Use VirtualStudy service from public VS controller

src/main/java/org/cbioportal/legacy/service/VirtualStudyService.java

@@ -2,27 +2,42 @@
 
 import java.util.List;
 import java.util.Map;
+import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
+import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException;
+import org.cbioportal.legacy.service.exception.DuplicateVirtualStudyException;
+import org.cbioportal.legacy.service.exception.StudyNotFoundException;
 import org.cbioportal.legacy.service.util.SessionServiceRequestHandler;
 import org.cbioportal.legacy.web.parameter.SampleIdentifier;
 import org.cbioportal.legacy.web.parameter.VirtualStudy;
 import org.cbioportal.legacy.web.parameter.VirtualStudyData;
 import org.cbioportal.legacy.web.parameter.VirtualStudySamples;
 import org.cbioportal.legacy.web.util.StudyViewFilterApplier;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
 
 @Service
 public class VirtualStudyService {
+  private static final Logger LOG = LoggerFactory.getLogger(VirtualStudyService.class);
+
+  public static final String ALL_USERS = "*";
   private final SessionServiceRequestHandler sessionServiceRequestHandler;
   private final StudyViewFilterApplier studyViewFilterApplier;
+  private final CancerTypeService cancerTypeService;
+  private final StudyService studyService;
 
   public VirtualStudyService(
       SessionServiceRequestHandler sessionServiceRequestHandler,
-      StudyViewFilterApplier studyViewFilterApplier) {
+      StudyViewFilterApplier studyViewFilterApplier,
+      CancerTypeService cancerTypeService,
+      StudyService studyService) {
     this.sessionServiceRequestHandler = sessionServiceRequestHandler;
     this.studyViewFilterApplier = studyViewFilterApplier;
+    this.cancerTypeService = cancerTypeService;
+    this.studyService = studyService;
   }
 
   public VirtualStudy getVirtualStudy(String id) {
@@ -59,6 +74,10 @@ public List<VirtualStudy> getUserVirtualStudies(String user) {
     return virtualStudies;
   }
 
