java.util.List; -import java.util.UUID; -import java.util.stream.Collectors; -import java.util.stream.StreamSupport; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; -import pl.poznan.put.schema.ModelComparisonDTO; -import pl.poznan.put.schema.ModelsDTO; -import pl.poznan.put.schema.TargetModelsDTO; -import pl.poznan.put.ws.entities.TrigonometricRepresentation; -import pl.poznan.put.ws.exceptions.ObjectNotFoundException; -import pl.poznan.put.ws.jpa.TrigonometricRepresentationCrudRepo; -import pl.poznan.put.ws.services.subservices.ComputationService; - -@Service -public class CompareService { - - private final ComputationService computationService; - - private final TrigonometricRepresentationCrudRepo trigonometricRepresentationCrudRepo; - - @Autowired - public CompareService( - ComputationService computationService, - TrigonometricRepresentationCrudRepo trigonometricRepresentationCrudRepo) { - this.computationService = computationService; - this.trigonometricRepresentationCrudRepo = trigonometricRepresentationCrudRepo; - } - - public List handleCompare(TargetModelsDTO targetModelsDTO) { - return handleCompare(targetModelsDTO.getModels(), targetModelsDTO.getTarget()); - } - - public List handleCompare(ModelsDTO modelsDTO) { - return handleCompare(modelsDTO.getModels(), null); - } - - public List handleCompare(List chains, String modelTarget) { - List trigonometricRepresentations = - new ArrayList(); - - trigonometricRepresentations = - StreamSupport.stream( - trigonometricRepresentationCrudRepo - .findAllById( - chains.stream() - .map(chain -> UUID.fromString(chain)) - .collect(Collectors.toList())) - .spliterator(), - false) - .collect(Collectors.toList()); - - if (modelTarget != null) { - List targets = - trigonometricRepresentationCrudRepo.findAllByInputId(UUID.fromString(modelTarget)); - if (targets.size() == 1) { - return computationService.compare(trigonometricRepresentations, targets.get(0)); - } else { - throw new ObjectNotFoundException(modelTarget, TrigonometricRepresentation.class); - } - } else { - return computationService.compare(trigonometricRepresentations); - } - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/services/UploadService.java b/mcq-ws/src/main/java/pl/poznan/put/ws/services/UploadService.java deleted file mode 100644 index cd4f6c97..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/services/UploadService.java +++ /dev/null @@ -1,63 +0,0 @@ -package pl.poznan.put.ws.services; - -import java.util.Optional; -import org.modelmapper.ModelMapper; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; -import pl.poznan.put.schema.StructureContentDTO; -import pl.poznan.put.schema.UploadDTO; -import pl.poznan.put.ws.entities.StructureContent; -import pl.poznan.put.ws.exceptions.PathVariableException; -import pl.poznan.put.ws.jpa.StructureContentCrudRepo; -import pl.poznan.put.ws.services.subservices.ComputationService; - -@Service -public class UploadService { - - private final ComputationService computationService; - - private final StructureContentCrudRepo structureContentCrudRepo; - - private final ModelMapper modelMapper; - - @Autowired - public UploadService( - ComputationService computationService, - StructureContentCrudRepo structureContentCrudRepo, - ModelMapper modelMapper) { - this.computationService = computationService; - this.structureContentCrudRepo = structureContentCrudRepo; - this.modelMapper = modelMapper; - } - - public UploadDTO handlePostUpload(StructureContentDTO structureContentDTO) { - Optional queryResult = - structureContentCrudRepo.findByData(structureContentDTO.getData()); - if (queryResult.isPresent()) { - return modelMapper.map(queryResult.get(), UploadDTO.class); - } else { - return modelMapper.map( - structureContentCrudRepo.save( - modelMapper.map(structureContentDTO, StructureContent.class)), - UploadDTO.class); - } - } - - public UploadDTO handlePostUpload(String pdbId, int assemblyId) { - validateParameters(pdbId, assemblyId); - StructureContentDTO loadedStructure = computationService.loadStructure(pdbId, assemblyId); - return handlePostUpload(loadedStructure); - } - - private void validateParameters(String pdbId, int assemblyId) { - if (pdbId.length() != 4) { - throw new PathVariableException( - "pdbId", pdbId, "This parameter has to contain 4 characters!"); - } - - if (assemblyId < 1) { - throw new PathVariableException( - "assemblyId", String.valueOf(assemblyId), "This number has to be positive!"); - } - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/services/VersionService.java b/mcq-ws/src/main/java/pl/poznan/put/ws/services/VersionService.java deleted file mode 100644 index b3fa456f..