diff --git a/build.sh b/build.sh
index ef4f10565705b3eb3d0fae54b60de23671f356bf..6a18d98ecec05885651675049490ca44c990ec7f 100755
--- a/build.sh
+++ b/build.sh
@@ -26,7 +26,7 @@ else
DOCKER="sudo docker"
fi
-IMAGE="hbpmip/portal-backend"
+IMAGE="kfilippopolitis/portal-backend"
VCS_REF=$(git describe --tags --dirty)
VERSION=$(git describe --tags --dirty)
diff --git a/pom.xml b/pom.xml
index 20a6f066122779eab771ca0d012dbcc4a8e8a208..87ef337aab0423568234cb76691ab29632ac265d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -211,13 +211,6 @@
<artifactId>jaxb-runtime</artifactId>
<version>2.4.0-b180830.0438</version>
</dependency>
-
- <dependency>
- <groupId>com.auth0</groupId>
- <artifactId>java-jwt</artifactId>
- <version>3.8.3</version>
- </dependency>
-
<!-- https://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j -->
<dependency>
<groupId>com.github.jmchilton.blend4j</groupId>
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index 8310973a308ec810853519552dc48855f494e4d7..fcde558b8c006b4d945a5eed51812d73a5e27891 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -8,7 +8,7 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.model.AlgorithmDTO;
+import eu.hbp.mip.model.DTOs.AlgorithmDTO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.galaxy.WorkflowDTO;
import eu.hbp.mip.utils.CustomResourceLoader;
diff --git a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java b/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
deleted file mode 100644
index d4eb46e9f3d072255e23be8a37a4e956add16873..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
+++ /dev/null
@@ -1,193 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-
-import com.github.slugify.Slugify;
-import eu.hbp.mip.model.Article;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.ArticleRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.*;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
-import java.io.IOException;
-import java.util.Date;
-import java.util.Iterator;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/articles", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/articles", description = "the articles API")
-public class ArticlesApi {
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private ArticleRepository articleRepository;
-
- @ApiOperation(value = "Get articles", response = Article.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<Iterable> getArticles(
- @ApiParam(value = "Only ask own articles") @RequestParam(value = "own", required = false) Boolean own,
- @ApiParam(value = "Only ask results matching status", allowableValues = "draft, published") @RequestParam(value = "status", required = false) String status
- ) {
- User user = userInfo.getUser();
- Iterable<Article> articles;
- Logging.LogUserAction(user.getUsername(), "(GET) /articles", "Loading articles...");
-
- if (own != null && own) {
- articles = articleRepository.findByCreatedBy(user);
- } else {
- articles = articleRepository.findByStatusOrCreatedBy("published", user);
- }
- int articlesSize = 0;
- if (status != null) {
- for (Iterator<Article> i = articles.iterator(); i.hasNext(); ) {
- Article a = i.next();
- if (!status.equals(a.getStatus())) {
- i.remove();
- }
- articlesSize++;
- }
- }
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles", "Successfully Loaded " + articlesSize + " articles");
-
- return ResponseEntity.ok(articles);
- }
-
-
- @ApiOperation(value = "Create an article")
- @ApiResponses(value = {@ApiResponse(code = 201, message = "Article created")})
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<Void> addAnArticle(
- @RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
- ) {
-
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Creating article...");
-
- article.setCreatedAt(new Date());
- if ("published".equals(article.getStatus())) {
- article.setPublishedAt(new Date());
- }
- article.setCreatedBy(user);
-
- long count = 1;
- for (int i = 1; count > 0; i++) {
- count = articleRepository.countByTitle(article.getTitle());
-
- if (count > 0) {
- String title = article.getTitle();
- if (i > 1) {
- title = title.substring(0, title.length() - 4);
- }
- article.setTitle(title + " (" + i + ")");
- }
- }
-
- String slug;
- try {
- slug = new Slugify().slugify(article.getTitle());
- } catch (IOException e) {
- slug = "";
- //LOGGER.trace("Cannot slugify title", e);
- }
-
- boolean alreadyExists = true;
- for (int i = 1; alreadyExists; i++) {
- alreadyExists = articleRepository.exists(slug);
- if (alreadyExists) {
- if (i > 1) {
- slug = slug.substring(0, slug.length() - 2);
- }
- slug += "-" + i;
- }
- article.setSlug(slug);
- }
- articleRepository.save(article);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Successfully created article with id : " + article.getSlug());
- return new ResponseEntity<>(HttpStatus.CREATED);
- }
-
-
- @ApiOperation(value = "Get an article", response = Article.class)
- @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
- public ResponseEntity<Article> getAnArticle(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Loading article with id : " + slug);
-
- User user = userInfo.getUser();
- Article article;
- article = articleRepository.findOne(slug);
-
- if (article == null) {
- //LOGGER.warn("Cannot find article : " + slug);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Article not found");
- return ResponseEntity.badRequest().body(null);
- }
-
- if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername())) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- Logging.LogUserAction(user.getUsername(), "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
-
- return ResponseEntity.ok(article);
- }
-
-
- @ApiOperation(value = "Update an article")
- @ApiResponses(value = {@ApiResponse(code = 204, message = "Article updated")})
- @RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
- public ResponseEntity<Void> updateAnArticle(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
- @RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Updating article with id : " + slug);
-
- User user = userInfo.getUser();
-
- String author = articleRepository.findOne(slug).getCreatedBy().getUsername();
-
- if (!user.getUsername().equals(author)) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- String oldTitle = articleRepository.findOne(slug).getTitle();
-
- String newTitle = article.getTitle();
-
- if (!newTitle.equals(oldTitle)) {
- long count = 1;
- for (int i = 1; count > 0 && !newTitle.equals(oldTitle); i++) {
- newTitle = article.getTitle();
- count = articleRepository.countByTitle(newTitle);
- if (count > 0 && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- article.setTitle(newTitle + " (" + i + ")");
- }
- }
- }
-
- articleRepository.save(article);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Successfully pdated article with id : " + slug);
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index f0515147455a391e409f4dcc63c32da1f54e1502..d28d8aac35cf08c7be49f96e64b1bfb5410e2662 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,43 +1,20 @@
package eu.hbp.mip.controllers;
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
-import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
-import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
-import com.google.common.collect.Lists;
-import com.google.gson.*;
-import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
-import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.model.*;
-import eu.hbp.mip.model.ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO;
-import eu.hbp.mip.model.galaxy.ErrorResponse;
-import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
-import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
-import eu.hbp.mip.repositories.ExperimentRepository;
-import eu.hbp.mip.repositories.ModelRepository;
-import eu.hbp.mip.utils.ClaimUtils;
-import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.Logging;
+import com.google.gson.Gson;
+import eu.hbp.mip.model.DTOs.ExperimentDTO;
+import eu.hbp.mip.model.UserInfo;
+import eu.hbp.mip.services.ExperimentService;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
-import org.codehaus.jettison.json.JSONException;
-import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.*;
-import retrofit2.Call;
-import retrofit2.Response;
-import java.io.IOException;
-import java.util.*;
+import java.util.List;
-import static java.lang.Thread.sleep;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
/*
@@ -50,784 +27,41 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/experiments")
public class ExperimentApi {
- private static final Gson gson = new Gson();
-
@Autowired
private UserInfo userInfo;
- private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
- .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
-
- @Value("#{'${services.exareme.queryExaremeUrl}'}")
- private String queryExaremeUrl;
-
- @Value("#{'${services.workflows.workflowUrl}'}")
- private String workflowUrl;
-
- @Value("#{'${services.workflows.jwtSecret}'}")
- private String jwtSecret;
-
- @Value("#{'${services.galaxy.galaxyUrl}'}")
- private String galaxyUrl;
-
- @Value("#{'${services.galaxy.galaxyApiKey}'}")
- private String galaxyApiKey;
-
- // Enable HBP collab authentication (1) or disable it (0). Default is 1
- @Value("#{'${hbp.authentication.enabled:1}'}")
- private boolean authenticationIsEnabled;
-
@Autowired
- private ModelRepository modelRepository;
+ private ExperimentService experimentService;
- @Autowired
- private ExperimentRepository experimentRepository;
+ @ApiOperation(value = "Get experiments", response = ExperimentDTO.class, responseContainer = "List")
+ @RequestMapping(method = RequestMethod.GET)
+ public ResponseEntity<String> getExperiments() {
+ return experimentService.getExperiments("(GET) /experiments");
+ }
- @ApiOperation(value = "get an experiment", response = Experiment.class)
+ @ApiOperation(value = "Get an experiment", response = ExperimentDTO.class)
@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
public ResponseEntity<String> getExperiment(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : " + uuid);
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Invalid Experiment UUID.");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
-
- if (experiment == null) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment Not found.");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
-
- if (!experiment.isShared() && !experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Accessing Experiment is unauthorized.");
- return new ResponseEntity<>("You don't have access to the experiment.", HttpStatus.UNAUTHORIZED);
- }
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid + ".");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
-
- @ApiOperation(value = "Create an experiment", response = Experiment.class)
- @RequestMapping(value = "/runAlgorithm", method = RequestMethod.POST)
- public ResponseEntity<String> runExperiment(Authentication authentication, @RequestBody ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- // Get the type and name of algorithm
- String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
- String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
- for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO params : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
- parametersLogMessage
- .append(" ")
- .append(params.getLabel())
- .append(" -> ")
- .append(params.getValue())
- .append("\n");
- }
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + parametersLogMessage);
-
- if (authenticationIsEnabled) {
- // Getting the dataset from the experiment parameters
- String experimentDatasets = null;
- for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO parameter : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
- if (parameter.getLabel().equals("dataset")) {
- experimentDatasets = parameter.getValue();
- break;
- }
- }
-
- if (experimentDatasets == null || experimentDatasets.equals("")) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "A dataset should be specified to run an algorithm.");
- return ResponseEntity.badRequest().body("Please provide at least one dataset to run the algorithm.");
- }
-
- // --- Validating proper access rights on the datasets ---
- if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
- return ResponseEntity.badRequest().body("You are not authorized to use these datasets.");
- }
- }
-
- // Run with the appropriate engine
- if (algorithmType.equals("workflow")) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Galaxy.");
- return runGalaxyWorkflow(experimentExecutionDTO);
- } else {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Exareme.");
- return runExaremeAlgorithm(experimentExecutionDTO);
- }
+ return experimentService.getExperiment(uuid, "(GET) /experiments/{uuid}");
}
- @ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsViewed", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsViewed(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Marking as viewed the experiment with uuid : " + uuid + ".");
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Invalid Experiment UUID" + uuid + ".");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "You're not the owner of this experiment");
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
- }
- experiment.setResultsViewed(true);
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Experiment with uuid: " + uuid + " was marked as viewed.");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ @ApiOperation(value = "Create an experiment", response = ExperimentDTO.class)
+ @RequestMapping(method = RequestMethod.POST)
+ public ResponseEntity<String> createExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
+ return experimentService.createExperiment(authentication, experimentDTO, "(POST) /experiments");
}
- @ApiOperation(value = "Mark an experiment as shared", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsShared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsShared(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAsShared", "Marking as shared the experiment with uuid : " + uuid + ".");
-
- return doMarkExperimentAsShared(uuid, true);
+ @ApiOperation(value = "Update an experiment", response = ExperimentDTO.class)
+ @RequestMapping(value = "/{uuid}", method = RequestMethod.PATCH)
+ public ResponseEntity<String> updateExperiment(@RequestBody ExperimentDTO experimentDTO,@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ return experimentService.updateExperiment(uuid, experimentDTO, "(PATCH) /experiments/{uuid}");
}
- @ApiOperation(value = "Mark an experiment as unshared", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsUnshared(
+ @ApiOperation(value = "Delete an experiment", response = boolean.class)
+ @RequestMapping(value = "/{uuid}", method = RequestMethod.DELETE)
+ public ResponseEntity<String> deleteExperiment(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAs/Unshared", "Marking as unshared the experiment with uuid : " + uuid + ".");
-
- return doMarkExperimentAsShared(uuid, false);
- }
-
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"maxResultCount"})
- public ResponseEntity<String> listExperiments(
- @ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
-
- List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
- public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
- @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Listing experiments with a maximum amount of :" + maxResultCount + "with modelSlug : " + modelSlug + ".");
-
- if (maxResultCount <= 0 || modelSlug == null || "".equals(modelSlug)) {
- return new ResponseEntity<>("You must provide at least a slug or a limit of result",
- HttpStatus.BAD_REQUEST);
- }
-
- List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Successfully listed my experiments.");
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- @ApiOperation(value = "list my experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"mine"})