+  public List<VirtualStudy> getPublicVirtualStudies() {
+    return getUserVirtualStudies(ALL_USERS);
+  }
+
   /**
    * This method populates the `virtualStudyData` object with a new set of sample IDs retrieved as
    * the result of executing a query based on virtual study view filters. It first applies the
@@ -107,4 +126,91 @@ private Map<String, Set<String>> groupSampleIdsByStudyId(
                 SampleIdentifier::getStudyId,
                 Collectors.mapping(SampleIdentifier::getSampleId, Collectors.toSet())));
   }
+
+  /**
+   * Publishes virtual study optionally updating metadata fields
+   *
+   * @param id - id of public virtual study to publish
+   * @param typeOfCancerId - if specified (not null) update type of cancer of published virtual
+   *     study
+   * @param pmid - if specified (not null) update PubMed ID of published virtual study
+   * @param virtualStudyData - if specified (not null) create new virtual study with this data,
+   *     otherwise updates virtual study with the given id
+   */
+  public void publishVirtualStudy(
+      String id, String typeOfCancerId, String pmid, VirtualStudyData virtualStudyData) {
+    if (virtualStudyData == null) {
+      VirtualStudy virtualStudyDataToPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
+      VirtualStudyData storedVirtualStudyData = virtualStudyDataToPublish.getData();
+      updateStudyMetadataFieldsIfSpecified(storedVirtualStudyData, typeOfCancerId, pmid);
+      storedVirtualStudyData.setUsers(Set.of(ALL_USERS));
+      sessionServiceRequestHandler.updateVirtualStudy(virtualStudyDataToPublish);
+    } else {
+      updateStudyMetadataFieldsIfSpecified(virtualStudyData, typeOfCancerId, pmid);
+      virtualStudyData.setUsers(Set.of(ALL_USERS));
+      try {
+        studyService.getStudy(id);
+        throw new DuplicateVirtualStudyException(
+            "The study with id="
+                + id
+                + " already exists. Use a different id for the virtual study.");
+      } catch (StudyNotFoundException e) {
+        LOG.debug(
+            "The study with id={} does not exist, proceeding to create a new virtual study.", id);
+      }
+      sessionServiceRequestHandler.createVirtualStudy(id, virtualStudyData);
+    }
+  }
+
+  /**
+   * Un-publish virtual study
+   *
+   * @param id - id of public virtual study to un-publish
+   */
+  public void unPublishVirtualStudy(String id) {
+    VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
+    if (virtualStudyToUnPublish == null) {
+      throw new NoSuchElementException(
+          "The virtual study with id=" + id + " has not been found in the public list.");
+    }
+    VirtualStudyData virtualStudyData = virtualStudyToUnPublish.getData();
+    checkIfVSWasPublished(id, virtualStudyData);
+    virtualStudyData.setUsers(Set.of(virtualStudyData.getOwner()));
+    sessionServiceRequestHandler.updateVirtualStudy(virtualStudyToUnPublish);
+  }
+
+  /**
+   * Drops public virtual study, removing it from the public list
+   *
+   * @param id - id of public virtual study to drop
+   */
+  public void dropPublicVirtualStudyById(String id) {
+    VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
+    checkIfVSWasPublished(id, virtualStudyToUnPublish.getData());
+    sessionServiceRequestHandler.dropVirtualStudy(id);
+  }
+
+  private static void checkIfVSWasPublished(String id, VirtualStudyData virtualStudyData) {
+    Set<String> users = virtualStudyData.getUsers();
+    if (users == null || users.isEmpty() || !users.contains(ALL_USERS)) {
+      throw new NoSuchElementException(
+          "The virtual study with id=" + id + " has not been found in the public list.");
+    }
+  }
+
+  private void updateStudyMetadataFieldsIfSpecified(
+      VirtualStudyData virtualStudyData, String typeOfCancerId, String pmid) {
+    if (typeOfCancerId != null) {
+      try {
+        cancerTypeService.getCancerType(typeOfCancerId);
+        virtualStudyData.setTypeOfCancerId(typeOfCancerId);
+      } catch (CancerTypeNotFoundException e) {
+        LOG.error("No cancer type with id={} were found.", typeOfCancerId);
+        throw new IllegalArgumentException("The cancer type is not valid: " + typeOfCancerId);
+      }
+    }
+    if (pmid != null) {
+      virtualStudyData.setPmid(pmid);
+    }
+  }
 }

src/main/java/org/cbioportal/legacy/web/PublicVirtualStudiesController.java

@@ -4,15 +4,9 @@
 import io.swagger.v3.oas.annotations.media.Schema;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import org.cbioportal.legacy.service.CancerTypeService;
-import org.cbioportal.legacy.service.StudyService;
+import org.cbioportal.legacy.service.VirtualStudyService;
 import org.cbioportal.legacy.service.exception.AccessForbiddenException;
-import org.cbioportal.legacy.service.exception.CancerTypeNotFoundException;
 import org.cbioportal.legacy.service.exception.DuplicateVirtualStudyException;
-import org.cbioportal.legacy.service.exception.StudyNotFoundException;
-import org.cbioportal.legacy.service.util.SessionServiceRequestHandler;
 import org.cbioportal.legacy.web.parameter.VirtualStudy;
 import org.cbioportal.legacy.web.parameter.VirtualStudyData;
 import org.slf4j.Logger;
@@ -36,25 +30,15 @@
 public class PublicVirtualStudiesController {
 
   private static final Logger LOG = LoggerFactory.getLogger(PublicVirtualStudiesController.class);
-
-  public static final String ALL_USERS = "*";
-
   private final String requiredPublisherApiKey;
 
