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
-
-
-
-