- public ResponseEntity<String> listMyExperiments(Authentication authentication, @ApiParam(value = "mine") @RequestParam("mine") boolean mine) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
- List<Experiment> expList = doListExperiments(true, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- private List<Experiment> doListExperiments(boolean mine, String modelSlug) {
- User user = userInfo.getUser();
-
- Iterable<Experiment> myExperiments = experimentRepository.findByCreatedBy(user);
- List<Experiment> expList = Lists.newLinkedList(myExperiments);
- if (!mine) {
- Iterable<Experiment> sharedExperiments = experimentRepository.findByShared(true);
- List<Experiment> sharedExpList = Lists.newLinkedList(sharedExperiments);
- expList.addAll(sharedExpList);
- }
-
- if (modelSlug != null && !"".equals(modelSlug)) {
- for (Iterator<Experiment> it = expList.iterator(); it.hasNext(); ) {
- Experiment e = it.next();
- e.setResult(null);
- e.setAlgorithms(null);
- e.setValidations(null);
- if (!e.getModel().getSlug().equals(modelSlug)) {
- it.remove();
- }
- }
- }
- return expList;
- }
-
- private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- //LOGGER.trace("Invalid UUID", iae);
- //LOGGER.warn("An invalid Experiment UUID was received !");
- Logging.LogUserAction(user.getUsername(), "List my experiments", "Listing my experiments.");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
-
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
-
- experiment.setShared(shared);
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "Experiment updated (marked as shared)", "");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
- /* ------------------------------- EXPERIMENT MODEL METHODS ----------------------------------------------------*/
-
- public Experiment createExperiment(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
-
- Experiment experiment = new Experiment();
- experiment.setUuid(UUID.randomUUID());
- experiment.setCreatedBy(user);
- experiment.setAlgorithms(gson.toJson(experimentExecutionDTO.getAlgorithms()));
- Model model = modelRepository.findOne(experimentExecutionDTO.getModel());
- experiment.setModel(model);
- experiment.setName(experimentExecutionDTO.getName());
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
- return experiment;
- }
-
- private void saveExperiment(Experiment experiment) {
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " historyId : " + experiment.getWorkflowHistoryId());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " status : " + experiment.getWorkflowStatus());
-
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Saved experiment");
- }
-
- private void finishExperiment(Experiment experiment) {
- experiment.setFinished(new Date());
- experimentRepository.save(experiment);
- }
-
- /* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
-
- /**
- * The runExaremeExperiment will POST the algorithm to the exareme client
- *
- * @param experimentExecutionDTO is the request with the experiment information
- * @return the response to be returned
- */
- public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
-
- Experiment experiment = createExperiment(experimentExecutionDTO);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
-
- // Run the 1st algorithm from the list
- String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- // Get the parameters
- List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> algorithmParameters
- = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
-
- String body = gson.toJson(algorithmParameters);
- String url = queryExaremeUrl + "/" + algorithmName;
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "url: " + url + ", body: " + body);
-
- ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Completed, returning: " + experiment.toString());
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Starting exareme execution thread");
- new Thread(() -> {
- // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, body, results);
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Algorithm finished with code: " + code);
-
- // Results are stored in the experiment object
- experiment.setResult("[" + results.toString() + "]");
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
- } catch (Exception e) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "There was an exception: " + e.getMessage());
-
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
-
- finishExperiment(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Finished the experiment: " + experiment.toString());
- }).start();
-
- return response;
- }
-
- /* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
-
-
- /**
- * The runWorkflow will POST the algorithm to the galaxy client
- *
- * @param experimentExecutionDTO is the request with the experiment information
- * @return the response to be returned
- */
- public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
-
- Experiment experiment = createExperiment(experimentExecutionDTO);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
-
-
- // Run the 1st algorithm from the list
- String workflowId = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- // Get the parameters
- List<AlgorithmExecutionParamDTO> algorithmParameters
- = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
-
- // Convert the parameters to workflow parameters
- HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
- if (algorithmParameters != null) {
- for (AlgorithmExecutionParamDTO param : algorithmParameters) {
- algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
- }
- }
-
- // Get all the algorithm parameters because the frontend provides only the non-null
- final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
- final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
- Workflow workflow = null;
- for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
- if (curWorkflow.getId().equals(workflowId)) {
- workflow = curWorkflow;
- break;
- }
- }
- if (workflow == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Could not find algorithm code: " + workflowId);
- return ResponseEntity.status(HttpStatus.BAD_REQUEST)
- .body(new ErrorResponse("Could not find galaxy algorithm.").toString());
- }
- final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
- for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
- if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
- algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
- }
- }
-
- // Create the body of the request
- HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
- requestBody.put("inputs", algorithmParamsIncludingEmpty);
- JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running Galaxy workflow with id: " + workflow.getId());
-
- // Call Galaxy to run the workflow
- Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
- try {
- Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
-
- if (response.code() == 200) { // Call succeeded
- String responseBody = gson.toJson(response.body());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Response: " + responseBody);
-
- String historyId = (String) new JSONObject(responseBody).get("history_id");
- experiment.setWorkflowHistoryId(historyId);
- experiment.setWorkflowStatus("running");
- experiment.setHasError(false);
- experiment.setHasServerError(response.code() >= 500);
-
- } else { // Something unexpected happened
- String msgErr = gson.toJson(response.errorBody());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Error Response: " + msgErr);
-
- // Values are read from streams.
- JSONObject jObjectError = new JSONObject(msgErr);
- String errMsg = jObjectError.get("err_msg").toString();
-
- experiment.setResult("[" + new ErrorResponse(errMsg).toString() + "]");
- experiment.setHasError(response.code() >= 400);
- experiment.setHasServerError(response.code() >= 500);
- }
-
- } catch (Exception e) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "An exception occurred: " + e.getMessage());
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
- saveExperiment(experiment);
-
- // Start the process of fetching the status
- updateWorkflowExperiment(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Run workflow completed!");
-
- return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
-
- /**
- * This method creates a thread that will fetch the workflow result when it is ready
- *
- * @param experiment will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
- * and the result should not already be fetched
- * @return nothing, just updates the experiment
- */
- public void updateWorkflowExperiment(Experiment experiment) {
- User user = userInfo.getUser();
-
- if (experiment == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "The experiment does not exist.");
- return;
- }
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- " Experiment id : " + experiment.getUuid());
- if (experiment.getWorkflowHistoryId() == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "History Id does not exist.");
- return;
- }
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Starting Thread...");
- new Thread(() -> {
- while (true) {
- // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread is running...");
-
- try {
- sleep(2000);
- } catch (InterruptedException e) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Sleep was disrupted: " + e.getMessage());
- }
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Fetching status for experiment Id: " + experiment.getUuid());
-
- String state = getWorkflowStatus(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "State is: " + state);
-
- switch (state) {
- case "running":
- // Do nothing, when the experiment is created the status is set to running
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Workflow is still running.");
- break;
-
- case "completed":
- // Get only the job result that is visible
- List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Results are: " + workflowJobsResults.toString());
-
- boolean resultFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getVisible()) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Visible result are: " + jobResult.getId());
-
- String result = getWorkflowResultBody(experiment, jobResult.getId());
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result: " + result);
- if (result == null) {
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- experiment.setResult("[" + result + "]");
- experiment.setWorkflowStatus("completed");
- resultFound = true;
- }
- }
-
- if (!resultFound) { // If there is no visible result
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No visible result");
- experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
-
- finishExperiment(experiment);
- break;
-
- case "error":
- // Get the job result that failed
- workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Error results are: " + workflowJobsResults.toString());
-
- boolean failedJobFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getState().equals("error")) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Failed job is: " + jobResult.getId());
-
- String result = getWorkflowJobError(jobResult.getId(), experiment);
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Job result: " + result);
- if (result == null) {
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- experiment.setResult("[" + result + "]");
- experiment.setWorkflowStatus("error");
- failedJobFound = true;
- }
- }
-
- if (!failedJobFound) { // If there is no visible failed job
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No failed result");
- experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- finishExperiment(experiment);
- break;
-
- default: // InternalError or unexpected result
- experiment.setResult("[" + new ErrorResponse("An unexpected error occurred.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- finishExperiment(experiment);
- break;
- }
-
- // If result exists return
- if (experiment.getResult() != null) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result exists: " + experiment.getResult());
- return;
- }
- }
- }).start();
- }
-
-
- /**
- * @param experiment The experiment of the workflow
- * @return "running" -> When the workflow is still running
- * "internalError" -> When an exception or a bad request occurred
- * "error" -> When the workflow produced an error
- * "completed" -> When the workflow completed successfully
- */
- public String getWorkflowStatus(Experiment experiment) {
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
-
- String result = null;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return "internalError";
- }
- result = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + result);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- String state = null;
- try {
- JSONObject resultJson = new JSONObject(result);
- state = resultJson.getString("state");
- } catch (JSONException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- switch (state) {
- case "ok":
- return "completed";
- case "error":
- return "error";
- case "running":
- case "new":
- case "waiting":
- case "queued":
- return "running";
- default:
- return "internalError";
- }
- }
-
- /**
- * @param experiment The experiment of the workflow
- * @return a List<GalaxyWorkflowResult> or null when an error occurred
- */
- public List<GalaxyWorkflowResult> getWorkflowResults(Experiment experiment) {
-
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
- Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
-
- List<GalaxyWorkflowResult> getGalaxyWorkflowResultList = null;
- try {
- Response<List<GalaxyWorkflowResult>> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- getGalaxyWorkflowResultList = response.body();
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + response.body());
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- return getGalaxyWorkflowResultList;
-
+ return experimentService.deleteExperiment(uuid, "(DELETE) /experiments/{uuid}");
}
-
- /**
- * @param experiment The experiment of the workflow
- * @param contentId the id of the job result that we want
- * @return the result of the specific workflow job, null if there was an error
- */
- public String getWorkflowResultBody(Experiment experiment, String contentId) {
-
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call =
- service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
-
- String resultJson = null;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- resultJson = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + resultJson);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId,
- " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- return resultJson;
- }
-
-
- /**
- * @param jobId the id of the workflow job that failed
- * @return the error that was produced or null if an error occurred
- */
- public String getWorkflowJobError(String jobId, Experiment experiment) {
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- Logging.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
-
- String fullError = null;
- String returnError = null;
- try {
- Response<Object> response = callError.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, "Response code: "
- + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
-
- // Parsing the stderr of the job that failed
- String jsonString = new Gson().toJson(response.body());
- JsonElement jsonElement = new JsonParser().parse(jsonString);
- JsonObject rootObject = jsonElement.getAsJsonObject();
- fullError = rootObject.get("stderr").getAsString();
- Logging.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
-
- String[] arrOfStr = fullError.split("ValueError", 0);
- String specError = arrOfStr[arrOfStr.length - 1];
- returnError = specError.substring(1);
- Logging.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
-
- return returnError;
- }
-
-
-}
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
deleted file mode 100644
index 69e7f3ba94702ee9b5465920d3234ca4dcac0248..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-import eu.hbp.mip.utils.Logging;
-
-/**
- * Created by mirco on 08.05.17.