-  private final SessionServiceRequestHandler sessionServiceRequestHandler;
-
-  private final CancerTypeService cancerTypeService;
-  private final StudyService studyService;
+  private final VirtualStudyService virtualStudyService;
 
   public PublicVirtualStudiesController(
       @Value("${session.endpoint.publisher-api-key:}") String requiredPublisherApiKey,
-      SessionServiceRequestHandler sessionServiceRequestHandler,
-      CancerTypeService cancerTypeService,
-      StudyService studyService) {
+      VirtualStudyService virtualStudyService) {
     this.requiredPublisherApiKey = requiredPublisherApiKey;
-    this.sessionServiceRequestHandler = sessionServiceRequestHandler;
-    this.cancerTypeService = cancerTypeService;
-    this.studyService = studyService;
+    this.virtualStudyService = virtualStudyService;
   }
 
   @GetMapping
@@ -63,8 +47,7 @@ public PublicVirtualStudiesController(
       description = "OK",
       content = @Content(schema = @Schema(implementation = VirtualStudy.class)))
   public ResponseEntity<List<VirtualStudy>> getPublicVirtualStudies() {
-    List<VirtualStudy> virtualStudies =
-        sessionServiceRequestHandler.getVirtualStudiesAccessibleToUser(ALL_USERS);
+    List<VirtualStudy> virtualStudies = virtualStudyService.getPublicVirtualStudies();
     return new ResponseEntity<>(virtualStudies, HttpStatus.OK);
   }
 
@@ -80,7 +63,7 @@ public ResponseEntity<Void> publishVirtualStudy(
       @RequestParam(required = false) String pmid,
       @RequestBody(required = false) VirtualStudyData virtualStudyData) {
     ensureProvidedPublisherApiKeyCorrect(providedPublisherApiKey);
-    publishVirtualStudy(id, typeOfCancerId, pmid, virtualStudyData);
+    virtualStudyService.publishVirtualStudy(id, typeOfCancerId, pmid, virtualStudyData);
     return ResponseEntity.ok().build();
   }
 
@@ -92,45 +75,17 @@ public ResponseEntity<Void> unPublishVirtualStudy(
       @RequestHeader(value = "X-PUBLISHER-API-KEY") String providedPublisherApiKey) {
     ensureProvidedPublisherApiKeyCorrect(providedPublisherApiKey);
     if (softDelete) {
-      unPublishVirtualStudy(id);
+      virtualStudyService.unPublishVirtualStudy(id);
     } else {
-      dropPublicVirtualStudyById(id);
+      virtualStudyService.dropPublicVirtualStudyById(id);
     }
     return ResponseEntity.ok().build();
   }
 
-  /**
-   * Publishes virtual study optionally updating metadata fields
-   *
-   * @param id - id of public virtual study to publish
-   * @param typeOfCancerId - if specified (not null) update type of cancer of published virtual
-   *     study
-   * @param pmid - if specified (not null) update PubMed ID of published virtual study
-   * @param virtualStudyData - if specified (not null) create new virtual study with this data,
-   *     otherwise updates virtual study with the given id
-   */
-  private void publishVirtualStudy(
-      String id, String typeOfCancerId, String pmid, VirtualStudyData virtualStudyData) {
-    if (virtualStudyData == null) {
-      VirtualStudy virtualStudyDataToPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
-      VirtualStudyData storedVirtualStudyData = virtualStudyDataToPublish.getData();
-      updateStudyMetadataFieldsIfSpecified(storedVirtualStudyData, typeOfCancerId, pmid);
-      storedVirtualStudyData.setUsers(Set.of(ALL_USERS));
-      sessionServiceRequestHandler.updateVirtualStudy(virtualStudyDataToPublish);
-    } else {
-      updateStudyMetadataFieldsIfSpecified(virtualStudyData, typeOfCancerId, pmid);
-      virtualStudyData.setUsers(Set.of(ALL_USERS));
-      try {
-        studyService.getStudy(id);
-        throw new DuplicateVirtualStudyException(
-            "The study with id="
-                + id
-                + " already exists. Use a different id for the virtual study.");
-      } catch (StudyNotFoundException e) {
-        LOG.debug(
-            "The study with id={} does not exist, proceeding to create a new virtual study.", id);
-      }
-      sessionServiceRequestHandler.createVirtualStudy(id, virtualStudyData);
+  private void ensureProvidedPublisherApiKeyCorrect(String providedPublisherApiKey) {
+    if (requiredPublisherApiKey.isBlank()
+        || !requiredPublisherApiKey.equals(providedPublisherApiKey)) {
+      throw new AccessForbiddenException("The provided publisher API key is not correct.");
     }
   }
 