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/services/VersionService.java +++ /dev/null @@ -1,25 +0,0 @@ -package pl.poznan.put.ws.services; - -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; -import pl.poznan.put.ws.components.Version; -import pl.poznan.put.ws.exceptions.NoGitPropertiesException; - -@Service -public class VersionService { - - private final Version version; - - @Autowired - public VersionService(Version version) { - this.version = version; - } - - public Version findVersion() { - if (version.getVersion().equals("${git.commit.id.describe-short}")) { - throw new NoGitPropertiesException(); - } else { - return version; - } - } -} diff --git a/mcq-ws/src/main/java/pl/poznan/put/ws/services/subservices/ComputationService.java b/mcq-ws/src/main/java/pl/poznan/put/ws/services/subservices/ComputationService.java deleted file mode 100644 index 3c362baa..00000000 --- a/mcq-ws/src/main/java/pl/poznan/put/ws/services/subservices/ComputationService.java +++ /dev/null @@ -1,27 +0,0 @@ -package pl.poznan.put.ws.services.subservices; - -import java.util.List; -import org.springframework.stereotype.Service; -import pl.poznan.put.schema.ModelComparisonDTO; -import pl.poznan.put.schema.StructureContentDTO; -import pl.poznan.put.ws.entities.TrigonometricRepresentation; - -@Service -public class ComputationService { - public StructureContentDTO loadStructure(String pdbId, int assemblyId) { - return null; - } - - public List computeTorsionAngles(StructureContentDTO structureContentDTO) { - return null; - } - - public List compare(List target) { - return null; - } - - public List compare( - List model, TrigonometricRepresentation target) { - return null; - } -} diff --git a/mcq-ws/src/main/resources/application.properties b/mcq-ws/src/main/resources/application.properties deleted file mode 100644 index db1be8d0..00000000 --- a/mcq-ws/src/main/resources/application.properties +++ /dev/null @@ -1,7 +0,0 @@ -spring.datasource.url=jdbc:h2:mem:db -spring.datasource.driverClassName=org.h2.Driver -spring.datasource.username=admin -spring.datasource.password=password -spring.h2.console.enabled=true -spring.h2.console.path=/console -debug=true \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/AnglesDTO.yaml b/mcq-ws/src/main/resources/schema/AnglesDTO.yaml deleted file mode 100644 index 370acaf4..00000000 --- a/mcq-ws/src/main/resources/schema/AnglesDTO.yaml +++ /dev/null @@ -1,55 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - alpha: - $id: '#/properties/alpha' - type: number - beta: - $id: '#/properties/beta' - type: number - gamma: - $id: '#/properties/gamma' - type: number - delta: - $id: '#/properties/delta' - type: number - epsilon: - $id: '#/properties/epsilon' - type: number - zeta: - $id: '#/properties/zeta' - type: number - nu0: - $id: '#/properties/nu0' - type: number - nu1: - $id: '#/properties/nu1' - type: number - nu2: - $id: '#/properties/nu2' - type: number - nu3: - $id: '#/properties/nu3' - type: number - nu4: - $id: '#/properties/nu4' - type: number - eta: - $id: '#/properties/eta' - type: number - theta: - $id: '#/properties/theta' - type: number - etaPrim: - $id: '#/properties/etaPrim' - type: number - tehtaPrim: - $id: '#/properties/tehtaPrim' - type: number - chi: - $id: '#/properties/chi' - type: number - pseudophasePucker: - $id: '#/properties/pseudophasePucker' - type: number \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ChainDTO.yaml b/mcq-ws/src/main/resources/schema/ChainDTO.yaml deleted file mode 100644 index 6cc04bf4..00000000 --- a/mcq-ws/src/main/resources/schema/ChainDTO.yaml +++ /dev/null @@ -1,14 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - name: - $id: '#/properties/name' - type: string - residueAngles: - $id: '#/properties/residueAngles' - type: array - items: - $id: '#/properties/residueAngles/items' - existingJavaType: 'pl.poznan.put.schema.ResidueAngelsDTO' - type: object \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ModelComparisonDTO.yaml b/mcq-ws/src/main/resources/schema/ModelComparisonDTO.yaml deleted file mode 100644 index 94ed0f4b..00000000 --- a/mcq-ws/src/main/resources/schema/ModelComparisonDTO.yaml +++ /dev/null @@ -1,26 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - firstId: - $id: '#/properties/firstId' - type: string - secondId: - $id: '#/properties/secondId' - type: string - residueComparison: - $id: '#/properties/residueComparison' - type: array - items: - $id: '#/properties/residueComparison/items' - existingJavaType: 'pl.poznan.put.schema.ResidueComparisonDTO' - type: object - mcd: - $id: '#/properties/mcd' - type: number - mcq: - $id: '#/properties/mcq' - type: number - medcq: - $id: '#/properties/medcq' - type: number \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ModelsDTO.yaml b/mcq-ws/src/main/resources/schema/ModelsDTO.yaml deleted file mode 100644 index 8e990b4c..00000000 --- a/mcq-ws/src/main/resources/schema/ModelsDTO.yaml +++ /dev/null @@ -1,10 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - models: - $id: '#/properties/models' - type: array - items: - $id: '#/properties/models/items' - type: string \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ResidueAngelsDTO.yaml b/mcq-ws/src/main/resources/schema/ResidueAngelsDTO.yaml deleted file mode 100644 index 385d879e..00000000 --- a/mcq-ws/src/main/resources/schema/ResidueAngelsDTO.yaml +++ /dev/null @@ -1,12 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - residue: - $id: '#/properties/residue' - existingJavaType: 'pl.poznan.put.schema.ResidueDTO' - type: object - angles: - $id: '#/properties/angles' - existingJavaType: 'pl.poznan.put.schema.AnglesDTO' - type: object \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ResidueComparisonDTO.yaml b/mcq-ws/src/main/resources/schema/ResidueComparisonDTO.yaml deleted file mode 100644 index 03469b19..00000000 --- a/mcq-ws/src/main/resources/schema/ResidueComparisonDTO.yaml +++ /dev/null @@ -1,25 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - first: - $id: '#/properties/first' - existingJavaType: 'pl.poznan.put.schema.ResidueDTO' - type: object - second: - $id: '#/properties/second' - existingJavaType: 'pl.poznan.put.schema.ResidueDTO' - type: object - differences: - $id: '#/properties/differences' - existingJavaType: 'pl.poznan.put.schema.ResidueDTO' - type: object - mcd: - $id: '#/properties/mcd' - type: number - mcq: - $id: '#/properties/mcq' - type: number - medcq: - $id: '#/properties/medcq' - type: number \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/ResidueDTO.yaml b/mcq-ws/src/main/resources/schema/ResidueDTO.yaml deleted file mode 100644 index d878c372..00000000 --- a/mcq-ws/src/main/resources/schema/ResidueDTO.yaml +++ /dev/null @@ -1,25 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - isMissing: - $id: '#/properties/isMissing' - type: boolean - standardResidueName: - $id: '#/properties/standardResidueName' - type: string - modifiedResidueName: - $id: '#/properties/modifiedResidueName' - type: string - oneLetterName: - $id: '#/properties/oneLetterName' - type: string - chain: - $id: '#/properties/chain' - type: string - residueNumber: - $id: '#/properties/residueNumber' - type: integer - insertionCode: - $id: '#/properties/insertionCode' - type: string \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/StructureContentDTO.yaml b/mcq-ws/src/main/resources/schema/StructureContentDTO.yaml deleted file mode 100644 index 6bef066f..00000000 --- a/mcq-ws/src/main/resources/schema/StructureContentDTO.yaml +++ /dev/null @@ -1,7 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - data: - $id: '#/properties/data' - type: string \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/TargetModelsDTO.yaml b/mcq-ws/src/main/resources/schema/TargetModelsDTO.yaml deleted file mode 100644 index baffc003..00000000 --- a/mcq-ws/src/main/resources/schema/TargetModelsDTO.yaml +++ /dev/null @@ -1,13 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - target: - $id: '#/properties/target' - type: string - models: - $id: '#/properties/target' - type: array - items: - $id: '#/properties/target/items' - type: string \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/TrigonometricRepresentationDTO.yaml b/mcq-ws/src/main/resources/schema/TrigonometricRepresentationDTO.yaml deleted file mode 100644 index cc8a8549..00000000 --- a/mcq-ws/src/main/resources/schema/TrigonometricRepresentationDTO.yaml +++ /dev/null @@ -1,17 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - id: - $id: '#/properties/id' - type: string - modelNumber: - $id: '#/properties/modelNumber' - type: number - chains: - $id: '#/properties/chains' - type: array - items: - $id: '#/properties/chains/items' - existingJavaType: 'pl.poznan.put.schema.ChainDTO' - type: object \ No newline at end of file diff --git a/mcq-ws/src/main/resources/schema/UploadDTO.yaml b/mcq-ws/src/main/resources/schema/UploadDTO.yaml deleted file mode 100644 index 62436400..00000000 --- a/mcq-ws/src/main/resources/schema/UploadDTO.yaml +++ /dev/null @@ -1,7 +0,0 @@ -$schema: http://json-schema.org/draft-07/schema -additionalProperties: false -default: {} -properties: - id: - $id: '#/properties/id' - type: string \ No newline at end of file diff --git a/pom.xml b/pom.xml index 68bd6bfd..e6bdce99 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,6 @@ mcq-clustering mcq-core mcq-gui - mcq-ws @@ -210,7 +209,7 @@ org.springframework.boot spring-boot-starter-validation - 2.7.10 + 3.1.5 @@ -345,43 +344,11 @@ versions-maven-plugin - - org.jsonschema2pojo - jsonschema2pojo-maven-plugin - 1.2.1 - - ${basedir}/src/main/resources/schema - pl.poznan.put.schema - yamlschema - true - true - true - - - org.springframework.boot spring-boot-maven-plugin 3.1.5 - - - pl.project13.maven - git-commit-id-plugin - 4.9.10 - - true - false - - - - get-the-git-infos - - revision - - - -