- */
-
-@RestController
-@RequestMapping(value = "/protected")
-@Api(value = "/protected", description = "the protected files API")
-public class FilesAPI {
-
-
- @Autowired
- private UserInfo userInfo;
-
- @ApiOperation(value = "Get protected files")
- @RequestMapping(value = "/{filename:.+}", method = RequestMethod.GET)
- public ResponseEntity<Void> getProtectedFile(
- @ApiParam(value = "filename", required = true) @PathVariable("filename") String filename
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}", "Loading protected file with filename : " + filename);
-
- String filepath = "/protected/" + filename;
- Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}" + filepath, "Downloaded protected file");
-
- HttpHeaders headers = new HttpHeaders();
- headers.add("X-Accel-Redirect", filepath);
-
- return new ResponseEntity<>(headers, HttpStatus.OK);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
deleted file mode 100644
index 6a198cc0d4571c58b1ff424e590bc418893a39f1..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.utils.HTTPUtil;
-
-import com.google.gson.Gson;
-
-import eu.hbp.mip.model.UserInfo;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import eu.hbp.mip.utils.Logging;
-
-
-import java.util.*;
-import java.io.IOException;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-/**
- * Created by mirco on 06.01.17.
- */
-@RestController
-@RequestMapping(value = "/mining", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/mining", description = "the mining API")
-public class MiningApi {
-
- private static final Gson gson = new Gson();
-
- @Autowired
- private UserInfo userInfo;
-
- @Value("#{'${services.exareme.queryExaremeUrl:http://localhost:9090/mining/query}'}")
- public String queryExaremeUrl;
-
- @ApiOperation(value = "Create a histogram on Exareme", response = String.class)
- @RequestMapping(value = "/histograms", method = RequestMethod.POST)
- public ResponseEntity runExaremeHistograms(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executing histogram...");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executed histogram with result :" + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Histogram algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
- @RequestMapping(value = "/descriptive_stats", method = RequestMethod.POST)
- public ResponseEntity runExaremeDescriptiveStats(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executing Exareme descriptive stats...");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executed descriptive stats with result : " + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Descriptive stats algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
- @RequestMapping(value = "/descriptive_stats_v2", method = RequestMethod.POST)
- public ResponseEntity runExaremeDescriptiveStatsV2(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Executing an Exareme descriptive stats v2");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS_v2";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Successfully executed descriptive stats v2 with results : " + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Descriptive stats v2 algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Check if a formula is valid", response = String.class)
- @RequestMapping(value = "/checkFormula", method = RequestMethod.POST)
- public ResponseEntity checkFormulaValidity(String formula) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/checkFormula", "Executing checkFormula ...");
-
- return ResponseEntity.ok("");
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
deleted file mode 100644
index 6f013ee336815bbb25514b37cdb764fe7710e8fd..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ /dev/null
@@ -1,259 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-import com.github.slugify.Slugify;
-import eu.hbp.mip.model.Model;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.model.Variable;
-import eu.hbp.mip.repositories.*;
-import io.swagger.annotations.*;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.utils.Logging;
-
-import java.io.IOException;
-import java.util.*;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/models", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/models", description = "the models API")
-public class ModelsApi {
-
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private DatasetRepository datasetRepository;
-
- @Autowired
- private ModelRepository modelRepository;
-
- @Autowired
- private QueryRepository queryRepository;
-
- @Autowired
- private ConfigRepository configRepository;
-
- @Autowired
- private VariableRepository variableRepository;
-
- @ApiOperation(value = "get models", response = Model.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getModels(
- @ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
- @ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Loading models ...");
-
- User user = userInfo.getUser();
-
- Iterable<Model> models;
- if (own != null && own) {
- models = modelRepository.findByCreatedByOrderByCreatedAt(user);
- } else {
- models = modelRepository.findByValidOrCreatedByOrderByCreatedAt(true, user);
- }
-
- if (valid != null && models != null) {
- for (Iterator<Model> i = models.iterator(); i.hasNext(); ) {
- Model m = i.next();
- if (valid != m.getValid()) {
- i.remove();
- }
- }
- }
-
- List<Object> modelsList = new LinkedList<>();
- models = models != null ? models : new LinkedList<>();
- for (Model m : models) {
- m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
- modelsList.add(m);
- }
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Successfully loaded " + modelsList.size() + " models.");
-
- return ResponseEntity.ok(modelsList);
- }
-
-
- @ApiOperation(value = "Create a model", response = Model.class)
- @ApiResponses(value = {@ApiResponse(code = 201, message = "Model created")})
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<Model> addAModel(
- @RequestBody @ApiParam(value = "Model to create", required = true) Model model
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /models", "Creating a model");
-
- model.setTitle(model.getConfig().getTitle().get("text"));
- model.setCreatedBy(user);
- model.setCreatedAt(new Date());
- if (model.getValid() == null) {
- model.setValid(false);
- }
-
- ensureTitleUniqueness(model);
- ensureSlugUniqueness(model);
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
-
- saveVariables(model.getQuery().getVariables());
- saveVariables(model.getQuery().getCovariables());
- saveVariables(model.getQuery().getGrouping());
- saveVariables(model.getQuery().getTrainingDatasets());
-
- configRepository.save(model.getConfig());
- queryRepository.save(model.getQuery());
- if (model.getDataset() != null) {
- datasetRepository.save(model.getDataset());
- }
- modelRepository.save(model);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /models", "Created model with id : " + model.getSlug() + ", model.config and model.query");
-
- return ResponseEntity.status(HttpStatus.CREATED).body(model);
- }
-
- private void saveVariables(@RequestBody @ApiParam(value = "Model to create", required = true) List<Variable> variables) {
- for (Variable var : variables) {
- variableRepository.save(var);
- }
- }
-
- private void ensureSlugUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
- String slug = createSlug(model.getTitle());
- boolean slugExists = true;
- for (int i = 1; slugExists; i++) {
- slugExists = modelRepository.exists(slug);
- if (slugExists) {
- if (i > 1) {
- slug = slug.substring(0, slug.length() - 2);
- }
- slug += "-" + i;
- }
- model.setSlug(slug);
- }
- }
-
- private String createSlug(@RequestBody @ApiParam(value = "Model to create", required = true) String title) {
- String slug;
- try {
- slug = new Slugify().slugify(title);
- } catch (IOException e) {
- slug = ""; // Should never happen
- //LOGGER.trace("Cannot slugify title", e);
- }
- return slug;
- }
-
- private void ensureTitleUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
- boolean titleExists = true;
- for (int i = 1; titleExists; i++) {
- String title = model.getTitle();
- titleExists = modelRepository.countByTitle(title) > 0;
- if (titleExists) {
- if (i > 1) {
- title = title.substring(0, title.length() - 4);
- }
- model.setTitle(title + " (" + i + ")");
- }
- }
- }
-
- @ApiOperation(value = "Get a model", response = Model.class)
- @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
- public ResponseEntity<Model> getAModel(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
-
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loading model with id : " + slug);
-
- Model model = modelRepository.findOne(slug);
- if (model == null) {
- //LOGGER.warn("Cannot find model : " + slug);
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Model was not found");
- return ResponseEntity.badRequest().body(null);
- }
-
- if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "You are not authorized to retrieve models. ");
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- List<String> yAxisVars = configRepository.findOne(model.getConfig().getId()).getyAxisVariables();
- Collection<String> yAxisVarsColl = new LinkedHashSet<>(yAxisVars);
- model.getConfig().setyAxisVariables(new LinkedList<>(yAxisVarsColl));
-
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loaded model with id : " + slug);
- return ResponseEntity.ok(model);
- }
-
-
- @ApiOperation(value = "Update a model", response = Void.class)
- @ApiResponses(value = {@ApiResponse(code = 204, message = "Model updated")})
- @RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
- public ResponseEntity<Void> updateAModel(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
- @RequestBody @ApiParam(value = "Model to update", required = true) Model model
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updating model with id : " + slug);
- Model oldModel = modelRepository.findOne(slug);
-
- if (!user.getUsername().equals(oldModel.getCreatedBy().getUsername())) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- model.setTitle(model.getConfig().getTitle().get("text"));
-
- String oldTitle = oldModel.getTitle();
- String newTitle = model.getTitle();
-
- // If title has been updated, ensure it is unique
- if (!newTitle.equals(oldTitle)) {
- boolean newTitleExists = true;
- for (int i = 1; newTitleExists && !newTitle.equals(oldTitle); i++) {
- newTitle = model.getTitle();
- newTitleExists = modelRepository.countByTitle(newTitle) > 0;
- if (newTitleExists && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- model.setTitle(newTitle + " (" + i + ")");
- }
- }
- }
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
-
- saveVariables(model.getQuery().getVariables());
- saveVariables(model.getQuery().getCovariables());
- saveVariables(model.getQuery().getGrouping());
- saveVariables(model.getQuery().getTrainingDatasets());
-
- configRepository.save(model.getConfig());
- queryRepository.save(model.getQuery());
- datasetRepository.save(model.getDataset());
- modelRepository.save(model);
-
- Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updated model and saved/updated model.config and model.query");
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index 77916981465827ae4e0806366663a16c7ad1e70b..66a97896bc805667e263b8a1e65565969ea1f63e 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -6,7 +6,7 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
-import eu.hbp.mip.model.PathologyDTO;
+import eu.hbp.mip.model.DTOs.PathologyDTO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.CustomResourceLoader;
diff --git a/src/main/java/eu/hbp/mip/controllers/StatsApi.java b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
deleted file mode 100644
index 8bd109e535b7c29b5dac96b68b2ba59329ca6a59..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Created by mirco on 18.01.16.
- */
-
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.model.GeneralStats;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.ArticleRepository;
-import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/stats", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/stats", description = "the stats API")
-public class StatsApi {
- @Autowired
- private UserRepository userRepository;
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private ArticleRepository articleRepository;
-
-
- @ApiOperation(value = "Get general statistics", response = GeneralStats.class)
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<GeneralStats> getGeneralStatistics() {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loading general statistics");
-
- GeneralStats stats = new GeneralStats();
-
- stats.setUsers(userRepository.count());
- stats.setArticles(articleRepository.count());
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loaded " + userRepository.count() + " user statistics and " + articleRepository.count() + " artcle statistics.");
- return ResponseEntity.ok(stats);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Article.java b/src/main/java/eu/hbp/mip/model/Article.java
index 95c7cbbae0701558b249dec7a5cf0b9a07bd3e92..b79f2a33a8275484a0e9a680a93619dbea2ea5c2 100644
--- a/src/main/java/eu/hbp/mip/model/Article.java
+++ b/src/main/java/eu/hbp/mip/model/Article.java
@@ -52,10 +52,6 @@ public class Article {
@JoinColumn(name = "updatedby_username")
private User updatedBy = null;
- @ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.PERSIST)
- private List<Tag> tags = new LinkedList<>();
-
-
public Article() {
/*
* Empty constructor is needed by Hibernate
@@ -154,13 +150,4 @@ public class Article {
this.updatedBy = updatedBy;
}
-
- public List<Tag> getTags() {
- return tags;
- }
-
- public void setTags(List<Tag> tags) {
- this.tags = tags;
- }
-
}
diff --git a/src/main/java/eu/hbp/mip/model/Config.java b/src/main/java/eu/hbp/mip/model/Config.java
deleted file mode 100644
index 2362194b2b8338d7ab7a0b781c7891e88acfd293..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Config.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/**
- * Created by mirco on 25.02.16.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-@Entity
-@Table(name = "`config`")
-@ApiModel
-@JsonIgnoreProperties(value = {"id"})
-public class Config {
-
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE)
- private Long id = null;
-
- private String type = null;
-
- private Integer height = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "config_yAxisVariables", joinColumns = @JoinColumn(name = "config_id"))
- private List<String> yAxisVariables = new LinkedList<>();
-
- private String xAxisVariable = null;
-
- private Boolean hasXAxis = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "config_title", joinColumns = @JoinColumn(name = "config_id"))
- private Map<String, String> title = new HashMap<>();
-
-
- public Config() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public Long getId() {
- return id;
- }
-
- public void setId(Long id) {
- this.id = id;
- }
-
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
-
- public Integer getHeight() {
- return height;
- }
-
- public void setHeight(Integer height) {
- this.height = height;
- }
-
-
- public List<String> getyAxisVariables() {
- return yAxisVariables;
- }
-
- public void setyAxisVariables(List<String> yAxisVariables) {
- this.yAxisVariables = yAxisVariables;
- }
-
-
- public String getxAxisVariable() {
- return xAxisVariable;
- }
-
- public void setxAxisVariable(String xAxisVariable) {
- this.xAxisVariable = xAxisVariable;
- }
-
-
- public Boolean getHasXAxis() {
- return hasXAxis;
- }
-
- public void setHasXAxis(Boolean hasXAxis) {
- this.hasXAxis = hasXAxis;
- }
-
-
- public Map<String, String> getTitle() {
- return title;
- }
-
- public void setTitle(Map<String, String> title) {
- this.title = title;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..682f121cea95c13bf88c83c71ddcd5815ffe7884
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
@@ -0,0 +1,203 @@
+package eu.hbp.mip.model.DAOs;
+
+import com.google.gson.Gson;
+import com.google.gson.annotations.Expose;
+import eu.hbp.mip.model.DTOs.AlgorithmDTO;
+import eu.hbp.mip.model.DTOs.ExperimentDTO;
+import eu.hbp.mip.model.User;
+import eu.hbp.mip.utils.JsonConverters;
+
+import javax.persistence.*;
+import java.util.Date;
+import java.util.UUID;
+
+/**
+ * Created by habfast on 21/04/16.
+ */
+@Entity
+@Table(name = "`experiment`")
+public class ExperimentDAO {
+
+ private static final Gson gson = new Gson();
+
+ @Id
+ @Column(columnDefinition = "uuid", updatable = false)
+ @org.hibernate.annotations.Type(type = "pg-uuid")
+ @Expose
+ private UUID uuid;
+
+ @Column(columnDefinition = "TEXT")
+ @Expose
+ private String name;
+
+ @Expose
+ @ManyToOne
+ @JoinColumn(name = "created_by_username")
+ private User createdBy;
+
+ @Column(name="workflow_history_id", columnDefinition = "TEXT")
+ @Expose
+ private String workflowHistoryId;
+
+ @Column(columnDefinition = "TEXT")
+ @Expose
+ private Status status;
+
+ @Column(columnDefinition = "TEXT")
+ @Expose
+ private String result;
+
+ @Expose
+ private Date finished;
+
+ @Expose
+ private String algorithm;
+
+ @Expose
+ private Date created = new Date();
+
+ @Expose
+ private boolean shared = false;
+
+ // whether or not the experiment's result have been viewed by its owner
+ @Expose
+ private boolean viewed = false;
+
+ public enum Status {
+ error,
+ pending,
+ success
+ }
+
+ public enum MimeTypes {
+ ERROR("text/plain+error"),
+ WARNING("text/plain+warning"),
+ USER_WARNING("text/plain+user_error"),
+ HIGHCHARTS("application/vnd.highcharts+json"),
+ JSON("application/json"),
+ JSONBTREE("application/binary-tree+json"),
+ PFA("application/pfa+json"),
+ JSONDATA("application/vnd.dataresource+json"),
+ HTML("text/html"),
+ TEXT("text/plain");
+
+ private String types;
+
+ //Constructor to initialize the instance variable
+ MimeTypes(String types) {
+ this.types = types;
+ }
+
+ public String getTypes() {
+ return this.types;
+ }
+ }
+
+ public ExperimentDAO() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
+ }
+
+ public ExperimentDTO convertToDTO()
+ {
+ ExperimentDTO experimentDTO = new ExperimentDTO();
+ experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, AlgorithmDTO.class));
+ experimentDTO.setCreated(this.created);
+ experimentDTO.setCreatedBy(this.createdBy.getUsername());
+ experimentDTO.setName(this.name);
+ experimentDTO.setResult(JsonConverters.convertJsonStringToObject(this.result, ExperimentDTO.ResultDTO.class));
+ experimentDTO.setShared(this.shared);
+ experimentDTO.setUuid(this.uuid.toString());
+ experimentDTO.setViewed(this.viewed);
+ return experimentDTO;
+ }
+
+ public String getAlgorithm() {
+ return algorithm;
+ }
+
+ public void setAlgorithm(String algorithm) {
+ this.algorithm = algorithm;
+ }
+
+ public String getWorkflowHistoryId() {
+ return workflowHistoryId;
+ }
+
+ public void setWorkflowHistoryId(String workflowHistoryId) {
+ this.workflowHistoryId = workflowHistoryId;
+ }
+
+ public Status getStatus() {
+ return status;
+ }
+
+ public void setStatus(Status status) {
+ this.status = status;
+ }
+
+ public String getResult() {
+ return result;
+ }
+
+ public void setResult(String result) {
+ this.result = result;
+ }
+
+ public Date getFinished() {
+ return finished;
+ }
+
+ public void setFinished(Date finished) {
+ this.finished = finished;
+ }
+
+ public Date getCreated() {
+ return created;
+ }
+
+ public void setCreated(Date created) {
+ this.created = created;
+ }
+
+ public UUID getUuid() {
+ return uuid;
+ }
+
+ public void setUuid(UUID uuid) {
+ this.uuid = uuid;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public User getCreatedBy() {
+ return createdBy;
+ }
+
+ public void setCreatedBy(User createdBy) {
+ this.createdBy = createdBy;
+ }
+
+ public boolean isViewed() {
+ return viewed;
+ }
+
+ public void setViewed(boolean viewed) {
+ this.viewed = viewed;
+ }
+
+ public boolean isShared() {
+ return shared;
+ }
+
+ public void setShared(boolean shared) {
+ this.shared = shared;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
rename to src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java
index ed0ef2a15606ef09f139bad65c90c3cf436c2474..0a49c5ad672aa0b14e6830bf6d683f95a08af6b4 100644
--- a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.model;
+package eu.hbp.mip.model.DTOs;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..b4214dd0a4de6aa50fa13f7aeb91652ce2c32137
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
@@ -0,0 +1,126 @@
+package eu.hbp.mip.model.DTOs;
+
+import eu.hbp.mip.model.DAOs.ExperimentDAO;
+
+import java.util.Date;
+import java.util.List;
+
+public class ExperimentDTO {
+
+ private String uuid;
+ private String name;
+ private String createdBy;
+ private Date created;
+ private Boolean shared;
+ private Boolean viewed;
+ private ExperimentDTO.ResultDTO result;
+ private ExperimentDAO.Status status;
+
+ private AlgorithmDTO algorithm;
+
+ public AlgorithmDTO getAlgorithm() {
+ return algorithm;
+ }
+
+ public void setAlgorithm(AlgorithmDTO algorithm) {
+ this.algorithm = algorithm;
+ }
+
+ public String getUuid() {
+ return uuid;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getCreatedBy() {
+ return createdBy;
+ }
+
+ public void setCreatedBy(String createdBy) {
+ this.createdBy = createdBy;
+ }
+
+ public Date getCreated() {
+ return created;
+ }
+
+ public void setCreated(Date created) {
+ this.created = created;
+ }
+
+ public Boolean getShared() {
+ return shared;
+ }
+
+ public void setShared(Boolean shared) {
+ this.shared = shared;
+ }
+
+ public Boolean getViewed() {
+ return viewed;
+ }
+
+ public void setViewed(Boolean viewed) {
+ this.viewed = viewed;
+ }
+
+ public ExperimentDTO.ResultDTO getResult() {
+ return result;
+ }
+
+ public void setResult(ExperimentDTO.ResultDTO result) {
+ this.result = result;
+ }
+
+ public ExperimentDAO.Status getStatus() {
+ return status;
+ }
+
+ public void setStatus(ExperimentDAO.Status status) {
+ this.status = status;
+ }
+
+ public static class OutputDTO {
+
+ private String data;
+ private ExperimentDAO.MimeTypes mimeTypes;
+
+ public String getData() {
+ return this.data;
+ }
+
+ public void setData(String data) {
+ this.data = data;
+ }
+
+ public ExperimentDAO.MimeTypes getMimeTypes() {
+ return mimeTypes;
+ }
+
+ public void setMimeTypes(ExperimentDAO.MimeTypes mimeTypes) {
+ this.mimeTypes = mimeTypes;
+ }
+ }
+
+ public static class ResultDTO {
+ private List<OutputDTO> result;
+
+ public List<OutputDTO> getResult() {
+ return this.result;
+ }
+
+ public void setResult(List<OutputDTO> result) {
+ this.result = result;
+ }
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/PathologyDTO.java b/src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java
similarity index 93%
rename from src/main/java/eu/hbp/mip/model/PathologyDTO.java
rename to src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java
index c58238b623e18aa5f7942d9e4816f905ce48f3f8..6a4580e81bbf9e7e371cf4c8297723d3b946f9c0 100644
--- a/src/main/java/eu/hbp/mip/model/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.model;
+package eu.hbp.mip.model.DTOs;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/Dataset.java b/src/main/java/eu/hbp/mip/model/Dataset.java
deleted file mode 100644
index d920571d9526dca8d29316d8d56578dc3d0b3b9b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Dataset.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
-
-// TODO: deprecate
-
-@Entity
-@Table(name = "`dataset`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Dataset {
-
- @Id
- private String code = null;
-
- private Date date = null;
-
- // Aka covariables
- @ElementCollection
- @CollectionTable(name = "dataset_header", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> header = new LinkedList<>();
-
- @ElementCollection
- @CollectionTable(name = "dataset_grouping", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> grouping = new LinkedList<>();
-
- @ElementCollection
- @CollectionTable(name = "dataset_variable", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> variable = new LinkedList<>();
-
- // TODO:
- @Transient
- @JsonProperty(access = JsonProperty.Access.READ_ONLY)
- private Object data = null;
-
-
- public Dataset() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
-
- public Date getDate() {
- return date;
- }
-
- public void setDate(Date date) {
- this.date = date;
- }
-
-
- public List<String> getHeader() {
- return header;
- }
-
- public void setHeader(List<String> header) {
- this.header = header;
- }
-
-
- public List<String> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<String> grouping) {
- this.grouping = grouping;
- }
-
-
- public List<String> getVariable() {
- return variable;
- }
-
- public void setVariable(List<String> variable) {
- this.variable = variable;
- }
-
- public Object getData() {
- return data;
- }
-
- public void setData(Object data) {
- this.data = data;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/DatasetDescription.java b/src/main/java/eu/hbp/mip/model/DatasetDescription.java
deleted file mode 100644
index c77c50aeab3a4256ecadf78aa2f25f89a05a0b92..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/DatasetDescription.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class DatasetDescription {
-
- private String code;
- private String label;
- private String description;
- private String anonymisationLevel;
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getDescription() {
- return description;
- }
-
- public void setDescription(String description) {
- this.description = description;
- }
-
- public String getAnonymisationLevel() {
- return anonymisationLevel;
- }
-
- public void setAnonymisationLevel(String anonymisationLevel) {
- this.anonymisationLevel = anonymisationLevel;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
deleted file mode 100644
index c40d91d3441ce131e45e5dbda0934c4a3ab0c30b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ /dev/null
@@ -1,232 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.*;
-import com.google.gson.annotations.Expose;
-import org.hibernate.annotations.Cascade;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.*;
-import java.util.*;
-
-/**
- * Created by habfast on 21/04/16.
- */
-@Entity
-@Table(name = "`experiment`")
-public class Experiment {
-
- private static final Gson gson = new Gson();
-
- @Id
- @Column(columnDefinition = "uuid")
- @org.hibernate.annotations.Type(type = "pg-uuid")
- @Expose
- private UUID uuid;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String name;
-
- @Expose
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private User createdBy;
-
- @ManyToOne
- @Cascade(org.hibernate.annotations.CascadeType.SAVE_UPDATE)
- @Expose
- private Model model;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String algorithms;
-
- @Column(columnDefinition = "TEXT")
- private String validations;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String workflowHistoryId;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String workflowStatus;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String result;
-
- @Expose
- private Date created = new Date();
-
- @Expose
- private Date finished;
-
- @Expose
- private boolean hasError = false;
-
- @Expose
- private boolean hasServerError = false;
-
- @Expose
- private boolean shared = false;
-
- // whether or not the experiment's result have been resultsViewed by its owner
- @Expose
- private boolean resultsViewed = false;
-
- public Experiment() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public JsonObject jsonify() {
- JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
- JsonParser parser = new JsonParser();
-
- if (this.algorithms != null) {
- exp.remove("algorithms");
- JsonArray jsonAlgorithms = parser.parse(this.algorithms).getAsJsonArray();
- exp.add("algorithms", jsonAlgorithms);
- }
-
- if (this.validations != null) {
- exp.remove("validations");
- JsonArray jsonValidations = parser.parse(this.validations).getAsJsonArray();
- exp.add("validations", jsonValidations);
- }
-
- if (this.result != null && !this.hasServerError) {
- exp.remove("result");
-
- JsonElement jsonResult = parser.parse(this.result);
- exp.add("result", jsonResult);
-
- }
-
- return exp;
- }
-
- public String getValidations() {
- return validations;
- }
-
- public void setValidations(String validations) {
- this.validations = validations;
- }
-
- public String getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(String algorithms) {
- this.algorithms = algorithms;
- }
-
- public Model getModel() {
- return model;
- }
-
- public void setModel(Model model) {
- this.model = model;
- }
-
- public boolean isHasError() {
- return hasError;
- }
-
- public void setHasError(boolean hasError) {
- this.hasError = hasError;
- }
-
- public String getWorkflowHistoryId() {
- return workflowHistoryId;
- }
-
- public void setWorkflowHistoryId(String workflowHistoryId) {
- this.workflowHistoryId = workflowHistoryId;
- }
-
- public String getWorkflowStatus() {
- return workflowStatus;
- }
-
- public void setWorkflowStatus(String workflowStatus) {
- this.workflowStatus = workflowStatus;
- }
-
- public String getResult() {
- return result;
- }
-
- public void setResult(String result) {
- this.result = result;
- }
-
- public Date getFinished() {
- return finished;
- }
-
- public void setFinished(Date finished) {
- this.finished = finished;
- }
-
- public Date getCreated() {
- return created;
- }
-
- public void setCreated(Date created) {
- this.created = created;
- }
-
- public UUID getUuid() {
- return uuid;
- }
-
- public void setUuid(UUID uuid) {
- this.uuid = uuid;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public User getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(User createdBy) {
- this.createdBy = createdBy;
- }
-
- public boolean isResultsViewed() {
- return resultsViewed;
- }
-
- public void setResultsViewed(boolean resultsViewed) {
- this.resultsViewed = resultsViewed;
- }
-
- public boolean isHasServerError() {
- return hasServerError;
- }
-
- public void setHasServerError(boolean hasServerError) {
- this.hasServerError = hasServerError;
- }
-
- public boolean isShared() {
- return shared;
- }
-
- public void setShared(boolean shared) {
- this.shared = shared;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
deleted file mode 100644
index a68cd9121d852503bc01eb6b2f0d23dd8af525dd..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-public class ExperimentExecutionDTO {
-
- private String name;
- private String model;
- private List<AlgorithmExecutionDTO> algorithms;
-
- public String getModel() {
- return model;
- }
-
- public void setModel(String model) {
- this.model = model;
- }
-
- public List<AlgorithmExecutionDTO> getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(List<AlgorithmExecutionDTO> algorithms) {
- this.algorithms = algorithms;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public static class AlgorithmExecutionDTO {
-
- private String name;
- private String label;
- private String type;
-
- private List<AlgorithmExecutionParamDTO> parameters;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> parameters) {
- this.parameters = parameters;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public static class AlgorithmExecutionParamDTO {
-
- private String name;
- private String label;
- private String value;
-
- public String getName() {
- return this.name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
- }
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Group.java b/src/main/java/eu/hbp/mip/model/Group.java
deleted file mode 100644
index abb195a932669d28785b407ad3738ab8087cffe7..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Group.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`group`")
-@ApiModel
-@JsonIgnoreProperties(value = {"parent"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Group {
-
- @Id
- private String code = null;
-
-
- public Group() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getCode() {
- return code;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Mining.java b/src/main/java/eu/hbp/mip/model/Mining.java
deleted file mode 100644
index 46cfd6c3ec64b0a7e552cd4f6e210a24a746fc1e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Mining.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.*;
-
-import java.util.Date;
-
-public class Mining {
-
- private static final Gson gson = new Gson();
-
- private final String jobId;
- private final String node;
- private final String function;
- private final String shape;
- private final Date timestamp;
- private final String data;
-
- public Mining(String jobId, String node, String function, String shape, Date timestamp, String data) {
- this.jobId = jobId;
- this.node = node;
- this.function = function;
- this.shape = shape;
- this.timestamp = timestamp;
- this.data = data;
- }
-
- public String getJobId() {
- return jobId;
- }
-
- public String getNode() {
- return node;
- }
-
- public String getFunction() {
- return function;
- }
-
- public String getShape() {
- return shape;
- }
-
- public Date getTimestamp() {
- return timestamp;
- }
-
- public String getData() {
- return data;
- }
-
- public JsonObject jsonify() {
- JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
- JsonParser parser = new JsonParser();
-
- if (this.data != null) {
- exp.remove("data");
- JsonElement jsonResult = parser.parse(this.data);
- exp.add("data", jsonResult);
- }
-
- return exp;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
deleted file mode 100644
index 171c55032eee4b3c5f63d636c137d6ae41bfe051..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.Gson;
-
-import java.util.LinkedList;
-import java.util.List;
-
-/**
- * Created by mirco on 06.01.17.
- */
-public class MiningQuery {
-
- private List<Variable> variables;
- private List<Variable> covariables;
- private List<Variable> grouping;
- private List<Variable> datasets;
- private String filters;
- private ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm;
-
- public MiningQuery() {
- this.variables = new LinkedList<>();
- this.covariables = new LinkedList<>();
- this.grouping = new LinkedList<>();
- this.datasets = new LinkedList<>();
- this.filters = "";
- }
-
- public List<Variable> getVariables() {
- return variables;
- }
-
- public void setVariables(List<Variable> variables) {
- this.variables = variables;
- }
-
- public void addVariable(Variable variable) {
- this.variables.add(variable);
- }
-
- public List<Variable> getCovariables() {
- return covariables;
- }
-
- public void setCovariables(List<Variable> covariables) {
- this.covariables = covariables;
- }
-
- public void addCovariable(Variable variable) {
- this.covariables.add(variable);
- }
-
- public List<Variable> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<Variable> grouping) {
- this.grouping = grouping;
- }
-
- public List<Variable> getDatasets() {
- return datasets;
- }
-
- public void setDataset(List<Variable> datasets) {
- this.datasets = datasets;
- }
-
- public void addDataset(Variable variable) {
- this.datasets.add(variable);
- }
-
- public void addGrouping(Variable variable) {
- this.grouping.add(variable);
- }
-
- public String getFilters() {
- return filters;
- }
-
- public void setFilters(String filters) {
- this.filters = filters;
- }
-
- public ExperimentExecutionDTO.AlgorithmExecutionDTO getAlgorithm() {
- return algorithm;
- }
-
- public void setAlgorithm(ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm) {
- this.algorithm = algorithm;
- }
-
- @Override
- public String toString() {
- return new Gson().toJson(this);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Model.java b/src/main/java/eu/hbp/mip/model/Model.java
deleted file mode 100644
index b1590803720c5a0c38538667ef48c940d644399c..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Model.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.google.gson.annotations.Expose;
-import io.swagger.annotations.ApiModel;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import javax.persistence.*;
-import java.util.Date;
-
-@Entity
-@Table(name = "`model`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Model {
-
- @Id
- @Expose
- private String slug = null;
-
- @Expose
- private String title = null;
-
- private String description = null;
-
- private Boolean valid = null;
-
- private Date createdAt = null;
-
- private Date updatedAt = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private eu.hbp.mip.model.Query query = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private Dataset dataset = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private Config config = null;
-
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private User createdBy = null;
-
- @ManyToOne
- @JoinColumn(name = "updatedby_username")
- private User updatedBy = null;
-
-
- public Model() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getTitle() {
- return title;
- }
-
- public void setTitle(String title) {
- this.title = title;
- }
-
-
- public String getSlug() {
- return slug;
- }
-
- public void setSlug(String slug) {
- this.slug = slug;
- }
-
-
- public String getDescription() {
- return description;
- }
-
- public void setDescription(String description) {
- this.description = description;
- }
-
-
- public eu.hbp.mip.model.Query getQuery() {
- return query;
- }
-
- public void setQuery(eu.hbp.mip.model.Query query) {
- this.query = query;
- }
-
-
- public Dataset getDataset() {
- return dataset;
- }
-
- public void setDataset(Dataset dataset) {
- this.dataset = dataset;
- }
-
-
- public Boolean getValid() {
- return valid;
- }
-
- public void setValid(Boolean valid) {
- this.valid = valid;
- }
-
-
- public Config getConfig() {
- return config;
- }
-
- public void setConfig(Config config) {
- this.config = config;
- }
-
-
- public Date getCreatedAt() {
- return createdAt;
- }
-
- public void setCreatedAt(Date createdAt) {
- this.createdAt = createdAt;
- }
-
-
- public Date getUpdatedAt() {
- return updatedAt;
- }
-
- public void setUpdatedAt(Date updatedAt) {
- this.updatedAt = updatedAt;
- }
-
-
- public User getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(User createdBy) {
- this.createdBy = createdBy;
- }
-
-
- public User getUpdatedBy() {
- return updatedBy;
- }
-
- public void setUpdatedBy(User updatedBy) {
- this.updatedBy = updatedBy;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Query.java b/src/main/java/eu/hbp/mip/model/Query.java
deleted file mode 100644
index 8e4d78dcbb1534052e9108aa9cf6d35be6ffa26e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Query.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.LinkedList;
-import java.util.List;
-
-@Entity
-@ApiModel
-@Table(name = "`query`")
-@JsonIgnoreProperties(value = {"id"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Query {
-
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE)
- private Long id = null;
-
- @ManyToMany
- @JoinTable(name = "query_variable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> variables = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_covariable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> covariables = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_grouping", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> grouping = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_training_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> trainingDatasets = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_testing_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> testingDatasets = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_validation_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> validationDatasets = new LinkedList<>();
-
- @Column(columnDefinition = "text")
- private String filters = "";
-
- @Column(columnDefinition = "text")
- private String pathology = "";
-
-
- public Query() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public Long getId() {
- return id;
- }
-
- public void setId(Long id) {
- this.id = id;
- }
-
-
- @JsonProperty("variables")
- public List<Variable> getVariables() {
- return variables;
- }
-
- public void setVariables(List<Variable> variables) {
- this.variables = variables;
- }
-
-
- @JsonProperty("coVariables")
- public List<Variable> getCovariables() {
- return covariables;
- }
-
- public void setCovariables(List<Variable> covariables) {
- this.covariables = covariables;
- }
-
-
- @JsonProperty("groupings")
- public List<Variable> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<Variable> grouping) {
- this.grouping = grouping;
- }
-
- @JsonProperty("trainingDatasets")
- public List<Variable> getTrainingDatasets() {
- return trainingDatasets;
- }
-
- public void setTrainingDatasets(List<Variable> trainingDatasets) {
- this.trainingDatasets = trainingDatasets;
- }
-
- @JsonProperty("testingDatasets")
- public List<Variable> getTestingDatasets() {
- return testingDatasets;
- }
-
- public void setTestingDatasets(List<Variable> testingDatasets) {
- this.testingDatasets = testingDatasets;
- }
-
- @JsonProperty("validationDatasets")
- public List<Variable> getValidationDatasets() {
- return validationDatasets;
- }
-
- public void setValidationDatasets(List<Variable> validationDatasets) {
- this.validationDatasets = validationDatasets;
- }
-
- public String getFilters() {
- return filters;
- }
-
- public void setFilters(String filters) {
- this.filters = filters;
- }
-
- public String getPathology() {
- return pathology;
- }
-
- public void setPathology(String pathology) {
- this.pathology = pathology;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Tag.java b/src/main/java/eu/hbp/mip/model/Tag.java
deleted file mode 100644
index 693c9865602ace72de50d067e3dd5e3eaac97526..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Tag.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`tag`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Tag {
-
- @Id
- private String name = null;
-
-
- public Tag() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/User.java b/src/main/java/eu/hbp/mip/model/User.java
index 64fee4b670e6285a0e06ada431975fd5c17cf50e..f1ee34059054493bfc3c37ad7d762ffacb486c6f 100644
--- a/src/main/java/eu/hbp/mip/model/User.java
+++ b/src/main/java/eu/hbp/mip/model/User.java
@@ -9,11 +9,11 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.annotations.Expose;
import io.swagger.annotations.ApiModel;
-import javax.persistence.*;
-import java.util.*;
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.Table;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import java.util.stream.Collectors;
@Entity
@Table(name = "`user`")
@@ -29,58 +29,9 @@ public class User {
@Expose
private String fullname = null;
- @Expose
- private String firstname = null;
-
- @Expose
- private String lastname = null;
-
- @Expose
- private String picture = null;
-
- @Expose
- private String web = null;
-
- @Expose
- private String phone = null;
-
- @Expose
- private String birthday = null;
-
- @Expose
- private String gender = null;
-
- @Expose
- private String city = null;
-
- @Expose
- private String country = null;
-
- @Expose
- private String password = null;
-
@Expose
private String email = null;
- @Expose
- private String apikey = null;
-
- @Expose
- private String team = null;
-
- @Expose
- private Boolean isActive = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "user_languages", joinColumns = @JoinColumn(name = "user_username"))
- @Expose
- private List<String> languages = new LinkedList<>();
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "user_roles", joinColumns = @JoinColumn(name = "user_username"))
- @Expose
- private List<String> roles = new LinkedList<>();
-
private Boolean agreeNDA = null;
@@ -113,49 +64,12 @@ public class User {
this.fullname = m.group(1);
}
- p = Pattern.compile("given_name=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.firstname = m.group(1);
- }
-
- p = Pattern.compile("family_name=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.lastname = m.group(1);
- }
-
p = Pattern.compile("email=([\\w.]+@[\\w.]+)");
m = p.matcher(userInfo);
if (m.find()) {
this.email = m.group(1);
}
- p = Pattern.compile("title=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- if ("Mr".equals(m.group(1))) {
- this.gender = "Male";
- } else {
- this.gender = "Female";
- }
- }
-
- p = Pattern.compile("contractor=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.team = m.group(1);
- }
-
- p = Pattern.compile("picture=([-a-zA-Z0-9+&@#/%=~_|.: ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.picture = m.group(1);
- }
-
- if (this.picture == null || this.picture.isEmpty()) {
- this.picture = "images/users/default_user.png";
- }
}
@@ -178,96 +92,6 @@ public class User {
}
- public String getFirstname() {
- return firstname;
- }
-
- public void setFirstname(String firstname) {
- this.firstname = firstname;
- }
-
-
- public String getLastname() {
- return lastname;
- }
-
- public void setLastname(String lastname) {
- this.lastname = lastname;
- }
-
-
- public String getPicture() {
- return picture;
- }
-
- public void setPicture(String picture) {
- this.picture = picture;
- }
-
-
- public String getWeb() {
- return web;
- }
-
- public void setWeb(String web) {
- this.web = web;
- }
-
-
- public String getPhone() {
- return phone;
- }
-
- public void setPhone(String phone) {
- this.phone = phone;
- }
-
-
- public String getBirthday() {
- return birthday;
- }
-
- public void setBirthday(String birthday) {
- this.birthday = birthday;
- }
-
-
- public String getGender() {
- return gender;
- }
-
- public void setGender(String gender) {
- this.gender = gender;
- }
-
-
- public String getCity() {
- return city;
- }
-
- public void setCity(String city) {
- this.city = city;
- }
-
-
- public String getCountry() {
- return country;
- }
-
- public void setCountry(String country) {
- this.country = country;
- }
-
-
- public String getPassword() {
- return password;
- }
-
- public void setPassword(String password) {
- this.password = password;
- }
-
-
public String getEmail() {
return email;
}
@@ -276,52 +100,6 @@ public class User {
this.email = email;
}
-
- public String getApikey() {
- return apikey;
- }
-
- public void setApikey(String apikey) {
- this.apikey = apikey;
- }
-
-
- public String getTeam() {
- return team;
- }
-
- public void setTeam(String team) {
- this.team = team;
- }
-
-
- public Boolean getIsActive() {
- return isActive;
- }
-
- public void setIsActive(Boolean isActive) {
- this.isActive = isActive;
- }
-
-
- public List<String> getLanguages() {
- return languages;
- }
-
- public void setLanguages(List<String> languages) {
- this.languages = languages;
- }
-
-
- public List<String> getRoles() {
- return roles;
- }
-
- public void setRoles(List<String> roles) {
- this.roles = roles;
- }
-
-
public Boolean getAgreeNDA() {
return agreeNDA;
}
diff --git a/src/main/java/eu/hbp/mip/model/UserInfo.java b/src/main/java/eu/hbp/mip/model/UserInfo.java
index 71eee3573b485d690c810b42c1344cc2170fb9f5..7bd9a97f3a8f16847410f73afc924fd05ff905cd 100644
--- a/src/main/java/eu/hbp/mip/model/UserInfo.java
+++ b/src/main/java/eu/hbp/mip/model/UserInfo.java
@@ -53,7 +53,6 @@ public class UserInfo {
user.setUsername("anonymous");
user.setFullname("anonymous");
user.setEmail("anonymous@anonymous.com");
- user.setPicture("images/users/default_user.png");
} else {
user = new User(getUserInfos());
}
diff --git a/src/main/java/eu/hbp/mip/model/Value.java b/src/main/java/eu/hbp/mip/model/Value.java
deleted file mode 100644
index 784452e591ffc8eb1f62ff5cc0c7f82694c78a3c..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Value.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`value`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Value {
-
- @Id
- private String code = null;
-
- private String label = null;
-
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Variable.java b/src/main/java/eu/hbp/mip/model/Variable.java
deleted file mode 100644
index 596be8d775673af068235dabed39323a4440de49..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Variable.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.google.gson.annotations.Expose;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-import java.util.List;
-
-@Entity
-@Table(name = "`variable`")
-@ApiModel
-@JsonIgnoreProperties(value = {"queries"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Variable {
-
- @Id
- @Expose
- private String code = null;
-
- /**
- * Empty constructor is needed by Hibernate
- */
- public Variable() {
- }
-
- public Variable(String code) {
- this.code = code;
- }
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public static String stringFromVariables(List<Variable> variables, String operator) {
- StringBuilder sb = new StringBuilder();
- int i = 0;
- for (Variable s : variables) {
- i++;
- sb.append(s.getCode());
- if (i < variables.size()) {
- sb.append(operator);
- }
- }
- return sb.toString();
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
index fa0cb4b336ef2f8276db39c1a03097f51a5c8ea7..4b01b38198d52e25d0f9455f770a9a5918d77874 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
@@ -2,7 +2,7 @@ package eu.hbp.mip.model.galaxy;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.model.AlgorithmDTO;
+import eu.hbp.mip.model.DTOs.AlgorithmDTO;
import java.util.*;
diff --git a/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java b/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java
deleted file mode 100644
index deb286150c0ba9c7833b4dfa66a61d3890c011c4..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Config;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ConfigRepository extends CrudRepository<Config, Long> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java b/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java
deleted file mode 100644
index 7c6da1e9745b8a144296d51a5d85434111213b96..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Dataset;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface DatasetRepository extends CrudRepository<Dataset, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index 2f6ae857d49018c5d9a3cb429f17cf3d2b80d313..eb1d254156e38529de29335a7f3cdfdd49cd7686 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.Experiment;
+import eu.hbp.mip.model.DAOs.ExperimentDAO;
import eu.hbp.mip.model.User;
import org.springframework.data.repository.CrudRepository;
@@ -10,8 +10,8 @@ import java.util.UUID;
* Created by mirco on 11.07.16.
*/
-public interface ExperimentRepository extends CrudRepository<Experiment, UUID> {
- Iterable<Experiment> findByCreatedBy(User user);
+public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID> {
+ Iterable<ExperimentDAO> findByCreatedBy(User user);
- Iterable<Experiment> findByShared(Boolean shared);
+ Iterable<ExperimentDAO> findByShared(Boolean shared);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java b/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
deleted file mode 100644
index c25b1e5bb6c4a5e888851b08ae3f0a801d5a4553..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Model;
-import eu.hbp.mip.model.User;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ModelRepository extends CrudRepository<Model, String> {
- Long countByTitle(String Title);
-
- Iterable<Model> findByCreatedByOrderByCreatedAt(User user);
-
- Iterable<Model> findByValidOrCreatedByOrderByCreatedAt(Boolean valid, User user);
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/QueryRepository.java b/src/main/java/eu/hbp/mip/repositories/QueryRepository.java
deleted file mode 100644
index f0b95d39c4c3a480fe2bec20ce75e46361889e71..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/QueryRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Query;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface QueryRepository extends CrudRepository<Query, Long> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/TagRepository.java b/src/main/java/eu/hbp/mip/repositories/TagRepository.java
deleted file mode 100644
index 4edb4090e0336ac034daf245d5ca3bb084a6f5ae..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/TagRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Tag;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface TagRepository extends CrudRepository<Tag, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/ValueRepository.java b/src/main/java/eu/hbp/mip/repositories/ValueRepository.java
deleted file mode 100644
index b41574d6082542ec1539f8e14203e61eb27e0614..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ValueRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Value;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ValueRepository extends CrudRepository<Value, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/VariableRepository.java b/src/main/java/eu/hbp/mip/repositories/VariableRepository.java
deleted file mode 100644
index 3ded949436f345143bb9e60a51bc0ee2ab20019b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/VariableRepository.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Variable;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 13.09.16.
- */
-public interface VariableRepository extends CrudRepository<Variable, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
new file mode 100644
index 0000000000000000000000000000000000000000..bd0bed3596c6de60154cacd291e6d34e9a4a74c1
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -0,0 +1,776 @@
+package eu.hbp.mip.services;
+
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
+import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
+import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
+import com.google.common.collect.Lists;
+import com.google.gson.*;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
+import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.model.DTOs.AlgorithmDTO;
+import eu.hbp.mip.model.DTOs.ExperimentDTO;
+import eu.hbp.mip.model.User;
+import eu.hbp.mip.model.UserInfo;
+import eu.hbp.mip.model.galaxy.ErrorResponse;
+import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.repositories.ExperimentRepository;
+import eu.hbp.mip.utils.ClaimUtils;
+import eu.hbp.mip.utils.HTTPUtil;
+import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Logging;
+import org.codehaus.jettison.json.JSONException;
+import org.codehaus.jettison.json.JSONObject;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.core.Authentication;
+import org.springframework.stereotype.Service;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.*;
+
+import static java.lang.Thread.sleep;
+
+@Service
+public class ExperimentService {
+
+ @Autowired
+ private UserInfo userInfo;
+
+ private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
+ .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
+
+ @Value("#{'${services.exareme.queryExaremeUrl}'}")
+ private String queryExaremeUrl;
+
+ @Value("#{'${services.workflows.workflowUrl}'}")
+ private String workflowUrl;
+
+ @Value("#{'${services.workflows.jwtSecret}'}")
+ private String jwtSecret;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
+ // Enable HBP collab authentication (1) or disable it (0). Default is 1
+ @Value("#{'${hbp.authentication.enabled:1}'}")
+ private boolean authenticationIsEnabled;
+
+ @Autowired
+ private ExperimentRepository experimentRepository;
+
+ private static final Gson gson = new Gson();
+
+ public ResponseEntity<String> getExperiment(String uuid, String endpoint) {
+
+ ExperimentDAO experimentDAO;
+ User user = userInfo.getUser();
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Loading Experiment with uuid : " + uuid);
+
+ experimentDAO = loadExperiment(uuid);
+
+ if (experimentDAO == null) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "Experiment Not found.");
+ return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
+ }
+
+ if (!experimentDAO.isShared() && !experimentDAO.getCreatedBy().getUsername().equals(user.getUsername())) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "Accessing Experiment is unauthorized.");
+ return new ResponseEntity<>("You don't have access to the experiment.", HttpStatus.UNAUTHORIZED);
+ }
+ ExperimentDTO experimentDTO = experimentDAO.convertToDTO();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Experiment was Loaded with uuid : " + uuid + ".");
+
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+ public ResponseEntity<String> createExperiment(Authentication authentication, ExperimentDTO experimentDTO, String endpoint) {
+ User user = userInfo.getUser();
+
+ //Checking if check (POST) /experiments has proper input.
+ if (checkPostExperimentProperInput(experimentDTO)){
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "Invalid input.");
+ return ResponseEntity.badRequest().body("Please provide proper input.");
+ }
+ // Get the type and name of algorithm
+ String algorithmType = experimentDTO.getAlgorithm().getType();
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+
+ StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
+ for (AlgorithmDTO.AlgorithmParamDTO params : experimentDTO.getAlgorithm().getParameters()) {
+ parametersLogMessage
+ .append(" ")
+ .append(params.getLabel())
+ .append(" -> ")
+ .append(params.getValue())
+ .append("\n");
+ }
+ Logging.LogUserAction(user.getUsername(), endpoint, "Executing " + algorithmName + parametersLogMessage);
+
+ if (authenticationIsEnabled) {
+ // Getting the dataset from the experiment parameters
+ String experimentDatasets = null;
+ for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
+ if (parameter.getLabel().equals("dataset")) {
+ experimentDatasets = parameter.getValue();
+ break;
+ }
+ }
+
+ if (experimentDatasets == null || experimentDatasets.equals("")) {
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "A dataset should be specified to run an algorithm.");
+ return ResponseEntity.badRequest().body("Please provide at least one dataset to run the algorithm.");
+ }
+
+ // --- Validating proper access rights on the datasets ---
+ if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
+ return ResponseEntity.badRequest().body("You are not authorized to use these datasets.");
+ }
+ }
+
+ // Run with the appropriate engine
+ if (algorithmType.equals("workflow")) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "Algorithm runs on Galaxy.");
+ return runGalaxyWorkflow(experimentDTO, endpoint);
+ } else {
+ Logging.LogUserAction(user.getUsername(), endpoint, "Algorithm runs on Exareme.");
+ return runExaremeAlgorithm(experimentDTO, endpoint);
+ }
+ }
+
+ public ResponseEntity<String> getExperiments( String endpoint) {
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Listing my experiments.");
+
+ Iterable<ExperimentDAO> myExperiments = experimentRepository.findByCreatedBy(user);
+ List<ExperimentDAO> expList = Lists.newLinkedList(myExperiments);
+ Iterable<ExperimentDAO> sharedExperiments = experimentRepository.findByShared(true);
+ List<ExperimentDAO> sharedExpList = Lists.newLinkedList(sharedExperiments);
+ expList.addAll(sharedExpList);
+ Logging.LogUserAction(user.getUsername(), endpoint, "Successfully listed my experiments.");
+ List<ExperimentDTO> experimentDTOs = new LinkedList<>();
+
+ for (ExperimentDAO experimentDAO: expList){
+ ExperimentDTO experimentDTO = experimentDAO.convertToDTO();
+ experimentDTOs.add(experimentDTO);
+ }
+ return new ResponseEntity<>(new Gson().toJson(experimentDTOs ), HttpStatus.OK);
+ }
+
+ public ResponseEntity<String> updateExperiment(String uuid, ExperimentDTO experimentDTO, String endpoint)
+ {
+ ExperimentDAO experimentDAO;
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Updating experiment with uuid : " + experimentDTO.getUuid() + ".");
+ //Checking if check (PUT) /experiments has proper input.
+ if (checkPutExperimentProperInput(experimentDTO)){
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "Invalid input.");
+ return ResponseEntity.badRequest().body("Please provide proper input.");
+ }
+
+ if((experimentDTO.getName() == null || experimentDTO.getName().length() == 0)
+ && experimentDTO.getShared() == null
+ && experimentDTO.getViewed() == null
+ && experimentDTO.getAlgorithm() == null)
+ {
+ return ResponseEntity.badRequest().body("Input is required.");
+ }
+
+ experimentDAO = loadExperiment(uuid);
+
+ if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
+
+ if(experimentDTO.getName() != null && experimentDTO.getName().length() != 0)
+ {
+ experimentDAO.setName(experimentDTO.getName());
+ }
+
+ if(experimentDTO.getShared() != null)
+ {
+ experimentDAO.setShared(experimentDTO.getShared());
+ }
+
+ if(experimentDTO.getViewed() != null)
+ {
+ experimentDAO.setViewed(experimentDTO.getViewed());
+ }
+
+ experimentRepository.save(experimentDAO);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Updated experiment with uuid : " + experimentDTO.getUuid() + ".");
+
+ experimentDTO = experimentDAO.convertToDTO();
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+ public ResponseEntity<String> deleteExperiment(String uuid, String endpoint)
+ {
+ ExperimentDAO experimentDAO;
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Deleting experiment with uuid : " + uuid + ".");
+
+ experimentDAO = loadExperiment(uuid);
+
+ if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>(endpoint, HttpStatus.UNAUTHORIZED);
+
+ experimentRepository.delete(experimentDAO);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Deleted experiment with uuid : " + uuid + ".");
+ return new ResponseEntity<>(HttpStatus.OK);
+ }
+
+ // /* ------------------------------- PRIVATE METHODS ----------------------------------------------------*/
+ private boolean checkPostExperimentProperInput(ExperimentDTO experimentDTO)
+ {
+ return experimentDTO.getShared() != null
+ || experimentDTO.getViewed() != null
+ || experimentDTO.getCreated() != null
+ || experimentDTO.getCreatedBy() != null
+ || experimentDTO.getResult() != null
+ || experimentDTO.getStatus() != null
+ || experimentDTO.getUuid() != null;
+ }
+
+ private boolean checkPutExperimentProperInput(ExperimentDTO experimentDTO)
+ {
+ return experimentDTO.getUuid() != null
+ || experimentDTO.getCreated() != null
+ || experimentDTO.getResult() != null
+ || experimentDTO.getStatus() != null;
+ }
+
+ private ExperimentDAO loadExperiment(String uuid){
+
+ UUID experimentUuid ;
+
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ } catch (IllegalArgumentException iae) {
+ return null;
+ }
+
+ return experimentRepository.findOne(experimentUuid);
+ }
+
+ private ExperimentDAO createExperiment(ExperimentDTO experimentDTO, String endpoint) {
+ User user = userInfo.getUser();
+
+ ExperimentDAO experimentDAO = new ExperimentDAO();
+ experimentDAO.setUuid(UUID.randomUUID());
+ experimentDAO.setCreatedBy(user);
+ experimentDAO.setAlgorithm(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithm()));
+ experimentDAO.setName(experimentDTO.getName());
+ experimentRepository.save(experimentDAO);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, " id : " + experimentDAO.getUuid());
+ Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithm());
+ Logging.LogUserAction(user.getUsername(), endpoint, " name : " + experimentDAO.getName());
+ return experimentDAO;
+ }
+
+ private void saveExperiment(ExperimentDAO experimentDAO, String endpoint) {
+ User user = userInfo.getUser();
+
+ Logging.LogUserAction(user.getUsername(), endpoint, " id : " + experimentDAO.getUuid());
+ Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithm());
+ Logging.LogUserAction(user.getUsername(), endpoint, " name : " + experimentDAO.getName());
+ Logging.LogUserAction(user.getUsername(), endpoint, " historyId : " + experimentDAO.getWorkflowHistoryId());
+ Logging.LogUserAction(user.getUsername(), endpoint, " status : " + experimentDAO.getStatus());
+
+ experimentRepository.save(experimentDAO);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Saved experiment");
+ }
+
+ private void finishExperiment(ExperimentDAO experimentDAO) {
+ experimentDAO.setFinished(new Date());
+ experimentRepository.save(experimentDAO);
+ }
+
+ /* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
+
+ /**
+ * The runExaremeExperiment will POST the algorithm to the exareme client
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runExaremeAlgorithm(ExperimentDTO experimentDTO, String endpoint) {
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Running the algorithm...");
+
+ ExperimentDAO experimentDAO = createExperiment(experimentDTO, endpoint);
+ Logging.LogUserAction(user.getUsername(), endpoint, "Created experiment with uuid :" + experimentDAO.getUuid());
+
+ // Run the 1st algorithm from the list
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ String body = gson.toJson(algorithmParameters);
+ String url = queryExaremeUrl + "/" + algorithmName;
+ Logging.LogUserAction(user.getUsername(), endpoint, "url: " + url + ", body: " + body);
+
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "Completed, returning: " + experimentDTO.toString());
+
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "Starting exareme execution thread");
+ new Thread(() -> {
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
+
+ try {
+ StringBuilder results = new StringBuilder();
+ int code = HTTPUtil.sendPost(url, body, results);
+
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Algorithm finished with code: " + code);
+
+ // Results are stored in the experiment object
+ ExperimentDTO.ResultDTO resultDTO = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.ResultDTO.class);
+
+ experimentDAO.setResult(JsonConverters.convertObjectToJsonString(resultDTO));
+// experimentDAO.setHasError(code >= 400);
+// experimentDAO.setHasServerError(code >= 500);
+ } catch (Exception e) {
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
+
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ experimentDAO.setResult(e.getMessage());
+ }
+
+ finishExperiment(experimentDAO);
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Finished the experiment: " + experimentDAO.toString());
+ }).start();
+ experimentDTO = experimentDAO.convertToDTO();
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+ /* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
+
+
+ /**
+ * The runWorkflow will POST the algorithm to the galaxy client
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runGalaxyWorkflow(ExperimentDTO experimentDTO, String endpoint) {
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), endpoint, "Running a workflow...");
+
+ ExperimentDAO experimentDAO = createExperiment(experimentDTO, endpoint);
+ Logging.LogUserAction(user.getUsername(), endpoint, "Created experiment with uuid :" + experimentDAO.getUuid());
+
+
+ // Run the 1st algorithm from the list
+ String workflowId = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ // Convert the parameters to workflow parameters
+ HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
+ if (algorithmParameters != null) {
+ for (AlgorithmDTO.AlgorithmParamDTO param : algorithmParameters) {
+ algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
+ }
+ }
+
+ // Get all the algorithm parameters because the frontend provides only the non-null
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+ Workflow workflow = null;
+ for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
+ if (curWorkflow.getId().equals(workflowId)) {
+ workflow = curWorkflow;
+ break;
+ }
+ }
+ if (workflow == null) {
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ "Could not find algorithm code: " + workflowId);
+ return ResponseEntity.badRequest()
+ .body(new ErrorResponse("Could not find galaxy algorithm.").toString());
+ }
+ final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
+ for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
+ if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
+ algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
+ }
+ }
+
+ // Create the body of the request
+ HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
+ requestBody.put("inputs", algorithmParamsIncludingEmpty);
+ JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Logging.LogUserAction(user.getUsername(), endpoint, "Running Galaxy workflow with id: " + workflow.getId());
+
+ // Call Galaxy to run the workflow
+ Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
+ try {
+ Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ String responseBody = gson.toJson(response.body());
+ Logging.LogUserAction(user.getUsername(), endpoint, "Response: " + responseBody);
+
+ String historyId = (String) new JSONObject(responseBody).get("history_id");
+ experimentDAO.setWorkflowHistoryId(historyId);
+ experimentDAO.setStatus(ExperimentDAO.Status.pending);
+// experimentDAO.setHasServerError(response.code() >= 500);
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ Logging.LogUserAction(user.getUsername(), endpoint, "Error Response: " + msgErr);
+
+ // Values are read from streams.
+ JSONObject jObjectError = new JSONObject(msgErr);
+ String errMsg = jObjectError.get("err_msg").toString();
+
+ experimentDAO.setResult(errMsg);
+// experimentDAO.setHasError(response.code() >= 400);
+// experimentDAO.setHasServerError(response.code() >= 500);
+ }
+
+ } catch (Exception e) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "An exception occurred: " + e.getMessage());
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ experimentDAO.setResult(e.getMessage());
+ }
+ saveExperiment(experimentDAO, endpoint);
+
+ // Start the process of fetching the status
+ updateWorkflowExperiment(experimentDAO, endpoint);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Run workflow completed!");
+
+ experimentDTO = experimentDAO.convertToDTO();
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+
+ /**
+ * This method creates a thread that will fetch the workflow result when it is ready
+ *
+ * @param experimentDAO will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
+ * and the result should not already be fetched
+ * @return nothing, just updates the experiment
+ */
+ public void updateWorkflowExperiment(ExperimentDAO experimentDAO, String endpoint) {
+ User user = userInfo.getUser();
+
+ if (experimentDAO == null) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "The experiment does not exist.");
+ return;
+ }
+
+ Logging.LogUserAction(user.getUsername(), endpoint,
+ " Experiment id : " + experimentDAO.getUuid());
+ if (experimentDAO.getWorkflowHistoryId() == null) {
+ Logging.LogUserAction(user.getUsername(), endpoint, "History Id does not exist.");
+ return;
+ }
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Starting Thread...");
+ new Thread(() -> {
+ while (true) {
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread is running...");
+
+ try {
+ sleep(2000);
+ } catch (InterruptedException e) {
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Sleep was disrupted: " + e.getMessage());
+ }
+
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Fetching status for experiment Id: " + experimentDAO.getUuid());
+
+ String state = getWorkflowStatus(experimentDAO);
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "State is: " + state);
+
+ switch (state) {
+ case "running":
+ // Do nothing, when the experiment is created the status is set to running
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Workflow is still running.");
+ break;
+
+ case "completed":
+ // Get only the job result that is visible
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Results are: " + workflowJobsResults.toString());
+
+ boolean resultFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getVisible()) {
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Visible result are: " + jobResult.getId());
+
+ String result = getWorkflowResultBody(experimentDAO, jobResult.getId());
+
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentDAO.setResult("[" + result + "]");
+ experimentDAO.setStatus(ExperimentDAO.Status.success);
+ resultFound = true;
+ }
+ }
+
+ if (!resultFound) { // If there is no visible result
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No visible result");
+ experimentDAO.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+
+ finishExperiment(experimentDAO);
+ break;
+
+ case "error":
+ // Get the job result that failed
+ workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Error results are: " + workflowJobsResults.toString());
+
+ boolean failedJobFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getState().equals("error")) {
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Failed job is: " + jobResult.getId());
+
+ String result = getWorkflowJobError(jobResult.getId(), experimentDAO);
+
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Job result: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentDAO.setResult("[" + result + "]");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ failedJobFound = true;
+ }
+ }
+
+ if (!failedJobFound) { // If there is no visible failed job
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No failed result");
+ experimentDAO.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ finishExperiment(experimentDAO);
+ break;
+
+ default: // InternalError or unexpected result
+ experimentDAO.setResult("[" + new ErrorResponse("An unexpected error occurred.").toString() + "]");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ finishExperiment(experimentDAO);
+ break;
+ }
+
+ // If result exists return
+ if (experimentDAO.getResult() != null) {
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
+ return;
+ }
+ }
+ }).start();
+ }
+
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return "running" -> When the workflow is still running
+ * "internalError" -> When an exception or a bad request occurred
+ * "error" -> When the workflow produced an error
+ * "completed" -> When the workflow completed successfully
+ */
+ public String getWorkflowStatus(ExperimentDAO experimentDAO) {
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
+ Logging.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
+
+ String result = null;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return "internalError";
+ }
+ result = new Gson().toJson(response.body());
+ Logging.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + result);
+
+ } catch (IOException e) {
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ String state = null;
+ try {
+ JSONObject resultJson = new JSONObject(result);
+ state = resultJson.getString("state");
+ } catch (JSONException e) {
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
+ switch (state) {
+ case "ok":
+ return "completed";
+ case "error":
+ return "error";
+ case "running":
+ case "new":
+ case "waiting":
+ case "queued":
+ return "running";
+ default:
+ return "internalError";
+ }
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return a List<GalaxyWorkflowResult> or null when an error occurred
+ */
+ public List<GalaxyWorkflowResult> getWorkflowResults(ExperimentDAO experimentDAO) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+ Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
+
+ List<GalaxyWorkflowResult> getGalaxyWorkflowResultList = null;
+ try {
+ Response<List<GalaxyWorkflowResult>> response = call.execute();
+ if (response.code() >= 400) {
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ getGalaxyWorkflowResultList = response.body();
+ Logging.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + response.body());
+
+ } catch (IOException e) {
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return getGalaxyWorkflowResultList;
+
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @param contentId the id of the job result that we want
+ * @return the result of the specific workflow job, null if there was an error
+ */
+ public String getWorkflowResultBody(ExperimentDAO experimentDAO, String contentId) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call =
+ service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
+
+ String resultJson = null;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ resultJson = new Gson().toJson(response.body());
+ Logging.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
+
+ } catch (IOException e) {
+ Logging.LogExperimentAction(experimentName, experimentId,
+ " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return resultJson;
+ }
+
+
+ /**
+ * @param jobId the id of the workflow job that failed
+ * @return the error that was produced or null if an error occurred
+ */
+ public String getWorkflowJobError(String jobId, ExperimentDAO experimentDAO) {
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logging.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
+
+ String fullError = null;
+ String returnError = null;
+ try {
+ Response<Object> response = callError.execute();
+ if (response.code() >= 400) {
+ Logging.LogExperimentAction(experimentName, experimentId, "Response code: "
+ + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+
+ // Parsing the stderr of the job that failed
+ String jsonString = new Gson().toJson(response.body());
+ JsonElement jsonElement = new JsonParser().parse(jsonString);
+ JsonObject rootObject = jsonElement.getAsJsonObject();
+ fullError = rootObject.get("stderr").getAsString();
+ Logging.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
+
+ String[] arrOfStr = fullError.split("ValueError", 0);
+ String specError = arrOfStr[arrOfStr.length - 1];
+ returnError = specError.substring(1);
+ Logging.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
+
+ } catch (IOException e) {
+ Logging.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
+ return null;
+ }
+
+ Logging.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
+
+ return returnError;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index e71d3f19083d03ae0067176b2fccfe4f06175915..5872819bc883efd98a453e363a46ad0a1cb537cd 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.utils;
import com.google.gson.Gson;
-import eu.hbp.mip.model.PathologyDTO;
+import eu.hbp.mip.model.DTOs.PathologyDTO;
import org.springframework.security.core.GrantedAuthority;
import java.util.ArrayList;
diff --git a/src/main/java/eu/hbp/mip/utils/JsonConverters.java b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
new file mode 100644
index 0000000000000000000000000000000000000000..52305124aff3c2078d6c87ba95c1b4235782da5a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
@@ -0,0 +1,27 @@
+package eu.hbp.mip.utils;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+
+import java.lang.reflect.Type;
+
+public class JsonConverters {
+ Gson gson = new Gson();
+
+ public static String convertObjectToJsonString(Object object) {
+ ObjectMapper mapper = new ObjectMapper();
+ //Converting the Object to JSONString
+ try {
+ return mapper.writeValueAsString(object);
+ } catch (JsonProcessingException e) {
+ return e.getMessage();
+ }
+ }
+
+ public static <T> T convertJsonStringToObject(String jsonString, Type typeOfT) {
+ if(jsonString == null || jsonString.isEmpty())
+ return null;
+ return new Gson().fromJson(jsonString, typeOfT);
+ }
+}
diff --git a/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql b/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql
new file mode 100644
index 0000000000000000000000000000000000000000..b69ae2b702742e36025e99ba04ebde23610c10f4
--- /dev/null
+++ b/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql
@@ -0,0 +1,45 @@
+ALTER TABLE experiment
+DROP COLUMN haserror,
+DROP COLUMN hasservererror,
+DROP COLUMN validations,
+DROP COLUMN model_slug;
+
+ALTER TABLE experiment
+RENAME algorithms TO algorithm;
+ALTER TABLE experiment
+RENAME createdby_username TO created_by_username;
+ALTER TABLE experiment
+RENAME workflowhistoryid TO workflow_history_id;
+ALTER TABLE experiment
+RENAME resultsviewed TO viewed;
+ALTER TABLE experiment
+RENAME workflowstatus TO status;
+
+ALTER TABLE "user"
+DROP COLUMN birthday,
+DROP COLUMN city,
+DROP COLUMN country,
+DROP COLUMN firstname,
+DROP COLUMN gender,
+DROP COLUMN isactive,
+DROP COLUMN lastname,
+DROP COLUMN password,
+DROP COLUMN phone,
+DROP COLUMN picture,
+DROP COLUMN team,
+DROP COLUMN web;
+
+DROP TABLE "config_title", "config_yaxisvariables";
+DROP TABLE "dataset_variable", "dataset_grouping", "dataset_data", "dataset_header";
+DROP TABLE "query_variable", "query_grouping", "query_filter", "query_covariable";
+DROP TABLE "article_tag", "tag";
+DROP TABLE "variable_value";
+DROP TABLE "query_training_datasets", "query_validation_datasets", "query_testing_datasets";
+DROP TABLE "variable", "value";
+DROP TABLE "group_group", "group";
+DROP TABLE "model";
+DROP TABLE "query";
+DROP TABLE "dataset";
+DROP TABLE "config";
+DROP TABLE "vote", "app";
+DROP TABLE "user_roles", "user_languages";
diff --git a/src/main/resources/logback.xml b/src/main/resources/logback.xml
index 0726d82f41564d850f92eaa301010d39ea89b068..eb9ace1a6b2ae5675fdd27e00077b4844873eaa4 100644
--- a/src/main/resources/logback.xml
+++ b/src/main/resources/logback.xml
@@ -10,8 +10,7 @@
<logger name="eu.hbp.mip">
<appender-ref ref="FILE1" />
</logger>
- <include resource="org/springframework/boot/logging/logback/base.xml"/>
- <logger name="org.springframework.web" level="ERROR">
+ <logger name="org.springframework.web" level="INFO">
<appender-ref ref="FILE1" />
</logger>
<logger name="eu.hbp.mip.utils" level="INFO" additivity="false">