@@ -140,63 +95,4 @@ public ResponseEntity<String> handleDuplicateVirtualStudyException(
     LOG.error("Duplicate virtual study error: {}", e.getMessage());
     return ResponseEntity.status(HttpStatus.CONFLICT).body(e.getMessage());
   }
-
-  /**
-   * Un-publish virtual study
-   *
-   * @param id - id of public virtual study to un-publish
-   */
-  private void unPublishVirtualStudy(String id) {
-    VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
-    if (virtualStudyToUnPublish == null) {
-      throw new NoSuchElementException(
-          "The virtual study with id=" + id + " has not been found in the public list.");
-    }
-    VirtualStudyData virtualStudyData = virtualStudyToUnPublish.getData();
-    checkIfVSWasPublished(id, virtualStudyData);
-    virtualStudyData.setUsers(Set.of(virtualStudyData.getOwner()));
-    sessionServiceRequestHandler.updateVirtualStudy(virtualStudyToUnPublish);
-  }
-
-  /**
-   * Drops public virtual study, removing it from the public list
-   *
-   * @param id - id of public virtual study to drop
-   */
-  private void dropPublicVirtualStudyById(String id) {
-    VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
-    checkIfVSWasPublished(id, virtualStudyToUnPublish.getData());
-    sessionServiceRequestHandler.dropVirtualStudy(id);
-  }
-
-  private static void checkIfVSWasPublished(String id, VirtualStudyData virtualStudyData) {
-    Set<String> users = virtualStudyData.getUsers();
-    if (users == null || users.isEmpty() || !users.contains(ALL_USERS)) {
-      throw new NoSuchElementException(
-          "The virtual study with id=" + id + " has not been found in the public list.");
-    }
-  }
-
-  private void ensureProvidedPublisherApiKeyCorrect(String providedPublisherApiKey) {
-    if (requiredPublisherApiKey.isBlank()
-        || !requiredPublisherApiKey.equals(providedPublisherApiKey)) {
-      throw new AccessForbiddenException("The provided publisher API key is not correct.");
-    }
-  }
-
-  private void updateStudyMetadataFieldsIfSpecified(
-      VirtualStudyData virtualStudyData, String typeOfCancerId, String pmid) {
-    if (typeOfCancerId != null) {
-      try {
-        cancerTypeService.getCancerType(typeOfCancerId);
-        virtualStudyData.setTypeOfCancerId(typeOfCancerId);
-      } catch (CancerTypeNotFoundException e) {
-        LOG.error("No cancer type with id={} were found.", typeOfCancerId);
-        throw new IllegalArgumentException("The cancer type is not valid: " + typeOfCancerId);
-      }
-    }
-    if (pmid != null) {
-      virtualStudyData.setPmid(pmid);
-    }
-  }
 }

src/main/java/org/cbioportal/legacy/web/SessionServiceController.java

@@ -1,6 +1,6 @@
 package org.cbioportal.legacy.web;
 
-import static org.cbioportal.legacy.web.PublicVirtualStudiesController.ALL_USERS;
+import static org.cbioportal.legacy.service.VirtualStudyService.ALL_USERS;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonProcessingException;